From 33aa68a4b0e20583bffb2d43806f9bb452229f91 Mon Sep 17 00:00:00 2001 From: slsevilla Date: Wed, 27 Sep 2023 17:06:02 -0400 Subject: [PATCH 1/5] chore: updates from biowulf to rhel8 --- carlisle | 18 +++------- resources/cluster_biowulf.yaml | 20 +++++++++-- resources/cluster_rhel8.yaml | 61 ---------------------------------- resources/tools_biowulf.yaml | 41 ++++++++++++----------- resources/tools_rhel8.yaml | 20 ----------- 5 files changed, 43 insertions(+), 117 deletions(-) delete mode 100644 resources/cluster_rhel8.yaml delete mode 100644 resources/tools_rhel8.yaml diff --git a/carlisle b/carlisle index c2e1ac0..3ba603c 100755 --- a/carlisle +++ b/carlisle @@ -21,17 +21,9 @@ SCRIPTBASENAME=$(readlink -f $(basename $0)) #define cluster, partitions dependent on host hostID=`echo $HOSTNAME` -if [[ $hostID == "biowulf.nih.gov" ]]; then - BUYINPARTITIONS=$(bash <(curl -s https://raw.githubusercontent.com/CCBR/Tools/master/Biowulf/get_buyin_partition_list.bash 2>/dev/null)) - PARTITIONS="norm,ccr" - cluster_specific_yaml="cluster_biowulf.yaml" - tools_specific_yaml="tools_biowulf.yaml" - #if [ $BUYINPARTITIONS ];then PARTITIONS="norm,$BUYINPARTITIONS";fi -elif [[ $hostID == "biowulf8.nih.gov" ]]; then - PARTITIONS="rhel8" - cluster_specific_yaml="cluster_rhel8.yaml" - tools_specific_yaml="tools_rhel8.yaml" -fi +PARTITIONS="norm,ccr" +cluster_specific_yaml="cluster_biowulf.yaml" +tools_specific_yaml="tools_biowulf.yaml" # essential files # these are relative to the workflows' base folder @@ -249,7 +241,7 @@ function testrun() { sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" ${PIPELINE_HOME}/.test/samples.test.tsv > $WORKDIR/config/samples.tsv cp ${PIPELINE_HOME}/.test/contrasts.test.tsv $WORKDIR/config/contrasts.tsv check_essential_files - dryrun + runslurm } function runslurm() { @@ -441,4 +433,4 @@ function main(){ } # call the main function -main "$@" +main "$@" \ No newline at end of file diff --git a/resources/cluster_biowulf.yaml b/resources/cluster_biowulf.yaml index eaa4d09..9711767 100644 --- a/resources/cluster_biowulf.yaml +++ b/resources/cluster_biowulf.yaml @@ -48,14 +48,28 @@ gopeaks_broad: ################################################################### findMotif: mem: 10g + time: 02-00:00:00 threads: 6 ################################################################### rose: - mem: 32g + mem: 64g threads: 2 - time: 00-06:00:00 + time: 00-12:00:00 ################################################################### go_enrichment: time: 02-00:00:00 mem: 10g -################################################################### \ No newline at end of file +################################################################### +deeptools_bw: + mem: 30g + time: 00-10:00:00 +################################################################### +deeptools_mat: + mem: 30g + threads: 16 + time: 01-00:00:00 +################################################################### +deeptools_heatmap: + mem: 30g + time: 01-00:00:00 +################################################################### diff --git a/resources/cluster_rhel8.yaml b/resources/cluster_rhel8.yaml deleted file mode 100644 index ea66fbf..0000000 --- a/resources/cluster_rhel8.yaml +++ /dev/null @@ -1,61 +0,0 @@ -# cluster configuration -################################################################### -__default__: - gres: lscratch:96 - mem: 40g - partition: rhel8 - time: 00-02:00:00 - threads: 2 - name: "{rule}.{wildcards}" - output: "logs/{rule}.${{SLURM_JOBID}}.%j.{wildcards}.out" - error: "logs/{rule}.${{SLURM_JOBID}}.%j.{wildcards}.err" -################################################################### -align: - mem: 200g - time: 00-12:00:00 - threads: 56 -################################################################### -qc_fastq_screen_validator: - mem: 20g - threads: 4 -################################################################### -create_reference: - mem: 200g - time: 00-12:00:00 - threads: 32 -################################################################### -bam2bg: - mem: 30g - time: 00-1:00:00 - threads: 4 -################################################################### -filter: - mem: 100g - time: 00-12:00:00 -################################################################### -trim: - mem: 200g - time: 00-12:00:00 - threads: 56 -################################################################### -gopeaks_narrow: - mem: 75g - threads: 8 -################################################################### -gopeaks_broad: - mem: 75g - threads: 8 -################################################################### -findMotif: - mem: 10g - threads: 6 -################################################################### -rose: - mem: 32g - threads: 2 - time: 00-06:00:00 -################################################################### -go_enrichment: - time: 02-00:00:00 - mem: 10g -################################################################### \ No newline at end of file diff --git a/resources/tools_biowulf.yaml b/resources/tools_biowulf.yaml index adfb54d..4955a67 100644 --- a/resources/tools_biowulf.yaml +++ b/resources/tools_biowulf.yaml @@ -1,20 +1,21 @@ -bedtools: "bedtools/2.30.0" -bedops: "bedops/2.4.40" -bowtie2: "bowtie/2-2.4.2" -cutadapt: "cutadapt/1.18" -fastqc: "fastqc/0.11.9" -fastq_screen: "fastq_screen/0.15.2" -fastxtoolkit: "fastxtoolkit/0.0.14" -homer: "homer/4.11.1" -macs2: "macs/2.2.7.1" -multiqc: "multiqc/1.14" -perl: "perl/5.34" -picard: "picard/2.26.9" -python3: "python/3.7" -R: "R/4.2.2" -rose: "ROSE/1.3.1" -samtools: "samtools/1.15" -seacr: "seacr/1.4-beta.2" -ucsc: "ucsc/407" -gopeaks: "/data/CCBR_Pipeliner/Pipelines/gopeaks/gopeaks" -fastq_val: "/data/CCBR_Pipeliner/iCLIP/bin/fastQValidator" \ No newline at end of file +bedtools: "bedtools/2.30.0" +bedops: "bedops/2.4.41" +bowtie2: "bowtie/2-2.4.5" +cutadapt: "cutadapt/4.0" +deeptools: "deeptools/3.5.1" +fastqc: "fastqc/0.11.9" +fastq_screen: "fastq_screen/0.15.2" +fastxtoolkit: "fastxtoolkit/0.0.14" +homer: "homer/4.11.1" +macs2: "macs/2.2.7.1" +multiqc: "multiqc/1.14" +perl: "perl/5.34" +picard: "picard/2.27.3" +python3: "python/3.9" +R: "R/4.2.2" +rose: "ROSE/1.3.1" +samtools: "samtools/1.15" +seacr: "SEACR/1.4-beta.2" +ucsc: "ucsc/445" +gopeaks: "/data/CCBR_Pipeliner/Pipelines/gopeaks/gopeaks" +fastq_val: "/data/CCBR_Pipeliner/bin/fastQValidator" \ No newline at end of file diff --git a/resources/tools_rhel8.yaml b/resources/tools_rhel8.yaml deleted file mode 100644 index 2f7e023..0000000 --- a/resources/tools_rhel8.yaml +++ /dev/null @@ -1,20 +0,0 @@ -bedtools: "bedtools/2.30.0" -bedops: "bedops/2.4.41" -bowtie2: "bowtie/2-2.4.5" -cutadapt: "cutadapt/4.0" -fastqc: "fastqc/0.11.9" -fastq_screen: "fastq_screen/0.15.2" -fastxtoolkit: "fastxtoolkit/0.0.14" -homer: "homer/4.11.1" -macs2: "macs/2.2.7.1" -multiqc: "multiqc/1.14" -perl: "perl/5.34" -picard: "picard/2.27.3" -python3: "python/3.9" -R: "R/4.2.2" -rose: "ROSE/1.3.1" -samtools: "samtools/1.15" -seacr: "SEACR/1.4-beta.2" -ucsc: "ucsc/445" -gopeaks: "/data/CCBR_Pipeliner/Pipelines/gopeaks/gopeaks" -fastq_val: "/data/CCBR_Pipeliner/iCLIP/bin/fastQValidator" \ No newline at end of file From 427f682151c7dc49745b0c8d34d37c9ebfd6d32f Mon Sep 17 00:00:00 2001 From: slsevilla Date: Wed, 27 Sep 2023 17:08:59 -0400 Subject: [PATCH 2/5] feature: create a control to treat dict --- workflow/rules/init.smk | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/workflow/rules/init.smk b/workflow/rules/init.smk index 441396f..6dbde8b 100644 --- a/workflow/rules/init.smk +++ b/workflow/rules/init.smk @@ -247,6 +247,13 @@ if config["run_contrasts"] == "Y": if os.path.exists(rg_file): os.remove(rg_file) # once file is removed it will be recreated by rule create_replicate_sample_table +# create CONTROL : TREATMENT dictionary +CONTROL_to_TREAT_DICT={} +for t in TREAT_to_CONTRL_DICT: + c=TREAT_to_CONTRL_DICT[t] + if c not in CONTROL_to_TREAT_DICT: + CONTROL_to_TREAT_DICT[c]=[] + CONTROL_to_TREAT_DICT[c].append(t) ######################################################### # READ IN TOOLS REQUIRED BY PIPELINE From f37b5fccea055e87a8f04b06a5639afe5b2fb43c Mon Sep 17 00:00:00 2001 From: slsevilla Date: Wed, 27 Sep 2023 17:23:35 -0400 Subject: [PATCH 3/5] feature: add deeptools to pipeline, fix minor bug in qc --- carlisle | 2 +- workflow/Snakefile | 43 ++++++++++++++++- workflow/rules/align.smk | 101 +++++++++++++++++++++++++++++++++++++++ 3 files changed, 143 insertions(+), 3 deletions(-) diff --git a/carlisle b/carlisle index 3ba603c..92cef8e 100755 --- a/carlisle +++ b/carlisle @@ -241,7 +241,7 @@ function testrun() { sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" ${PIPELINE_HOME}/.test/samples.test.tsv > $WORKDIR/config/samples.tsv cp ${PIPELINE_HOME}/.test/contrasts.test.tsv $WORKDIR/config/contrasts.tsv check_essential_files - runslurm + dryrun } function runslurm() { diff --git a/workflow/Snakefile b/workflow/Snakefile index 02370e9..40ad256 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -14,6 +14,29 @@ def run_library_norm(wildcards): files.extend(lib) return files +def run_deeptools_bw(wildcards): + files=[] + b1=expand(join(RESULTSDIR,"deeptools","clean","{replicate}.{dupstatus}.clean.bam"),replicate=REPLICATES,dupstatus=DUPSTATUS) + files.extend(b1) + b2=expand(join(RESULTSDIR,"deeptools","clean","{replicate}.{dupstatus}.clean.bam.bai"),replicate=REPLICATES,dupstatus=DUPSTATUS) + files.extend(b2) + b3=expand(join(RESULTSDIR,"deeptools","clean","{replicate}.{dupstatus}.clean.bigwig"),replicate=REPLICATES,dupstatus=DUPSTATUS) + files.extend(b3) + return files + +def run_deeptools_heatmap(wildcards): + files=[] + GROUP = [a+b for a in TREATMENTS+["all_samples"] for b in ["", ".prot"]] + p1=expand(join(RESULTSDIR,"deeptools","{group}.{dupstatus}.metagene_heatmap.pdf"),group=GROUP,dupstatus=DUPSTATUS) + files.extend(p1) + p2=expand(join(RESULTSDIR,"deeptools","{group}.{dupstatus}.TSS_heatmap.pdf"),group=GROUP,dupstatus=DUPSTATUS) + files.extend(p2) + p3=expand(join(RESULTSDIR,"deeptools","{group}.{dupstatus}.metagene_profile.pdf"),group=GROUP,dupstatus=DUPSTATUS) + files.extend(p3) + p4=expand(join(RESULTSDIR,"deeptools","{group}.{dupstatus}.TSS_profile.pdf"),group=GROUP,dupstatus=DUPSTATUS) + files.extend(p4) + return files + def run_macs2(wildcards): files=[] if "macs2_narrow" in PEAKTYPE: @@ -60,13 +83,14 @@ def run_qc(wildcards): files=[] if ("gopeaks_narrow" in PEAKTYPE) or ("gopeaks_broad" in PEAKTYPE): q=expand(join(RESULTSDIR,'qc', 'multiqc_report_{qthresholds}.html'),qthresholds=QTRESHOLDS) + files.extend(q) else: q=join(RESULTSDIR,'qc', 'multiqc_report.html') - files.extend(q) + files.append(q) if ("SPIKEIN" == NORM_METHOD) and ("ecoli" == spikein_genome): html=join(RESULTSDIR,'qc',"spikein_qc_report.html"), - files.extend(html) + files.append(html) return files def run_contrasts(wildcards): @@ -167,6 +191,12 @@ rule all: # manifests unpack(run_pipe_prep), + # ALIGN / deeptools_bw + unpack(run_deeptools_bw), + + # ALIGN / deeptools_heatmap + unpack(run_deeptools_heatmap), + # ALIGN / create_library_norm_scales unpack(run_library_norm), @@ -229,4 +259,13 @@ rule all: expand(join(RESULTSDIR,"fragments","{replicate}.{dupstatus}.fragments.bed"),replicate=REPLICATES,dupstatus=DUPSTATUS), expand(join(RESULTSDIR,"bedgraph","{replicate}.{dupstatus}.bedgraph"),replicate=REPLICATES,dupstatus=DUPSTATUS), expand(join(RESULTSDIR,"bigwig","{replicate}.{dupstatus}.bigwig"),replicate=REPLICATES,dupstatus=DUPSTATUS), + + # ALIGN / deeptools_heatmap + expand(join(RESULTSDIR,"deeptools","clean", "{sample}.{dupstatus}.deeptools_prep"), sample=TREATMENTS, dupstatus=DUPSTATUS), + expand(join(RESULTSDIR,"deeptools","clean", "{sample}.prot.{dupstatus}.deeptools_prep"), sample=TREATMENTS, dupstatus=DUPSTATUS), + expand(join(RESULTSDIR,"deeptools","clean", "all_samples.{dupstatus}.deeptools_prep"), dupstatus=DUPSTATUS), + expand(join(RESULTSDIR,"deeptools","clean", "all_samples.prot.{dupstatus}.deeptools_prep"), dupstatus=DUPSTATUS), + expand(join(RESULTSDIR,"deeptools","clean", "{group}.{dupstatus}.metagene.mat.gz"),group=[a+b for a in TREATMENTS+["all_samples"] for b in ["", ".prot"]],dupstatus=DUPSTATUS), + expand(join(RESULTSDIR,"deeptools","clean", "{group}.{dupstatus}.TSS.mat.gz"),group=[a+b for a in TREATMENTS+["all_samples"] for b in ["", ".prot"]],dupstatus=DUPSTATUS), + expand(join(RESULTSDIR,"deeptools","clean", "{group}.{dupstatus}.geneinfo.bed"),group=[a+b for a in TREATMENTS+["all_samples"] for b in ["", ".prot"]],dupstatus=DUPSTATUS), """ \ No newline at end of file diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk index 6017f27..7a0b8c9 100644 --- a/workflow/rules/align.smk +++ b/workflow/rules/align.smk @@ -367,4 +367,105 @@ rule bam2bg: # add to YAML echo "spikein_scaling_factor=$spikein_scale" > {output.sf_yaml} + """ + +rule deeptools_bw: + input: + bam = join(RESULTSDIR,"bam","{replicate}.{dupstatus}.bam"), + genome_len = join(BOWTIE2_INDEX,"genome.len") + output: + clean_bam = join(RESULTSDIR,"deeptools","clean","{replicate}.{dupstatus}.clean.bam"), + clean_bai = join(RESULTSDIR,"deeptools","clean","{replicate}.{dupstatus}.clean.bam.bai"), + bw = join(RESULTSDIR,"deeptools","clean","{replicate}.{dupstatus}.clean.bigwig"), + envmodules: + TOOLS["samtools"], + TOOLS["deeptools"], + shell: + """ + genome_size=`cat {input.genome_len} | awk '{{ sum+=$2 }} END{{ print sum }}'` + samtools view -b -@4 {input.bam} chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY | samtools sort -@4 -o {output.clean_bam} + samtools index {output.clean_bam} + bamCoverage --bam {output.clean_bam} -o {output.bw} --binSize 25 --smoothLength 75 --numberOfProcessors 32 --normalizeUsing RPGC --effectiveGenomeSize $genome_size --centerReads + """ + +rule deeptools_prep: + input: + bw = expand(join(RESULTSDIR,"deeptools","clean","{replicate}.{dupstatus}.clean.bigwig"), replicate=REPLICATES,dupstatus=DUPSTATUS), + output: + deeptools_prep = temp(expand(join(RESULTSDIR,"deeptools","clean", "{group}.{dupstatus}.deeptools_prep"),group=[a+b for a in TREATMENTS+["all_samples"] for b in ["", ".prot"]],dupstatus=DUPSTATUS)), + run: + for dupstatus in DUPSTATUS: + for i in ["","prot."]: + for item in TREATMENT_CONTROL_LIST: + labels = item.split('_vs_') + treatment, control = labels + bws = [join(RESULTSDIR,"deeptools","clean","{}.{}.clean.bigwig".format(item, dupstatus)) for item in labels] + f=open(join(RESULTSDIR,"deeptools","clean","{}.{}{}.deeptools_prep".format(treatment, i, dupstatus) ),'w') + f.write("{}\n".format(dupstatus)) + f.write("{}\n".format(" ".join(bws))) + f.write("{}\n".format(" ".join(labels))) + f.close() + + for dupstatus in DUPSTATUS: + labels = [] + for c in CONTROL_to_TREAT_DICT: + labels += CONTROL_to_TREAT_DICT[c] + labels.append(c) + bws = [join(RESULTSDIR,"deeptools","clean","{}.{}.clean.bigwig".format(item, dupstatus)) for item in labels] + + for i in ["","prot."]: + f_all=open(join(RESULTSDIR,"deeptools","clean","all_samples.{}{}.deeptools_prep".format(i, dupstatus)),'w') + f_all.write("all_samples\n") + f_all.write("{}\n".format(" ".join(bws))) + f_all.write("{}\n".format(" ".join(labels))) + f_all.close() + +rule deeptools_mat: + input: + deeptools_prep = join(RESULTSDIR,"deeptools","clean", "{group}.{dupstatus}.deeptools_prep"), + bw = expand(join(RESULTSDIR,"deeptools","clean","{replicate}.{dupstatus}.clean.bigwig"), replicate=REPLICATES,dupstatus=DUPSTATUS), + output: + metamat=temp(join(RESULTSDIR,"deeptools","clean", "{group}.{dupstatus}.metagene.mat.gz")), + TSSmat=temp(join(RESULTSDIR,"deeptools","clean","{group}.{dupstatus}.TSS.mat.gz")), + bed=temp(join(RESULTSDIR,"deeptools","clean","{group}.{dupstatus}.geneinfo.bed")), + params: + prebed="/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/geneinfo.bed", + pythonver=TOOLS["python3"], + deeptoolsver=TOOLS["deeptools"], + threads: + getthreads("deeptools_mat"), + run: + import re + commoncmd="module load {params.deeptoolsver}; module load {params.pythonver};" + listfile=list(map(lambda z:z.strip().split(),open(input.deeptools_prep,'r').readlines())) + ext=listfile[0][0] + bws=listfile[1] + labels=listfile[2] + if "prot" in wildcards.group: + cmd1="grep --line-buffered 'protein_coding' "+ params.prebed +" | awk -v OFS='\t' -F'\t' '{{print $1, $2, $3, $5, \".\", $4}}' > "+output.bed + else: + cmd1="awk -v OFS='\t' -F'\t' '{{print $1, $2, $3, $5, \".\", $4}}' "+params.prebed+" > "+output.bed + cmd2="computeMatrix scale-regions -S "+" ".join(bws)+" -R "+output.bed+" -p 16 --upstream 1000 --regionBodyLength 2000 --downstream 1000 --skipZeros -o "+output.metamat+" --samplesLabel "+" ".join(labels) + cmd3="computeMatrix reference-point -S "+" ".join(bws)+" -R "+output.bed+" -p 16 --referencePoint TSS --upstream 3000 --downstream 3000 --skipZeros -o "+output.TSSmat+" --samplesLabel "+" ".join(labels) + shell(commoncmd+cmd1) + shell(commoncmd+cmd2) + shell(commoncmd+cmd3) + +rule deeptools_heatmap: + input: + metamat=rules.deeptools_mat.output.metamat, + TSSmat=rules.deeptools_mat.output.TSSmat, + output: + metaheat=join(RESULTSDIR,"deeptools","{group}.{dupstatus}.metagene_heatmap.pdf"), + TSSheat=join(RESULTSDIR,"deeptools","{group}.{dupstatus}.TSS_heatmap.pdf"), + metaline=join(RESULTSDIR,"deeptools","{group}.{dupstatus}.metagene_profile.pdf"), + TSSline=join(RESULTSDIR,"deeptools","{group}.{dupstatus}.TSS_profile.pdf"), + envmodules: + TOOLS["deeptools"], + shell: + """ + plotHeatmap -m {input.metamat} -out {output.metaheat} --colorMap 'PuOr_r' --zMin auto --zMax auto --yAxisLabel 'average RPGC' --regionsLabel 'genes' --legendLocation 'none' + plotHeatmap -m {input.TSSmat} -out {output.TSSheat} --colorMap 'RdBu_r' --zMin auto --zMax auto --yAxisLabel 'average RPGC' --regionsLabel 'genes' --legendLocation 'none' + plotProfile -m {input.metamat} -out {output.metaline} --plotHeight 15 --plotWidth 15 --perGroup --yAxisLabel 'average RPGC' --plotType 'se' --legendLocation upper-right + plotProfile -m {input.TSSmat} -out {output.TSSline} --plotHeight 15 --plotWidth 15 --perGroup --yAxisLabel 'average RPGC' --plotType 'se' --legendLocation upper-left """ \ No newline at end of file From 3d3b11983e9bc50a59e8678d3ef04969af2139a8 Mon Sep 17 00:00:00 2001 From: slsevilla Date: Wed, 27 Sep 2023 17:38:46 -0400 Subject: [PATCH 4/5] feature: adding tiny test option for dev --- .test/contrasts.tinytest.tsv | 2 ++ .test/samples.tinytest.tsv | 4 ++++ carlisle | 9 +++++++++ workflow/Snakefile | 36 ++++++++++++++++++------------------ 4 files changed, 33 insertions(+), 18 deletions(-) create mode 100644 .test/contrasts.tinytest.tsv create mode 100644 .test/samples.tinytest.tsv diff --git a/.test/contrasts.tinytest.tsv b/.test/contrasts.tinytest.tsv new file mode 100644 index 0000000..c69fab0 --- /dev/null +++ b/.test/contrasts.tinytest.tsv @@ -0,0 +1,2 @@ +condition1 condition2 +53_H3K4me3 HN6_H3K4me3 \ No newline at end of file diff --git a/.test/samples.tinytest.tsv b/.test/samples.tinytest.tsv new file mode 100644 index 0000000..fbf6aef --- /dev/null +++ b/.test/samples.tinytest.tsv @@ -0,0 +1,4 @@ +sampleName replicateNumber isControl controlName controlReplicateNumber path_to_R1 path_to_R2 +53_H3K4me3 1 N HN6_IgG_rabbit_negative_control 1 PIPELINE_HOME/.test/53_H3K4me3_1.R1.fastq.gz PIPELINE_HOME/.test/53_H3K4me3_1.R2.fastq.gz +HN6_H3K4me3 1 N HN6_IgG_rabbit_negative_control 1 PIPELINE_HOME/.test/HN6_H3K4me3_1.R1.fastq.gz PIPELINE_HOME/.test/HN6_H3K4me3_1.R2.fastq.gz +HN6_IgG_rabbit_negative_control 1 Y - - PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R1.fastq.gz PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R2.fastq.gz \ No newline at end of file diff --git a/carlisle b/carlisle index 92cef8e..1302420 100755 --- a/carlisle +++ b/carlisle @@ -244,6 +244,14 @@ function testrun() { dryrun } +function tinytestrun() { + check_essential_files + sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" ${PIPELINE_HOME}/.test/samples.tinytest.tsv > $WORKDIR/config/samples.tsv + cp ${PIPELINE_HOME}/.test/contrasts.tinytest.tsv $WORKDIR/config/contrasts.tsv + check_essential_files + dryrun +} + function runslurm() { # Submit the execution of the pipeline to the biowulf job scheduler (slurm) runcheck @@ -422,6 +430,7 @@ function main(){ runlocal) runlocal && exit 0;; reset) reset && exit 0;; testrun) testrun && exit 0;; + tinytestrun) tinytestrun && exit 0;; # hidden option for debugging dry) dryrun && exit 0;; # hidden option local) runlocal && exit 0;; # hidden option reconfig) reconfig && exit 0;; # hidden option for debugging diff --git a/workflow/Snakefile b/workflow/Snakefile index 40ad256..0167e70 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -197,30 +197,30 @@ rule all: # ALIGN / deeptools_heatmap unpack(run_deeptools_heatmap), - # ALIGN / create_library_norm_scales - unpack(run_library_norm), + # # ALIGN / create_library_norm_scales + # unpack(run_library_norm), - # ALIGN / alignstats - expand(join(RESULTSDIR,"alignment_stats","{replicate}.alignment_stats.yaml"),replicate=REPLICATES), + # # ALIGN / alignstats + # expand(join(RESULTSDIR,"alignment_stats","{replicate}.alignment_stats.yaml"),replicate=REPLICATES), - # ALIGN / gather_alignstats - join(RESULTSDIR,"alignment_stats","alignment_stats.tsv"), + # # ALIGN / gather_alignstats + # join(RESULTSDIR,"alignment_stats","alignment_stats.tsv"), - # PEAKCALLS / macs2_narrow, macs2_broad, seacr_stringent, seacr_relaxed, gopeaks_narrow, gopeaks_broad - unpack(run_macs2), - unpack(run_seacr), - unpack(run_gopeaks), + # # PEAKCALLS / macs2_narrow, macs2_broad, seacr_stringent, seacr_relaxed, gopeaks_narrow, gopeaks_broad + # unpack(run_macs2), + # unpack(run_seacr), + # unpack(run_gopeaks), - # QC - unpack(run_qc), + # # QC + # unpack(run_qc), - # DIFF / create_contrast_data_files - unpack(run_contrasts), + # # DIFF / create_contrast_data_files + # unpack(run_contrasts), - # ANNOTATION / findMotif, rose, create_contrast_peakcaller_files, go_enrichment - unpack(get_motifs), - unpack(get_rose), - unpack(get_enrichment) + # # ANNOTATION / findMotif, rose, create_contrast_peakcaller_files, go_enrichment + # unpack(get_motifs), + # unpack(get_rose), + # unpack(get_enrichment) """ ########################################## ### intermediate files From de5c62c3197e4ecc4075fc8832fab89f809ab3ae Mon Sep 17 00:00:00 2001 From: slsevilla Date: Thu, 28 Sep 2023 07:26:20 -0400 Subject: [PATCH 5/5] style: remove cols with spaces and pipes --- resources/blacklistbed/hg19.bed | 822 ++++++------ resources/blacklistbed/hg38.bed | 2099 +++++++++++++++---------------- resources/blacklistbed/mm10.bed | 1119 ++++++++-------- 3 files changed, 2019 insertions(+), 2021 deletions(-) mode change 100755 => 100644 resources/blacklistbed/hg19.bed diff --git a/resources/blacklistbed/hg19.bed b/resources/blacklistbed/hg19.bed old mode 100755 new mode 100644 index a37f048..ee2de95 --- a/resources/blacklistbed/hg19.bed +++ b/resources/blacklistbed/hg19.bed @@ -1,411 +1,411 @@ -chr1 564449 570371 High_Mappability_island 1000 . -chr1 724136 727043 Satellite_repeat 1000 . -chr1 825006 825115 BSR/Beta 1000 . -chr1 2583334 2634374 Low_mappability_island 1000 . -chr1 4363064 4363242 (CATTC)n 1000 . -chr1 5725866 5736651 Low_mappability_island 1000 . -chr1 16839923 16841396 Low_mappability_island 1000 . -chr1 38077347 38077423 Low_mappability_island 1000 . -chr1 91852785 91853147 LSU-rRNA_Hsa 1000 . -chr1 104163724 104163860 Low_mappability_island 1000 . -chr1 108112972 108113707 LSU-rRNA_Hsa 1000 . -chr1 121351474 121487059 centromeric_repeat 1000 . -chr1 142535434 142543081 Satellite_repeat 1000 . -chr1 142723256 142723968 Low_mappability_island 1000 . -chr1 142792613 142793303 Low_mappability_island 1000 . -chr1 142835822 142837333 Low_mappability_island 1000 . -chr1 143274490 143284340 centromeric_repeat 1000 . -chr1 145277108 145277572 LSU-rRNA_Hsa 1000 . -chr1 149033183 149035829 Satellite_repeat 1000 . -chr1 156186169 156186712 High_Mappability_island 1000 . -chr1 224199390 224204260 Satellite_repeat 1000 . -chr1 233318467 233318516 (CATTC)n 1000 . -chr1 236260366 236260821 Low_mappability_island 1000 . -chr1 237766308 237766764 LSU-rRNA_Hsa 1000 . -chr1 238105345 238105511 Low_mappability_island 1000 . -chr1 238108025 238108378 Low_mappability_island 1000 . -chr1 238108645 238109697 Low_mappability_island 1000 . -chr10 18841533 18862467 (CATTC)n 1000 . -chr10 20035661 20037171 Low_mappability_island 1000 . -chr10 36722282 36723650 Low_mappability_island 1000 . -chr10 38772277 38819357 Satellite_repeat 1000 . -chr10 38868892 38889025 Satellite_repeat 1000 . -chr10 39076515 39155771 Satellite_repeat 1000 . -chr10 42354835 42548642 centromeric_repeat 1000 . -chr10 42596676 42602082 Satellite_repeat 1000 . -chr10 42596700 42602110 Satellite_repeat 1000 . -chr10 42661264 42667623 Satellite_repeat 1000 . -chr10 42790522 42818398 Satellite_repeat 1000 . -chr10 135498649 135502716 Satellite_repeat 1000 . -chr11 6831669 6831838 ALR/Alpha 1000 . -chr11 10529403 10531969 Low_mappability_island 1000 . -chr11 48671444 48902406 centromeric_repeat 1000 . -chr11 48931242 48964015 centromeric_repeat 1000 . -chr11 50318471 50784078 centromeric_repeat 1000 . -chr11 51090700 51374066 centromeric_repeat 1000 . -chr11 51567242 51594226 centromeric_repeat 1000 . -chr11 54694046 55027975 centromeric_repeat 1000 . -chr11 73221660 73221946 Low_mappability_island 1000 . -chr11 85194913 85195322 LSU-rRNA_Hsa 1000 . -chr11 87524468 87525005 Low_mappability_island 1000 . -chr11 103275584 103281729 Low_mappability_island 1000 . -chr11 122874287 122874443 Low_mappability_island 1000 . -chr12 20704285 20704583 SSU-rRNA_Hsa 1000 . -chr12 34372315 34372825 LSU-rRNA_Hsa 1000 . -chr12 34432130 34857010 centromeric_repeat 1000 . -chr12 37989447 38441828 centromeric_repeat 1000 . -chr12 38531376 38531930 LSU-rRNA_Hsa 1000 . -chr12 41757383 41757545 Low_mappability_island 1000 . -chr12 127650407 127651075 LSU-rRNA_Hsa 1000 . -chr12 132061320 132062046 Low_mappability_island 1000 . -chr13 56545728 56545925 Low_mappability_island 1000 . -chr13 110076444 110076782 Low_mappability_island 1000 . -chr14 18999935 19056900 centromeric_repeat 1000 . -chr14 32953263 32954381 Low_mappability_island 1000 . -chr14 84637832 84639038 Low_mappability_island 1000 . -chr14 90341302 90341516 SSU-rRNA_Hsa 1000 . -chr15 19999941 20044132 centromeric_repeat 1000 . -chr16 32493036 32570826 ALR/Alpha 1000 . -chr16 32590063 32598801 ALR/Alpha 1000 . -chr16 33237130 33241330 Low_mappability_island 1000 . -chr16 33864355 34023306 centromeric_repeat 1000 . -chr16 34180542 34197081 Satellite_repeat 1000 . -chr16 34530115 34542632 BSR/Beta 1000 . -chr16 35193580 35285885 centromeric_repeat 1000 . -chr16 46385718 46456668 Satellite_repeat 1000 . -chr16 46497639 46500515 Satellite_repeat 1000 . -chr16 47538629 47539297 LSU-rRNA_Hsa 1000 . -chr17 19355538 19356096 LSU-rRNA_Hsa 1000 . -chr17 19502495 19506773 Low_mappability_island 1000 . -chr17 21905167 21906712 centromeric_repeat 1000 . -chr17 22018524 22032049 Low_mappability_island 1000 . -chr17 22221073 22263006 centromeric_repeat 1000 . -chr17 25263010 25268059 Satellite_repeat 1000 . -chr17 25415551 25417559 telomeric_repeat 1000 . -chr17 31149365 31149981 High_Mappability_island 1000 . -chr17 33478114 33478372 LSU-rRNA_Hsa 1000 . -chr17 41381502 41382591 High_Mappability_island 1000 . -chr17 41463538 41464075 High_Mappability_island 1000 . -chr17 41464478 41465015 snRNA 1000 . -chr17 41465562 41467288 High_Mappability_island 1000 . -chr17 51183038 51183763 Low_mappability_island 1000 . -chr17 55868618 55868752 LSU-rRNA_Hsa 1000 . -chr17 75158031 75158430 LSU-rRNA_Hsa 1000 . -chr18 96416 97552 Satellite_repeat 1000 . -chr18 105658 112233 Satellite_repeat 1000 . -chr18 2842252 2842356 Low_mappability_island 1000 . -chr18 15393801 15393992 centromeric_repeat 1000 . -chr18 18510894 18520356 centromeric_repeat 1000 . -chr18 44126235 44126593 (CATTC)n 1000 . -chr18 45379603 45379864 Low_mappability_island 1000 . -chr18 50319086 50319301 Low_mappability_island 1000 . -chr18 77772846 77773065 LSU-rRNA_Hsa 1000 . -chr19 246006 247844 TAR1 1000 . -chr19 22877614 22877696 SSU-rRNA_Hsa 1000 . -chr19 23235030 23235504 BSR/Beta 1000 . -chr19 24182398 24186210 LSU-rRNA_Hsa 1000 . -chr19 24385474 24633168 centromeric_repeat 1000 . -chr19 27730611 28262682 centromeric_repeat 1000 . -chr19 36066445 36066810 LSU-rRNA_Hsa 1000 . -chr19 36756398 36800948 centromeric_repeat 1000 . -chr19 37759473 37797722 centromeric_repeat 1000 . -chr19 44914313 44916340 ACRO1 1000 . -chr19 44960681 44962681 ACRO1 1000 . -chr2 739925 740994 Low_mappability_island 1000 . -chr2 49456729 49457067 Low_mappability_island 1000 . -chr2 88124390 88124903 Low_mappability_island 1000 . -chr2 89830421 89880514 Satellite_repeat 1000 . -chr2 90371401 90394776 Satellite_repeat 1000 . -chr2 90443001 90545431 Low_mappability_island 1000 . -chr2 91595080 91616015 Satellite_repeat 1000 . -chr2 92267428 92326280 centromeric_repeat 1000 . -chr2 115695017 115695281 LSU-rRNA_Hsa 1000 . -chr2 117781085 117781300 Low_mappability_island 1000 . -chr2 132966248 132989300 centromeric_repeat 1000 . -chr2 132994855 133007983 ALR/Alpha 1000 . -chr2 133011824 133013298 SSU-rRNA_Hsa 1000 . -chr2 133036250 133040042 LSU-rRNA_Hsa 1000 . -chr2 133044095 133045945 ACRO1 1000 . -chr2 143848503 143848792 Low_mappability_island 1000 . -chr2 148022736 148022878 Low_mappability_island 1000 . -chr2 149639207 149639515 Low_mappability_island 1000 . -chr2 156120500 156120610 Low_mappability_island 1000 . -chr2 162135000 162139241 Low_mappability_island 1000 . -chr2 230045426 230045796 LSU-rRNA_Hsa 1000 . -chr20 26257032 26320267 centromeric_repeat 1000 . -chr20 29517710 29521147 centromeric_repeat 1000 . -chr20 29803876 29833334 centromeric_repeat 1000 . -chr20 55932703 55936114 chrM 1000 . -chr20 62916702 62918053 telomeric_repeat 1000 . -chr21 9647205 9648529 Low_mappability_island 1000 . -chr21 9694896 9704962 centromeric_repeat 1000 . -chr21 9825451 9827612 High_Mappability_island 1000 . -chr21 9827612 9845233 Low_mappability_island 1000 . -chr21 9881895 9882569 TAR1 1000 . -chr21 10084922 10088004 Satellite_repeat 1000 . -chr21 10492876 10493049 Low_mappability_island 1000 . -chr21 10599428 10599915 TAR1 1000 . -chr21 10697886 10860890 centromeric_repeat 1000 . -chr21 11186054 11188131 Satellite_repeat 1000 . -chr21 14338127 14369791 centromeric_repeat 1000 . -chr21 18800575 18800997 (GAGTG)n 1000 . -chr21 27228003 27228242 SSU-rRNA_Hsa 1000 . -chr21 46796081 46796336 Low_mappability_island 1000 . -chr22 16847814 16862659 Satellite_repeat 1000 . -chr22 18876789 18884510 Satellite_repeat 1000 . -chr3 25508897 25509131 Low_mappability_island 1000 . -chr3 73159606 73161131 snRNA 1000 . -chr3 75696297 75699304 BSR/Beta 1000 . -chr3 75717841 75720426 Satellite_repeat 1000 . -chr3 80995858 81014459 ALR/Alpha 1000 . -chr3 90311686 90507410 centromeric_repeat 1000 . -chr3 93504815 93519133 centromeric_repeat 1000 . -chr3 96335934 96337436 Low_mappability_island 1000 . -chr3 160665423 160665642 Low_mappability_island 1000 . -chr3 196625514 196625860 Satellite_repeat 1000 . -chr3 197825427 197834080 Low_mappability_island 1000 . -chr4 9987 12694 telomeric_repeat 1000 . -chr4 12276463 12292424 ALR/Alpha 1000 . -chr4 12641862 12642305 Low_mappability_island 1000 . -chr4 21583630 21583719 (GAATG)n 1000 . -chr4 27732004 27732240 Low_mappability_island 1000 . -chr4 47774268 47774416 Low_mappability_island 1000 . -chr4 49085372 49342114 centromeric_repeat 1000 . -chr4 49488472 49662085 centromeric_repeat 1000 . -chr4 52659961 52688986 centromeric_repeat 1000 . -chr4 56194229 56194584 Low_mappability_island 1000 . -chr4 65473858 65473941 Low_mappability_island 1000 . -chr4 68264186 68266830 centromeric_repeat 1000 . -chr4 70296565 70296841 LSU-rRNA_Hsa 1000 . -chr4 76807083 76807320 LSU-rRNA_Hsa 1000 . -chr4 78929660 78929920 Low_mappability_island 1000 . -chr4 156374749 156377226 chrM 1000 . -chr4 156384860 156387314 Low_mappability_island 1000 . -chr4 163342479 163342744 Low_mappability_island 1000 . -chr4 190190746 190203442 Low_mappability_island 1000 . -chr4 190801869 190802909 Low_mappability_island 1000 . -chr4 190943802 190943962 Satellite_repeat 1000 . -chr4 190987268 190990949 Satellite_repeat 1000 . -chr4 191026302 191044344 telomeric_repeat 1000 . -chr5 17517177 17600940 Low_mappability_island 1000 . -chr5 21477365 21497415 Low_mappability_island 1000 . -chr5 34177882 34197574 Low_mappability_island 1000 . -chr5 45908253 46411114 centromeric_repeat 1000 . -chr5 49405493 49554574 centromeric_repeat 1000 . -chr5 71146650 71146996 LSU-rRNA_Hsa 1000 . -chr5 79945807 79948223 Low_mappability_island 1000 . -chr5 93903068 93906726 Low_mappability_island 1000 . -chr5 97746525 97746679 Low_mappability_island 1000 . -chr5 99381556 99390873 Low_mappability_island 1000 . -chr5 105889063 105889263 chrM 1000 . -chr5 123095972 123097432 chrM 1000 . -chr5 134258949 134264271 Low_mappability_island 1000 . -chr5 174541634 174542177 SSU-rRNA_Hsa 1000 . -chr6 58735349 58739031 centromeric_repeat 1000 . -chr6 58745955 58780547 centromeric_repeat 1000 . -chr6 61880095 61944008 centromeric_repeat 1000 . -chr6 62189892 62206612 ALR/Alpha 1000 . -chr6 62207809 62230644 ALR/Alpha 1000 . -chr6 62283966 62284581 Low_mappability_island 1000 . -chr6 133593944 133594201 LSU-rRNA_Hsa 1000 . -chr6 137059142 137059326 SSU-rRNA_Hsa 1000 . -chr6 150665074 150665281 SSU-rRNA_Hsa 1000 . -chr6 157731310 157735525 Low_mappability_island 1000 . -chr7 43878355 43878530 TAR1 1000 . -chr7 45291517 45291740 Low_mappability_island 1000 . -chr7 56437808 56442977 Low_mappability_island 1000 . -chr7 57253980 57254183 Low_mappability_island 1000 . -chr7 57255310 57255444 Low_mappability_island 1000 . -chr7 57261829 57261998 Low_mappability_island 1000 . -chr7 57544726 57556913 Satellite_repeat 1000 . -chr7 57811488 57836990 centromeric_repeat 1000 . -chr7 57939184 58055539 centromeric_repeat 1000 . -chr7 61054285 62454680 centromeric_repeat 1000 . -chr7 64059157 64066183 BSR/Beta 1000 . -chr7 64951348 64956223 centromeric_repeat 1000 . -chr7 68201468 68201673 Low_mappability_island 1000 . -chr7 68527370 68527788 LSU-rRNA_Hsa 1000 . -chr7 80962907 80963147 SSU-rRNA_Hsa 1000 . -chr7 100550640 100551321 Low_mappability_island 1000 . -chr7 142372972 142375638 Low_mappability_island 1000 . -chr7 145694403 145694561 Low_mappability_island 1000 . -chr8 155512 157639 TAR1 1000 . -chr8 21455971 21456306 LSU-rRNA_Hsa 1000 . -chr8 32868966 32873279 Low_mappability_island 1000 . -chr8 43092737 43097573 Satellite_repeat 1000 . -chr8 43399486 43843604 centromeric_repeat 1000 . -chr8 46838215 47457541 centromeric_repeat 1000 . -chr8 47739043 47742797 Low_mappability_island 1000 . -chr8 47750844 47776101 BSR/Beta 1000 . -chr8 56754955 56755418 LSU-rRNA_Hsa 1000 . -chr8 69218401 69218922 LSU-rRNA_Hsa 1000 . -chr8 70602248 70602620 LSU-rRNA_Hsa 1000 . -chr8 77114154 77114389 Low_mappability_island 1000 . -chr8 100508010 100508287 Low_mappability_island 1000 . -chr9 10435 11574 TAR1 1000 . -chr9 4799734 4800000 SSU-rRNA_Hsa 1000 . -chr9 33656606 33659249 Low_mappability_island 1000 . -chr9 42819021 42832395 centromeric_repeat 1000 . -chr9 44070617 44070871 Low_mappability_island 1000 . -chr9 44873123 44902307 centromeric_repeat 1000 . -chr9 45355954 45357644 telomeric_repeat 1000 . -chr9 45435109 45443517 centromeric_repeat 1000 . -chr9 66494170 66494805 TAR1 1000 . -chr9 66767710 66864329 centromeric_repeat 1000 . -chr9 66970914 67005594 centromeric_repeat 1000 . -chr9 67315122 67321036 centromeric_repeat 1000 . -chr9 67789868 67792893 centromeric_repeat 1000 . -chr9 68410775 68435115 Low_mappability_island 1000 . -chr9 69677073 69687998 centromeric_repeat 1000 . -chr9 69689770 69711497 centromeric_repeat 1000 . -chr9 69947961 70011196 centromeric_repeat 1000 . -chr9 70076144 70076855 centromeric_repeat 1000 . -chr9 70318723 70327683 centromeric_repeat 1000 . -chr9 72653073 72653572 Satellite_repeat 1000 . -chr9 78790077 78790255 (GAATG)n 1000 . -chr9 79186574 79187026 LSU-rRNA_Hsa 1000 . -chr9 141019938 141021783 TAR1 1000 . -chrM 1 16571 chrM 1000 . -chrX 55206111 55206740 Low_mappability_island 1000 . -chrX 55207753 55208152 Low_mappability_island 1000 . -chrX 55208300 55208643 Low_mappability_island 1000 . -chrX 55208980 55209208 Low_mappability_island 1000 . -chrX 55209655 55210006 Low_mappability_island 1000 . -chrX 58330488 58330843 centromeric_repeat 1000 . -chrX 58373806 58373962 centromeric_repeat 1000 . -chrX 58377680 58377864 centromeric_repeat 1000 . -chrX 58415350 58416387 centromeric_repeat 1000 . -chrX 58432411 58432680 centromeric_repeat 1000 . -chrX 58485887 58486241 centromeric_repeat 1000 . -chrX 58488898 58494528 centromeric_repeat 1000 . -chrX 58499466 58504235 centromeric_repeat 1000 . -chrX 58506076 58528214 centromeric_repeat 1000 . -chrX 58528184 58536883 centromeric_repeat 1000 . -chrX 58544061 58582415 centromeric_repeat 1000 . -chrX 61681834 61919683 centromeric_repeat 1000 . -chrX 62003205 62041580 centromeric_repeat 1000 . -chrX 83658929 83659019 Low_mappability_island 1000 . -chrX 108297348 108297886 LSU-rRNA_Hsa 1000 . -chrX 114959057 115006437 Low_mappability_island 1000 . -chrX 125605623 125607351 Low_mappability_island 1000 . -chrX 125714985 125715338 Low_mappability_island 1000 . -chrX 125864844 125864980 Low_mappability_island 1000 . -chrX 125865719 125865874 Low_mappability_island 1000 . -chrY 313470 313613 ALR/Alpha 1000 . -chrY 3004989 3005175 LSU-rRNA_Hsa 1000 . -chrY 4212807 4212910 Low_mappability_island 1000 . -chrY 7671817 7694928 BSR/Beta 1000 . -chrY 7726064 7730229 BSR/Beta 1000 . -chrY 7730734 7731598 BSR/Beta 1000 . -chrY 7735811 7752887 BSR/Beta 1000 . -chrY 7785067 7806311 BSR/Beta 1000 . -chrY 7806856 7814704 BSR/Beta 1000 . -chrY 7815230 7820478 BSR/Beta 1000 . -chrY 7829937 7832032 BSR/Beta 1000 . -chrY 7832744 7848695 BSR/Beta 1000 . -chrY 7870343 7873582 BSR/Beta 1000 . -chrY 7874115 7874584 BSR/Beta 1000 . -chrY 7875409 7885257 BSR/Beta 1000 . -chrY 7886545 7894591 BSR/Beta 1000 . -chrY 7898927 7916812 BSR/Beta 1000 . -chrY 7918790 7921352 BSR/Beta 1000 . -chrY 7926344 7936705 BSR/Beta 1000 . -chrY 7941130 7947438 BSR/Beta 1000 . -chrY 7948790 7964448 BSR/Beta 1000 . -chrY 8179010 8181143 BSR/Beta 1000 . -chrY 8181757 8213330 BSR/Beta 1000 . -chrY 8214629 8215637 BSR/Beta 1000 . -chrY 8220421 8230061 BSR/Beta 1000 . -chrY 8230686 8231546 BSR/Beta 1000 . -chrY 8240772 8265916 BSR/Beta 1000 . -chrY 8291535 8292942 BSR/Beta 1000 . -chrY 8294002 8295175 BSR/Beta 1000 . -chrY 8296944 8321375 BSR/Beta 1000 . -chrY 8325813 8325929 BSR/Beta 1000 . -chrY 8326678 8333466 BSR/Beta 1000 . -chrY 8334027 8342387 BSR/Beta 1000 . -chrY 8356544 8369346 BSR/Beta 1000 . -chrY 8909560 8909925 TAR1 1000 . -chrY 8979478 8979585 Low_mappability_island 1000 . -chrY 9072781 9072993 TAR1 1000 . -chrY 9908430 9925608 centromeric_repeat 1000 . -chrY 9981952 9982126 BSR/Beta 1000 . -chrY 10034864 10036712 SSU-rRNA_Hsa 1000 . -chrY 10040627 10045657 ALR/Alpha 1000 . -chrY 10047773 10052533 ALR/Alpha 1000 . -chrY 10053695 10057722 ALR/Alpha 1000 . -chrY 10059394 10073694 ALR/Alpha 1000 . -chrY 10075082 10075781 ALR/Alpha 1000 . -chrY 10080736 10104539 ALR/Alpha 1000 . -chrY 13104530 13144368 centromeric_repeat 1000 . -chrY 13193966 13196535 Low_mappability_island 1000 . -chrY 13252193 13259484 centromeric_repeat 1000 . -chrY 13290177 13290667 chrM 1000 . -chrY 13445957 13490591 Satellite_repeat 1000 . -chrY 13642186 13749784 Satellite_repeat 1000 . -chrY 13798522 13870984 Satellite_repeat 1000 . -chrY 19691913 19692524 LSU-rRNA_Hsa 1000 . -chrY 19764063 19776198 ALR/Alpha 1000 . -chrY 19780600 19781704 ALR/Alpha 1000 . -chrY 19783669 19796396 ALR/Alpha 1000 . -chrY 19800068 19801419 ALR/Alpha 1000 . -chrY 19808085 19817100 ALR/Alpha 1000 . -chrY 19944298 19944581 TAR1 1000 . -chrY 20235195 20235478 TAR1 1000 . -chrY 20362679 20371694 ALR/Alpha 1000 . -chrY 20378360 20379711 ALR/Alpha 1000 . -chrY 20383383 20396110 ALR/Alpha 1000 . -chrY 20398075 20399179 ALR/Alpha 1000 . -chrY 20403581 20415713 ALR/Alpha 1000 . -chrY 20487248 20487859 LSU-rRNA_Hsa 1000 . -chrY 23124788 23125577 BSR/Beta 1000 . -chrY 23149027 23151205 BSR/Beta 1000 . -chrY 23157969 23158245 BSR/Beta 1000 . -chrY 23159001 23167737 BSR/Beta 1000 . -chrY 23178886 23181770 BSR/Beta 1000 . -chrY 23220740 23223625 BSR/Beta 1000 . -chrY 23234125 23235822 BSR/Beta 1000 . -chrY 23236898 23248080 BSR/Beta 1000 . -chrY 23248729 23248851 BSR/Beta 1000 . -chrY 23899295 23899388 TAR1 1000 . -chrY 23956449 23956628 TAR1 1000 . -chrY 24247659 24247700 TAR1 1000 . -chrY 24630999 24631040 TAR1 1000 . -chrY 24953159 24975657 BSR/Beta 1000 . -chrY 24980997 24991235 BSR/Beta 1000 . -chrY 25022753 25039185 BSR/Beta 1000 . -chrY 25040153 25042421 BSR/Beta 1000 . -chrY 25048332 25059258 BSR/Beta 1000 . -chrY 25060235 25064798 BSR/Beta 1000 . -chrY 25099139 25121882 BSR/Beta 1000 . -chrY 25122419 25160800 BSR/Beta 1000 . -chrY 25182404 25192372 BSR/Beta 1000 . -chrY 25217722 25219409 BSR/Beta 1000 . -chrY 25493588 25495275 BSR/Beta 1000 . -chrY 26148315 26148450 TAR1 1000 . -chrY 26586905 26609405 BSR/Beta 1000 . -chrY 26614745 26624983 BSR/Beta 1000 . -chrY 26656502 26672934 BSR/Beta 1000 . -chrY 26673902 26676170 BSR/Beta 1000 . -chrY 26682081 26693007 BSR/Beta 1000 . -chrY 26693984 26698547 BSR/Beta 1000 . -chrY 26732883 26755623 BSR/Beta 1000 . -chrY 26756160 26794538 BSR/Beta 1000 . -chrY 26816148 26826116 BSR/Beta 1000 . -chrY 26851466 26853153 BSR/Beta 1000 . -chrY 27109247 27110934 BSR/Beta 1000 . -chrY 27136281 27146249 BSR/Beta 1000 . -chrY 27167859 27206241 BSR/Beta 1000 . -chrY 27206778 27229502 BSR/Beta 1000 . -chrY 27263848 27268411 BSR/Beta 1000 . -chrY 27269388 27280315 BSR/Beta 1000 . -chrY 27286226 27288494 BSR/Beta 1000 . -chrY 27289462 27305895 BSR/Beta 1000 . -chrY 27337415 27347656 BSR/Beta 1000 . -chrY 27352996 27375497 BSR/Beta 1000 . -chrY 27813984 27814119 TAR1 1000 . -chrY 28555026 28555353 TAR1 1000 . -chrY 28784129 28819695 Satellite_repeat 1000 . -chrY 58819367 58917648 (CATTC)n 1000 . -chrY 58971913 58997782 (CATTC)n 1000 . -chrY 59361267 59362785 TAR1 1000 . +chr1 564449 570371 +chr1 724136 727043 +chr1 825006 825115 +chr1 2583334 2634374 +chr1 4363064 4363242 +chr1 5725866 5736651 +chr1 16839923 16841396 +chr1 38077347 38077423 +chr1 91852785 91853147 +chr1 104163724 104163860 +chr1 108112972 108113707 +chr1 121351474 121487059 +chr1 142535434 142543081 +chr1 142723256 142723968 +chr1 142792613 142793303 +chr1 142835822 142837333 +chr1 143274490 143284340 +chr1 145277108 145277572 +chr1 149033183 149035829 +chr1 156186169 156186712 +chr1 224199390 224204260 +chr1 233318467 233318516 +chr1 236260366 236260821 +chr1 237766308 237766764 +chr1 238105345 238105511 +chr1 238108025 238108378 +chr1 238108645 238109697 +chr10 18841533 18862467 +chr10 20035661 20037171 +chr10 36722282 36723650 +chr10 38772277 38819357 +chr10 38868892 38889025 +chr10 39076515 39155771 +chr10 42354835 42548642 +chr10 42596676 42602082 +chr10 42596700 42602110 +chr10 42661264 42667623 +chr10 42790522 42818398 +chr10 135498649 135502716 +chr11 6831669 6831838 +chr11 10529403 10531969 +chr11 48671444 48902406 +chr11 48931242 48964015 +chr11 50318471 50784078 +chr11 51090700 51374066 +chr11 51567242 51594226 +chr11 54694046 55027975 +chr11 73221660 73221946 +chr11 85194913 85195322 +chr11 87524468 87525005 +chr11 103275584 103281729 +chr11 122874287 122874443 +chr12 20704285 20704583 +chr12 34372315 34372825 +chr12 34432130 34857010 +chr12 37989447 38441828 +chr12 38531376 38531930 +chr12 41757383 41757545 +chr12 127650407 127651075 +chr12 132061320 132062046 +chr13 56545728 56545925 +chr13 110076444 110076782 +chr14 18999935 19056900 +chr14 32953263 32954381 +chr14 84637832 84639038 +chr14 90341302 90341516 +chr15 19999941 20044132 +chr16 32493036 32570826 +chr16 32590063 32598801 +chr16 33237130 33241330 +chr16 33864355 34023306 +chr16 34180542 34197081 +chr16 34530115 34542632 +chr16 35193580 35285885 +chr16 46385718 46456668 +chr16 46497639 46500515 +chr16 47538629 47539297 +chr17 19355538 19356096 +chr17 19502495 19506773 +chr17 21905167 21906712 +chr17 22018524 22032049 +chr17 22221073 22263006 +chr17 25263010 25268059 +chr17 25415551 25417559 +chr17 31149365 31149981 +chr17 33478114 33478372 +chr17 41381502 41382591 +chr17 41463538 41464075 +chr17 41464478 41465015 +chr17 41465562 41467288 +chr17 51183038 51183763 +chr17 55868618 55868752 +chr17 75158031 75158430 +chr18 96416 97552 +chr18 105658 112233 +chr18 2842252 2842356 +chr18 15393801 15393992 +chr18 18510894 18520356 +chr18 44126235 44126593 +chr18 45379603 45379864 +chr18 50319086 50319301 +chr18 77772846 77773065 +chr19 246006 247844 +chr19 22877614 22877696 +chr19 23235030 23235504 +chr19 24182398 24186210 +chr19 24385474 24633168 +chr19 27730611 28262682 +chr19 36066445 36066810 +chr19 36756398 36800948 +chr19 37759473 37797722 +chr19 44914313 44916340 +chr19 44960681 44962681 +chr2 739925 740994 +chr2 49456729 49457067 +chr2 88124390 88124903 +chr2 89830421 89880514 +chr2 90371401 90394776 +chr2 90443001 90545431 +chr2 91595080 91616015 +chr2 92267428 92326280 +chr2 115695017 115695281 +chr2 117781085 117781300 +chr2 132966248 132989300 +chr2 132994855 133007983 +chr2 133011824 133013298 +chr2 133036250 133040042 +chr2 133044095 133045945 +chr2 143848503 143848792 +chr2 148022736 148022878 +chr2 149639207 149639515 +chr2 156120500 156120610 +chr2 162135000 162139241 +chr2 230045426 230045796 +chr20 26257032 26320267 +chr20 29517710 29521147 +chr20 29803876 29833334 +chr20 55932703 55936114 +chr20 62916702 62918053 +chr21 9647205 9648529 +chr21 9694896 9704962 +chr21 9825451 9827612 +chr21 9827612 9845233 +chr21 9881895 9882569 +chr21 10084922 10088004 +chr21 10492876 10493049 +chr21 10599428 10599915 +chr21 10697886 10860890 +chr21 11186054 11188131 +chr21 14338127 14369791 +chr21 18800575 18800997 +chr21 27228003 27228242 +chr21 46796081 46796336 +chr22 16847814 16862659 +chr22 18876789 18884510 +chr3 25508897 25509131 +chr3 73159606 73161131 +chr3 75696297 75699304 +chr3 75717841 75720426 +chr3 80995858 81014459 +chr3 90311686 90507410 +chr3 93504815 93519133 +chr3 96335934 96337436 +chr3 160665423 160665642 +chr3 196625514 196625860 +chr3 197825427 197834080 +chr4 9987 12694 +chr4 12276463 12292424 +chr4 12641862 12642305 +chr4 21583630 21583719 +chr4 27732004 27732240 +chr4 47774268 47774416 +chr4 49085372 49342114 +chr4 49488472 49662085 +chr4 52659961 52688986 +chr4 56194229 56194584 +chr4 65473858 65473941 +chr4 68264186 68266830 +chr4 70296565 70296841 +chr4 76807083 76807320 +chr4 78929660 78929920 +chr4 156374749 156377226 +chr4 156384860 156387314 +chr4 163342479 163342744 +chr4 190190746 190203442 +chr4 190801869 190802909 +chr4 190943802 190943962 +chr4 190987268 190990949 +chr4 191026302 191044344 +chr5 17517177 17600940 +chr5 21477365 21497415 +chr5 34177882 34197574 +chr5 45908253 46411114 +chr5 49405493 49554574 +chr5 71146650 71146996 +chr5 79945807 79948223 +chr5 93903068 93906726 +chr5 97746525 97746679 +chr5 99381556 99390873 +chr5 105889063 105889263 +chr5 123095972 123097432 +chr5 134258949 134264271 +chr5 174541634 174542177 +chr6 58735349 58739031 +chr6 58745955 58780547 +chr6 61880095 61944008 +chr6 62189892 62206612 +chr6 62207809 62230644 +chr6 62283966 62284581 +chr6 133593944 133594201 +chr6 137059142 137059326 +chr6 150665074 150665281 +chr6 157731310 157735525 +chr7 43878355 43878530 +chr7 45291517 45291740 +chr7 56437808 56442977 +chr7 57253980 57254183 +chr7 57255310 57255444 +chr7 57261829 57261998 +chr7 57544726 57556913 +chr7 57811488 57836990 +chr7 57939184 58055539 +chr7 61054285 62454680 +chr7 64059157 64066183 +chr7 64951348 64956223 +chr7 68201468 68201673 +chr7 68527370 68527788 +chr7 80962907 80963147 +chr7 100550640 100551321 +chr7 142372972 142375638 +chr7 145694403 145694561 +chr8 155512 157639 +chr8 21455971 21456306 +chr8 32868966 32873279 +chr8 43092737 43097573 +chr8 43399486 43843604 +chr8 46838215 47457541 +chr8 47739043 47742797 +chr8 47750844 47776101 +chr8 56754955 56755418 +chr8 69218401 69218922 +chr8 70602248 70602620 +chr8 77114154 77114389 +chr8 100508010 100508287 +chr9 10435 11574 +chr9 4799734 4800000 +chr9 33656606 33659249 +chr9 42819021 42832395 +chr9 44070617 44070871 +chr9 44873123 44902307 +chr9 45355954 45357644 +chr9 45435109 45443517 +chr9 66494170 66494805 +chr9 66767710 66864329 +chr9 66970914 67005594 +chr9 67315122 67321036 +chr9 67789868 67792893 +chr9 68410775 68435115 +chr9 69677073 69687998 +chr9 69689770 69711497 +chr9 69947961 70011196 +chr9 70076144 70076855 +chr9 70318723 70327683 +chr9 72653073 72653572 +chr9 78790077 78790255 +chr9 79186574 79187026 +chr9 141019938 141021783 +chrM 1 16571 +chrX 55206111 55206740 +chrX 55207753 55208152 +chrX 55208300 55208643 +chrX 55208980 55209208 +chrX 55209655 55210006 +chrX 58330488 58330843 +chrX 58373806 58373962 +chrX 58377680 58377864 +chrX 58415350 58416387 +chrX 58432411 58432680 +chrX 58485887 58486241 +chrX 58488898 58494528 +chrX 58499466 58504235 +chrX 58506076 58528214 +chrX 58528184 58536883 +chrX 58544061 58582415 +chrX 61681834 61919683 +chrX 62003205 62041580 +chrX 83658929 83659019 +chrX 108297348 108297886 +chrX 114959057 115006437 +chrX 125605623 125607351 +chrX 125714985 125715338 +chrX 125864844 125864980 +chrX 125865719 125865874 +chrY 313470 313613 +chrY 3004989 3005175 +chrY 4212807 4212910 +chrY 7671817 7694928 +chrY 7726064 7730229 +chrY 7730734 7731598 +chrY 7735811 7752887 +chrY 7785067 7806311 +chrY 7806856 7814704 +chrY 7815230 7820478 +chrY 7829937 7832032 +chrY 7832744 7848695 +chrY 7870343 7873582 +chrY 7874115 7874584 +chrY 7875409 7885257 +chrY 7886545 7894591 +chrY 7898927 7916812 +chrY 7918790 7921352 +chrY 7926344 7936705 +chrY 7941130 7947438 +chrY 7948790 7964448 +chrY 8179010 8181143 +chrY 8181757 8213330 +chrY 8214629 8215637 +chrY 8220421 8230061 +chrY 8230686 8231546 +chrY 8240772 8265916 +chrY 8291535 8292942 +chrY 8294002 8295175 +chrY 8296944 8321375 +chrY 8325813 8325929 +chrY 8326678 8333466 +chrY 8334027 8342387 +chrY 8356544 8369346 +chrY 8909560 8909925 +chrY 8979478 8979585 +chrY 9072781 9072993 +chrY 9908430 9925608 +chrY 9981952 9982126 +chrY 10034864 10036712 +chrY 10040627 10045657 +chrY 10047773 10052533 +chrY 10053695 10057722 +chrY 10059394 10073694 +chrY 10075082 10075781 +chrY 10080736 10104539 +chrY 13104530 13144368 +chrY 13193966 13196535 +chrY 13252193 13259484 +chrY 13290177 13290667 +chrY 13445957 13490591 +chrY 13642186 13749784 +chrY 13798522 13870984 +chrY 19691913 19692524 +chrY 19764063 19776198 +chrY 19780600 19781704 +chrY 19783669 19796396 +chrY 19800068 19801419 +chrY 19808085 19817100 +chrY 19944298 19944581 +chrY 20235195 20235478 +chrY 20362679 20371694 +chrY 20378360 20379711 +chrY 20383383 20396110 +chrY 20398075 20399179 +chrY 20403581 20415713 +chrY 20487248 20487859 +chrY 23124788 23125577 +chrY 23149027 23151205 +chrY 23157969 23158245 +chrY 23159001 23167737 +chrY 23178886 23181770 +chrY 23220740 23223625 +chrY 23234125 23235822 +chrY 23236898 23248080 +chrY 23248729 23248851 +chrY 23899295 23899388 +chrY 23956449 23956628 +chrY 24247659 24247700 +chrY 24630999 24631040 +chrY 24953159 24975657 +chrY 24980997 24991235 +chrY 25022753 25039185 +chrY 25040153 25042421 +chrY 25048332 25059258 +chrY 25060235 25064798 +chrY 25099139 25121882 +chrY 25122419 25160800 +chrY 25182404 25192372 +chrY 25217722 25219409 +chrY 25493588 25495275 +chrY 26148315 26148450 +chrY 26586905 26609405 +chrY 26614745 26624983 +chrY 26656502 26672934 +chrY 26673902 26676170 +chrY 26682081 26693007 +chrY 26693984 26698547 +chrY 26732883 26755623 +chrY 26756160 26794538 +chrY 26816148 26826116 +chrY 26851466 26853153 +chrY 27109247 27110934 +chrY 27136281 27146249 +chrY 27167859 27206241 +chrY 27206778 27229502 +chrY 27263848 27268411 +chrY 27269388 27280315 +chrY 27286226 27288494 +chrY 27289462 27305895 +chrY 27337415 27347656 +chrY 27352996 27375497 +chrY 27813984 27814119 +chrY 28555026 28555353 +chrY 28784129 28819695 +chrY 58819367 58917648 +chrY 58971913 58997782 +chrY 59361267 59362785 diff --git a/resources/blacklistbed/hg38.bed b/resources/blacklistbed/hg38.bed index 2075b4d..a96479e 100644 --- a/resources/blacklistbed/hg38.bed +++ b/resources/blacklistbed/hg38.bed @@ -1,1050 +1,1049 @@ -Chr Start End Detailed Annotation Nearest TSS Mappability Overlap with ENCODE -chr1 124610979 124625614 ALR/Alpha|Satellite|centr EMBP1 Mappable ENCODE Overlap -chr1 124347449 124349827 ALR/Alpha|Satellite|centr EMBP1 Mappable ENCODE Overlap -chr1 123681389 123697714 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 124755617 124756133 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 228644488 228646810 TTS (NR_023363).10 RNA5S8 Mappable Unique -chr1 122763761 122771648 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 123074471 123077388 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 123698751 123699028 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 124082237 124085912 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 124195003 124199252 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 122822805 122852412 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 124079072 124081761 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 124637048 124650716 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 123923101 123930829 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 123947775 123954907 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 2651096 2657690 "intron (NM_001242672, intron 5 of 7)" MMEL1 Mappable Unique -chr1 123772279 123772518 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 123888372 123895580 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 124132073 124137242 ALR/Alpha|Satellite|centr EMBP1 Mappable ENCODE Overlap -chr1 123421242 123424555 ALR/Alpha|Satellite|centr EMBP1 Mappable ENCODE Overlap -chr1 122792518 122792713 ALR/Alpha|Satellite|centr EMBP1 Mappable ENCODE Overlap -chr1 123575612 123580150 ALR/Alpha|Satellite|centr EMBP1 Mappable ENCODE Overlap -chr1 123730701 123737589 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124192450 124193252 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122864530 122892414 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123457393 123461993 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124416522 124429776 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124488952 124492689 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123761364 123765317 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122974321 122975357 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124573689 124577060 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 2660041 2662057 "intron (NM_001242672, intron 5 of 7)" MMEL1 Lowly ENCODE Overlap -chr1 124666337 124666578 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124444870 124447910 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124628401 124632935 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123955788 123976252 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123749402 123749623 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123788987 123792333 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123353813 123358798 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123487838 123493348 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124185193 124186084 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 121742016 121776960 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124389047 124390123 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 248944611 248947412 (AGGGTT)n|Simple_repeat|Simple_repeat PGBD2 Lowly ENCODE Overlap -chr1 16615621 16615795 Intergenic NBPF1 Lowly ENCODE Overlap -chr1 124162104 124174735 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123769824 123771521 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122976387 122979388 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124046457 124046514 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123828506 123829677 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124487499 124487838 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123454191 123456805 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123831264 123840597 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123866133 123870135 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123207871 123216816 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123067262 123071930 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123671098 123680501 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123680799 123681034 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123787966 123788535 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 143183597 143277030 Intergenic LSP1P5 Lowly ENCODE Overlap -chr1 123841498 123841592 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123777239 123787683 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123004659 123060219 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123410850 123411000 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122967648 122973395 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 228608508 228616048 TTS (NR_023363).2 RNA5S3 Lowly ENCODE Overlap -chr1 124312508 124313152 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 2663197 2666377 "intron (NM_001242672, intron 5 of 7)" MMEL1 Lowly ENCODE Overlap -chr1 124037252 124040943 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 2658437 2659484 "intron (NM_001242672, intron 5 of 7)" MMEL1 Lowly ENCODE Overlap -chr1 123638914 123647813 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122758317 122763284 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123310280 123312959 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123944700 123947541 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 2696387 2697700 "intron (NM_001242672, intron 5 of 7)" MMEL1 Lowly ENCODE Overlap -chr1 123993045 123993143 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 228616110 228616994 TTS (NR_023363).4 RNA5S8 Lowly ENCODE Overlap -chr1 123809159 123825290 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123700538 123701366 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123292604 123293199 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124524705 124536570 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122853507 122863783 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124396134 124398614 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124462900 124469384 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 789517 792613 (GGAATG)n|Simple_repeat|Simple_repeat LOC100288069 Lowly ENCODE Overlap -chr1 122565737 122597777 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122660352 122712552 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123465637 123470989 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 16512350 16514335 TTS (NR_004400) RNU1-1 Lowly ENCODE Overlap -chr1 124711528 124748035 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123515909 123517288 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122906144 122915306 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123871258 123876903 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123990369 123992936 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123449989 123452433 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123658013 123658426 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 161460728 161466377 CpG FCGR2A Lowly ENCODE Overlap -chr1 124430835 124441228 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124633057 124633319 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123757476 123761007 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124652111 124665269 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123124556 123125047 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123793121 123804898 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123319246 123324771 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123314679 123317444 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123387599 123390748 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124303939 124311225 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124558602 124573677 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 2675075 2675937 "intron (NM_001242672, intron 5 of 7)" MMEL1 Lowly ENCODE Overlap -chr1 122813930 122821753 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122892854 122906013 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123183593 123187242 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124594049 124605596 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 16614858 16615354 Intergenic NBPF1 Lowly ENCODE Overlap -chr1 122599644 122617908 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 2755311 2760203 "intron (NM_001242672, intron 5 of 7)" TTC34 Lowly ENCODE Overlap -chr1 123955043 123955348 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123295606 123295739 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124024633 124024799 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123633969 123634047 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122502392 122558766 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123904701 123908708 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 2676476 2689992 "intron (NM_001242672, intron 5 of 7)" MMEL1 Lowly ENCODE Overlap -chr1 124593326 124593327 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124243016 124255477 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124193388 124194092 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122812476 122812926 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123187448 123187650 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123246292 123252731 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123345950 123353178 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123908832 123909015 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123865900 123866108 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123880442 123887992 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124605974 124606640 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123478972 123483857 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124127325 124131808 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123392121 123395225 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122655572 122659623 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 16725841 16728094 Intergenic ESPNP Lowly ENCODE Overlap -chr1 123471069 123472466 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123257533 123267929 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123487155 123487680 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123878887 123880095 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123721481 123724576 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123293396 123293989 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123648151 123653550 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123806472 123807799 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123484321 123484872 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123223300 123229067 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122988286 122988566 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124334073 124339709 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 228636195 228644351 GA-rich|Low_complexity|Low_complexity RHOU Lowly ENCODE Overlap -chr1 123750069 123757183 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123366175 123373760 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123133630 123149853 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124142769 124151448 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122750334 122757705 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124543344 124551494 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123463500 123464152 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123337837 123338665 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 228617880 228620677 promoter-TSS (NR_023363).5 RNA5S8 Lowly ENCODE Overlap -chr1 122559146 122563373 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124449186 124459787 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123705983 123709138 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123717922 123720330 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124553805 124556586 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124022068 124023445 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123774014 123776700 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124112936 124127192 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123703028 123703309 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123338733 123341125 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123534158 123538816 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122921571 122965108 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123739630 123746731 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123473265 123473765 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123078634 123090349 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123634201 123638786 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123267951 123272997 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 236712612 236716056 "intron (NM_001278344, intron 1 of 22)" ACTN2 Lowly ENCODE Overlap -chr1 124537250 124541856 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124058577 124074991 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123426130 123440706 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124634253 124634854 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124493000 124494360 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123977871 123982318 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123601299 123632580 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124233326 124233698 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124496911 124521316 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123581424 123587147 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123152211 123160608 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124295346 124303919 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 2667718 2674721 "intron (NM_001242672, intron 5 of 7)" MMEL1 Lowly ENCODE Overlap -chr1 161442212 161459350 CpG FCGR2A Lowly ENCODE Overlap -chr1 124236503 124241894 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123595138 123599775 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124416165 124416369 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122981432 122981579 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124558348 124558487 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122918760 122919060 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124401333 124410007 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123909020 123916403 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123567201 123572421 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123983540 123986717 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124460404 124460735 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123090393 123124055 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122989513 122991506 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123545968 123562717 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123725476 123729267 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124047216 124058353 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123125721 123129029 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124748208 124754755 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123709361 123710441 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123192365 123205196 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124157846 124161487 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123274274 123277786 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 161466446 161472738 CpG FCGR2A Lowly ENCODE Overlap -chr1 123232086 123238851 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123600135 123600404 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122981905 122984908 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124410105 124415973 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123000144 123004503 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123710782 123716188 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124042426 124046077 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124153959 124157292 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124523859 124524670 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124391089 124393688 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123160743 123179378 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124340068 124346843 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123078238 123078262 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123463270 123463288 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124288111 124292489 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 228620723 228624068 promoter-TSS (NR_023363).6 RNA5S17 Lowly ENCODE Overlap -chr1 122985198 122987949 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123501642 123505110 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123494306 123500148 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123299360 123308922 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123477134 123478791 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123918014 123920972 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123564074 123564609 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124187392 124191846 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123860085 123865862 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124137450 124141973 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123231456 123232068 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124668405 124698204 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123660028 123667802 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124029009 124035852 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124314206 124330916 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 628088 635923 TTS (NR_162149) MIR12136 Lowly ENCODE Overlap -chr1 124698889 124710105 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123654707 123657707 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122564484 122564628 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123327187 123336366 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124756241 124765560 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124587185 124593255 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123993263 124017467 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124577276 124577641 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123936407 123941483 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 144102590 144105633 (TGGCTGGCT)n|Simple_repeat|Simple_repeat FAM72C Lowly ENCODE Overlap -chr1 123063967 123066571 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 91386236 91388535 LSU-rRNA_Hsa|rRNA|rRNA HFM1 Lowly ENCODE Overlap -chr1 121965774 121969623 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123506859 123512351 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124203810 124232742 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124177846 124182735 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 224010839 224015910 (AATGG)n|Simple_repeat|Simple_repeat LOC100287497 Lowly ENCODE Overlap -chr1 123442350 123448859 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123336600 123336731 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123724579 123724815 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123668135 123668950 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123411051 123420183 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124350457 124387136 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 125165251 125171959 Intergenic EMBP1 Lowly ENCODE Overlap -chr1 122617993 122622038 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123587727 123593407 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123240864 123243602 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123452734 123453336 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123252764 123256027 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124024808 124027897 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123318612 123318659 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122712809 122715970 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123217618 123218459 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122716926 122720666 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124091699 124105529 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124470643 124487474 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123766306 123769701 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124579298 124584106 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123899406 123904231 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124018297 124021565 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123825521 123828486 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123517950 123531595 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122793709 122809534 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123485159 123486942 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124075556 124076291 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 2691502 2693971 "intron (NM_001242672, intron 5 of 7)" MMEL1 Lowly ENCODE Overlap -chr1 123374374 123383121 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123899167 123899184 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123073383 123074327 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122622921 122655193 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 125172600 125185576 Intergenic EMBP1 Lowly ENCODE Overlap -chr1 122772071 122792107 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123222073 123222104 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 123395736 123410588 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 124521887 124523497 ALR/Alpha|Satellite|centr EMBP1 Mappable ENCODE Overlap -chr1 122915620 122915759 ALR/Alpha|Satellite|centr EMBP1 Mappable ENCODE Overlap -chr1 16612489 16614272 "5' UTR (NM_017940, exon 1 of 29)" NBPF1 Mappable ENCODE Overlap -chr1 122720823 122749445 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 122992665 122999602 ALR/Alpha|Satellite|centr EMBP1 Mappable ENCODE Overlap -chr1 124551762 124552236 ALR/Alpha|Satellite|centr EMBP1 Lowly ENCODE Overlap -chr1 122916012 122916101 ALR/Alpha|Satellite|centr EMBP1 Mappable ENCODE Overlap -chr1 2747597 2755052 "intron (NM_001242672, intron 5 of 7)" TTC34 Mappable ENCODE Overlap -chr1 123841803 123858444 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 122810096 122810306 ALR/Alpha|Satellite|centr EMBP1 Lowly Unique -chr1 124586233 124586899 ALR/Alpha|Satellite|centr EMBP1 Lowly Unique -chr1 123187673 123191050 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 124258930 124285568 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 123279142 123292202 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 124765617 124785370 ALR/Alpha|Satellite|centr EMBP1 Mappable Unique -chr1 123129823 123133340 ALR/Alpha|Satellite|centr EMBP1 Mappable ENCODE Overlap -chr1 228624085 228635970 TTS (NR_023363).9 RNA5S14 Mappable ENCODE Overlap -chr1_KI270709v1_random 1 19452 Intergenic Lowly Unique -chr1_KI270711v1_random 7349 10549 Intergenic Lowly Unique -chr1_KI270712v1_random 57044 59379 (TGGCTGGCT)n|Simple_repeat|Simple_repeat Lowly Unique -chr1_KI270713v1_random 19745 23499 TTS (NR_004400).9 RNU1-2 Lowly Unique -chr10 38917532 38921312 (GAATG)n|Satellite|Satellite ACTR3BP5 Mappable ENCODE Overlap -chr10 38485929 38490812 Intergenic LINC00999 Mappable ENCODE Overlap -chr10 40555218 40558145 ALR/Alpha|Satellite|centr LOC441666 Mappable ENCODE Overlap -chr10 40184616 40184779 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 40085143 40086546 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 42316454 42321742 Intergenic LOC441666 Mappable ENCODE Overlap -chr10 40394887 40394946 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 40134029 40136698 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 41123812 41126690 ALR/Alpha|Satellite|centr LOC441666 Mappable ENCODE Overlap -chr10 42302263 42306136 Intergenic LOC441666 Mappable ENCODE Overlap -chr10 40975016 40977643 ALR/Alpha|Satellite|centr LOC441666 Mappable ENCODE Overlap -chr10 38784990 38787946 (TTCCA)n|Simple_repeat|Simple_repeat ACTR3BP5 Mappable ENCODE Overlap -chr10 42307404 42315736 Intergenic LOC441666 Lowly ENCODE Overlap -chr10 126946285 126949389 "intron (NM_001290223, intron 1 of 51)" DOCK1 Mappable ENCODE Overlap -chr10 40681674 40683032 ALR/Alpha|Satellite|centr LOC441666 Mappable ENCODE Overlap -chr10 40412067 40415257 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 40185985 40187776 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 40890943 40893719 ALR/Alpha|Satellite|centr LOC441666 Mappable ENCODE Overlap -chr10 40395146 40397876 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 41016424 41019108 ALR/Alpha|Satellite|centr LOC441666 Lowly ENCODE Overlap -chr10 40510552 40510803 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 40815111 40818385 ALR/Alpha|Satellite|centr LOC441666 Mappable ENCODE Overlap -chr10 40199982 40200234 ALR/Alpha|Satellite|centr ACTR3BP5 Lowly ENCODE Overlap -chr10 39968185 39968710 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 40667639 40670355 ALR/Alpha|Satellite|centr LOC441666 Mappable ENCODE Overlap -chr10 38807376 38810540 (TTCCA)n|Simple_repeat|Simple_repeat ACTR3BP5 Mappable ENCODE Overlap -chr10 42065293 42106174 Intergenic LOC441666 Lowly ENCODE Overlap -chr10 38799302 38801295 (TTCCA)n|Simple_repeat|Simple_repeat ACTR3BP5 Lowly ENCODE Overlap -chr10 40129941 40131107 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 38497910 38501672 Intergenic LINC00999 Mappable ENCODE Overlap -chr10 133685504 133691455 BSR/Beta|Satellite|Satellite FRG2B Mappable ENCODE Overlap -chr10 40961499 40963218 ALR/Alpha|Satellite|centr LOC441666 Mappable ENCODE Overlap -chr10 40287965 40290809 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 38572473 38574967 (AATGG)n|Simple_repeat|Simple_repeat ACTR3BP5 Mappable ENCODE Overlap -chr10 42315741 42315752 Intergenic LOC441666 Mappable ENCODE Overlap -chr10 40128252 40129424 ALR/Alpha|Satellite|centr ACTR3BP5 Lowly ENCODE Overlap -chr10 42165072 42168883 Intergenic LOC441666 Mappable ENCODE Overlap -chr10 38789940 38793846 (TTCCA)n|Simple_repeat|Simple_repeat ACTR3BP5 Mappable ENCODE Overlap -chr10 40933603 40935552 ALR/Alpha|Satellite|centr LOC441666 Mappable ENCODE Overlap -chr10 40366986 40369532 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable ENCODE Overlap -chr10 38903116 38905607 (GAATGGAATG)n|Simple_repeat|Simple_repeat ACTR3BP5 Mappable ENCODE Overlap -chr10 41842047 41917264 (ATGGA)n|Simple_repeat|Simple_repeat LOC441666 Mappable ENCODE Overlap -chr10 40509472 40509493 ALR/Alpha|Satellite|centr ACTR3BP5 Mappable Unique -chr10 42296616 42299414 Intergenic LOC441666 Mappable ENCODE Overlap -chr10 40767435 40770603 ALR/Alpha|Satellite|centr LOC441666 Mappable ENCODE Overlap -chr10 40539939 40542976 ALR/Alpha|Satellite|centr LOC441666 Mappable ENCODE Overlap -chr10 133679108 133679154 CpG FRG2B Mappable ENCODE Overlap -chr10 38523266 38530846 Intergenic LINC00999 Mappable ENCODE Overlap -chr10 133761260 133765408 BSR/Beta|Satellite|Satellite FRG2B Mappable ENCODE Overlap -chr10 40476591 40478349 ALR/Alpha|Satellite|centr ACTR3BP5 Lowly ENCODE Overlap -chr10 38577833 38582050 (AATGG)n|Simple_repeat|Simple_repeat ACTR3BP5 Lowly ENCODE Overlap -chr10 38494933 38497542 Intergenic LINC00999 Mappable ENCODE Overlap -chr10 133679249 133679353 CpG FRG2B Mappable ENCODE Overlap -chr11 3652764 3655645 "intron (NM_004314, intron 1 of 4)" ART1 Mappable ENCODE Overlap -chr11 94236861 94237383 L1PA2|LINE|L1 IZUMO1R Mappable ENCODE Overlap -chr11 10506890 10510998 promoter-TSS (NR_039705) MTRNR2L8 Mappable ENCODE Overlap -chr11 94237393 94239001 L1PA2|LINE|L1 IZUMO1R Lowly ENCODE Overlap -chr11 1016509 1018503 "exon (NM_005961, exon 31 of 33).2" MUC6 Mappable ENCODE Overlap -chr12 9003 11550 (CTAACC)n|Simple_repeat|Simple_repeat WASH8P Mappable ENCODE Overlap -chr12 35613810 35616091 ALR/Alpha|Satellite|centr ALG10 Mappable ENCODE Overlap -chr12 37245547 37247397 ALR/Alpha|Satellite|centr ALG10B Mappable ENCODE Overlap -chr12 37235710 37241245 ALR/Alpha|Satellite|centr ALG10B Mappable ENCODE Overlap -chr12 132239864 132243684 "intron (NM_001122636, intron 6 of 10)" LOC100130238 Mappable ENCODE Overlap -chr12 37265352 37266527 ALR/Alpha|Satellite|centr ALG10B Mappable ENCODE Overlap -chr13 17896880 17897978 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 18013137 18015392 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17053353 17056060 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17745515 17746936 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16244034 16244112 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17942778 17944168 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17711883 17712069 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16599254 16600279 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17150303 17151628 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16249181 16254341 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17643597 17646367 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16606651 16609402 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17095168 17096475 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16414425 16417030 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16672385 16672426 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17856076 17857762 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17721328 17721413 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17381911 17382356 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17303579 17306666 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17939255 17939991 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17416373 17416917 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17791894 17792146 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17182716 17184870 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16656928 16657044 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 18020584 18020716 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17935600 17938924 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17604283 17609260 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16697589 16697682 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17923781 17923923 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17143546 17146577 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17946624 17951696 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17117485 17119711 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16153317 16156028 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 18210701 18213661 HSATI|Satellite|Satellite FAM230C Lowly ENCODE Overlap -chr13 17877701 17877809 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17887934 17890703 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17664615 17669171 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17347058 17351187 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16923463 16927889 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17295139 17297764 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17750720 17753323 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17654891 17657917 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17219173 17219270 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16698050 16700278 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17328621 17328826 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17932523 17933722 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17531675 17534979 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17624570 17628053 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16484559 16486098 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17127062 17130174 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17120016 17120463 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16116481 16116678 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17884216 17887064 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17079136 17081535 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16697688 16698031 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17988261 17988436 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16918603 16921651 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16133786 16137594 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17239848 17243306 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17367784 17369863 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17372849 17378158 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16113312 16116428 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17543368 17544311 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17165760 17168258 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16116799 16116843 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17946055 17946089 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16462827 16463822 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17978596 17979303 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16497927 16500817 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17927090 17930378 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17536172 17536268 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17031820 17031985 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17582870 17585687 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 18029662 18029877 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17018417 17020181 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17585846 17585987 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17020904 17021039 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17400299 17405427 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17071688 17074162 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17845879 17848465 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16765152 16767662 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17912704 17915217 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16235967 16243773 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17154977 17158374 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17703323 17705629 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17826681 17832106 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16487849 16488103 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17874543 17877647 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16930162 16931331 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16687382 16691490 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17706732 17709513 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17877832 17878000 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 18000459 18005465 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17952346 17954794 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16597142 16599029 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17538263 17541448 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16255195 16257054 Intergenic FAM230C Lowly ENCODE Overlap -chr13 17318152 17320974 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17148028 17148998 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17206641 17209469 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17007241 17007246 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17309664 17311163 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17032633 17034654 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17642351 17643155 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17679715 17684928 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17878036 17880528 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17718673 17721311 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17026785 17030773 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 18030080 18032798 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17410217 17411716 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17113803 17116579 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17999420 18000378 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 109423125 109425342 Intergenic LINC00399 Lowly ENCODE Overlap -chr13 17792424 17795278 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17564083 17565098 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17216765 17218395 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16392184 16394696 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17738851 17745243 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17417100 17417333 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17798860 17802270 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16437130 16439835 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17628400 17631725 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17671567 17672338 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16159974 16162705 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17915249 17915268 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16244242 16246123 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17354483 17356857 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17923002 17923725 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17988560 17991066 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17922091 17922212 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 18009819 18013052 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16146408 16149034 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17485116 17487318 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 18005756 18008782 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17070384 17071097 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17791405 17791779 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 18021232 18022958 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16600613 16601047 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17094313 17094390 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17854761 17855955 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16882765 16884187 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16656324 16656785 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17004782 17007171 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17841209 17842722 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17916147 17917119 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16848379 16848894 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17391380 17393955 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16942345 16944804 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17839923 17841144 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16923061 16923291 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16856329 16856452 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17323756 17325638 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16229236 16235037 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17177841 17180742 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17788889 17790682 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17993993 17998725 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16246475 16246855 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17817804 17822642 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16826275 16827838 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17417958 17419021 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17031088 17031801 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17955477 17956002 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17697792 17700499 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 18025886 18028639 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17756295 17759896 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17860073 17865089 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17263467 17266339 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17515140 17519684 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 16851515 16851797 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17979450 17981547 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17230401 17233567 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17243411 17245204 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17778067 17780938 ALR/Alpha|Satellite|centr FAM230C Lowly ENCODE Overlap -chr13 17172503 17175298 ALR/Alpha|Satellite|centr FAM230C Mappable ENCODE Overlap -chr13 17993819 17993835 ALR/Alpha|Satellite|centr FAM230C Mappable ENCODE Overlap -chr14 16091961 16105537 (ATTCC)n|Simple_repeat|Simple_repeat OR11H12 Mappable ENCODE Overlap -chr14 105230006 105232915 "intron (NM_001242789, intron 1 of 12)" BRF1 Mappable ENCODE Overlap -chr14_GL000225v1_random 105690 136390 BSR/Beta|Satellite|Satellite Lowly Unique -chr14_GL000225v1_random 89351 104131 BSR/Beta|Satellite|Satellite Lowly Unique -chr14_GL000225v1_random 136395 140413 BSR/Beta|Satellite|Satellite Lowly Unique -chr14_GL000225v1_random 1666 8760 BSR/Beta|Satellite|Satellite Lowly Unique -chr14_GL000225v1_random 37408 38072 Intergenic Lowly Unique -chr14_GL000225v1_random 39176 89339 CpG Lowly Unique -chr14_GL000225v1_random 30656 36652 BSR/Beta|Satellite|Satellite Lowly Unique -chr14_GL000225v1_random 9530 30503 BSR/Beta|Satellite|Satellite Lowly Unique -chr14_GL000225v1_random 195384 199785 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr14_KI270723v1_random 33989 38115 Intergenic Lowly Unique -chr14_KI270724v1_random 1 2096 LSAU|Satellite|Satellite Lowly Unique -chr15 19774748 19781046 ALR/Alpha|Satellite|centr CHEK2P2 Mappable ENCODE Overlap -chr15 17079519 17084551 (GGAAT)n|Simple_repeat|Simple_repeat CHEK2P2 Mappable ENCODE Overlap -chr15 19781269 19782029 ALR/Alpha|Satellite|centr CHEK2P2 Mappable ENCODE Overlap -chr16 38264960 38268929 ALR/Alpha|Satellite|centr LINC02167 Mappable Unique -chr16 33335395 33340544 (TGGCTTGGC)n|Simple_repeat|Simple_repeat LOC105369266 Mappable ENCODE Overlap -chr16 90115865 90118991 "intron (NR_126161, intron 3 of 3)" FAM157C Mappable ENCODE Overlap -chr16 34609198 34611771 Intergenic CCNYL3 Mappable ENCODE Overlap -chr16 38274918 38281137 ALR/Alpha|Satellite|centr LINC02167 Mappable ENCODE Overlap -chr16 46379683 46402990 Intergenic ANKRD26P1 Mappable ENCODE Overlap -chr16 34570511 34577757 (GAATG)n|Satellite|Satellite CCNYL3 Mappable ENCODE Overlap -chr16 34095258 34100789 Intergenic MIR9901 Mappable ENCODE Overlap -chr16 34579966 34597675 Intergenic CCNYL3 Mappable ENCODE Overlap -chr16 34697614 34698226 Intergenic CCNYL3 Mappable ENCODE Overlap -chr16 34061433 34067253 AluYh9|SINE|Alu MIR9901 Mappable ENCODE Overlap -chr17 23015137 23017694 ALR/Alpha|Satellite|centr MTRNR2L1 Mappable ENCODE Overlap -chr17 26567361 26568148 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 26935184 26941957 (GAATG)n|Satellite|Satellite LOC105371703 Mappable ENCODE Overlap -chr17 25388774 25391334 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 43234260 43235297 promoter-TSS (NR_002716) RNU2-1 Mappable ENCODE Overlap -chr17 22520192 22522698 Intergenic MTRNR2L1 Mappable ENCODE Overlap -chr17 26824538 26827116 Intergenic LOC105371703 Mappable ENCODE Overlap -chr17 25787486 25789678 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 25351848 25354673 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 26827179 26830212 Intergenic LOC105371703 Mappable ENCODE Overlap -chr17 24149445 24152769 ALR/Alpha|Satellite|centr MTRNR2L1 Mappable ENCODE Overlap -chr17 26624404 26626919 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 25568022 25570460 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 115876 119087 Intergenic SCGB1C2 Mappable ENCODE Overlap -chr17 26602416 26605714 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 23581842 23584984 ALR/Alpha|Satellite|centr MTRNR2L1 Mappable ENCODE Overlap -chr17 26784244 26785873 Intergenic LOC105371703 Mappable ENCODE Overlap -chr17 43281692 43285869 TTS (NR_002716).8 RNU2-1 Lowly ENCODE Overlap -chr17 43232334 43233864 TTS (NR_002716) RNU2-1 Lowly ENCODE Overlap -chr17 25571866 25574916 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 43276929 43279827 promoter-TSS (NR_002716).7 RNU2-1 Mappable ENCODE Overlap -chr17 26872121 26872359 (GAATG)n|Satellite|Satellite LOC105371703 Mappable ENCODE Overlap -chr17 21851874 21854502 (AATGG)n|Simple_repeat|Simple_repeat KCNJ18 Mappable ENCODE Overlap -chr17 26593506 26597692 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 26139235 26142549 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 23067523 23070190 ALR/Alpha|Satellite|centr MTRNR2L1 Mappable ENCODE Overlap -chr17 25382608 25385005 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 26547832 26550522 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 43250513 43253389 promoter-TSS (NR_002716).5 RNU2-1 Mappable ENCODE Overlap -chr17 1062389 1066145 "intron (NM_001322840, intron 10 of 22).2" ABR Mappable ENCODE Overlap -chr17 24186508 24189789 ALR/Alpha|Satellite|centr MTRNR2L1 Mappable ENCODE Overlap -chr17 43287867 43290714 Intergenic RNU2-1 Mappable ENCODE Overlap -chr17 25073233 25075710 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 26878005 26886980 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 313684 316768 "intron (NM_006987, intron 5 of 9).2" LOC100506388 Mappable ENCODE Overlap -chr17 43245212 43247867 promoter-TSS (NR_002716).4 RNU2-1 Mappable ENCODE Overlap -chr17 22976412 22977953 ALR/Alpha|Satellite|centr MTRNR2L1 Mappable ENCODE Overlap -chr17 43264248 43267017 L1PA8|LINE|L1 RNU2-1 Mappable ENCODE Overlap -chr17 21856405 21856412 (AATGG)n|Simple_repeat|Simple_repeat KCNJ18 Mappable ENCODE Overlap -chr17 23189141 23191663 ALR/Alpha|Satellite|centr MTRNR2L1 Mappable ENCODE Overlap -chr17 26618168 26621523 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 25919036 25921580 ALR/Alpha|Satellite|centr LOC105371703 Mappable ENCODE Overlap -chr17 21967190 21993012 (ATGGA)n|Simple_repeat|Simple_repeat UBBP4 Mappable ENCODE Overlap -chr17 26854870 26856944 (TGGAA)n|Simple_repeat|Simple_repeat LOC105371703 Mappable ENCODE Overlap -chr17 121351 125557 L1MC3|LINE|L1 SCGB1C2 Mappable ENCODE Overlap -chr17_GL000205v2_random 86989 90907 Intergenic MGC70870 Lowly Unique -chr17_GL000205v2_random 26 3428 CER|Satellite|Satellite MGC70870 Lowly Unique -chr17_GL000205v2_random 7379 7759 CER|Satellite|Satellite MGC70870 Lowly Unique -chr17_GL000205v2_random 3848 7071 CER|Satellite|Satellite MGC70870 Lowly Unique -chr17_KI270729v1_random 160013 162123 Intergenic Lowly Unique -chr17_KI270729v1_random 19213 29747 (GAATG)n|Satellite|Satellite Lowly Unique -chr17_KI270729v1_random 45511 48698 (GAATG)n|Satellite|Satellite Lowly Unique -chr17_KI270729v1_random 1 7213 (TTCCA)n|Simple_repeat|Simple_repeat Lowly Unique -chr17_KI270729v1_random 9482 14680 (ATTCC)n|Simple_repeat|Simple_repeat Lowly Unique -chr17_KI270729v1_random 55466 60276 (GAATGGAATG)n|Simple_repeat|Simple_repeat Lowly Unique -chr17_KI270730v1_random 101867 111086 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr17_KI270730v1_random 95356 100621 (GAATG)n|Satellite|Satellite Lowly Unique -chr17_KI270730v1_random 80509 93823 (GAATG)n|Satellite|Satellite Lowly Unique -chr18 9028 11550 (CCCTAA)n|Simple_repeat|Simple_repeat LINC02564 Mappable ENCODE Overlap -chr18 20560617 20563418 ALR/Alpha|Satellite|centr ROCK1 Mappable ENCODE Overlap -chr18 105276 113531 "non-coding (NR_033770, exon 1 of 5)" ROCK1P1 Mappable ENCODE Overlap -chr18 79618344 79620846 Intergenic LOC284240 Mappable ENCODE Overlap -chr19 54188605 54191272 promoter-TSS (NM_001146056).2 MBOAT7 Mappable ENCODE Overlap -chr19 36279514 36282602 SST1|Satellite|centr LOC100134317 Mappable ENCODE Overlap -chr19 37291909 37295660 (ACAG)n|Simple_repeat|Simple_repeat ZNF875 Lowly ENCODE Overlap -chr19 7449308 7452123 "intron (NM_001130955, intron 5 of 19)" ARHGEF18 Mappable ENCODE Overlap -chr19 37290463 37291465 CpG ZNF875 Mappable ENCODE Overlap -chr19 36300186 36303419 SST1|Satellite|centr LOC100134317 Mappable ENCODE Overlap -chr19 24890430 24896738 ALR/Alpha|Satellite|centr HAVCR1P1 Mappable Unique -chr2 89822969 89823237 (ATTCC)n|Simple_repeat|Simple_repeat LOC101927050 Mappable ENCODE Overlap -chr2 89818404 89821968 (ATTCC)n|Simple_repeat|Simple_repeat LOC101927050 Mappable ENCODE Overlap -chr2 89814061 89814505 (ATTCC)n|Simple_repeat|Simple_repeat LOC101927050 Mappable ENCODE Overlap -chr2 89810575 89813442 (ATTCC)n|Simple_repeat|Simple_repeat LOC101927050 Mappable ENCODE Overlap -chr2 89814629 89817620 (ATTCC)n|Simple_repeat|Simple_repeat LOC101927050 Mappable ENCODE Overlap -chr2 91420365 91423530 Intergenic LSP1P4 Mappable ENCODE Overlap -chr2 89805597 89807370 (ATCAAATGGA)n|Simple_repeat|Simple_repeat LOC101927050 Mappable ENCODE Overlap -chr2 90379564 90403503 Intergenic LOC101927050 Mappable ENCODE Overlap -chr2 89823396 89842268 (ATTCC)n|Simple_repeat|Simple_repeat LOC101927050 Mappable ENCODE Overlap -chr20 31232160 31233573 Intergenic DEFB115 Mappable ENCODE Overlap -chr20 31176519 31179840 (GGAAT)n|Simple_repeat|Simple_repeat DEFB115 Lowly ENCODE Overlap -chr20 28818144 28818512 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr20 28511375 28514724 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr20 28784667 28786930 ALR/Alpha|Satellite|centr FRG1CP Lowly ENCODE Overlap -chr20 31181856 31189491 (GGAAT)n|Simple_repeat|Simple_repeat DEFB115 Mappable ENCODE Overlap -chr20 28516883 28518637 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr20 28815563 28816341 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr20 31228459 31231680 Intergenic DEFB115 Lowly ENCODE Overlap -chr20 27180808 27182094 ALR/Alpha|Satellite|centr MIR663AHG Mappable ENCODE Overlap -chr20 28839720 28842865 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr20 26540721 26543455 ALR/Alpha|Satellite|centr MIR663AHG Mappable ENCODE Overlap -chr20 29884447 29885678 ALR/Alpha|Satellite|centr MIR4477A Mappable ENCODE Overlap -chr20 31050520 31077638 (GGAAT)n|Simple_repeat|Simple_repeat DEFB115 Mappable ENCODE Overlap -chr20 28888219 28891252 Intergenic FRG1DP Mappable ENCODE Overlap -chr20 26489265 26489874 ALR/Alpha|Satellite|centr MIR663AHG Mappable ENCODE Overlap -chr20 31224415 31227417 Intergenic DEFB115 Mappable ENCODE Overlap -chr20 28819957 28823272 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr20 26601374 26608712 ALR/Alpha|Satellite|centr MIR663AHG Mappable ENCODE Overlap -chr20 28805290 28808241 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr20 31239887 31243476 Intergenic DEFB115 Mappable ENCODE Overlap -chr20 31166568 31167807 (AATGG)n|Simple_repeat|Simple_repeat DEFB115 Mappable ENCODE Overlap -chr20 29261354 29264856 ALR/Alpha|Satellite|centr FRG2EP Mappable Unique -chr20 28307014 28309467 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr20 28781706 28784563 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr20 31170535 31172967 (GGAAT)n|Simple_repeat|Simple_repeat DEFB115 Mappable ENCODE Overlap -chr20 31168211 31169703 (GGAAT)n|Simple_repeat|Simple_repeat DEFB115 Mappable ENCODE Overlap -chr20 28896358 28899883 (CCATT)n|Simple_repeat|Simple_repeat FRG1DP Mappable ENCODE Overlap -chr20 31090368 31091746 (GGAAT)n|Simple_repeat|Simple_repeat DEFB115 Mappable ENCODE Overlap -chr20 31173003 31173426 (GGAAT)n|Simple_repeat|Simple_repeat DEFB115 Mappable ENCODE Overlap -chr20 31156073 31160110 (TGGAA)n|Simple_repeat|Simple_repeat DEFB115 Mappable ENCODE Overlap -chr20 59234 67210 Intergenic DEFB125 Mappable ENCODE Overlap -chr20 28493663 28499706 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr20 29121594 29123538 MER5A1|DNA|hAT-Charlie FRG1DP Mappable ENCODE Overlap -chr20 31190204 31190333 (GGAAT)n|Simple_repeat|Simple_repeat DEFB115 Mappable ENCODE Overlap -chr20 28548723 28550182 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr20 28787339 28787377 ALR/Alpha|Satellite|centr FRG1CP Mappable ENCODE Overlap -chr21 10653993 10663675 (TCCATTCCAT)n|Simple_repeat|Simple_repeat TPTE Mappable ENCODE Overlap -chr21 10699029 10699402 (TTCCA)n|Simple_repeat|Simple_repeat TPTE Mappable ENCODE Overlap -chr21 10428560 10428597 "intron (NM_001187, intron 3 of 4)" BAGE2 Mappable ENCODE Overlap -chr21 7256313 7262762 (TGGAA)n|Simple_repeat|Simple_repeat LOC102724219 Mappable ENCODE Overlap -chr21 10687705 10698999 (TTCCA)n|Simple_repeat|Simple_repeat TPTE Mappable ENCODE Overlap -chr21 10683389 10686769 (TTCCA)n|Simple_repeat|Simple_repeat TPTE Mappable ENCODE Overlap -chr21 10700414 10710804 (TTCCA)n|Simple_repeat|Simple_repeat TPTE Mappable ENCODE Overlap -chr21 10268901 10273604 (TA)n|Simple_repeat|Simple_repeat BAGE Mappable ENCODE Overlap -chr21 9245189 9250252 Intergenic TEKT4P2 Mappable ENCODE Overlap -chr21 10752005 10756855 ALR/Alpha|Satellite|centr TPTE Mappable ENCODE Overlap -chr21 10719044 10720169 (TTCCA)n|Simple_repeat|Simple_repeat TPTE Mappable ENCODE Overlap -chr21 10796208 10798236 ALR/Alpha|Satellite|centr TPTE Mappable Unique -chr21 10729126 10738634 (TCCAT)n|Simple_repeat|Simple_repeat TPTE Mappable Unique -chr21 10391655 10393390 L2|LINE|L2 BAGE Mappable ENCODE Overlap -chr21 10798373 10799432 ALR/Alpha|Satellite|centr TPTE Mappable ENCODE Overlap -chr21 8808979 8812258 ACRO1|Satellite|acro MIR3648-1 Mappable ENCODE Overlap -chr21 7932046 7935094 (ATTCCATTCC)n|Simple_repeat|Simple_repeat KCNE1B Mappable ENCODE Overlap -chr21 10361620 10363358 L1MA2|LINE|L1 BAGE Mappable ENCODE Overlap -chr21 7935422 7940005 (ATTCCATTCC)n|Simple_repeat|Simple_repeat KCNE1B Mappable ENCODE Overlap -chr21 7914978 7919785 (ATTCCATTCC)n|Simple_repeat|Simple_repeat KCNE1B Mappable ENCODE Overlap -chr21 8201552 8261964 AluSz|SINE|Alu MIR6724-4 Mappable ENCODE Overlap -chr21 10710911 10718875 (TTCCA)n|Simple_repeat|Simple_repeat TPTE Mappable ENCODE Overlap -chr21 10720474 10728504 (TCCAT)n|Simple_repeat|Simple_repeat TPTE Mappable ENCODE Overlap -chr21 10804494 10807620 ALR/Alpha|Satellite|centr TPTE Mappable ENCODE Overlap -chr21 5326890 5330910 AluYj4|SINE|Alu LOC102724159 Mappable ENCODE Overlap -chr21 6368536 6373565 Intergenic CBS Mappable ENCODE Overlap -chr21 7940721 7945695 (ATTCCATTCC)n|Simple_repeat|Simple_repeat KCNE1B Mappable ENCODE Overlap -chr21 10665364 10681351 (TTCCA)n|Simple_repeat|Simple_repeat TPTE Mappable ENCODE Overlap -chr21 7922196 7931111 (ATTCCATTCC)n|Simple_repeat|Simple_repeat KCNE1B Mappable ENCODE Overlap -chr21 10807667 10808020 ALR/Alpha|Satellite|centr TPTE Mappable ENCODE Overlap -chr21 10800154 10800890 ALR/Alpha|Satellite|centr TPTE Mappable ENCODE Overlap -chr21 7946160 7958748 (CATTC)n|Satellite|Satellite KCNE1B Mappable ENCODE Overlap -chr21 8985911 8989787 TTS (NR_037421).2 MIR10396A Mappable ENCODE Overlap -chr21 10324539 10327338 HSATI|Satellite|Satellite BAGE Mappable ENCODE Overlap -chr21 10686799 10686855 (TTCCA)n|Simple_repeat|Simple_repeat TPTE Mappable ENCODE Overlap -chr21 10426777 10428455 "intron (NM_001187, intron 3 of 4)" BAGE2 Mappable ENCODE Overlap -chr21 8384656 8473309 AluSp|SINE|Alu MIR6724-1 Mappable ENCODE Overlap -chr22 11210160 11215577 SAR|Satellite|Satellite FRG1FP Mappable ENCODE Overlap -chr22 18729480 18731694 AluSc8|SINE|Alu FAM230E Mappable ENCODE Overlap -chr22 12174634 12177777 ACRO1|Satellite|acro LOC102723769 Mappable ENCODE Overlap -chr22 12690973 12694171 BSR/Beta|Satellite|Satellite LOC102723769 Mappable ENCODE Overlap -chr22 18895123 18897647 AluSc8|SINE|Alu FAM230F Mappable ENCODE Overlap -chr22 50806876 50809467 (AGGGTT)n|Simple_repeat|Simple_repeat RPL23AP82 Mappable ENCODE Overlap -chr22 11022253 11024389 Intergenic FRG1FP Mappable ENCODE Overlap -chr22 16345779 16354945 (GGAAT)n|Simple_repeat|Simple_repeat CCT8L2 Mappable ENCODE Overlap -chr22 11367998 11371880 ALR/Alpha|Satellite|centr FRG1FP Mappable ENCODE Overlap -chr22 10716070 10731276 (TCCATTCCAT)n|Simple_repeat|Simple_repeat FRG1FP Mappable ENCODE Overlap -chr22 16356082 16361451 (GGAAT)n|Simple_repeat|Simple_repeat CCT8L2 Mappable ENCODE Overlap -chr22 11812787 11816849 ACRO1|Satellite|acro LOC102723769 Mappable ENCODE Overlap -chr22_KI270733v1_random 117288 179772 AluSz|SINE|Alu RNA28SN2 Lowly Unique -chr22_KI270734v1_random 120388 122914 AluSc8|SINE|Alu LOC102724770 Lowly Unique -chr22_KI270735v1_random 38514 42811 (ATTCC)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 86945 87728 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 47146 51395 (TGGAGTGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 63231 66185 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 81973 86084 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 136134 140350 (GAATG)n|Satellite|Satellite Lowly Unique -chr22_KI270736v1_random 131362 135297 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 76967 77087 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 161047 164535 (GAATG)n|Satellite|Satellite Lowly Unique -chr22_KI270736v1_random 165492 168910 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 51786 54840 (TGGAGTGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 153598 154722 (GAATG)n|Satellite|Satellite Lowly Unique -chr22_KI270736v1_random 144303 153354 (GAATG)n|Satellite|Satellite Lowly Unique -chr22_KI270736v1_random 95664 105091 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 109434 110514 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 128647 129777 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 111003 115086 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 169771 176702 Intergenic Lowly Unique -chr22_KI270736v1_random 178428 181920 Intergenic Lowly Unique -chr22_KI270736v1_random 88590 92411 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 129980 130603 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 230 3329 (ATGGA)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 154901 159132 (GAATG)n|Satellite|Satellite Lowly Unique -chr22_KI270736v1_random 60991 62109 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 58693 60667 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 115254 122892 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 77202 81530 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 72297 75263 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270736v1_random 123794 128009 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270737v1_random 79010 80504 Intergenic Lowly Unique -chr22_KI270737v1_random 30421 40521 (TCCAT)n|Simple_repeat|Simple_repeat Lowly Unique -chr22_KI270737v1_random 23114 29485 (TCCAT)n|Simple_repeat|Simple_repeat Lowly Unique -chr3 93469362 93471801 SAR|Satellite|Satellite PROS1 Mappable ENCODE Overlap -chr3 93711664 93712437 ALR/Alpha|Satellite|centr PROS1 Mappable ENCODE Overlap -chr3 91548591 91554130 ALR/Alpha|Satellite|centr PROS1 Mappable ENCODE Overlap -chr3 197389421 197389902 Intergenic DLG1 Mappable ENCODE Overlap -chr3 198172030 198174477 (AGGGTT)n|Simple_repeat|Simple_repeat FAM157A Mappable ENCODE Overlap -chr3 198167382 198170281 "intron (NR_146164, intron 4 of 17)" FAM157A Lowly ENCODE Overlap -chr3 9002 11842 (CTAACC)n|Simple_repeat|Simple_repeat LINC01986 Mappable ENCODE Overlap -chr3 93706888 93710048 ALR/Alpha|Satellite|centr PROS1 Mappable ENCODE Overlap -chr3 75667816 75670647 CpG LINC00960 Mappable ENCODE Overlap -chr3 96616287 96619133 Intergenic EPHA6 Mappable ENCODE Overlap -chr4 49322045 49325033 ACRO1|Satellite|acro CWH43 Mappable ENCODE Overlap -chr4 49630300 49659095 (GAATG)n|Satellite|Satellite CWH43 Mappable ENCODE Overlap -chr4 49708071 49712961 SAR|Satellite|Satellite CWH43 Mappable ENCODE Overlap -chr4 190175302 190182802 BSR/Beta|Satellite|Satellite DUX4 Mappable ENCODE Overlap -chr4 190082751 190083066 CpG DUX4 Mappable ENCODE Overlap -chr4 190020660 190023773 CpG FRG2 Mappable ENCODE Overlap -chr4 1433989 1436603 Intergenic NKX1-1 Mappable ENCODE Overlap -chr4 190121457 190124076 (AGGGTT)n|Simple_repeat|Simple_repeat DUX4 Mappable ENCODE Overlap -chr4 49090233 49157664 (TCCAT)n|Simple_repeat|Simple_repeat CWH43 Lowly ENCODE Overlap -chr4 51106159 51108566 SAR|Satellite|Satellite DCUN1D4 Mappable ENCODE Overlap -chr4 49510010 49516194 (CA)n|Simple_repeat|Simple_repeat CWH43 Mappable ENCODE Overlap -chr4_GL000008v2_random 1 8337 Intergenic ANKRD20A12P Lowly Unique -chr5 9009 12786 (TAACCC)n|Simple_repeat|Simple_repeat PLEKHG4B Mappable ENCODE Overlap -chr5 49620931 49628481 ALR/Alpha|Satellite|centr EMB Mappable ENCODE Overlap -chr5 80649491 80652837 promoter-TSS (NM_001190470) MTRNR2L2 Mappable ENCODE Overlap -chr5 50139509 50139815 ALR/Alpha|Satellite|centr EMB Mappable ENCODE Overlap -chr5 17591996 17597406 MLT1E3|LTR|ERVL-MaLR H3.Y Lowly ENCODE Overlap -chr5 17524212 17529170 Intergenic LINC02218 Mappable ENCODE Overlap -chr5 34188278 34193784 "non-coding (NR_157803, exon 1 of 1)" LOC646652 Mappable ENCODE Overlap -chr5 134924083 134928692 "intron (NM_032151, intron 2 of 3)" PCBD2 Mappable ENCODE Overlap -chr5 17597460 17599261 Intergenic H3.Y Mappable ENCODE Overlap -chr5 49598396 49604131 (TGGAA)n|Simple_repeat|Simple_repeat EMB Mappable ENCODE Overlap -chr5 17584091 17585523 Intergenic H3.Y Mappable ENCODE Overlap -chr5 49629731 49634740 ALR/Alpha|Satellite|centr EMB Mappable ENCODE Overlap -chr5 34186729 34187148 "intron (NR_146599, intron 2 of 11)" LOC646652 Mappable ENCODE Overlap -chr5 47295868 47300778 ALR/Alpha|Satellite|centr HCN1 Mappable ENCODE Overlap -chr5 2144865 2147341 Intergenic LOC100506858 Mappable ENCODE Overlap -chr5 49665174 49668431 (CATTC)n|Satellite|Satellite EMB Mappable ENCODE Overlap -chr5 50141319 50141921 ALR/Alpha|Satellite|centr EMB Mappable ENCODE Overlap -chr5 49608847 49619600 ALR/Alpha|Satellite|centr EMB Mappable ENCODE Overlap -chr5 49640990 49647802 ALR/Alpha|Satellite|centr EMB Lowly ENCODE Overlap -chr5 17517750 17523690 AluSx|SINE|Alu LINC02218 Mappable ENCODE Overlap -chr5 49655272 49662871 (TCCAT)n|Simple_repeat|Simple_repeat EMB Mappable ENCODE Overlap -chr5 47306576 47310036 ALR/Alpha|Satellite|centr HCN1 Mappable ENCODE Overlap -chr5_GL000208v1_random 90558 92621 ALR/Alpha|Satellite|centr Lowly Unique -chr6 157309365 157315191 "intron (NM_018452, intron 3 of 3)" TMEM242 Mappable ENCODE Overlap -chr6 59718138 59718529 ALR/Alpha|Satellite|centr LINC00680-GUSBP4 Mappable ENCODE Overlap -chr6 170397348 170400442 "intron (NM_001286381, intron 7 of 8).2" MIR4644 Lowly ENCODE Overlap -chr6 862141 864174 Intergenic LOC101927691 Mappable ENCODE Overlap -chr6 59640507 59641284 ALR/Alpha|Satellite|centr LINC00680-GUSBP4 Lowly ENCODE Overlap -chr6 58783432 58784719 ALR/Alpha|Satellite|centr LINC00680-GUSBP4 Lowly ENCODE Overlap -chr6 58996337 58998871 ALR/Alpha|Satellite|centr LINC00680-GUSBP4 Mappable ENCODE Overlap -chr6 58793187 58793265 ALR/Alpha|Satellite|centr LINC00680-GUSBP4 Mappable ENCODE Overlap -chr6 58784734 58786253 ALR/Alpha|Satellite|centr LINC00680-GUSBP4 Lowly ENCODE Overlap -chr6 58792241 58793118 ALR/Alpha|Satellite|centr LINC00680-GUSBP4 Mappable ENCODE Overlap -chr6 60231805 60232035 ALR/Alpha|Satellite|centr MTRNR2L9 Mappable ENCODE Overlap -chr6 370247 373135 (AGCAGC)n|Simple_repeat|Simple_repeat IRF4 Mappable ENCODE Overlap -chr7 57495340 57497718 Intergenic ZNF716 Mappable ENCODE Overlap -chr7 60309518 60312051 ALR/Alpha|Satellite|centr ZNF716 Mappable ENCODE Overlap -chr7 58034763 58037384 Intergenic ZNF716 Mappable ENCODE Overlap -chr7 100956534 100959960 "exon (NM_005960, exon 2 of 12)" MUC3A Mappable ENCODE Overlap -chr7 158914463 158916767 "intron (NM_001350918, intron 16 of 26)" WDR60 Mappable ENCODE Overlap -chr7 58032104 58034587 Intergenic ZNF716 Mappable ENCODE Overlap -chr7 57493144 57494128 Intergenic ZNF716 Lowly ENCODE Overlap -chr7 61055086 61056354 Intergenic ZNF733P Lowly ENCODE Overlap -chr7 62349293 62351966 Intergenic ZNF733P Mappable ENCODE Overlap -chr7 57486422 57491361 Intergenic ZNF716 Mappable ENCODE Overlap -chr7 158145977 158150149 "intron (NM_130843, intron 6 of 21)" LOC100506585 Mappable ENCODE Overlap -chr7 56369384 56375717 Intergenic LOC650226 Mappable ENCODE Overlap -chr7 65488410 65491158 (CCATT)n|Simple_repeat|Simple_repeat LOC101929322 Mappable ENCODE Overlap -chr7 59292148 59293599 ALR/Alpha|Satellite|centr ZNF716 Mappable ENCODE Overlap -chr7 58796711 58798922 ALR/Alpha|Satellite|centr ZNF716 Mappable ENCODE Overlap -chr8 85783148 85787786 Intergenic REXO1L2P Mappable ENCODE Overlap -chr8 85763464 85765991 promoter-TSS (NR_003594).6 REXO1L2P Mappable ENCODE Overlap -chr8 85794512 85818706 Intergenic REXO1L2P Mappable ENCODE Overlap -chr8 85725563 85725893 Intergenic REXO1L2P Lowly ENCODE Overlap -chr8 43236617 43243359 SAR|Satellite|Satellite POTEA Mappable ENCODE Overlap -chr8 85646151 85663321 "non-coding (NR_003594, exon 1 of 1)" REXO1L2P Mappable ENCODE Overlap -chr8 85731042 85746666 L1PA5|LINE|L1 REXO1L2P Mappable ENCODE Overlap -chr8 85768408 85778392 L1PA5|LINE|L1 REXO1L2P Mappable ENCODE Overlap -chr8 85820021 85822957 L1MA8|LINE|L1 REXO1L2P Lowly ENCODE Overlap -chr8 85714761 85722035 L1PA5|LINE|L1 REXO1L2P Lowly ENCODE Overlap -chr8 85825873 85828618 "non-coding (NR_003594, exon 1 of 1).10" REXO1L2P Mappable ENCODE Overlap -chr8 85755743 85762636 L1PA5|LINE|L1 REXO1L2P Mappable ENCODE Overlap -chr8 85788653 85793679 "non-coding (NR_003594, exon 1 of 1).8" REXO1L2P Mappable ENCODE Overlap -chr8 85793779 85794442 Intergenic REXO1L2P Lowly ENCODE Overlap -chr9 60631611 60632719 ALR/Alpha|Satellite|centr SPATA31A5 Mappable ENCODE Overlap -chr9 43944548 43947643 ALR/Alpha|Satellite|centr LOC102724904 Mappable ENCODE Overlap -chr9 60610639 60611482 ALR/Alpha|Satellite|centr SPATA31A5 Mappable ENCODE Overlap -chr9 137326772 137329485 "intron (NM_017820, intron 17 of 21)" NRARP Mappable ENCODE Overlap -chr9 41229428 41231548 Intergenic MIR4477A Mappable ENCODE Overlap -chr9 40911805 40913197 CER|Satellite|Satellite MIR1299 Mappable ENCODE Overlap -chr9 43317735 43320170 (TTCGA)n|Simple_repeat|Simple_repeat LOC102724904 Mappable ENCODE Overlap -chr9 61855439 61858036 SST1|Satellite|centr FAM27C Mappable ENCODE Overlap -chr9 138230383 138234257 "intron (NR_146178, intron 5 of 14)" FAM157B Mappable ENCODE Overlap -chrM 1 16569 promoter-TSS (NR_162149).2 MIR12136 Lowly ENCODE Overlap -chrUn_GL000195v1 31055 32367 Intergenic LOC389831 Lowly Unique -chrUn_GL000214v1 63140 66720 Intergenic Lowly Unique -chrUn_GL000214v1 116380 137718 Intergenic Lowly Unique -chrUn_GL000216v2 52643 53625 (TTCCATTCCA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_GL000216v2 59665 59760 (TTCCATTCCA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_GL000216v2 47923 48574 (TTCCATTCCA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_GL000216v2 75829 81867 (TTCCATTCCA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_GL000216v2 39980 43542 (CATTC)n|Satellite|Satellite Lowly Unique -chrUn_GL000216v2 68368 74161 (TTCCATTCCA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_GL000216v2 1 31022 (CATTC)n|Satellite|Satellite Lowly Unique -chrUn_GL000216v2 44910 47898 (TTCCATTCCA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_GL000216v2 60966 60982 (TTCCATTCCA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_GL000216v2 137856 143789 BSR/Beta|Satellite|Satellite Lowly Unique -chrUn_GL000216v2 61141 67547 (TTCCATTCCA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_GL000216v2 144039 144681 Intergenic Lowly Unique -chrUn_GL000216v2 82320 86892 (TTCCATTCCA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_GL000216v2 50490 50550 (TTCCATTCCA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_GL000216v2 144999 173107 BSR/Beta|Satellite|Satellite Lowly Unique -chrUn_GL000216v2 33316 39801 (CATTC)n|Satellite|Satellite Lowly Unique -chrUn_GL000220v1 100564 161802 (TCTC)n|Simple_repeat|Simple_repeat MIR6724-1 Lowly Unique -chrUn_GL000224v1 1 20377 L1MB8|LINE|L1 LOC100505874 Lowly Unique -chrUn_GL000226v1 1 15008 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270303v1 1 1942 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270304v1 1 2165 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270310v1 1 1201 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270311v1 1 2240 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270317v1 135 2580 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270317v1 35352 37690 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270330v1 1 1652 L1MB8|LINE|L1 Lowly Unique -chrUn_KI270333v1 1 2699 SAR|Satellite|Satellite Lowly Unique -chrUn_KI270336v1 1 1026 SAR|Satellite|Satellite Lowly Unique -chrUn_KI270337v1 1 1121 SAR|Satellite|Satellite Lowly Unique -chrUn_KI270411v1 1 2646 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270435v1 90752 92983 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270435v1 94 3221 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270438v1 45534 48569 (GGAAT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270438v1 68235 72651 (GGAATGGAAT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270438v1 78544 79227 (GGAATGGAAT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270438v1 66554 68124 (GGAATGGAAT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270438v1 99571 112505 (GGAATGGAAT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270442v1 39052 44270 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270442v1 32884 34371 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270442v1 1 1666 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270442v1 67250 72057 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270442v1 45626 46874 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270442v1 12306 15717 (GAATG)n|Satellite|Satellite Lowly Unique -chrUn_KI270442v1 31259 32442 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270442v1 99605 100217 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270442v1 73967 78664 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270442v1 22807 26003 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270442v1 78839 98090 (AATGG)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270465v1 1 1774 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270466v1 1 1233 SAR|Satellite|Satellite Lowly Unique -chrUn_KI270467v1 1 3920 SAR|Satellite|Satellite Lowly Unique -chrUn_KI270512v1 20303 22689 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270519v1 135213 138126 (TGGAA)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270519v1 82280 82552 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270519v1 134919 134971 L1PA4|LINE|L1 Lowly Unique -chrUn_KI270519v1 87087 87726 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270519v1 83709 84963 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270519v1 85036 85246 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270538v1 52315 55319 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270538v1 82664 85364 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270538v1 87289 90766 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270538v1 79641 82654 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270544v1 1 1202 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270589v1 40521 44474 (CATTC)n|Satellite|Satellite Lowly Unique -chrUn_KI270590v1 1791 4364 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270591v1 3788 5796 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270743v1 150742 153388 ACRO1|Satellite|acro Lowly Unique -chrUn_KI270743v1 155199 157860 ACRO1|Satellite|acro Lowly Unique -chrUn_KI270744v1 104492 126444 Intergenic Lowly Unique -chrUn_KI270744v1 10020 15078 Intergenic Lowly Unique -chrUn_KI270751v1 148528 150742 L1P1|LINE|L1 Lowly Unique -chrUn_KI270751v1 37373 41073 Intergenic Lowly Unique -chrUn_KI270754v1 37970 40191 SST1|Satellite|centr Lowly Unique -chrUn_KI270756v1 13229 17851 (CCATTCCATT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270756v1 63263 65792 Intergenic Lowly Unique -chrUn_KI270756v1 23904 23957 (CCATTCCATT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270756v1 60584 60646 Intergenic Lowly Unique -chrUn_KI270756v1 61107 61240 Intergenic Lowly Unique -chrUn_KI270756v1 24602 28567 (CCATTCCATT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270756v1 1 8666 (CCATTCCATT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270756v1 17930 19177 (CCATTCCATT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270756v1 45923 49371 Intergenic Lowly Unique -chrUn_KI270756v1 53222 53315 Intergenic Lowly Unique -chrUn_KI270756v1 29479 30611 (CCATTCCATT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270756v1 74181 75098 Intergenic Lowly Unique -chrUn_KI270756v1 20853 23813 (CCATTCCATT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270756v1 41049 44746 Intergenic Lowly Unique -chrUn_KI270756v1 20484 20705 (CCATTCCATT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270756v1 57080 60437 Intergenic Lowly Unique -chrUn_KI270756v1 12442 13205 (CCATTCCATT)n|Simple_repeat|Simple_repeat Lowly Unique -chrUn_KI270757v1 59339 62855 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270757v1 69004 69630 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270757v1 58790 58869 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270757v1 64050 68303 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270757v1 68531 68702 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270757v1 58678 58783 ALR/Alpha|Satellite|centr Lowly Unique -chrUn_KI270757v1 13326 17787 AluYj4|SINE|Alu Lowly Unique -chrX 115731592 115734123 CpG DANT1 Lowly ENCODE Overlap -chrX 115727364 115729136 CpG DANT1 Lowly ENCODE Overlap -chrX 267916 270529 Intergenic PLCXD1 Mappable ENCODE Overlap -chrX 156029043 156031753 (TTAGGG)n|Simple_repeat|Simple_repeat DDX11L16 Mappable ENCODE Overlap -chrX 270737 271685 Intergenic PLCXD1 Lowly ENCODE Overlap -chrY 10886323 10890931 (TTCCA)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 11316283 11316300 Intergenic GYG2P1 Mappable ENCODE Overlap -chrY 10858033 10859502 (TCCAT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 11308226 11316021 BSR/Beta|Satellite|Satellite GYG2P1 Mappable ENCODE Overlap -chrY 11012810 11016490 (ATTCC)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10878587 10881982 (TCCAT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10931592 10932136 (TTCCA)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10753641 10757873 FRAM|SINE|Alu TTTY23 Mappable ENCODE Overlap -chrY 10956930 10957024 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10661754 10661806 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10758153 10766392 (CCATT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10746721 10753487 (CCATT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10920106 10922590 (TCCAT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10774388 10778018 (CCATT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10778911 10782860 (ATTCC)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10894385 10895918 (TTCCA)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10954990 10956549 (TCCAC)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10840925 10841313 (TCCAT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 11686805 11691549 Intergenic GYG2P1 Mappable ENCODE Overlap -chrY 10820442 10823253 (ATTCC)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10981359 10990942 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10681540 10688008 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 11720926 11724374 (GAATG)n|Satellite|Satellite GYG2P1 Mappable ENCODE Overlap -chrY 10969891 10973436 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10646251 10650980 (CCATT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 56824781 56852466 BSR/Beta|Satellite|Satellite SPRY3 Mappable ENCODE Overlap -chrY 11003946 11005824 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10794838 10810653 (ATTCC)n|Simple_repeat|Simple_repeat TTTY23 Lowly ENCODE Overlap -chrY 10898026 10900773 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10883316 10886262 (TCCAT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10784961 10787467 (ATTCC)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10794605 10794735 (ATTCC)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10766649 10766865 (CCATT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 26638739 26641562 (AATGG)n|Simple_repeat|Simple_repeat TTTY3 Mappable ENCODE Overlap -chrY 10948249 10952190 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10841985 10843556 (TCCAT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10911064 10913946 BSR/Beta|Satellite|Satellite TTTY23 Mappable ENCODE Overlap -chrY 11030435 11031351 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10957101 10960925 (CATTC)n|Satellite|Satellite TTTY23 Mappable ENCODE Overlap -chrY 10628917 10632667 AluYj4|SINE|Alu TTTY23 Lowly ENCODE Overlap -chrY 10998021 11001808 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10890947 10891357 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10767048 10774082 (CCATT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 11289677 11307587 (ATTCC)n|Simple_repeat|Simple_repeat GYG2P1 Mappable ENCODE Overlap -chrY 10923983 10929299 (TTCCA)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 11021350 11022613 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10991016 10991138 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10665517 10668057 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 11745782 11749552 (GAATG)n|Satellite|Satellite GYG2P1 Mappable ENCODE Overlap -chrY 10824136 10826667 (ATTCC)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 11316916 11335434 BSR/Beta|Satellite|Satellite GYG2P1 Lowly ENCODE Overlap -chrY 10891370 10894050 SVA_C|Retroposon|SVA TTTY23 Mappable ENCODE Overlap -chrY 11002737 11003086 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10866943 10870405 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10943432 10946724 (TTCCA)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 11023543 11023560 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10932277 10941762 Intergenic TTTY23 Mappable ENCODE Overlap -chrY 10992538 10994331 AluJo|SINE|Alu TTTY23 Mappable ENCODE Overlap -chrY 10655846 10661087 (CCATT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10766897 10766903 (CCATT)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap -chrY 10788274 10794462 (ATTCC)n|Simple_repeat|Simple_repeat TTTY23 Mappable ENCODE Overlap \ No newline at end of file +chr1 124610979 124625614 +chr1 124347449 124349827 +chr1 123681389 123697714 +chr1 124755617 124756133 +chr1 228644488 228646810 +chr1 122763761 122771648 +chr1 123074471 123077388 +chr1 123698751 123699028 +chr1 124082237 124085912 +chr1 124195003 124199252 +chr1 122822805 122852412 +chr1 124079072 124081761 +chr1 124637048 124650716 +chr1 123923101 123930829 +chr1 123947775 123954907 +chr1 2651096 2657690 +chr1 123772279 123772518 +chr1 123888372 123895580 +chr1 124132073 124137242 +chr1 123421242 123424555 +chr1 122792518 122792713 +chr1 123575612 123580150 +chr1 123730701 123737589 +chr1 124192450 124193252 +chr1 122864530 122892414 +chr1 123457393 123461993 +chr1 124416522 124429776 +chr1 124488952 124492689 +chr1 123761364 123765317 +chr1 122974321 122975357 +chr1 124573689 124577060 +chr1 2660041 2662057 +chr1 124666337 124666578 +chr1 124444870 124447910 +chr1 124628401 124632935 +chr1 123955788 123976252 +chr1 123749402 123749623 +chr1 123788987 123792333 +chr1 123353813 123358798 +chr1 123487838 123493348 +chr1 124185193 124186084 +chr1 121742016 121776960 +chr1 124389047 124390123 +chr1 248944611 248947412 +chr1 16615621 16615795 +chr1 124162104 124174735 +chr1 123769824 123771521 +chr1 122976387 122979388 +chr1 124046457 124046514 +chr1 123828506 123829677 +chr1 124487499 124487838 +chr1 123454191 123456805 +chr1 123831264 123840597 +chr1 123866133 123870135 +chr1 123207871 123216816 +chr1 123067262 123071930 +chr1 123671098 123680501 +chr1 123680799 123681034 +chr1 123787966 123788535 +chr1 143183597 143277030 +chr1 123841498 123841592 +chr1 123777239 123787683 +chr1 123004659 123060219 +chr1 123410850 123411000 +chr1 122967648 122973395 +chr1 228608508 228616048 +chr1 124312508 124313152 +chr1 2663197 2666377 +chr1 124037252 124040943 +chr1 2658437 2659484 +chr1 123638914 123647813 +chr1 122758317 122763284 +chr1 123310280 123312959 +chr1 123944700 123947541 +chr1 2696387 2697700 +chr1 123993045 123993143 +chr1 228616110 228616994 +chr1 123809159 123825290 +chr1 123700538 123701366 +chr1 123292604 123293199 +chr1 124524705 124536570 +chr1 122853507 122863783 +chr1 124396134 124398614 +chr1 124462900 124469384 +chr1 789517 792613 +chr1 122565737 122597777 +chr1 122660352 122712552 +chr1 123465637 123470989 +chr1 16512350 16514335 +chr1 124711528 124748035 +chr1 123515909 123517288 +chr1 122906144 122915306 +chr1 123871258 123876903 +chr1 123990369 123992936 +chr1 123449989 123452433 +chr1 123658013 123658426 +chr1 161460728 161466377 +chr1 124430835 124441228 +chr1 124633057 124633319 +chr1 123757476 123761007 +chr1 124652111 124665269 +chr1 123124556 123125047 +chr1 123793121 123804898 +chr1 123319246 123324771 +chr1 123314679 123317444 +chr1 123387599 123390748 +chr1 124303939 124311225 +chr1 124558602 124573677 +chr1 2675075 2675937 +chr1 122813930 122821753 +chr1 122892854 122906013 +chr1 123183593 123187242 +chr1 124594049 124605596 +chr1 16614858 16615354 +chr1 122599644 122617908 +chr1 2755311 2760203 +chr1 123955043 123955348 +chr1 123295606 123295739 +chr1 124024633 124024799 +chr1 123633969 123634047 +chr1 122502392 122558766 +chr1 123904701 123908708 +chr1 2676476 2689992 +chr1 124593326 124593327 +chr1 124243016 124255477 +chr1 124193388 124194092 +chr1 122812476 122812926 +chr1 123187448 123187650 +chr1 123246292 123252731 +chr1 123345950 123353178 +chr1 123908832 123909015 +chr1 123865900 123866108 +chr1 123880442 123887992 +chr1 124605974 124606640 +chr1 123478972 123483857 +chr1 124127325 124131808 +chr1 123392121 123395225 +chr1 122655572 122659623 +chr1 16725841 16728094 +chr1 123471069 123472466 +chr1 123257533 123267929 +chr1 123487155 123487680 +chr1 123878887 123880095 +chr1 123721481 123724576 +chr1 123293396 123293989 +chr1 123648151 123653550 +chr1 123806472 123807799 +chr1 123484321 123484872 +chr1 123223300 123229067 +chr1 122988286 122988566 +chr1 124334073 124339709 +chr1 228636195 228644351 +chr1 123750069 123757183 +chr1 123366175 123373760 +chr1 123133630 123149853 +chr1 124142769 124151448 +chr1 122750334 122757705 +chr1 124543344 124551494 +chr1 123463500 123464152 +chr1 123337837 123338665 +chr1 228617880 228620677 +chr1 122559146 122563373 +chr1 124449186 124459787 +chr1 123705983 123709138 +chr1 123717922 123720330 +chr1 124553805 124556586 +chr1 124022068 124023445 +chr1 123774014 123776700 +chr1 124112936 124127192 +chr1 123703028 123703309 +chr1 123338733 123341125 +chr1 123534158 123538816 +chr1 122921571 122965108 +chr1 123739630 123746731 +chr1 123473265 123473765 +chr1 123078634 123090349 +chr1 123634201 123638786 +chr1 123267951 123272997 +chr1 236712612 236716056 +chr1 124537250 124541856 +chr1 124058577 124074991 +chr1 123426130 123440706 +chr1 124634253 124634854 +chr1 124493000 124494360 +chr1 123977871 123982318 +chr1 123601299 123632580 +chr1 124233326 124233698 +chr1 124496911 124521316 +chr1 123581424 123587147 +chr1 123152211 123160608 +chr1 124295346 124303919 +chr1 2667718 2674721 +chr1 161442212 161459350 +chr1 124236503 124241894 +chr1 123595138 123599775 +chr1 124416165 124416369 +chr1 122981432 122981579 +chr1 124558348 124558487 +chr1 122918760 122919060 +chr1 124401333 124410007 +chr1 123909020 123916403 +chr1 123567201 123572421 +chr1 123983540 123986717 +chr1 124460404 124460735 +chr1 123090393 123124055 +chr1 122989513 122991506 +chr1 123545968 123562717 +chr1 123725476 123729267 +chr1 124047216 124058353 +chr1 123125721 123129029 +chr1 124748208 124754755 +chr1 123709361 123710441 +chr1 123192365 123205196 +chr1 124157846 124161487 +chr1 123274274 123277786 +chr1 161466446 161472738 +chr1 123232086 123238851 +chr1 123600135 123600404 +chr1 122981905 122984908 +chr1 124410105 124415973 +chr1 123000144 123004503 +chr1 123710782 123716188 +chr1 124042426 124046077 +chr1 124153959 124157292 +chr1 124523859 124524670 +chr1 124391089 124393688 +chr1 123160743 123179378 +chr1 124340068 124346843 +chr1 123078238 123078262 +chr1 123463270 123463288 +chr1 124288111 124292489 +chr1 228620723 228624068 +chr1 122985198 122987949 +chr1 123501642 123505110 +chr1 123494306 123500148 +chr1 123299360 123308922 +chr1 123477134 123478791 +chr1 123918014 123920972 +chr1 123564074 123564609 +chr1 124187392 124191846 +chr1 123860085 123865862 +chr1 124137450 124141973 +chr1 123231456 123232068 +chr1 124668405 124698204 +chr1 123660028 123667802 +chr1 124029009 124035852 +chr1 124314206 124330916 +chr1 628088 635923 +chr1 124698889 124710105 +chr1 123654707 123657707 +chr1 122564484 122564628 +chr1 123327187 123336366 +chr1 124756241 124765560 +chr1 124587185 124593255 +chr1 123993263 124017467 +chr1 124577276 124577641 +chr1 123936407 123941483 +chr1 144102590 144105633 +chr1 123063967 123066571 +chr1 91386236 91388535 +chr1 121965774 121969623 +chr1 123506859 123512351 +chr1 124203810 124232742 +chr1 124177846 124182735 +chr1 224010839 224015910 +chr1 123442350 123448859 +chr1 123336600 123336731 +chr1 123724579 123724815 +chr1 123668135 123668950 +chr1 123411051 123420183 +chr1 124350457 124387136 +chr1 125165251 125171959 +chr1 122617993 122622038 +chr1 123587727 123593407 +chr1 123240864 123243602 +chr1 123452734 123453336 +chr1 123252764 123256027 +chr1 124024808 124027897 +chr1 123318612 123318659 +chr1 122712809 122715970 +chr1 123217618 123218459 +chr1 122716926 122720666 +chr1 124091699 124105529 +chr1 124470643 124487474 +chr1 123766306 123769701 +chr1 124579298 124584106 +chr1 123899406 123904231 +chr1 124018297 124021565 +chr1 123825521 123828486 +chr1 123517950 123531595 +chr1 122793709 122809534 +chr1 123485159 123486942 +chr1 124075556 124076291 +chr1 2691502 2693971 +chr1 123374374 123383121 +chr1 123899167 123899184 +chr1 123073383 123074327 +chr1 122622921 122655193 +chr1 125172600 125185576 +chr1 122772071 122792107 +chr1 123222073 123222104 +chr1 123395736 123410588 +chr1 124521887 124523497 +chr1 122915620 122915759 +chr1 16612489 16614272 +chr1 122720823 122749445 +chr1 122992665 122999602 +chr1 124551762 124552236 +chr1 122916012 122916101 +chr1 2747597 2755052 +chr1 123841803 123858444 +chr1 122810096 122810306 +chr1 124586233 124586899 +chr1 123187673 123191050 +chr1 124258930 124285568 +chr1 123279142 123292202 +chr1 124765617 124785370 +chr1 123129823 123133340 +chr1 228624085 228635970 +chr1_KI270709v1_random 1 19452 +chr1_KI270711v1_random 7349 10549 +chr1_KI270712v1_random 57044 59379 +chr1_KI270713v1_random 19745 23499 +chr10 38917532 38921312 +chr10 38485929 38490812 +chr10 40555218 40558145 +chr10 40184616 40184779 +chr10 40085143 40086546 +chr10 42316454 42321742 +chr10 40394887 40394946 +chr10 40134029 40136698 +chr10 41123812 41126690 +chr10 42302263 42306136 +chr10 40975016 40977643 +chr10 38784990 38787946 +chr10 42307404 42315736 +chr10 126946285 126949389 +chr10 40681674 40683032 +chr10 40412067 40415257 +chr10 40185985 40187776 +chr10 40890943 40893719 +chr10 40395146 40397876 +chr10 41016424 41019108 +chr10 40510552 40510803 +chr10 40815111 40818385 +chr10 40199982 40200234 +chr10 39968185 39968710 +chr10 40667639 40670355 +chr10 38807376 38810540 +chr10 42065293 42106174 +chr10 38799302 38801295 +chr10 40129941 40131107 +chr10 38497910 38501672 +chr10 133685504 133691455 +chr10 40961499 40963218 +chr10 40287965 40290809 +chr10 38572473 38574967 +chr10 42315741 42315752 +chr10 40128252 40129424 +chr10 42165072 42168883 +chr10 38789940 38793846 +chr10 40933603 40935552 +chr10 40366986 40369532 +chr10 38903116 38905607 +chr10 41842047 41917264 +chr10 40509472 40509493 +chr10 42296616 42299414 +chr10 40767435 40770603 +chr10 40539939 40542976 +chr10 133679108 133679154 +chr10 38523266 38530846 +chr10 133761260 133765408 +chr10 40476591 40478349 +chr10 38577833 38582050 +chr10 38494933 38497542 +chr10 133679249 133679353 +chr11 3652764 3655645 +chr11 94236861 94237383 +chr11 10506890 10510998 +chr11 94237393 94239001 +chr11 1016509 1018503 +chr12 9003 11550 +chr12 35613810 35616091 +chr12 37245547 37247397 +chr12 37235710 37241245 +chr12 132239864 132243684 +chr12 37265352 37266527 +chr13 17896880 17897978 +chr13 18013137 18015392 +chr13 17053353 17056060 +chr13 17745515 17746936 +chr13 16244034 16244112 +chr13 17942778 17944168 +chr13 17711883 17712069 +chr13 16599254 16600279 +chr13 17150303 17151628 +chr13 16249181 16254341 +chr13 17643597 17646367 +chr13 16606651 16609402 +chr13 17095168 17096475 +chr13 16414425 16417030 +chr13 16672385 16672426 +chr13 17856076 17857762 +chr13 17721328 17721413 +chr13 17381911 17382356 +chr13 17303579 17306666 +chr13 17939255 17939991 +chr13 17416373 17416917 +chr13 17791894 17792146 +chr13 17182716 17184870 +chr13 16656928 16657044 +chr13 18020584 18020716 +chr13 17935600 17938924 +chr13 17604283 17609260 +chr13 16697589 16697682 +chr13 17923781 17923923 +chr13 17143546 17146577 +chr13 17946624 17951696 +chr13 17117485 17119711 +chr13 16153317 16156028 +chr13 18210701 18213661 +chr13 17877701 17877809 +chr13 17887934 17890703 +chr13 17664615 17669171 +chr13 17347058 17351187 +chr13 16923463 16927889 +chr13 17295139 17297764 +chr13 17750720 17753323 +chr13 17654891 17657917 +chr13 17219173 17219270 +chr13 16698050 16700278 +chr13 17328621 17328826 +chr13 17932523 17933722 +chr13 17531675 17534979 +chr13 17624570 17628053 +chr13 16484559 16486098 +chr13 17127062 17130174 +chr13 17120016 17120463 +chr13 16116481 16116678 +chr13 17884216 17887064 +chr13 17079136 17081535 +chr13 16697688 16698031 +chr13 17988261 17988436 +chr13 16918603 16921651 +chr13 16133786 16137594 +chr13 17239848 17243306 +chr13 17367784 17369863 +chr13 17372849 17378158 +chr13 16113312 16116428 +chr13 17543368 17544311 +chr13 17165760 17168258 +chr13 16116799 16116843 +chr13 17946055 17946089 +chr13 16462827 16463822 +chr13 17978596 17979303 +chr13 16497927 16500817 +chr13 17927090 17930378 +chr13 17536172 17536268 +chr13 17031820 17031985 +chr13 17582870 17585687 +chr13 18029662 18029877 +chr13 17018417 17020181 +chr13 17585846 17585987 +chr13 17020904 17021039 +chr13 17400299 17405427 +chr13 17071688 17074162 +chr13 17845879 17848465 +chr13 16765152 16767662 +chr13 17912704 17915217 +chr13 16235967 16243773 +chr13 17154977 17158374 +chr13 17703323 17705629 +chr13 17826681 17832106 +chr13 16487849 16488103 +chr13 17874543 17877647 +chr13 16930162 16931331 +chr13 16687382 16691490 +chr13 17706732 17709513 +chr13 17877832 17878000 +chr13 18000459 18005465 +chr13 17952346 17954794 +chr13 16597142 16599029 +chr13 17538263 17541448 +chr13 16255195 16257054 +chr13 17318152 17320974 +chr13 17148028 17148998 +chr13 17206641 17209469 +chr13 17007241 17007246 +chr13 17309664 17311163 +chr13 17032633 17034654 +chr13 17642351 17643155 +chr13 17679715 17684928 +chr13 17878036 17880528 +chr13 17718673 17721311 +chr13 17026785 17030773 +chr13 18030080 18032798 +chr13 17410217 17411716 +chr13 17113803 17116579 +chr13 17999420 18000378 +chr13 109423125 109425342 +chr13 17792424 17795278 +chr13 17564083 17565098 +chr13 17216765 17218395 +chr13 16392184 16394696 +chr13 17738851 17745243 +chr13 17417100 17417333 +chr13 17798860 17802270 +chr13 16437130 16439835 +chr13 17628400 17631725 +chr13 17671567 17672338 +chr13 16159974 16162705 +chr13 17915249 17915268 +chr13 16244242 16246123 +chr13 17354483 17356857 +chr13 17923002 17923725 +chr13 17988560 17991066 +chr13 17922091 17922212 +chr13 18009819 18013052 +chr13 16146408 16149034 +chr13 17485116 17487318 +chr13 18005756 18008782 +chr13 17070384 17071097 +chr13 17791405 17791779 +chr13 18021232 18022958 +chr13 16600613 16601047 +chr13 17094313 17094390 +chr13 17854761 17855955 +chr13 16882765 16884187 +chr13 16656324 16656785 +chr13 17004782 17007171 +chr13 17841209 17842722 +chr13 17916147 17917119 +chr13 16848379 16848894 +chr13 17391380 17393955 +chr13 16942345 16944804 +chr13 17839923 17841144 +chr13 16923061 16923291 +chr13 16856329 16856452 +chr13 17323756 17325638 +chr13 16229236 16235037 +chr13 17177841 17180742 +chr13 17788889 17790682 +chr13 17993993 17998725 +chr13 16246475 16246855 +chr13 17817804 17822642 +chr13 16826275 16827838 +chr13 17417958 17419021 +chr13 17031088 17031801 +chr13 17955477 17956002 +chr13 17697792 17700499 +chr13 18025886 18028639 +chr13 17756295 17759896 +chr13 17860073 17865089 +chr13 17263467 17266339 +chr13 17515140 17519684 +chr13 16851515 16851797 +chr13 17979450 17981547 +chr13 17230401 17233567 +chr13 17243411 17245204 +chr13 17778067 17780938 +chr13 17172503 17175298 +chr13 17993819 17993835 +chr14 16091961 16105537 +chr14 105230006 105232915 +chr14_GL000225v1_random 105690 136390 +chr14_GL000225v1_random 89351 104131 +chr14_GL000225v1_random 136395 140413 +chr14_GL000225v1_random 1666 8760 +chr14_GL000225v1_random 37408 38072 +chr14_GL000225v1_random 39176 89339 +chr14_GL000225v1_random 30656 36652 +chr14_GL000225v1_random 9530 30503 +chr14_GL000225v1_random 195384 199785 +chr14_KI270723v1_random 33989 38115 +chr14_KI270724v1_random 1 2096 +chr15 19774748 19781046 +chr15 17079519 17084551 +chr15 19781269 19782029 +chr16 38264960 38268929 +chr16 33335395 33340544 +chr16 90115865 90118991 +chr16 34609198 34611771 +chr16 38274918 38281137 +chr16 46379683 46402990 +chr16 34570511 34577757 +chr16 34095258 34100789 +chr16 34579966 34597675 +chr16 34697614 34698226 +chr16 34061433 34067253 +chr17 23015137 23017694 +chr17 26567361 26568148 +chr17 26935184 26941957 +chr17 25388774 25391334 +chr17 43234260 43235297 +chr17 22520192 22522698 +chr17 26824538 26827116 +chr17 25787486 25789678 +chr17 25351848 25354673 +chr17 26827179 26830212 +chr17 24149445 24152769 +chr17 26624404 26626919 +chr17 25568022 25570460 +chr17 115876 119087 +chr17 26602416 26605714 +chr17 23581842 23584984 +chr17 26784244 26785873 +chr17 43281692 43285869 +chr17 43232334 43233864 +chr17 25571866 25574916 +chr17 43276929 43279827 +chr17 26872121 26872359 +chr17 21851874 21854502 +chr17 26593506 26597692 +chr17 26139235 26142549 +chr17 23067523 23070190 +chr17 25382608 25385005 +chr17 26547832 26550522 +chr17 43250513 43253389 +chr17 1062389 1066145 +chr17 24186508 24189789 +chr17 43287867 43290714 +chr17 25073233 25075710 +chr17 26878005 26886980 +chr17 313684 316768 +chr17 43245212 43247867 +chr17 22976412 22977953 +chr17 43264248 43267017 +chr17 21856405 21856412 +chr17 23189141 23191663 +chr17 26618168 26621523 +chr17 25919036 25921580 +chr17 21967190 21993012 +chr17 26854870 26856944 +chr17 121351 125557 +chr17_GL000205v2_random 86989 90907 +chr17_GL000205v2_random 26 3428 +chr17_GL000205v2_random 7379 7759 +chr17_GL000205v2_random 3848 7071 +chr17_KI270729v1_random 160013 162123 +chr17_KI270729v1_random 19213 29747 +chr17_KI270729v1_random 45511 48698 +chr17_KI270729v1_random 1 7213 +chr17_KI270729v1_random 9482 14680 +chr17_KI270729v1_random 55466 60276 +chr17_KI270730v1_random 101867 111086 +chr17_KI270730v1_random 95356 100621 +chr17_KI270730v1_random 80509 93823 +chr18 9028 11550 +chr18 20560617 20563418 +chr18 105276 113531 +chr18 79618344 79620846 +chr19 54188605 54191272 +chr19 36279514 36282602 +chr19 37291909 37295660 +chr19 7449308 7452123 +chr19 37290463 37291465 +chr19 36300186 36303419 +chr19 24890430 24896738 +chr2 89822969 89823237 +chr2 89818404 89821968 +chr2 89814061 89814505 +chr2 89810575 89813442 +chr2 89814629 89817620 +chr2 91420365 91423530 +chr2 89805597 89807370 +chr2 90379564 90403503 +chr2 89823396 89842268 +chr20 31232160 31233573 +chr20 31176519 31179840 +chr20 28818144 28818512 +chr20 28511375 28514724 +chr20 28784667 28786930 +chr20 31181856 31189491 +chr20 28516883 28518637 +chr20 28815563 28816341 +chr20 31228459 31231680 +chr20 27180808 27182094 +chr20 28839720 28842865 +chr20 26540721 26543455 +chr20 29884447 29885678 +chr20 31050520 31077638 +chr20 28888219 28891252 +chr20 26489265 26489874 +chr20 31224415 31227417 +chr20 28819957 28823272 +chr20 26601374 26608712 +chr20 28805290 28808241 +chr20 31239887 31243476 +chr20 31166568 31167807 +chr20 29261354 29264856 +chr20 28307014 28309467 +chr20 28781706 28784563 +chr20 31170535 31172967 +chr20 31168211 31169703 +chr20 28896358 28899883 +chr20 31090368 31091746 +chr20 31173003 31173426 +chr20 31156073 31160110 +chr20 59234 67210 +chr20 28493663 28499706 +chr20 29121594 29123538 +chr20 31190204 31190333 +chr20 28548723 28550182 +chr20 28787339 28787377 +chr21 10653993 10663675 +chr21 10699029 10699402 +chr21 10428560 10428597 +chr21 7256313 7262762 +chr21 10687705 10698999 +chr21 10683389 10686769 +chr21 10700414 10710804 +chr21 10268901 10273604 +chr21 9245189 9250252 +chr21 10752005 10756855 +chr21 10719044 10720169 +chr21 10796208 10798236 +chr21 10729126 10738634 +chr21 10391655 10393390 +chr21 10798373 10799432 +chr21 8808979 8812258 +chr21 7932046 7935094 +chr21 10361620 10363358 +chr21 7935422 7940005 +chr21 7914978 7919785 +chr21 8201552 8261964 +chr21 10710911 10718875 +chr21 10720474 10728504 +chr21 10804494 10807620 +chr21 5326890 5330910 +chr21 6368536 6373565 +chr21 7940721 7945695 +chr21 10665364 10681351 +chr21 7922196 7931111 +chr21 10807667 10808020 +chr21 10800154 10800890 +chr21 7946160 7958748 +chr21 8985911 8989787 +chr21 10324539 10327338 +chr21 10686799 10686855 +chr21 10426777 10428455 +chr21 8384656 8473309 +chr22 11210160 11215577 +chr22 18729480 18731694 +chr22 12174634 12177777 +chr22 12690973 12694171 +chr22 18895123 18897647 +chr22 50806876 50809467 +chr22 11022253 11024389 +chr22 16345779 16354945 +chr22 11367998 11371880 +chr22 10716070 10731276 +chr22 16356082 16361451 +chr22 11812787 11816849 +chr22_KI270733v1_random 117288 179772 +chr22_KI270734v1_random 120388 122914 +chr22_KI270735v1_random 38514 42811 +chr22_KI270736v1_random 86945 87728 +chr22_KI270736v1_random 47146 51395 +chr22_KI270736v1_random 63231 66185 +chr22_KI270736v1_random 81973 86084 +chr22_KI270736v1_random 136134 140350 +chr22_KI270736v1_random 131362 135297 +chr22_KI270736v1_random 76967 77087 +chr22_KI270736v1_random 161047 164535 +chr22_KI270736v1_random 165492 168910 +chr22_KI270736v1_random 51786 54840 +chr22_KI270736v1_random 153598 154722 +chr22_KI270736v1_random 144303 153354 +chr22_KI270736v1_random 95664 105091 +chr22_KI270736v1_random 109434 110514 +chr22_KI270736v1_random 128647 129777 +chr22_KI270736v1_random 111003 115086 +chr22_KI270736v1_random 169771 176702 +chr22_KI270736v1_random 178428 181920 +chr22_KI270736v1_random 88590 92411 +chr22_KI270736v1_random 129980 130603 +chr22_KI270736v1_random 230 3329 +chr22_KI270736v1_random 154901 159132 +chr22_KI270736v1_random 60991 62109 +chr22_KI270736v1_random 58693 60667 +chr22_KI270736v1_random 115254 122892 +chr22_KI270736v1_random 77202 81530 +chr22_KI270736v1_random 72297 75263 +chr22_KI270736v1_random 123794 128009 +chr22_KI270737v1_random 79010 80504 +chr22_KI270737v1_random 30421 40521 +chr22_KI270737v1_random 23114 29485 +chr3 93469362 93471801 +chr3 93711664 93712437 +chr3 91548591 91554130 +chr3 197389421 197389902 +chr3 198172030 198174477 +chr3 198167382 198170281 +chr3 9002 11842 +chr3 93706888 93710048 +chr3 75667816 75670647 +chr3 96616287 96619133 +chr4 49322045 49325033 +chr4 49630300 49659095 +chr4 49708071 49712961 +chr4 190175302 190182802 +chr4 190082751 190083066 +chr4 190020660 190023773 +chr4 1433989 1436603 +chr4 190121457 190124076 +chr4 49090233 49157664 +chr4 51106159 51108566 +chr4 49510010 49516194 +chr4_GL000008v2_random 1 8337 +chr5 9009 12786 +chr5 49620931 49628481 +chr5 80649491 80652837 +chr5 50139509 50139815 +chr5 17591996 17597406 +chr5 17524212 17529170 +chr5 34188278 34193784 +chr5 134924083 134928692 +chr5 17597460 17599261 +chr5 49598396 49604131 +chr5 17584091 17585523 +chr5 49629731 49634740 +chr5 34186729 34187148 +chr5 47295868 47300778 +chr5 2144865 2147341 +chr5 49665174 49668431 +chr5 50141319 50141921 +chr5 49608847 49619600 +chr5 49640990 49647802 +chr5 17517750 17523690 +chr5 49655272 49662871 +chr5 47306576 47310036 +chr5_GL000208v1_random 90558 92621 +chr6 157309365 157315191 +chr6 59718138 59718529 +chr6 170397348 170400442 +chr6 862141 864174 +chr6 59640507 59641284 +chr6 58783432 58784719 +chr6 58996337 58998871 +chr6 58793187 58793265 +chr6 58784734 58786253 +chr6 58792241 58793118 +chr6 60231805 60232035 +chr6 370247 373135 +chr7 57495340 57497718 +chr7 60309518 60312051 +chr7 58034763 58037384 +chr7 100956534 100959960 +chr7 158914463 158916767 +chr7 58032104 58034587 +chr7 57493144 57494128 +chr7 61055086 61056354 +chr7 62349293 62351966 +chr7 57486422 57491361 +chr7 158145977 158150149 +chr7 56369384 56375717 +chr7 65488410 65491158 +chr7 59292148 59293599 +chr7 58796711 58798922 +chr8 85783148 85787786 +chr8 85763464 85765991 +chr8 85794512 85818706 +chr8 85725563 85725893 +chr8 43236617 43243359 +chr8 85646151 85663321 +chr8 85731042 85746666 +chr8 85768408 85778392 +chr8 85820021 85822957 +chr8 85714761 85722035 +chr8 85825873 85828618 +chr8 85755743 85762636 +chr8 85788653 85793679 +chr8 85793779 85794442 +chr9 60631611 60632719 +chr9 43944548 43947643 +chr9 60610639 60611482 +chr9 137326772 137329485 +chr9 41229428 41231548 +chr9 40911805 40913197 +chr9 43317735 43320170 +chr9 61855439 61858036 +chr9 138230383 138234257 +chrM 1 16569 +chrUn_GL000195v1 31055 32367 +chrUn_GL000214v1 63140 66720 +chrUn_GL000214v1 116380 137718 +chrUn_GL000216v2 52643 53625 +chrUn_GL000216v2 59665 59760 +chrUn_GL000216v2 47923 48574 +chrUn_GL000216v2 75829 81867 +chrUn_GL000216v2 39980 43542 +chrUn_GL000216v2 68368 74161 +chrUn_GL000216v2 1 31022 +chrUn_GL000216v2 44910 47898 +chrUn_GL000216v2 60966 60982 +chrUn_GL000216v2 137856 143789 +chrUn_GL000216v2 61141 67547 +chrUn_GL000216v2 144039 144681 +chrUn_GL000216v2 82320 86892 +chrUn_GL000216v2 50490 50550 +chrUn_GL000216v2 144999 173107 +chrUn_GL000216v2 33316 39801 +chrUn_GL000220v1 100564 161802 +chrUn_GL000224v1 1 20377 +chrUn_GL000226v1 1 15008 +chrUn_KI270303v1 1 1942 +chrUn_KI270304v1 1 2165 +chrUn_KI270310v1 1 1201 +chrUn_KI270311v1 1 2240 +chrUn_KI270317v1 135 2580 +chrUn_KI270317v1 35352 37690 +chrUn_KI270330v1 1 1652 +chrUn_KI270333v1 1 2699 +chrUn_KI270336v1 1 1026 +chrUn_KI270337v1 1 1121 +chrUn_KI270411v1 1 2646 +chrUn_KI270435v1 90752 92983 +chrUn_KI270435v1 94 3221 +chrUn_KI270438v1 45534 48569 +chrUn_KI270438v1 68235 72651 +chrUn_KI270438v1 78544 79227 +chrUn_KI270438v1 66554 68124 +chrUn_KI270438v1 99571 112505 +chrUn_KI270442v1 39052 44270 +chrUn_KI270442v1 32884 34371 +chrUn_KI270442v1 1 1666 +chrUn_KI270442v1 67250 72057 +chrUn_KI270442v1 45626 46874 +chrUn_KI270442v1 12306 15717 +chrUn_KI270442v1 31259 32442 +chrUn_KI270442v1 99605 100217 +chrUn_KI270442v1 73967 78664 +chrUn_KI270442v1 22807 26003 +chrUn_KI270442v1 78839 98090 +chrUn_KI270465v1 1 1774 +chrUn_KI270466v1 1 1233 +chrUn_KI270467v1 1 3920 +chrUn_KI270512v1 20303 22689 +chrUn_KI270519v1 135213 138126 +chrUn_KI270519v1 82280 82552 +chrUn_KI270519v1 134919 134971 +chrUn_KI270519v1 87087 87726 +chrUn_KI270519v1 83709 84963 +chrUn_KI270519v1 85036 85246 +chrUn_KI270538v1 52315 55319 +chrUn_KI270538v1 82664 85364 +chrUn_KI270538v1 87289 90766 +chrUn_KI270538v1 79641 82654 +chrUn_KI270544v1 1 1202 +chrUn_KI270589v1 40521 44474 +chrUn_KI270590v1 1791 4364 +chrUn_KI270591v1 3788 5796 +chrUn_KI270743v1 150742 153388 +chrUn_KI270743v1 155199 157860 +chrUn_KI270744v1 104492 126444 +chrUn_KI270744v1 10020 15078 +chrUn_KI270751v1 148528 150742 +chrUn_KI270751v1 37373 41073 +chrUn_KI270754v1 37970 40191 +chrUn_KI270756v1 13229 17851 +chrUn_KI270756v1 63263 65792 +chrUn_KI270756v1 23904 23957 +chrUn_KI270756v1 60584 60646 +chrUn_KI270756v1 61107 61240 +chrUn_KI270756v1 24602 28567 +chrUn_KI270756v1 1 8666 +chrUn_KI270756v1 17930 19177 +chrUn_KI270756v1 45923 49371 +chrUn_KI270756v1 53222 53315 +chrUn_KI270756v1 29479 30611 +chrUn_KI270756v1 74181 75098 +chrUn_KI270756v1 20853 23813 +chrUn_KI270756v1 41049 44746 +chrUn_KI270756v1 20484 20705 +chrUn_KI270756v1 57080 60437 +chrUn_KI270756v1 12442 13205 +chrUn_KI270757v1 59339 62855 +chrUn_KI270757v1 69004 69630 +chrUn_KI270757v1 58790 58869 +chrUn_KI270757v1 64050 68303 +chrUn_KI270757v1 68531 68702 +chrUn_KI270757v1 58678 58783 +chrUn_KI270757v1 13326 17787 +chrX 115731592 115734123 +chrX 115727364 115729136 +chrX 267916 270529 +chrX 156029043 156031753 +chrX 270737 271685 +chrY 10886323 10890931 +chrY 11316283 11316300 +chrY 10858033 10859502 +chrY 11308226 11316021 +chrY 11012810 11016490 +chrY 10878587 10881982 +chrY 10931592 10932136 +chrY 10753641 10757873 +chrY 10956930 10957024 +chrY 10661754 10661806 +chrY 10758153 10766392 +chrY 10746721 10753487 +chrY 10920106 10922590 +chrY 10774388 10778018 +chrY 10778911 10782860 +chrY 10894385 10895918 +chrY 10954990 10956549 +chrY 10840925 10841313 +chrY 11686805 11691549 +chrY 10820442 10823253 +chrY 10981359 10990942 +chrY 10681540 10688008 +chrY 11720926 11724374 +chrY 10969891 10973436 +chrY 10646251 10650980 +chrY 56824781 56852466 +chrY 11003946 11005824 +chrY 10794838 10810653 +chrY 10898026 10900773 +chrY 10883316 10886262 +chrY 10784961 10787467 +chrY 10794605 10794735 +chrY 10766649 10766865 +chrY 26638739 26641562 +chrY 10948249 10952190 +chrY 10841985 10843556 +chrY 10911064 10913946 +chrY 11030435 11031351 +chrY 10957101 10960925 +chrY 10628917 10632667 +chrY 10998021 11001808 +chrY 10890947 10891357 +chrY 10767048 10774082 +chrY 11289677 11307587 +chrY 10923983 10929299 +chrY 11021350 11022613 +chrY 10991016 10991138 +chrY 10665517 10668057 +chrY 11745782 11749552 +chrY 10824136 10826667 +chrY 11316916 11335434 +chrY 10891370 10894050 +chrY 11002737 11003086 +chrY 10866943 10870405 +chrY 10943432 10946724 +chrY 11023543 11023560 +chrY 10932277 10941762 +chrY 10992538 10994331 +chrY 10655846 10661087 +chrY 10766897 10766903 +chrY 10788274 10794462 diff --git a/resources/blacklistbed/mm10.bed b/resources/blacklistbed/mm10.bed index 449a0a4..66dc024 100644 --- a/resources/blacklistbed/mm10.bed +++ b/resources/blacklistbed/mm10.bed @@ -1,560 +1,559 @@ -Chr Start End Detailed Annotation Nearest TSS Mappability Overlap with ENCODE -chr4 147638286 147647439 promoter-TSS (NM_145078) Zfp979 Mappable Unique -chr16 3338542 3338708 RLTR11A|LTR|ERVK Olfr161 Mappable Unique -chr1 181741994 181745061 Intergenic Lbr Mappable ENCODE Overlap -chr1 43776659 43779916 "intron (NM_001368287, intron 7 of 14)" Ecrg4 Mappable ENCODE Overlap -chr1 85452903 85466403 Lx5|LINE|L1 Sp110 Mappable ENCODE Overlap -chr1 84989001 84996294 Intergenic Slc16a14 Mappable ENCODE Overlap -chr1 88210785 88225860 "exon (NM_013701, exon 5 of 5)" Ugt1a1 Mappable ENCODE Overlap -chr1 133593455 133597064 Intergenic Snrpe Mappable ENCODE Overlap -chr1 85527647 85528664 Intergenic Sp110 Mappable ENCODE Overlap -chr1 84961182 84967761 Intergenic Slc16a14 Mappable ENCODE Overlap -chr1 195370720 195372965 (TTAGGG)n|Simple_repeat|Simple_repeat Cr2 Mappable ENCODE Overlap -chr1 85065013 85065017 L1Md_A|LINE|L1 A530032D15Rik Mappable ENCODE Overlap -chr1 85230698 85268061 "intron (NM_001037909, intron 5 of 6)" C130026I21Rik Mappable ENCODE Overlap -chr1 88296835 88310839 Intergenic Trpm8 Mappable ENCODE Overlap -chr1 85041960 85048233 (TTCC)n|Simple_repeat|Simple_repeat A530032D15Rik Mappable ENCODE Overlap -chr1 191396111 191398516 promoter-TSS (NM_144880) Ppp2r5a Lowly ENCODE Overlap -chr1 63629211 63631806 "intron (NM_001081658, intron 14 of 14)" Gm39653 Mappable ENCODE Overlap -chr1 85159040 85172333 Intergenic Gm7609 Mappable ENCODE Overlap -chr1 85570638 85570772 Intergenic Sp110 Mappable ENCODE Overlap -chr1 85268122 85335650 L1Md_F|LINE|L1 C130026I21Rik Mappable ENCODE Overlap -chr1 171068450 171072576 CpG Mir6546 Mappable ENCODE Overlap -chr1 85477779 85508363 Intergenic Sp110 Mappable ENCODE Overlap -chr1 88270612 88293020 B1_Mus2|SINE|Alu Hjurp Lowly ENCODE Overlap -chr1 85154287 85155709 B2_Mm2|SINE|B2 Gm7609 Mappable ENCODE Overlap -chr1 85212954 85213093 "exon (NM_001081746, exon 4 of 4)" Gm7609 Mappable ENCODE Overlap -chr1 85027461 85031109 Intergenic A530032D15Rik Mappable ENCODE Overlap -chr1 85578857 85636049 Lx10|LINE|L1 Sp110 Mappable ENCODE Overlap -chr1 88226083 88262450 "intron (NM_001281466, intron 22 of 41)" Mroh2a Mappable ENCODE Overlap -chr1 171073261 171076658 Intergenic Mir6546 Mappable ENCODE Overlap -chr1 84984333 84986162 L1Md_F2|LINE|L1 Slc16a14 Mappable ENCODE Overlap -chr1 88263593 88269113 "exon (NM_172505, exon 5 of 5)" 6430706D22Rik Mappable ENCODE Overlap -chr1 85196271 85200746 Intergenic Gm7609 Mappable ENCODE Overlap -chr1 85570878 85573531 ORR1E-int|LTR|ERVL-MaLR Sp110 Mappable ENCODE Overlap -chr1 7396936 7398946 CpG Pcmtd1 Mappable ENCODE Overlap -chr1 86524974 86527723 promoter-TSS (NM_001360830) Ptma Mappable ENCODE Overlap -chr1 85215765 85216434 Intergenic Gm7609 Mappable ENCODE Overlap -chr1 88293232 88293622 B1_Mur4|SINE|Alu Trpm8 Mappable ENCODE Overlap -chr1 26685234 26689325 "exon (NM_001033764, exon 1 of 2)" 4931408C20Rik Mappable Unique -chr1 183298135 183300594 RLTR33|LTR|ERVK Brox Mappable ENCODE Overlap -chr1 88294911 88296733 Intergenic Trpm8 Mappable ENCODE Overlap -chr1 24610534 24617184 Intergenic Col19a1 Mappable ENCODE Overlap -chr1 16072734 16074144 "intron (NM_001243238, intron 3 of 4)" 4930444P10Rik Mappable ENCODE Overlap -chr1 171080207 171081317 CpG Mir6546 Mappable ENCODE Overlap -chr1 171067673 171068300 Intergenic Mir6546 Mappable ENCODE Overlap -chr1 171063539 171065867 promoter-TSS (NR_106103) Mir6546 Mappable ENCODE Overlap -chr1 100179097 100181396 L1Md_F2|LINE|L1 Cntnap5b Mappable ENCODE Overlap -chr1 85523638 85527190 Intergenic Sp110 Mappable Unique -chr1 85549826 85555898 RSINE1|SINE|B4 Sp110 Mappable ENCODE Overlap -chr1 85003103 85013260 Intergenic Slc16a14 Mappable ENCODE Overlap -chr1 85646518 85649958 Intergenic Sp100 Mappable ENCODE Overlap -chr1 95450930 95453225 (TAAA)n|Simple_repeat|Simple_repeat Fam174a Mappable ENCODE Overlap -chr1 78572727 78575645 Intergenic Mogat1 Mappable ENCODE Overlap -chr1 85123828 85124899 ORR1E-int|LTR|ERVL-MaLR A530032D15Rik Lowly ENCODE Overlap -chr1 190299616 190304517 Intergenic Gm29678 Mappable ENCODE Overlap -chr1 85037170 85041259 Intergenic A530032D15Rik Mappable ENCODE Overlap -chr1 84960769 84961175 Intergenic Slc16a14 Mappable ENCODE Overlap -chr1 85178595 85185186 L1MB5|LINE|L1 Gm7609 Mappable Unique -chr1 85073737 85116916 B3|SINE|B2 A530032D15Rik Mappable ENCODE Overlap -chr1 195240544 195243014 CpG Cr2 Mappable ENCODE Overlap -chr1 85565428 85567696 Lx5|LINE|L1 Sp110 Mappable ENCODE Overlap -chr1 85337842 85347901 Intergenic C130026I21Rik Mappable ENCODE Overlap -chr10 81177053 81179869 promoter-TSS (NR_028549) Snord37 Mappable ENCODE Overlap -chr10 22469495 22472214 PB1D7|SINE|Alu Gm10825 Mappable Unique -chr10 130593319 130595993 (TTAGGG)n|Simple_repeat|Simple_repeat Vmn2r87 Mappable Unique -chr10 58220313 58235253 Intergenic Dux Mappable ENCODE Overlap -chr10 58236676 58240755 Intergenic Gm4981 Mappable ENCODE Overlap -chr10 80621024 80623632 promoter-TSS (NM_134002) Csnk1g2 Mappable Unique -chr10 3108427 3118165 Intergenic 9230019H11Rik Mappable ENCODE Overlap -chr10 27818052 27823177 L1Md_A|LINE|L1 Lama2 Mappable Unique -chr10 81319569 81322199 promoter-TSS (NM_027381) Cactin Mappable ENCODE Overlap -chr10 27823584 27824808 L1Md_A|LINE|L1 Lama2 Mappable ENCODE Overlap -chr10 22140821 22144273 "intron (NM_001254744, intron 1 of 1)" E030030I06Rik Mappable ENCODE Overlap -chr11 34680652 34684369 RLTR44-int|LTR|ERVK Dock2 Mappable ENCODE Overlap -chr11 3118245 3201063 MTD|LTR|ERVL-MaLR Sfi1 Mappable ENCODE Overlap -chr11 109010646 109013122 LSU-rRNA_Hsa|rRNA|rRNA Axin2 Mappable ENCODE Overlap -chr11 107197587 107200468 SYNREP_MM|Satellite|Satellite Nol11 Mappable ENCODE Overlap -chr11 54139006 54141736 (GGA)n|Simple_repeat|Simple_repeat P4ha2 Mappable ENCODE Overlap -chr11 106946994 106948324 B3|SINE|B2 Smurf2 Mappable ENCODE Overlap -chr11 34542542 34546090 RLTR44-int|LTR|ERVK Insyn2b Mappable Unique -chr11 3111164 3116055 Intergenic Pisd-ps1 Lowly ENCODE Overlap -chr11 3099001 3105930 GSAT_MM|Satellite|Satellite Pisd-ps1 Mappable ENCODE Overlap -chr11 96976407 96979082 promoter-TSS (NM_030220) Sp2 Mappable ENCODE Overlap -chr11 88967559 88970540 RMER16-int|LTR|ERVK Elobl Mappable ENCODE Overlap -chr11 5167853 5170298 Intergenic Emid1 Mappable ENCODE Overlap -chr12 78349869 78352172 LSU-rRNA_Hsa|rRNA|rRNA Gphn Mappable ENCODE Overlap -chr12 69158390 69160592 promoter-TSS (NM_009093) Rps29 Mappable ENCODE Overlap -chr12 120027628 120030022 (TTAGGG)n|Simple_repeat|Simple_repeat Tmem196 Mappable ENCODE Overlap -chr12 5057005 5057046 Intergenic Atad2b Mappable ENCODE Overlap -chr12 20225728 20228048 MMERGLN-int|LTR|ERV1 1700030C10Rik Mappable ENCODE Overlap -chr12 112776555 112784927 Intergenic Pld4 Lowly ENCODE Overlap -chr12 4218421 4222747 "intron (NM_001361641, intron 2 of 5)" Cenpo Mappable ENCODE Overlap -chr12 5057140 5060225 Intergenic Atad2b Mappable Unique -chr12 97060428 97062789 Intergenic 1700019M22Rik Mappable Unique -chr12 3108865 3111202 GSAT_MM|Satellite|Satellite Rab10os Mappable ENCODE Overlap -chr12 113423488 113426173 (CAGCT)n|Simple_repeat|Simple_repeat Adam6b Mappable ENCODE Overlap -chr12 67058082 67060960 GSAT_MM|Satellite|Satellite Mdga2 Mappable ENCODE Overlap -chr12 93575971 93578239 (TTAGGG)n|Simple_repeat|Simple_repeat 4930559C10Rik Mappable ENCODE Overlap -chr12 59035707 59037804 B2_Mm2|SINE|B2 Gemin2 Mappable ENCODE Overlap -chr12 20228876 20235430 MMERGLN-int|LTR|ERV1 1700030C10Rik Mappable ENCODE Overlap -chr12 74802840 74805506 GSAT_MM|Satellite|Satellite Kcnh5 Mappable ENCODE Overlap -chr12 69360184 69362481 7SLRNA|srpRNA|srpRNA Nemf Mappable ENCODE Overlap -chr12 20228316 20228624 MMERGLN-int|LTR|ERV1 1700030C10Rik Mappable Unique -chr13 74527428 74532026 (CACAG)n|Simple_repeat|Simple_repeat Zfp825 Mappable ENCODE Overlap -chr13 58346715 58349853 "intron (NM_175214, intron 1 of 16)" Kif27 Mappable ENCODE Overlap -chr13 110742967 110745548 (CCCTAA)n|Simple_repeat|Simple_repeat Gm38397 Mappable ENCODE Overlap -chr13 119488974 119491395 "intron (NM_001370627, intron 1 of 2)" Tmem267 Mappable ENCODE Overlap -chr13 120320412 120322639 (TTAGGG)n|Simple_repeat|Simple_repeat Tcstv3 Mappable ENCODE Overlap -chr13 9010688 9013168 (GGA)n|Simple_repeat|Simple_repeat Gtpbp4 Mappable Unique -chr13 3371585 3375531 Intergenic 2810429I04Rik Mappable Unique -chr13 119594610 119604524 "intron (NM_001370626, intron 2 of 2)" Ccl28 Mappable ENCODE Overlap -chr13 60095990 60098591 (CACAG)n|Simple_repeat|Simple_repeat A530065N20Rik Mappable ENCODE Overlap -chr13 119605201 119605920 "intron (NM_001370626, intron 2 of 2)" Ccl28 Mappable ENCODE Overlap -chr13 13859610 13862009 (TTAGGG)n|Simple_repeat|Simple_repeat Gng4 Mappable ENCODE Overlap -chr13 77437837 77440058 GSAT_MM|Satellite|Satellite Fam172a Mappable ENCODE Overlap -chr13 119607969 119617588 L1Md_F2|LINE|L1 Ccl28 Mappable ENCODE Overlap -chr13 44868572 44871024 LSU-rRNA_Hsa|rRNA|rRNA Dtnbp1 Mappable ENCODE Overlap -chr13 12829672 12831385 IAPLTR3-int|LTR|ERVK Prl2c3 Mappable ENCODE Overlap -chr13 9833306 9835494 L1Md_T|LINE|L1 Zmynd11 Mappable ENCODE Overlap -chr13 13753022 13756110 "intron (NM_010748, intron 46 of 52)" Gng4 Mappable ENCODE Overlap -chr14 120476521 120479308 promoter-TSS (NM_029519) Rap2a Mappable ENCODE Overlap -chr14 6636208 6638572 Intergenic Gm3636 Mappable ENCODE Overlap -chr14 7869742 7872517 "intron (NM_001081427, intron 3 of 45)" Flnb Mappable Unique -chr14 19414676 19420702 GSAT_MM|Satellite|Satellite Gm5458 Mappable Unique -chr14 67714647 67717104 promoter-TSS (NM_175384) Cdca2 Mappable Unique -chr14 69161004 69163446 (CCCTAA)n|Simple_repeat|Simple_repeat Nkx2-6 Mappable ENCODE Overlap -chr14 21499408 21502069 CpG Kat6b Mappable Unique -chr14 124800549 124803244 (TTAGGG)n|Simple_repeat|Simple_repeat Fgf14 Mappable ENCODE Overlap -chr14 8285634 8287903 Intergenic Fam107a Mappable ENCODE Overlap -chr14 55559045 55561737 promoter-TSS (NM_001199009) Dcaf11 Mappable ENCODE Overlap -chr15 75084455 75088047 B1_Mm|SINE|Alu Ly6c2 Mappable ENCODE Overlap -chr15 9014687 9017345 (CACG)n|Simple_repeat|Simple_repeat Ranbp3l Mappable ENCODE Overlap -chr15 91905616 91911402 (CCA)n|Simple_repeat|Simple_repeat Smgc Mappable ENCODE Overlap -chr15 102404624 102407389 promoter-TSS (NM_013672) Sp1 Mappable Unique -chr15 58437815 58440686 "intron (NM_145959, intron 15 of 23)" Fam91a1 Mappable Unique -chr15 91992118 91993703 L1Md_A|LINE|L1 Cntn1 Mappable ENCODE Overlap -chr15 76102012 76105870 "exon (NM_144848, exon 2 of 2)" Nrbp2 Mappable ENCODE Overlap -chr16 86819786 86822244 Intergenic Gm32461 Mappable ENCODE Overlap -chr16 3348513 3353138 Intergenic Olfr161 Mappable ENCODE Overlap -chr16 3112455 3118056 (TTTC)n|Simple_repeat|Simple_repeat Olfr161 Mappable ENCODE Overlap -chr16 11142906 11145315 LSU-rRNA_Hsa|rRNA|rRNA Txndc11 Lowly ENCODE Overlap -chr16 3337067 3337248 MMERGLN_LTR|LTR|ERV1 Olfr161 Mappable ENCODE Overlap -chr16 24582361 24584934 (TTAGGG)n|Simple_repeat|Simple_repeat Morf4l1-ps1 Mappable ENCODE Overlap -chr16 3270724 3273299 Lx6|LINE|L1 Olfr161 Mappable ENCODE Overlap -chr16 3121810 3124730 B1_Mus1|SINE|Alu Olfr161 Mappable ENCODE Overlap -chr16 93991773 93994368 "intron (NM_019500, intron 1 of 2)" Cldn14 Mappable ENCODE Overlap -chr16 10974067 10976278 GSAT_MM|Satellite|Satellite Litaf Mappable ENCODE Overlap -chr16 93788192 93790384 (CCCTAA)n|Simple_repeat|Simple_repeat 2310043M15Rik Mappable ENCODE Overlap -chr16 3338885 3339554 RLTR22_Mus|LTR|ERVK Olfr161 Mappable Unique -chr16 57390113 57392676 LSU-rRNA_Hsa|rRNA|rRNA Filip1l Mappable Unique -chr16 98106437 98108768 (TTAGGG)n|Simple_repeat|Simple_repeat A630089N07Rik Mappable ENCODE Overlap -chr16 3267680 3269997 Lx|LINE|L1 Olfr161 Mappable ENCODE Overlap -chr16 3340104 3341863 L1_Mur3|LINE|L1 Olfr161 Mappable ENCODE Overlap -chr16 38087847 38090558 promoter-TSS (NR_033221) BC031361 Mappable ENCODE Overlap -chr16 3230586 3249217 Intergenic Olfr161 Mappable ENCODE Overlap -chr16 17221214 17223525 LSU-rRNA_Hsa|rRNA|rRNA Hic2 Mappable ENCODE Overlap -chr17 84460688 84464659 "intron (NM_183021, intron 2 of 37)" Thada Mappable ENCODE Overlap -chr17 67740307 67742635 (CCCTAA)n|Simple_repeat|Simple_repeat Lama1 Mappable Unique -chr17 39841997 39849829 "non-coding (NR_046233, exon 1 of 1)" Rn45s Mappable ENCODE Overlap -chr17 3075361 3085806 "intron (NR_003519, intron 2 of 7)" Pisd-ps2 Mappable ENCODE Overlap -chr17 13584722 13592605 Intergenic 2700054A10Rik Mappable ENCODE Overlap -chr17 4625167 4627603 (CACTC)n|Simple_repeat|Simple_repeat 4930517M08Rik Mappable ENCODE Overlap -chr17 23533391 23533512 Intergenic 6330415G19Rik Mappable Unique -chr17 13547119 13554228 (CTGTG)n|Simple_repeat|Simple_repeat 2700054A10Rik Mappable ENCODE Overlap -chr17 3004168 3039892 (TACTG)n|Simple_repeat|Simple_repeat Pisd-ps2 Lowly ENCODE Overlap -chr17 29101439 29109513 Intergenic Rab44 Mappable ENCODE Overlap -chr17 13653613 13656298 Intergenic 2700054A10Rik Mappable ENCODE Overlap -chr17 22875275 22877883 LSU-rRNA_Hsa|rRNA|rRNA Zfp945 Mappable ENCODE Overlap -chr17 13304955 13307295 (CTGTG)n|Simple_repeat|Simple_repeat Tcp10c Mappable ENCODE Overlap -chr17 23530536 23533349 Intergenic 6330415G19Rik Mappable ENCODE Overlap -chr17 70962658 70964891 LSU-rRNA_Hsa|rRNA|rRNA Myl12b Mappable ENCODE Overlap -chr17 36230224 36232605 CpG Rpp21 Mappable ENCODE Overlap -chr18 40307015 40309403 "intron (NM_026135, intron 2 of 2)" Mappable ENCODE Overlap -chr18 82160214 82171948 Intergenic Mir5127 Mappable ENCODE Overlap -chr18 20619926 20621235 L1M3e|LINE|L1 Ttr Mappable Unique -chr18 20624339 20624494 L1M3e|LINE|L1 Ttr Mappable Unique -chr18 20617575 20617982 L1M3e|LINE|L1 Ttr Lowly Unique -chr18 85696926 85699291 LSU-rRNA_Hsa|rRNA|rRNA Neto1 Mappable Unique -chr18 3113805 3120973 Intergenic Vmn1r238 Mappable ENCODE Overlap -chr18 90601089 90603639 (TTAGGG)n|Simple_repeat|Simple_repeat Gm45871 Mappable ENCODE Overlap -chr18 4195753 4198816 B3A|SINE|B2 Lyzl1 Mappable ENCODE Overlap -chr18 36559007 36561036 promoter-TSS (NM_175375) Ankhd1 Mappable ENCODE Overlap -chr18 3002806 3013833 ERVB4_1B-I_MM-int|LTR|ERVK Vmn1r238 Mappable ENCODE Overlap -chr19 45648970 45651272 B2_Mm2|SINE|B2 Fbxw4 Mappable ENCODE Overlap -chr19 53775785 53776977 "intron (NM_001170847, intron 1 of 13)" Rbm20 Mappable ENCODE Overlap -chr19 58112241 58114641 (CACAG)n|Simple_repeat|Simple_repeat Mir5623 Mappable ENCODE Overlap -chr19 39258730 39261328 MTA_Mm-int|LTR|ERVL-MaLR Cyp2c29 Mappable ENCODE Overlap -chr19 39262753 39264236 MTA_Mm|LTR|ERVL-MaLR Cyp2c29 Mappable ENCODE Overlap -chr19 61330275 61332566 (TTAGGG)n|Simple_repeat|Simple_repeat Csf2ra Mappable ENCODE Overlap -chr19 61262650 61268164 Intergenic Csf2ra Mappable ENCODE Overlap -chr2 182011584 182014223 (TTAGGG)n|Simple_repeat|Simple_repeat Gm14496 Mappable ENCODE Overlap -chr2 3049003 3052125 B1F1|SINE|Alu Fam171a1 Mappable ENCODE Overlap -chr2 51946088 51948860 (GGA)n|Simple_repeat|Simple_repeat Rbm43 Lowly Unique -chr2 57628489 57630727 (TTAGGG)n|Simple_repeat|Simple_repeat Galnt5 Mappable ENCODE Overlap -chr2 92092600 92094775 (CCCTAA)n|Simple_repeat|Simple_repeat Creb3l1 Mappable ENCODE Overlap -chr2 84714187 84716735 promoter-TSS (NM_144887) Zdhhc5 Mappable ENCODE Overlap -chr2 181927046 181933525 RLTR33|LTR|ERVK Gm14496 Mappable ENCODE Overlap -chr2 22002667 22006682 L1Md_A|LINE|L1 Myo3a Mappable ENCODE Overlap -chr2 5378040 5380376 promoter-TSS (NR_030601) Mir466d Mappable Unique -chr2 177313551 177316626 MMSAT4|Satellite|Satellite Zfp970 Mappable ENCODE Overlap -chr2 66188206 66190462 (CCCTAA)n|Simple_repeat|Simple_repeat Galnt3 Mappable Unique -chr2 181915695 181920273 Intergenic Polr3k Mappable ENCODE Overlap -chr2 53190369 53192471 promoter-TSS (NM_022989) Mappable Unique -chr2 20898864 20901198 LSU-rRNA_Hsa|rRNA|rRNA Arhgap21 Mappable ENCODE Overlap -chr2 28182997 28185655 (CCCTAA)n|Simple_repeat|Simple_repeat Olfm1 Mappable ENCODE Overlap -chr2 98661230 98668337 RMER13A1|LTR|ERVK Lrrc4c Mappable ENCODE Overlap -chr2 22586502 22591198 Intergenic Gad2 Mappable ENCODE Overlap -chr2 22738413 22741056 Intergenic Apbb1ip Mappable ENCODE Overlap -chr2 121521321 121522185 "intron (NM_001290987, intron 4 of 11)" Wdr76 Mappable ENCODE Overlap -chr2 52695533 52700035 "intron (NM_019667, intron 13 of 13)" Cacnb4 Mappable ENCODE Overlap -chr2 80811835 80815984 L1Md_A|LINE|L1 Nup35 Mappable ENCODE Overlap -chr3 91097737 91098269 L1Md_A|LINE|L1 9130204L05Rik Mappable ENCODE Overlap -chr3 159938404 159940680 TTS (NM_001356350) Wls Mappable ENCODE Overlap -chr3 149051473 149053935 (TTAGGG)n|Simple_repeat|Simple_repeat Adgrl2 Mappable ENCODE Overlap -chr3 95014321 95016552 promoter-TSS (NM_030074) Zfp687 Mappable ENCODE Overlap -chr3 3003499 3005583 Intergenic Hnf4g Mappable ENCODE Overlap -chr3 5859339 5861826 LSU-rRNA_Hsa|rRNA|rRNA Pex2 Mappable ENCODE Overlap -chr3 3008518 3016611 Intergenic Hnf4g Mappable ENCODE Overlap -chr3 123676652 123679345 C-rich|Low_complexity|Low_complexity Ndst3 Mappable ENCODE Overlap -chr3 3000306 3003485 Intergenic Hnf4g Mappable Unique -chr3 8243566 8247573 B2_Mm2|SINE|B2 Gm6194 Mappable Unique -chr3 56574432 56576750 GSAT_MM|Satellite|Satellite Nbea Mappable ENCODE Overlap -chr3 96043520 96046044 "intron (NM_013841, intron 7 of 14)" Vps45 Mappable ENCODE Overlap -chr3 62158100 62160335 LSU-rRNA_Hsa|rRNA|rRNA Arhgef26 Mappable Unique -chr3 3027935 3033946 Intergenic Hnf4g Mappable ENCODE Overlap -chr3 60044058 60047062 (CACAG)n|Simple_repeat|Simple_repeat Aadac Mappable ENCODE Overlap -chr3 99980113 99982394 GSAT_MM|Satellite|Satellite Spag17 Mappable ENCODE Overlap -chr4 31775994 31778602 L1Md_A|LINE|L1 Map3k7 Lowly ENCODE Overlap -chr4 146599418 146600571 L1_Mur1|LINE|L1 1700095A21Rik Mappable ENCODE Overlap -chr4 145839807 145842678 Intergenic Gm13238 Mappable ENCODE Overlap -chr4 146262474 146263179 RMER3D-int|LTR|ERVK Zfp991 Mappable ENCODE Overlap -chr4 147255924 147259118 Intergenic Mappable ENCODE Overlap -chr4 3088184 3092574 GSAT_MM|Satellite|Satellite Vmn1r2 Mappable ENCODE Overlap -chr4 146165466 146171513 "intron (NM_001177546, intron 2 of 4)" Zfp600 Mappable ENCODE Overlap -chr4 146497127 146497191 MLTR18A_MM|LTR|ERVK Zfp981 Mappable ENCODE Overlap -chr4 118546006 118549737 G-rich|Low_complexity|Low_complexity Tmem125 Mappable ENCODE Overlap -chr4 147120785 147128930 CpG 4933438K21Rik Mappable ENCODE Overlap -chr4 146498137 146500659 RLTR40|LTR|ERVK Zfp981 Mappable ENCODE Overlap -chr4 145843517 145849997 Intergenic Gm13238 Lowly Unique -chr4 146451432 146455458 "intron (NM_001085522, intron 1 of 3)" Zfp992 Mappable ENCODE Overlap -chr4 147623285 147624916 "intron (NM_145078, intron 2 of 4)" Zfp979 Mappable ENCODE Overlap -chr4 156355655 156358892 Intergenic Vmn2r123 Mappable ENCODE Overlap -chr4 145700850 145703586 "exon (NM_001103158, exon 5 of 5)" Zfp980 Mappable ENCODE Overlap -chr4 147435763 147435792 (GAAA)n|Simple_repeat|Simple_repeat Mappable ENCODE Overlap -chr4 147448735 147450095 "intron (NM_001371349, intron 1 of 3)" Mappable ENCODE Overlap -chr4 146713610 146714207 Intergenic 1700095A21Rik Mappable ENCODE Overlap -chr4 147028189 147033108 "intron (NM_001177767, intron 2 of 4)" Rex2 Mappable ENCODE Overlap -chr4 147389133 147392158 MMSAT4|Satellite|Satellite Mappable ENCODE Overlap -chr4 147452010 147452668 Lx8|LINE|L1 Mappable ENCODE Overlap -chr4 70377117 70379256 GSAT_MM|Satellite|Satellite Cdk5rap2 Mappable ENCODE Overlap -chr4 147093921 147096533 L1VL4|LINE|L1 4933438K21Rik Mappable ENCODE Overlap -chr4 147369561 147370310 Lx3B|LINE|L1 Mappable ENCODE Overlap -chr4 147447353 147448412 "intron (NM_001371349, intron 1 of 3)" Mappable ENCODE Overlap -chr4 147331641 147333833 MMSAT4|Satellite|Satellite Mappable ENCODE Overlap -chr4 3174089 3178413 Intergenic Vmn1r2 Mappable ENCODE Overlap -chr4 145447894 145450160 Lx2|LINE|L1 Smarca5-ps Lowly ENCODE Overlap -chr4 151860870 151863546 promoter-TSS (NM_001195565) Camta1 Mappable ENCODE Overlap -chr4 3087794 3087824 MTA_Mm-int|LTR|ERVL-MaLR Vmn1r2 Lowly ENCODE Overlap -chr4 145779810 145780077 Intergenic Zfp991 Mappable ENCODE Overlap -chr4 147517884 147524409 Intergenic Zfp982 Mappable ENCODE Overlap -chr4 146259718 146261663 Lx4A|LINE|L1 Zfp991 Mappable ENCODE Overlap -chr4 146521337 146522409 Lx3B|LINE|L1 Zfp981 Mappable ENCODE Overlap -chr4 145834584 145838868 promoter-TSS (NR_033612) Gm13238 Mappable ENCODE Overlap -chr4 146714489 146716653 B2_Mm2|SINE|B2 1700095A21Rik Mappable ENCODE Overlap -chr4 147635572 147636208 RMER6A|LTR|ERVK Zfp979 Mappable ENCODE Overlap -chr4 147368968 147369146 (TATG)n|Simple_repeat|Simple_repeat Mappable ENCODE Overlap -chr4 28175809 28178165 SYNREP_MM|Satellite|Satellite Epha7 Lowly ENCODE Overlap -chr4 146475151 146476549 Intergenic Zfp981 Mappable ENCODE Overlap -chr4 147394988 147407328 RLTR10-int|LTR|ERVK Mappable ENCODE Overlap -chr4 147179879 147180585 Intergenic 4933438K21Rik Mappable ENCODE Overlap -chr4 147377003 147378516 Intergenic Mappable ENCODE Overlap -chr4 3057927 3057951 MTA_Mm-int|LTR|ERVL-MaLR Vmn1r2 Mappable ENCODE Overlap -chr4 147197835 147200824 Intergenic 4933438K21Rik Mappable ENCODE Overlap -chr4 147280125 147280832 Lx|LINE|L1 Mappable ENCODE Overlap -chr4 146172343 146177455 B2_Mm1a|SINE|B2 Zfp600 Mappable ENCODE Overlap -chr4 145685329 145689863 "intron (NM_001103158, intron 2 of 4)" Zfp980 Mappable ENCODE Overlap -chr4 145828383 145829917 "non-coding (NR_040355, exon 5 of 5)" Gm13238 Mappable ENCODE Overlap -chr4 146716992 146721348 MMSAT4|Satellite|Satellite 1700095A21Rik Mappable ENCODE Overlap -chr4 147348882 147351051 Intergenic Mappable ENCODE Overlap -chr4 147309454 147310788 RMER6A|LTR|ERVK Mappable ENCODE Overlap -chr4 146436307 146436832 "intron (NM_001083918, intron 3 of 6).2" Zfp992 Mappable ENCODE Overlap -chr4 147636285 147638009 Lx8|LINE|L1 Zfp979 Mappable ENCODE Overlap -chr4 3078688 3087634 Intergenic Vmn1r2 Mappable ENCODE Overlap -chr4 147450308 147451358 "intron (NM_001371349, intron 1 of 3)" Mappable ENCODE Overlap -chr4 147365623 147366636 Intergenic Mappable ENCODE Overlap -chr4 156339577 156344853 Intergenic Vmn2r123 Lowly ENCODE Overlap -chr4 147418158 147435518 Intergenic Mappable ENCODE Overlap -chr4 146273258 146273750 Lx8|LINE|L1 Zfp991 Lowly ENCODE Overlap -chr4 146477296 146496949 Intergenic Zfp981 Lowly ENCODE Overlap -chr4 147057335 147058419 "exon (NM_001177767, exon 5 of 5)" 4933438K21Rik Lowly ENCODE Overlap -chr4 145830595 145831382 "non-coding (NR_040355, exon 5 of 5)" Gm13238 Lowly ENCODE Overlap -chr4 147414962 147417956 Intergenic Mappable ENCODE Overlap -chr4 3179430 3183184 Intergenic Vmn1r3 Mappable ENCODE Overlap -chr4 147435947 147440573 Lx3_Mus|LINE|L1 Mappable ENCODE Overlap -chr4 3228412 3229946 LTR16C|LTR|ERVL Vmn1r3 Mappable ENCODE Overlap -chr4 146514744 146515880 "intron (NM_001243139, intron 1 of 3)" Zfp981 Mappable ENCODE Overlap -chr4 3057958 3070939 Intergenic Vmn1r2 Mappable ENCODE Overlap -chr4 147334486 147346844 B3A|SINE|B2 Mappable ENCODE Overlap -chr4 147119579 147119821 L1_Mur1|LINE|L1 4933438K21Rik Mappable ENCODE Overlap -chr4 145679625 145681903 "intron (NM_001103158, intron 2 of 4)" Zfp980 Mappable ENCODE Overlap -chr4 147231094 147237178 Intergenic 4933438K21Rik Mappable ENCODE Overlap -chr4 147512797 147513189 "exon (NM_001371348, exon 5 of 5)" Zfp982 Mappable ENCODE Overlap -chr4 3049009 3057589 Intergenic Vmn1r2 Lowly ENCODE Overlap -chr4 3178935 3178988 Intergenic Vmn1r3 Mappable ENCODE Overlap -chr4 3224191 3227875 MER90a|LTR|ERV1 Vmn1r3 Lowly ENCODE Overlap -chr4 146164049 146164808 "intron (NM_001177546, intron 2 of 4)" Zfp600 Lowly ENCODE Overlap -chr4 147355319 147357412 MLTR18A_MM|LTR|ERVK Lowly ENCODE Overlap -chr4 147362443 147364013 Lx8|LINE|L1 Mappable ENCODE Overlap -chr4 149809055 149811758 Intergenic Slc25a33 Mappable ENCODE Overlap -chr4 147755337 147756655 "exon (NM_001127189, exon 6 of 6)" Zfp534 Mappable ENCODE Overlap -chr4 147407719 147414944 Lx2|LINE|L1 Mappable Unique -chr4 147194720 147197718 RLTR13D3|LTR|ERVK 4933438K21Rik Mappable ENCODE Overlap -chr4 145438840 145440729 Intergenic Smarca5-ps Mappable ENCODE Overlap -chr5 15615268 15615413 ORR1A1-int|LTR|ERVL-MaLR Speer4d Mappable ENCODE Overlap -chr5 14957881 14964120 "intron (NR_001584, intron 2 of 3)" Speer8-ps1 Mappable ENCODE Overlap -chr5 14913423 14914073 "intron (NM_198666, intron 1 of 4)" Gm9758 Mappable ENCODE Overlap -chr5 15586655 15587094 Lx5c|LINE|L1 Gm21083 Mappable ENCODE Overlap -chr5 15034396 15046044 Lx2A1|LINE|L1 Gm17019 Mappable ENCODE Overlap -chr5 15687776 15694810 "intron (NR_001585, intron 1 of 4)" Speer4cos Mappable ENCODE Overlap -chr5 125388874 125389027 B1_Mus1|SINE|Alu Ubc Lowly ENCODE Overlap -chr5 14940146 14942209 ORR1A1|LTR|ERVL-MaLR Speer4e Mappable ENCODE Overlap -chr5 15634328 15634761 ORR1A3|LTR|ERVL-MaLR Speer4d Mappable ENCODE Overlap -chr5 14917775 14921130 ORR1A1-int|LTR|ERVL-MaLR Gm9758 Mappable ENCODE Overlap -chr5 15677087 15682991 promoter-TSS (NR_001585) Speer4cos Mappable ENCODE Overlap -chr5 15026604 15026773 L1_Mur2|LINE|L1 Gm17019 Mappable ENCODE Overlap -chr5 114921404 114923609 promoter-TSS (NM_145209) Oasl1 Mappable ENCODE Overlap -chr5 25815652 25819492 (CTGTG)n|Simple_repeat|Simple_repeat Actr3b Mappable ENCODE Overlap -chr5 15497437 15500155 Lx7|LINE|L1 Gm21190 Mappable ENCODE Overlap -chr5 15613353 15614537 RLTR19|LTR|ERVK Speer4d Mappable ENCODE Overlap -chr5 104329746 104333160 (CACAG)n|Simple_repeat|Simple_repeat Mepe Mappable ENCODE Overlap -chr5 14932264 14933958 TTS (NM_001122661) Speer4e Mappable ENCODE Overlap -chr5 14951800 14952432 "intron (NR_001584, intron 1 of 3)" Speer8-ps1 Mappable ENCODE Overlap -chr5 32732901 32735224 Intergenic Pisd Mappable ENCODE Overlap -chr5 109556534 109559507 "intron (NM_001310694, intron 1 of 7)" Crlf2 Mappable ENCODE Overlap -chr5 15478820 15485756 RMER6BA|LTR|ERVK Gm21190 Mappable ENCODE Overlap -chr5 15507626 15518299 L1_Mm|LINE|L1 Gm21190 Mappable ENCODE Overlap -chr5 15459668 15464106 Intergenic Gm21190 Mappable ENCODE Overlap -chr5 14934781 14935308 "exon (NM_001122661, exon 4 of 5)" Speer4e Mappable ENCODE Overlap -chr5 32736914 32739312 "exon (NM_001347332, exon 8 of 9)" Pisd Mappable ENCODE Overlap -chr5 14953678 14957075 Lx|LINE|L1 Speer8-ps1 Mappable ENCODE Overlap -chr5 137151217 137153727 "exon (NM_010843, exon 3 of 13)" Muc3 Mappable ENCODE Overlap -chr5 14985270 14992323 ORR1A3|LTR|ERVL-MaLR Gm10354 Mappable ENCODE Overlap -chr5 15486560 15489053 Intergenic Gm21190 Mappable ENCODE Overlap -chr5 15629147 15633869 Intergenic Speer4d Mappable ENCODE Overlap -chr5 15709317 15713682 "intron (NR_001585, intron 4 of 4)" Speer4c Mappable ENCODE Overlap -chr5 15017202 15021309 Intergenic Gm17019 Mappable ENCODE Overlap -chr5 15551423 15556883 MTD|LTR|ERVL-MaLR Gm21083 Mappable ENCODE Overlap -chr5 14950778 14951661 "intron (NR_001584, intron 1 of 3)" Speer8-ps1 Mappable ENCODE Overlap -chr5 15579113 15583633 "intron (NM_001310450, intron 4 of 4)" Gm21083 Mappable ENCODE Overlap -chr5 14909644 14910139 TTS (NM_198666) Gm9758 Mappable ENCODE Overlap -chr5 14950133 14950691 MTEa|LTR|ERVL-MaLR Speer8-ps1 Mappable ENCODE Overlap -chr5 14971252 14974797 L1_Mus4|LINE|L1 Gm10354 Mappable ENCODE Overlap -chr5 15010328 15011975 RMER17A|LTR|ERVK Gm17019 Mappable ENCODE Overlap -chr5 14942455 14942460 ORR1A1-int|LTR|ERVL-MaLR Speer8-ps1 Mappable ENCODE Overlap -chr5 15466369 15466693 Intergenic Gm21190 Mappable ENCODE Overlap -chr5 14983568 14984680 RLTR19|LTR|ERVK Gm10354 Mappable ENCODE Overlap -chr5 15003599 15009785 Intergenic Gm17019 Mappable ENCODE Overlap -chr5 14993381 14998101 Intergenic Gm10354 Mappable ENCODE Overlap -chr5 15639785 15646403 Intergenic 4930572O03Rik Mappable ENCODE Overlap -chr5 15021751 15024895 Intergenic Gm17019 Mappable ENCODE Overlap -chr5 135148198 135150687 promoter-TSS (NM_013763) Tbl2 Mappable ENCODE Overlap -chr5 146259978 146262365 LSU-rRNA_Hsa|rRNA|rRNA Cdk8 Mappable ENCODE Overlap -chr5 15605403 15608337 MTD|LTR|ERVL-MaLR Speer4d Mappable ENCODE Overlap -chr5 15702276 15704787 "intron (NR_001585, intron 2 of 4)" Speer4c Mappable ENCODE Overlap -chr5 14979650 14983004 Intergenic Gm10354 Mappable ENCODE Overlap -chr5 36659924 36662570 "intron (NM_001081232, intron 2 of 8)" D5Ertd579e Mappable ENCODE Overlap -chr5 15620009 15626203 "intron (NM_025759, intron 4 of 4)" Speer4d Mappable ENCODE Overlap -chr5 15650145 15656407 "intron (NR_073011, intron 4 of 4)" 4930572O03Rik Mappable ENCODE Overlap -chr5 125385640 125388609 "exon (NM_019639, exon 2 of 2)" Ubc Mappable ENCODE Overlap -chr5 15658545 15663465 ORR1A1-int|LTR|ERVL-MaLR 4930572O03Rik Mappable ENCODE Overlap -chr5 15657677 15657682 promoter-TSS (NR_073011) 4930572O03Rik Mappable ENCODE Overlap -chr5 15619206 15619829 "intron (NM_025759, intron 1 of 4)" Speer4d Mappable Unique -chr5 15526874 15529178 "exon (NM_001310449, exon 2 of 5)" Gm21190 Mappable Unique -chr5 15636219 15639197 RMER17A|LTR|ERVK Speer4d Mappable Unique -chr5 15589001 15591949 RMER6D|LTR|ERVK Gm21083 Mappable Unique -chr5 15595224 15597954 RMER17A|LTR|ERVK Gm21083 Mappable ENCODE Overlap -chr5 32725095 32731380 Lx9|LINE|L1 Pisd Mappable ENCODE Overlap -chr5 36629423 36631766 "intron (NM_001081232, intron 2 of 8)" Tbc1d14 Mappable Unique -chr5 15576662 15577621 "5' UTR (NM_001310450, exon 1 of 5)" Gm21083 Mappable Unique -chr5 15050630 15055837 Intergenic Gm17019 Mappable ENCODE Overlap -chr5 15696564 15699401 L1_Mus3|LINE|L1 Speer4c Mappable Unique -chr5 15670223 15673356 Intergenic Speer4cos Mappable Unique -chr5 15530483 15530524 RLTR19|LTR|ERVK Gm21190 Mappable Unique -chr5 15466890 15474923 Intergenic Gm21190 Mappable ENCODE Overlap -chr5 15600186 15600717 Intergenic Speer4d Mappable ENCODE Overlap -chr5 147610435 147612632 (TTAGGG)n|Simple_repeat|Simple_repeat Flt1 Mappable Unique -chr6 47770689 47773524 CpG Rn4.5s Mappable ENCODE Overlap -chr6 103648046 103650294 SYNREP_MM|Satellite|Satellite Chl1 Mappable ENCODE Overlap -chr6 3049424 3052069 Intergenic Gm8579 Mappable ENCODE Overlap -chr6 4922733 4925199 (CCCTAA)n|Simple_repeat|Simple_repeat Ppp1r9a Mappable ENCODE Overlap -chr6 47650957 47687580 RMER12B|LTR|ERVK Rn4.5s Mappable ENCODE Overlap -chr6 29746689 29750155 (CTGTG)n|Simple_repeat|Simple_repeat Smo Mappable ENCODE Overlap -chr6 47737204 47770613 promoter-TSS (NR_002841).3 Rn4.5s Mappable ENCODE Overlap -chr6 53082921 53085555 (TTAGGG)n|Simple_repeat|Simple_repeat Jazf1 Mappable ENCODE Overlap -chr6 114340023 114343200 (CACAG)n|Simple_repeat|Simple_repeat Hrh1 Mappable Unique -chr6 47776922 47778288 Intergenic Rn4.5s Mappable ENCODE Overlap -chr6 3199768 3202671 SSU-rRNA_Hsa|rRNA|rRNA Gm8579 Mappable ENCODE Overlap -chr7 123021275 123023624 (GGA)n|Simple_repeat|Simple_repeat Rbbp6 Mappable ENCODE Overlap -chr7 64072406 64091442 Intergenic Trpm1 Mappable Unique -chr7 59765859 59773433 "intron (NR_146211, intron 58 of 171)" Snord116l2 Mappable Unique -chr7 127026136 127028492 promoter-TSS (NM_010772) Maz Mappable ENCODE Overlap -chr7 59735343 59738480 "intron (NR_146211, intron 68 of 171)" Gm26504 Mappable ENCODE Overlap -chr7 56160687 56162801 "intron (NM_001360080, intron 48 of 92)" Oca2 Mappable ENCODE Overlap -chr7 59750257 59750403 "intron (NR_146211, intron 64 of 171)" Snord116l1 Mappable ENCODE Overlap -chr7 19227265 19229911 CpG Opa3 Lowly ENCODE Overlap -chr7 59743058 59744898 "intron (NR_146211, intron 66 of 171)" Snord116l1 Mappable ENCODE Overlap -chr7 128185847 128189343 "intron (NM_001029872, intron 11 of 30)" Itgad Mappable ENCODE Overlap -chr7 59860606 59861165 "intron (NR_146211, intron 43 of 171)" Snord116l2 Mappable ENCODE Overlap -chr7 59777820 59777966 (TG)n|Simple_repeat|Simple_repeat Snord116l2 Mappable ENCODE Overlap -chr7 72651872 72653772 L1Md_A|LINE|L1 Mctp2 Mappable ENCODE Overlap -chr7 12009344 12017164 Intergenic Vmn1r77 Mappable ENCODE Overlap -chr7 79828758 79830562 "intron (NM_008486, intron 15 of 20)" Anpep Mappable ENCODE Overlap -chr7 59867127 59870112 "intron (NR_146211, intron 41 of 171)" Snord64 Mappable ENCODE Overlap -chr7 25266685 25269342 "intron (NM_001302811, intron 1 of 20)" Cic Mappable ENCODE Overlap -chr7 59861276 59863853 "intron (NR_146211, intron 43 of 171)" Snord116l2 Mappable ENCODE Overlap -chr7 145339924 145342459 (TTAGGG)n|Simple_repeat|Simple_repeat Mrgprd Mappable ENCODE Overlap -chr7 59734760 59735130 (TG)n|Simple_repeat|Simple_repeat Gm26504 Mappable Unique -chr7 59797261 59797920 "intron (NR_146211, intron 47 of 171)" Snord116l2 Mappable ENCODE Overlap -chr7 64466765 64472321 Intergenic Apba2 Mappable Unique -chr7 64472787 64495602 Intergenic Apba2 Mappable Unique -chr7 59777436 59777688 "intron (NR_146211, intron 55 of 171)" Snord116l2 Mappable ENCODE Overlap -chr7 112636731 112640157 Intergenic Tead1 Mappable ENCODE Overlap -chr8 20108891 20117932 Lx4A|LINE|L1 6820431F20Rik Mappable ENCODE Overlap -chr8 20634388 20634922 "intron (NM_001270553, intron 6 of 9)" Gm21119 Mappable ENCODE Overlap -chr8 20628419 20628940 Lx5|LINE|L1 Gm21119 Mappable ENCODE Overlap -chr8 58094780 58097224 L1Md_A|LINE|L1 Galnt7 Mappable ENCODE Overlap -chr8 55345108 55356208 Intergenic Gpm6a Mappable ENCODE Overlap -chr8 20557580 20561181 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 19914830 19917323 L1_Mus4|LINE|L1 4930467E23Rik Mappable ENCODE Overlap -chr8 83755700 83757986 (CCCTAA)n|Simple_repeat|Simple_repeat Adgre5 Mappable ENCODE Overlap -chr8 20093115 20105279 Intergenic 6820431F20Rik Mappable ENCODE Overlap -chr8 19721390 19737352 promoter-TSS (NM_001270553).2 Gm21119 Mappable ENCODE Overlap -chr8 20054693 20062207 "intron (NM_001270553, intron 7 of 9).2" 6820431F20Rik Mappable ENCODE Overlap -chr8 20541398 20553100 B1_Mus1|SINE|Alu Gm21119 Mappable ENCODE Overlap -chr8 20029253 20029457 "intron (NM_001270553, intron 6 of 9).2" 6820431F20Rik Mappable ENCODE Overlap -chr8 20501720 20533726 L1_Mus3|LINE|L1 2610005L07Rik Mappable ENCODE Overlap -chr8 19712220 19714063 (GA)n|Simple_repeat|Simple_repeat Gm21119 Mappable ENCODE Overlap -chr8 55358111 55361564 Intergenic Gpm6a Mappable ENCODE Overlap -chr8 19758478 19761260 "intron (NM_001270553, intron 6 of 9).2" 4930467E23Rik Mappable ENCODE Overlap -chr8 20565579 20567175 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 20047169 20052201 L1Md_A|LINE|L1 6820431F20Rik Mappable ENCODE Overlap -chr8 20634276 20634295 "intron (NM_001270553, intron 6 of 9)" Gm21119 Mappable ENCODE Overlap -chr8 20263088 20264957 ID4_|SINE|ID 6820431F20Rik Mappable ENCODE Overlap -chr8 19782859 19787731 "intron (NM_001270553, intron 6 of 9).2" 4930467E23Rik Mappable ENCODE Overlap -chr8 19774084 19778539 Lx4A|LINE|L1 4930467E23Rik Mappable ENCODE Overlap -chr8 20258137 20261081 Intergenic 6820431F20Rik Lowly ENCODE Overlap -chr8 20023802 20026328 "intron (NM_001270553, intron 6 of 9).2" 6820431F20Rik Mappable ENCODE Overlap -chr8 20136729 20150793 L1_Mus2|LINE|L1 6820431F20Rik Mappable ENCODE Overlap -chr8 20641086 20651070 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 20079982 20087319 Intergenic 6820431F20Rik Lowly ENCODE Overlap -chr8 19903843 19914679 L1Md_F3|LINE|L1 4930467E23Rik Mappable ENCODE Overlap -chr8 55369073 55376371 Intergenic Gpm6a Mappable ENCODE Overlap -chr8 20494398 20499504 L1_Mus4|LINE|L1 2610005L07Rik Mappable ENCODE Overlap -chr8 19766333 19767937 L1_Mus4|LINE|L1 4930467E23Rik Mappable ENCODE Overlap -chr8 19692938 19693198 B2_Mm2|SINE|B2 Gm21119 Mappable ENCODE Overlap -chr8 20400724 20414672 L1_Mus2|LINE|L1 2610005L07Rik Mappable ENCODE Overlap -chr8 123567489 123568730 Intergenic Gm22291 Mappable ENCODE Overlap -chr8 20690916 20707927 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 20026678 20028442 L1VL4|LINE|L1 6820431F20Rik Mappable ENCODE Overlap -chr8 23094430 23096804 GSAT_MM|Satellite|Satellite Ank1 Mappable ENCODE Overlap -chr8 15518786 15521117 LSU-rRNA_Hsa|rRNA|rRNA Myom2 Mappable ENCODE Overlap -chr8 20415237 20426499 "intron (NR_028428, intron 1 of 5)" 2610005L07Rik Mappable ENCODE Overlap -chr8 20348879 20352973 Lx5|LINE|L1 Gm15319 Mappable ENCODE Overlap -chr8 20124703 20135310 RLTR13A2|LTR|ERVK 6820431F20Rik Mappable ENCODE Overlap -chr8 20322407 20323195 L1_Mus4|LINE|L1 6820431F20Rik Mappable ENCODE Overlap -chr8 20710569 20711926 L1_Mus3|LINE|L1 Gm21119 Mappable ENCODE Overlap -chr8 20119951 20124094 Intergenic 6820431F20Rik Mappable ENCODE Overlap -chr8 19926961 19936891 "intron (NM_001270553, intron 6 of 9).2" 4930467E23Rik Mappable ENCODE Overlap -chr8 20688029 20688503 Lx4A|LINE|L1 Gm21119 Mappable ENCODE Overlap -chr8 20635506 20640770 "intron (NM_001270553, intron 8 of 9)" Gm21119 Mappable ENCODE Overlap -chr8 19697279 19711741 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 20653638 20670423 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 20432980 20442727 L1_Mus2|LINE|L1 2610005L07Rik Mappable ENCODE Overlap -chr8 123542674 123544268 TTS (NR_046155).5 Gm22291 Mappable ENCODE Overlap -chr8 20272587 20304081 "intron (NR_030708, intron 1 of 4)" 6820431F20Rik Mappable ENCODE Overlap -chr8 55112933 55124672 Intergenic Gpm6a Mappable ENCODE Overlap -chr8 20628957 20634183 L1_Mus4|LINE|L1 Gm21119 Mappable ENCODE Overlap -chr8 20811277 20835155 Intergenic Gm21944 Mappable ENCODE Overlap -chr8 20327105 20348063 TTS (NM_001177408) Gm15319 Mappable ENCODE Overlap -chr8 20358921 20399684 URR1A|DNA|hAT-Charlie Gm15319 Mappable ENCODE Overlap -chr8 20428997 20432208 Intergenic 2610005L07Rik Mappable ENCODE Overlap -chr8 20119222 20119824 Intergenic 6820431F20Rik Mappable ENCODE Overlap -chr8 20534489 20541206 L1_Mus4|LINE|L1 Gm21119 Mappable ENCODE Overlap -chr8 20570366 20628202 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 19751688 19754146 "3' UTR (NM_001039553, exon 10 of 10)" 4930467E23Rik Mappable ENCODE Overlap -chr8 20265183 20269007 Intergenic 6820431F20Rik Lowly ENCODE Overlap -chr8 20062360 20062381 "3' UTR (NM_001270553, exon 10 of 10).2" 6820431F20Rik Mappable ENCODE Overlap -chr8 19789587 19792874 "intron (NM_001270553, intron 6 of 9).2" 4930467E23Rik Mappable ENCODE Overlap -chr8 55361851 55365675 Intergenic Gpm6a Mappable ENCODE Overlap -chr8 20068168 20073790 Intergenic 6820431F20Rik Mappable ENCODE Overlap -chr8 20066904 20068123 ORR1D1|LTR|ERVL-MaLR 6820431F20Rik Mappable ENCODE Overlap -chr8 123544585 123546137 TTS (NR_046147) Gm22291 Lowly ENCODE Overlap -chr8 20152642 20156368 L2c|LINE|L2 6820431F20Rik Mappable ENCODE Overlap -chr8 123539730 123539879 promoter-TSS (NR_046127) Gm25212 Lowly ENCODE Overlap -chr8 19715034 19721099 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 20312042 20315103 L1_Mus2|LINE|L1 6820431F20Rik Mappable ENCODE Overlap -chr8 123554758 123555015 TTS (NR_046152).4 Gm22291 Mappable ENCODE Overlap -chr8 19681132 19684756 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 14305741 14308369 "intron (NM_001145965, intron 2 of 14)" Dlgap2 Mappable ENCODE Overlap -chr8 20534339 20534342 L1_Mus4|LINE|L1 Gm21119 Mappable ENCODE Overlap -chr8 20022728 20023668 "intron (NM_001270553, intron 6 of 9).2" 6820431F20Rik Mappable ENCODE Overlap -chr8 20033974 20044377 "intron (NM_001270553, intron 6 of 9).2" 6820431F20Rik Mappable Unique -chr8 20563416 20563632 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 19691377 19692371 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 71840086 71840699 L1Md_F2|LINE|L1 Zfp709 Lowly ENCODE Overlap -chr8 20017164 20019193 MLTR11A|LTR|ERVK 6820431F20Rik Lowly ENCODE Overlap -chr8 20674137 20686766 Intergenic Gm21119 Mappable ENCODE Overlap -chr8 19801145 19802211 "intron (NM_001270553, intron 6 of 9).2" 4930467E23Rik Lowly ENCODE Overlap -chr8 20151869 20152461 LTRIS2|LTR|ERV1 6820431F20Rik Mappable ENCODE Overlap -chr9 24540850 24543161 Intergenic Dpy19l1 Mappable ENCODE Overlap -chr9 13826077 13828641 promoter-TSS (NM_001310721) Cep57 Mappable ENCODE Overlap -chr9 121040718 121043408 CpG Mir7090 Mappable Unique -chr9 3257636 3260113 LSU-rRNA_Hsa|rRNA|rRNA 4930433N12Rik Mappable ENCODE Overlap -chr9 124255276 124259014 Intergenic 2010315B03Rik Mappable ENCODE Overlap -chr9 2999001 3039419 GSAT_MM|Satellite|Satellite Mir101c Mappable ENCODE Overlap -chr9 35304216 35306651 GSAT_MM|Satellite|Satellite 4933422A05Rik Mappable Unique -chr9 69098573 69101274 (CTGTG)n|Simple_repeat|Simple_repeat Rora Mappable Unique -chr9 80956734 80958661 L1Md_T|LINE|L1 Impg1 Mappable Unique -chr9 56222572 56224955 LSU-rRNA_Hsa|rRNA|rRNA Tspan3 Mappable Unique -chr9 123460769 123463292 "3' UTR (NM_001348168, exon 22 of 22)" Limd1 Mappable ENCODE Overlap -chr9 123923333 123927203 CpG Ccr1 Mappable ENCODE Overlap -chr9 57074846 57077403 promoter-TSS (NM_001110350) 2700012I20Rik Mappable ENCODE Overlap -chr9 70622071 70624471 (CTGTG)n|Simple_repeat|Simple_repeat Mindy2 Mappable ENCODE Overlap -chrM 1 16299 Intergenic Mappable ENCODE Overlap -chrX 66493813 66495424 L1Md_F|LINE|L1 Slitrk2 Lowly Unique -chrX 170859260 170860477 Intergenic Asmt Mappable ENCODE Overlap -chrX 94885885 94886140 T-rich|Low_complexity|Low_complexity Zxda Mappable Unique -chrX 170863437 170864018 Intergenic Asmt Mappable ENCODE Overlap -chrX 91841304 91844066 L1Md_T|LINE|L1 Mageb5 Lowly ENCODE Overlap -chrX 94880959 94881406 Intergenic Zxda Lowly ENCODE Overlap -chrX 135041381 135044770 "intron (NR_040282, intron 2 of 3)" 3632454L22Rik Mappable ENCODE Overlap -chrX 94890211 94890326 Intergenic Zxda Mappable ENCODE Overlap -chrX 170861113 170861516 Intergenic Asmt Mappable ENCODE Overlap -chrX 169985134 170023444 Intergenic G530011O06Rik Mappable ENCODE Overlap -chrX 112369696 112372262 "intron (NM_026565, intron 8 of 8)" Satl1 Lowly Unique -chrX 94902538 94903991 Intergenic Zxda Mappable ENCODE Overlap -chrX 170879924 170882299 (TTAGGG)n|Simple_repeat|Simple_repeat Asmt Mappable ENCODE Overlap -chrX 94912627 94916014 Intergenic Spin4 Mappable ENCODE Overlap -chrX 170854230 170858346 Intergenic Asmt Mappable ENCODE Overlap -chrX 76597457 76600136 SYNREP_MM|Satellite|Satellite Cldn34d Mappable ENCODE Overlap -chrX 94907642 94908233 B1_Mus1|SINE|Alu Zxda Mappable ENCODE Overlap -chrX 170732207 170739180 Intergenic Asmt Mappable ENCODE Overlap -chrX 170840190 170853863 Intergenic Asmt Lowly ENCODE Overlap -chrX 170757171 170759511 (TTAGGG)n|Simple_repeat|Simple_repeat Asmt Lowly ENCODE Overlap -chrX 170830178 170834176 Intergenic Asmt Mappable ENCODE Overlap -chrX 143482005 143484125 SYNREP_MM|Satellite|Satellite Pak3 Mappable ENCODE Overlap -chrX 135051996 135055944 "intron (NR_040282, intron 2 of 3)" 3632454L22Rik Mappable ENCODE Overlap -chrX 170808829 170820055 Intergenic Asmt Mappable ENCODE Overlap -chrX 170741375 170743177 Intergenic Asmt Mappable ENCODE Overlap -chrX 170671790 170674598 "intron (NM_001199212, intron 1 of 7)" Asmt Lowly ENCODE Overlap -chrX 126770204 126772565 Intergenic 4932411N23Rik Lowly ENCODE Overlap -chrX 117087776 117090043 L1Md_F|LINE|L1 H2afb1 Lowly ENCODE Overlap -chrY 139572 147435 (TAGA)n|Simple_repeat|Simple_repeat 1700020D14Rik Mappable ENCODE Overlap -chrY 90810927 90814974 (TTAGGG)n|Simple_repeat|Simple_repeat G530011O06Rik Mappable ENCODE Overlap -chrY 11856804 11859498 Intergenic Gm20877 Mappable ENCODE Overlap -chrY 90762580 90802093 Intergenic Erdr1 Mappable ENCODE Overlap -chrY 90802573 90810712 "intron (NM_133362, intron 2 of 3)" Erdr1 Mappable ENCODE Overlap -chrY 90759628 90760408 B2_Mm1a|SINE|B2 G530011O06Rik Mappable ENCODE Overlap -chrY 90733806 90745852 Intergenic G530011O06Rik Mappable ENCODE Overlap -chrY 257193 264671 (TCTA)n|Simple_repeat|Simple_repeat Gm29089 Mappable ENCODE Overlap \ No newline at end of file +chr4 147638286 147647439 +chr16 3338542 3338708 +chr1 181741994 181745061 +chr1 43776659 43779916 +chr1 85452903 85466403 +chr1 84989001 84996294 +chr1 88210785 88225860 +chr1 133593455 133597064 +chr1 85527647 85528664 +chr1 84961182 84967761 +chr1 195370720 195372965 +chr1 85065013 85065017 +chr1 85230698 85268061 +chr1 88296835 88310839 +chr1 85041960 85048233 +chr1 191396111 191398516 +chr1 63629211 63631806 +chr1 85159040 85172333 +chr1 85570638 85570772 +chr1 85268122 85335650 +chr1 171068450 171072576 +chr1 85477779 85508363 +chr1 88270612 88293020 +chr1 85154287 85155709 +chr1 85212954 85213093 +chr1 85027461 85031109 +chr1 85578857 85636049 +chr1 88226083 88262450 +chr1 171073261 171076658 +chr1 84984333 84986162 +chr1 88263593 88269113 +chr1 85196271 85200746 +chr1 85570878 85573531 +chr1 7396936 7398946 +chr1 86524974 86527723 +chr1 85215765 85216434 +chr1 88293232 88293622 +chr1 26685234 26689325 +chr1 183298135 183300594 +chr1 88294911 88296733 +chr1 24610534 24617184 +chr1 16072734 16074144 +chr1 171080207 171081317 +chr1 171067673 171068300 +chr1 171063539 171065867 +chr1 100179097 100181396 +chr1 85523638 85527190 +chr1 85549826 85555898 +chr1 85003103 85013260 +chr1 85646518 85649958 +chr1 95450930 95453225 +chr1 78572727 78575645 +chr1 85123828 85124899 +chr1 190299616 190304517 +chr1 85037170 85041259 +chr1 84960769 84961175 +chr1 85178595 85185186 +chr1 85073737 85116916 +chr1 195240544 195243014 +chr1 85565428 85567696 +chr1 85337842 85347901 +chr10 81177053 81179869 +chr10 22469495 22472214 +chr10 130593319 130595993 +chr10 58220313 58235253 +chr10 58236676 58240755 +chr10 80621024 80623632 +chr10 3108427 3118165 +chr10 27818052 27823177 +chr10 81319569 81322199 +chr10 27823584 27824808 +chr10 22140821 22144273 +chr11 34680652 34684369 +chr11 3118245 3201063 +chr11 109010646 109013122 +chr11 107197587 107200468 +chr11 54139006 54141736 +chr11 106946994 106948324 +chr11 34542542 34546090 +chr11 3111164 3116055 +chr11 3099001 3105930 +chr11 96976407 96979082 +chr11 88967559 88970540 +chr11 5167853 5170298 +chr12 78349869 78352172 +chr12 69158390 69160592 +chr12 120027628 120030022 +chr12 5057005 5057046 +chr12 20225728 20228048 +chr12 112776555 112784927 +chr12 4218421 4222747 +chr12 5057140 5060225 +chr12 97060428 97062789 +chr12 3108865 3111202 +chr12 113423488 113426173 +chr12 67058082 67060960 +chr12 93575971 93578239 +chr12 59035707 59037804 +chr12 20228876 20235430 +chr12 74802840 74805506 +chr12 69360184 69362481 +chr12 20228316 20228624 +chr13 74527428 74532026 +chr13 58346715 58349853 +chr13 110742967 110745548 +chr13 119488974 119491395 +chr13 120320412 120322639 +chr13 9010688 9013168 +chr13 3371585 3375531 +chr13 119594610 119604524 +chr13 60095990 60098591 +chr13 119605201 119605920 +chr13 13859610 13862009 +chr13 77437837 77440058 +chr13 119607969 119617588 +chr13 44868572 44871024 +chr13 12829672 12831385 +chr13 9833306 9835494 +chr13 13753022 13756110 +chr14 120476521 120479308 +chr14 6636208 6638572 +chr14 7869742 7872517 +chr14 19414676 19420702 +chr14 67714647 67717104 +chr14 69161004 69163446 +chr14 21499408 21502069 +chr14 124800549 124803244 +chr14 8285634 8287903 +chr14 55559045 55561737 +chr15 75084455 75088047 +chr15 9014687 9017345 +chr15 91905616 91911402 +chr15 102404624 102407389 +chr15 58437815 58440686 +chr15 91992118 91993703 +chr15 76102012 76105870 +chr16 86819786 86822244 +chr16 3348513 3353138 +chr16 3112455 3118056 +chr16 11142906 11145315 +chr16 3337067 3337248 +chr16 24582361 24584934 +chr16 3270724 3273299 +chr16 3121810 3124730 +chr16 93991773 93994368 +chr16 10974067 10976278 +chr16 93788192 93790384 +chr16 3338885 3339554 +chr16 57390113 57392676 +chr16 98106437 98108768 +chr16 3267680 3269997 +chr16 3340104 3341863 +chr16 38087847 38090558 +chr16 3230586 3249217 +chr16 17221214 17223525 +chr17 84460688 84464659 +chr17 67740307 67742635 +chr17 39841997 39849829 +chr17 3075361 3085806 +chr17 13584722 13592605 +chr17 4625167 4627603 +chr17 23533391 23533512 +chr17 13547119 13554228 +chr17 3004168 3039892 +chr17 29101439 29109513 +chr17 13653613 13656298 +chr17 22875275 22877883 +chr17 13304955 13307295 +chr17 23530536 23533349 +chr17 70962658 70964891 +chr17 36230224 36232605 +chr18 40307015 40309403 +chr18 82160214 82171948 +chr18 20619926 20621235 +chr18 20624339 20624494 +chr18 20617575 20617982 +chr18 85696926 85699291 +chr18 3113805 3120973 +chr18 90601089 90603639 +chr18 4195753 4198816 +chr18 36559007 36561036 +chr18 3002806 3013833 +chr19 45648970 45651272 +chr19 53775785 53776977 +chr19 58112241 58114641 +chr19 39258730 39261328 +chr19 39262753 39264236 +chr19 61330275 61332566 +chr19 61262650 61268164 +chr2 182011584 182014223 +chr2 3049003 3052125 +chr2 51946088 51948860 +chr2 57628489 57630727 +chr2 92092600 92094775 +chr2 84714187 84716735 +chr2 181927046 181933525 +chr2 22002667 22006682 +chr2 5378040 5380376 +chr2 177313551 177316626 +chr2 66188206 66190462 +chr2 181915695 181920273 +chr2 53190369 53192471 +chr2 20898864 20901198 +chr2 28182997 28185655 +chr2 98661230 98668337 +chr2 22586502 22591198 +chr2 22738413 22741056 +chr2 121521321 121522185 +chr2 52695533 52700035 +chr2 80811835 80815984 +chr3 91097737 91098269 +chr3 159938404 159940680 +chr3 149051473 149053935 +chr3 95014321 95016552 +chr3 3003499 3005583 +chr3 5859339 5861826 +chr3 3008518 3016611 +chr3 123676652 123679345 +chr3 3000306 3003485 +chr3 8243566 8247573 +chr3 56574432 56576750 +chr3 96043520 96046044 +chr3 62158100 62160335 +chr3 3027935 3033946 +chr3 60044058 60047062 +chr3 99980113 99982394 +chr4 31775994 31778602 +chr4 146599418 146600571 +chr4 145839807 145842678 +chr4 146262474 146263179 +chr4 147255924 147259118 +chr4 3088184 3092574 +chr4 146165466 146171513 +chr4 146497127 146497191 +chr4 118546006 118549737 +chr4 147120785 147128930 +chr4 146498137 146500659 +chr4 145843517 145849997 +chr4 146451432 146455458 +chr4 147623285 147624916 +chr4 156355655 156358892 +chr4 145700850 145703586 +chr4 147435763 147435792 +chr4 147448735 147450095 +chr4 146713610 146714207 +chr4 147028189 147033108 +chr4 147389133 147392158 +chr4 147452010 147452668 +chr4 70377117 70379256 +chr4 147093921 147096533 +chr4 147369561 147370310 +chr4 147447353 147448412 +chr4 147331641 147333833 +chr4 3174089 3178413 +chr4 145447894 145450160 +chr4 151860870 151863546 +chr4 3087794 3087824 +chr4 145779810 145780077 +chr4 147517884 147524409 +chr4 146259718 146261663 +chr4 146521337 146522409 +chr4 145834584 145838868 +chr4 146714489 146716653 +chr4 147635572 147636208 +chr4 147368968 147369146 +chr4 28175809 28178165 +chr4 146475151 146476549 +chr4 147394988 147407328 +chr4 147179879 147180585 +chr4 147377003 147378516 +chr4 3057927 3057951 +chr4 147197835 147200824 +chr4 147280125 147280832 +chr4 146172343 146177455 +chr4 145685329 145689863 +chr4 145828383 145829917 +chr4 146716992 146721348 +chr4 147348882 147351051 +chr4 147309454 147310788 +chr4 146436307 146436832 +chr4 147636285 147638009 +chr4 3078688 3087634 +chr4 147450308 147451358 +chr4 147365623 147366636 +chr4 156339577 156344853 +chr4 147418158 147435518 +chr4 146273258 146273750 +chr4 146477296 146496949 +chr4 147057335 147058419 +chr4 145830595 145831382 +chr4 147414962 147417956 +chr4 3179430 3183184 +chr4 147435947 147440573 +chr4 3228412 3229946 +chr4 146514744 146515880 +chr4 3057958 3070939 +chr4 147334486 147346844 +chr4 147119579 147119821 +chr4 145679625 145681903 +chr4 147231094 147237178 +chr4 147512797 147513189 +chr4 3049009 3057589 +chr4 3178935 3178988 +chr4 3224191 3227875 +chr4 146164049 146164808 +chr4 147355319 147357412 +chr4 147362443 147364013 +chr4 149809055 149811758 +chr4 147755337 147756655 +chr4 147407719 147414944 +chr4 147194720 147197718 +chr4 145438840 145440729 +chr5 15615268 15615413 +chr5 14957881 14964120 +chr5 14913423 14914073 +chr5 15586655 15587094 +chr5 15034396 15046044 +chr5 15687776 15694810 +chr5 125388874 125389027 +chr5 14940146 14942209 +chr5 15634328 15634761 +chr5 14917775 14921130 +chr5 15677087 15682991 +chr5 15026604 15026773 +chr5 114921404 114923609 +chr5 25815652 25819492 +chr5 15497437 15500155 +chr5 15613353 15614537 +chr5 104329746 104333160 +chr5 14932264 14933958 +chr5 14951800 14952432 +chr5 32732901 32735224 +chr5 109556534 109559507 +chr5 15478820 15485756 +chr5 15507626 15518299 +chr5 15459668 15464106 +chr5 14934781 14935308 +chr5 32736914 32739312 +chr5 14953678 14957075 +chr5 137151217 137153727 +chr5 14985270 14992323 +chr5 15486560 15489053 +chr5 15629147 15633869 +chr5 15709317 15713682 +chr5 15017202 15021309 +chr5 15551423 15556883 +chr5 14950778 14951661 +chr5 15579113 15583633 +chr5 14909644 14910139 +chr5 14950133 14950691 +chr5 14971252 14974797 +chr5 15010328 15011975 +chr5 14942455 14942460 +chr5 15466369 15466693 +chr5 14983568 14984680 +chr5 15003599 15009785 +chr5 14993381 14998101 +chr5 15639785 15646403 +chr5 15021751 15024895 +chr5 135148198 135150687 +chr5 146259978 146262365 +chr5 15605403 15608337 +chr5 15702276 15704787 +chr5 14979650 14983004 +chr5 36659924 36662570 +chr5 15620009 15626203 +chr5 15650145 15656407 +chr5 125385640 125388609 +chr5 15658545 15663465 +chr5 15657677 15657682 +chr5 15619206 15619829 +chr5 15526874 15529178 +chr5 15636219 15639197 +chr5 15589001 15591949 +chr5 15595224 15597954 +chr5 32725095 32731380 +chr5 36629423 36631766 +chr5 15576662 15577621 +chr5 15050630 15055837 +chr5 15696564 15699401 +chr5 15670223 15673356 +chr5 15530483 15530524 +chr5 15466890 15474923 +chr5 15600186 15600717 +chr5 147610435 147612632 +chr6 47770689 47773524 +chr6 103648046 103650294 +chr6 3049424 3052069 +chr6 4922733 4925199 +chr6 47650957 47687580 +chr6 29746689 29750155 +chr6 47737204 47770613 +chr6 53082921 53085555 +chr6 114340023 114343200 +chr6 47776922 47778288 +chr6 3199768 3202671 +chr7 123021275 123023624 +chr7 64072406 64091442 +chr7 59765859 59773433 +chr7 127026136 127028492 +chr7 59735343 59738480 +chr7 56160687 56162801 +chr7 59750257 59750403 +chr7 19227265 19229911 +chr7 59743058 59744898 +chr7 128185847 128189343 +chr7 59860606 59861165 +chr7 59777820 59777966 +chr7 72651872 72653772 +chr7 12009344 12017164 +chr7 79828758 79830562 +chr7 59867127 59870112 +chr7 25266685 25269342 +chr7 59861276 59863853 +chr7 145339924 145342459 +chr7 59734760 59735130 +chr7 59797261 59797920 +chr7 64466765 64472321 +chr7 64472787 64495602 +chr7 59777436 59777688 +chr7 112636731 112640157 +chr8 20108891 20117932 +chr8 20634388 20634922 +chr8 20628419 20628940 +chr8 58094780 58097224 +chr8 55345108 55356208 +chr8 20557580 20561181 +chr8 19914830 19917323 +chr8 83755700 83757986 +chr8 20093115 20105279 +chr8 19721390 19737352 +chr8 20054693 20062207 +chr8 20541398 20553100 +chr8 20029253 20029457 +chr8 20501720 20533726 +chr8 19712220 19714063 +chr8 55358111 55361564 +chr8 19758478 19761260 +chr8 20565579 20567175 +chr8 20047169 20052201 +chr8 20634276 20634295 +chr8 20263088 20264957 +chr8 19782859 19787731 +chr8 19774084 19778539 +chr8 20258137 20261081 +chr8 20023802 20026328 +chr8 20136729 20150793 +chr8 20641086 20651070 +chr8 20079982 20087319 +chr8 19903843 19914679 +chr8 55369073 55376371 +chr8 20494398 20499504 +chr8 19766333 19767937 +chr8 19692938 19693198 +chr8 20400724 20414672 +chr8 123567489 123568730 +chr8 20690916 20707927 +chr8 20026678 20028442 +chr8 23094430 23096804 +chr8 15518786 15521117 +chr8 20415237 20426499 +chr8 20348879 20352973 +chr8 20124703 20135310 +chr8 20322407 20323195 +chr8 20710569 20711926 +chr8 20119951 20124094 +chr8 19926961 19936891 +chr8 20688029 20688503 +chr8 20635506 20640770 +chr8 19697279 19711741 +chr8 20653638 20670423 +chr8 20432980 20442727 +chr8 123542674 123544268 +chr8 20272587 20304081 +chr8 55112933 55124672 +chr8 20628957 20634183 +chr8 20811277 20835155 +chr8 20327105 20348063 +chr8 20358921 20399684 +chr8 20428997 20432208 +chr8 20119222 20119824 +chr8 20534489 20541206 +chr8 20570366 20628202 +chr8 19751688 19754146 +chr8 20265183 20269007 +chr8 20062360 20062381 +chr8 19789587 19792874 +chr8 55361851 55365675 +chr8 20068168 20073790 +chr8 20066904 20068123 +chr8 123544585 123546137 +chr8 20152642 20156368 +chr8 123539730 123539879 +chr8 19715034 19721099 +chr8 20312042 20315103 +chr8 123554758 123555015 +chr8 19681132 19684756 +chr8 14305741 14308369 +chr8 20534339 20534342 +chr8 20022728 20023668 +chr8 20033974 20044377 +chr8 20563416 20563632 +chr8 19691377 19692371 +chr8 71840086 71840699 +chr8 20017164 20019193 +chr8 20674137 20686766 +chr8 19801145 19802211 +chr8 20151869 20152461 +chr9 24540850 24543161 +chr9 13826077 13828641 +chr9 121040718 121043408 +chr9 3257636 3260113 +chr9 124255276 124259014 +chr9 2999001 3039419 +chr9 35304216 35306651 +chr9 69098573 69101274 +chr9 80956734 80958661 +chr9 56222572 56224955 +chr9 123460769 123463292 +chr9 123923333 123927203 +chr9 57074846 57077403 +chr9 70622071 70624471 +chrM 1 16299 +chrX 66493813 66495424 +chrX 170859260 170860477 +chrX 94885885 94886140 +chrX 170863437 170864018 +chrX 91841304 91844066 +chrX 94880959 94881406 +chrX 135041381 135044770 +chrX 94890211 94890326 +chrX 170861113 170861516 +chrX 169985134 170023444 +chrX 112369696 112372262 +chrX 94902538 94903991 +chrX 170879924 170882299 +chrX 94912627 94916014 +chrX 170854230 170858346 +chrX 76597457 76600136 +chrX 94907642 94908233 +chrX 170732207 170739180 +chrX 170840190 170853863 +chrX 170757171 170759511 +chrX 170830178 170834176 +chrX 143482005 143484125 +chrX 135051996 135055944 +chrX 170808829 170820055 +chrX 170741375 170743177 +chrX 170671790 170674598 +chrX 126770204 126772565 +chrX 117087776 117090043 +chrY 139572 147435 +chrY 90810927 90814974 +chrY 11856804 11859498 +chrY 90762580 90802093 +chrY 90802573 90810712 +chrY 90759628 90760408 +chrY 90733806 90745852 +chrY 257193 264671