# HG changeset patch
# User iuc
# Date 1567548729 14400
# Node ID 66ff749232244b1dc5fbf949236a4121896164bf

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"

diff -r 000000000000 -r 66ff74923224 telescope_assign.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/telescope_assign.xml	Tue Sep 03 18:12:09 2019 -0400
@@ -0,0 +1,173 @@
+<?xml version="1.0"?>
+<tool id="telescope_assign" name="Reassign reads" version="@VERSION@">
+    <description>with TELESCOPE using a statistical model</description>
+    <macros>
+        <token name="@VERSION@">1.0.3</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">telescope</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir tempdir &&
+        mkdir outdir &&
+        telescope assign '$input_alignment' '$input_gtf'
+            --tempdir tempdir
+            --outdir outdir
+            --ncpu \${GALAXY_SLOTS:-1}
+            $updated_sam
+            #if str($advanced.advanced_options) == 'select':
+                --reassign_mode $advanced.reassign_mode
+                --conf_prob $advanced.conf_prob
+                --overlap_mode $advanced.overlap_mode
+                --overlap_threshold $advanced.overlap_threshold
+                --annotation_class $advanced.annotation_class
+                --pi_prior $advanced.pi_prior
+                --theta_prior $advanced.theta_prior
+                --em_epsilon $advanced.em_epsilon
+                --max_iter $advanced.max_iter
+                $advanced.use_likelihood
+            #end if
+        #if $updated_sam
+            &&
+            if [ -f outdir/telescope-updated.bam ] ; then
+                samtools sort outdir/telescope-updated.bam > '$updated_alignment' ;
+            else
+                echo 'Updated alignment file not found.' ;
+                exit 1 ;
+            fi
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="input_alignment" type="data" format="sam,bam" label="Input SAM or BAM file" />
+        <param name="input_gtf" type="data" format="gtf" label="Input annotation" />
+        <param argument="--updated_sam" type="boolean" truevalue="--updated_sam" falsevalue="" label="Also output an updated BAM file with reassigned reads" />
+        <conditional name="advanced">
+            <param name="advanced_options" type="select" label="Advanced options">
+                <option value="defaults">Use defaults</option>
+                <option value="select">Select values</option>
+            </param>
+            <when value="defaults" />
+            <when value="select">
+                <param argument="--reassign_mode" type="select" label="Reassignment mode"
+                    help="After EM is complete, each fragment is reassigned according to the expected value of its membership weights. The reassignment method is the method for resolving the &quot;best&quot; reassignment for fragments that have multiple possible reassignments. Available modes are: &quot;exclude&quot; - fragments with multiple best assignments are excluded from the final counts; &quot;choose&quot; - the best assignment is randomly chosen from among the set of best assignments; &quot;average&quot; - the fragment is divided evenly among the best assignments; &quot;conf&quot; - only assignments that exceed a certain threshold (see --conf_prob) are accepted; &quot;unique&quot; - only uniquely aligned reads are included. NOTE: Results using all assignment modes are included in the Telescope report by default. This argument determines what mode will be used for the &quot;final counts&quot; column. (default: exclude)">
+                    <option value="exclude">Exclude</option>
+                    <option value="choose">Choose</option>
+                    <option value="average">Average</option>
+                    <option value="conf">Conf</option>
+                    <option value="unique">Unique</option>
+                </param>
+                <param argument="--conf_prob" type="float" value="0.9" min="0" max="1" label="Minimum probability for high confidence assignment" />
+                <param argument="--overlap_mode" type="select" label="Overlap mode" help="The method used to determine whether a fragment overlaps feature">
+                    <option value="threshold">Threshold</option>
+                    <option value="intersection-strict">Strict intersection</option>
+                    <option value="union">Union</option>
+                </param>
+                <param argument="--overlap_threshold" type="float" value="0.2" min="0" max="1" label="Fraction of fragment that must be contained within a feature to be assigned to that locus" help="Ignored unless overlap mode is 'threshold'" />
+                <param argument="--annotation_class" type="select" label="Annotation class" help="Both htseq and intervaltree appear to yield identical results. Performance differences are TBD.">
+                    <option value="intervaltree">Interval tree</option>
+                    <option value="htseq">HTSeq</option>
+                </param>
+                <param argument="--pi_prior" type="integer" value="0" label="Prior on &#960;" help="Equivalent to adding n unique reads." />
+                <param argument="--theta_prior" type="integer" value="0" label="Prior on &#952;" help="Equivalent to adding n non-unique reads." />
+                <param argument="--em_epsilon" type="float" value="0.0000001" label="EM Algorithm &#965; cutoff" help="Default: 1e-7" />
+                <param argument="--max_iter" type="integer" value="100" label="EM Algorithm maximum iterations" help="Default: 100" />
+                <param argument="--use_likelihood" type="boolean" truevalue="--use_likelihood" falsevalue="" label="Use difference in log-likelihood as convergence criteria" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" from_work_dir="outdir/telescope-telescope_report.tsv" />
+        <data name="updated_alignment" format="bam">
+            <filter>updated_sam</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_alignment" value="telescope-in1.bam" />
+            <param name="input_gtf" value="telescope-in1.gtf" />
+            <param name="updated_sam" value="true" />
+            <output name="output" file="telescope-out1.tabular" />
+            <output name="updated_alignment" file="telescope-out1.bam" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Output
+------
+
+Telescope has two main output files: the telescope report and an updated
+SAM file (optional). The report file is most important for downstream
+differential expression analysis since it contains the fragment count
+estimates. The updated SAM file is useful for downstream locus-specific
+analyses.
+
+Telescope report
+~~~~~~~~~~~~~~~~
+
+The first line in the telescope report is a comment (starting with a
+“#”) that contains information about the run such as the number of
+fragments processed, number of mapped fragments, number of uniquely and
+ambiguously mapped fragments, and number of fragments mapping to the
+annotation. The total number of mapped fragments may be useful for
+normalization.
+
+The rest of the report is a table with calculated expression values for
+individual transposable element locations. The columns of the table are:
+
+-  ``transcript`` - Transcript ID, by default from "locus" field. See
+   --attribute argument to use a different attribute.
+-  ``transcript_length`` - Approximate length of transcript. This is
+   calculated from the annotation, not the data, and is equal to the
+   spanning length of the annotation minus any non-model regions.
+-  ``final_count`` - Total number of fragments assigned to transcript
+   after fitting the Telescope model. This is the column to use for
+   downstream analysis that models data as negative binomial, i.e.
+   DESeq2.
+-  ``final_conf`` - Final confident fragments. The number of fragments
+   assigned to transcript whose posterior probability exceeds a cutoff,
+   0.9 by default. Set this using the --conf_prob argument.
+-  ``final_prop`` - Final proportion of fragments represented by
+   transcript. This is the final estimate of the π parameter.
+-  ``init_aligned`` - Initial number of fragments aligned to transcript.
+   A given fragment will contribute +1 to each transcript that it is
+   aligned to, thus the sum of this will be greater than the number of
+   fragments if there are multimapped reads.
+-  ``unique_count`` - Unique count. Number of fragments aligning
+   uniquely to this transcript.
+-  ``init_best`` - Initial number of fragments aligned to transcript
+   that have the "best" alignment score for that fragment. Fragments
+   that have the same best alignment score to multiple transcripts will
+   contribute +1 to each transcript.
+-  ``init_best_random`` - Initial number of fragments aligned to
+   transcript that have the "best" alignment score for that fragment.
+   Fragments that have the same best alignment score to multiple
+   transcripts will be randomly assigned to one transcript.
+
+Updated BAM file
+~~~~~~~~~~~~~~~~
+
+The updated BAM file contains those fragments that has at least 1
+initial alignment to a transposable element. The final assignment and
+probabilities are encoded in the SAM tags:
+
+-  ``ZF:Z`` Assigned Feature - The name of the feature that alignment is
+   assigned to.
+-  ``ZT:Z`` Telescope tag - A value of ``PRI`` indicates that this
+   alignment is the best hit for the feature and is used in the
+   likelihood calculations. Otherwise the value will be ``SEC``, meaning
+   that another alignment to the same feature has a higher score.
+-  ``ZB:Z`` Best Feature = The name(s) of the highest scoring feature(s)
+   for the fragment.
+-  ``YC:Z`` Specifies color for alignment as R,G,B. UCSC sanctioned tag,
+   see documentation `here.`_
+-  ``XP:Z`` Alignment probability - estimated posterior probability for
+   this alignment.
+
+.. _here.: http://genome.ucsc.edu/goldenpath/help/hgBamTrackHelp.html
+
+    ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1101/398172</citation>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 66ff74923224 test-data/telescope-in1.bam
Binary file test-data/telescope-in1.bam has changed
diff -r 000000000000 -r 66ff74923224 test-data/telescope-in1.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/telescope-in1.gtf	Tue Sep 03 18:12:09 2019 -0400
@@ -0,0 +1,548 @@
+### HML2_1p36.21a ###								
+chr1	rmsk	gene	12780115	12785935	.	-	.	gene_id "HML2_1p36.21a"; transcript_id "HML2_1p36.21a"; locus "HML2_1p36.21a"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0001"; model_cov "4813"; model_pct "63.9";
+chr1	rmsk	exon	12780115	12784947	27645	-	.	gene_id "HML2_1p36.21a"; transcript_id "HML2_1p36.21a"; locus "HML2_1p36.21a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0001"; repClass "LTR"; repEnd "4816"; repFamily "ERVK"; repLeft "3"; repStart "-2720";
+chr1	rmsk	exon	12784950	12785935	7601	-	.	gene_id "HML2_1p36.21a"; transcript_id "HML2_1p36.21a"; locus "HML2_1p36.21a"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0001"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_1p36.21b ###								
+chr1	rmsk	gene	13012447	13021988	.	-	.	gene_id "HML2_1p36.21b"; transcript_id "HML2_1p36.21b"; locus "HML2_1p36.21b"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0002"; model_cov "7448"; model_pct "98.8";
+chr1	rmsk	exon	13012447	13013444	8041	-	.	gene_id "HML2_1p36.21b"; transcript_id "HML2_1p36.21b"; locus "HML2_1p36.21b"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0002"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr1	rmsk	exon	13013534	13020171	21384	-	.	gene_id "HML2_1p36.21b"; transcript_id "HML2_1p36.21b"; locus "HML2_1p36.21b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0002"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "743"; repStart "-89";
+chr1	rmsk	exon	13020264	13020996	4529	-	.	gene_id "HML2_1p36.21b"; transcript_id "HML2_1p36.21b"; locus "HML2_1p36.21b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0002"; repClass "LTR"; repEnd "746"; repFamily "ERVK"; repLeft "2"; repStart "-6790";
+chr1	rmsk	exon	13020998	13021988	7851	-	.	gene_id "HML2_1p36.21b"; transcript_id "HML2_1p36.21b"; locus "HML2_1p36.21b"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0002"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_1p36.21c ###								
+chr1	rmsk	gene	13206972	13216513	.	+	.	gene_id "HML2_1p36.21c"; transcript_id "HML2_1p36.21c"; locus "HML2_1p36.21c"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0003"; model_cov "7448"; model_pct "98.8";
+chr1	rmsk	exon	13206972	13207962	7851	+	.	gene_id "HML2_1p36.21c"; transcript_id "HML2_1p36.21c"; locus "HML2_1p36.21c"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0003"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr1	rmsk	exon	13207964	13208696	4529	+	.	gene_id "HML2_1p36.21c"; transcript_id "HML2_1p36.21c"; locus "HML2_1p36.21c"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0003"; repClass "LTR"; repEnd "746"; repFamily "ERVK"; repLeft "-6790"; repStart "2";
+chr1	rmsk	exon	13208789	13215426	21447	+	.	gene_id "HML2_1p36.21c"; transcript_id "HML2_1p36.21c"; locus "HML2_1p36.21c"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0003"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "-89"; repStart "743";
+chr1	rmsk	exon	13215516	13216513	7965	+	.	gene_id "HML2_1p36.21c"; transcript_id "HML2_1p36.21c"; locus "HML2_1p36.21c"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0003"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_1p36.21d ###								
+chr1	rmsk	gene	13352736	13362257	.	+	.	gene_id "HML2_1p36.21d"; transcript_id "HML2_1p36.21d"; locus "HML2_1p36.21d"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0004"; model_cov "7449"; model_pct "98.8";
+chr1	rmsk	exon	13352736	13353726	7746	+	.	gene_id "HML2_1p36.21d"; transcript_id "HML2_1p36.21d"; locus "HML2_1p36.21d"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0004"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr1	rmsk	exon	13353727	13354460	4505	+	.	gene_id "HML2_1p36.21d"; transcript_id "HML2_1p36.21d"; locus "HML2_1p36.21d"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0004"; repClass "LTR"; repEnd "746"; repFamily "ERVK"; repLeft "-6790"; repStart "1";
+chr1	rmsk	exon	13354553	13361170	21857	+	.	gene_id "HML2_1p36.21d"; transcript_id "HML2_1p36.21d"; locus "HML2_1p36.21d"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0004"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "-89"; repStart "743";
+chr1	rmsk	exon	13361260	13362257	8099	+	.	gene_id "HML2_1p36.21d"; transcript_id "HML2_1p36.21d"; locus "HML2_1p36.21d"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0004"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_1p34.3 ###								
+chr1	rmsk	gene	36488984	36491127	.	-	.	gene_id "HML2_1p34.3"; transcript_id "HML2_1p34.3"; locus "HML2_1p34.3"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0006"; model_cov "1096"; model_pct "14.5";
+chr1	rmsk	exon	36488984	36489934	5851	-	.	gene_id "HML2_1p34.3"; transcript_id "HML2_1p34.3"; locus "HML2_1p34.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0006"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr1	rmsk	exon	36490048	36490378	2634	-	.	gene_id "HML2_1p34.3"; transcript_id "HML2_1p34.3"; locus "HML2_1p34.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0006"; repClass "LTR"; repEnd "7417"; repFamily "ERVK"; repLeft "7087"; repStart "-119";
+chr1	rmsk	exon	36490359	36491127	5815	-	.	gene_id "HML2_1p34.3"; transcript_id "HML2_1p34.3"; locus "HML2_1p34.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0006"; repClass "LTR"; repEnd "5868"; repFamily "ERVK"; repLeft "5102"; repStart "-1668";
+### HML2_1p31.1 ###								
+chr1	rmsk	gene	75377086	75383458	.	+	.	gene_id "HML2_1p31.1"; transcript_id "HML2_1p31.1"; locus "HML2_1p31.1"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0007"; model_cov "4355"; model_pct "57.8";
+chr1	rmsk	exon	75377086	75378053	8811	+	.	gene_id "HML2_1p31.1"; transcript_id "HML2_1p31.1"; locus "HML2_1p31.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0007"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr1	rmsk	exon	75378054	75380597	22845	+	.	gene_id "HML2_1p31.1"; transcript_id "HML2_1p31.1"; locus "HML2_1p31.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0007"; repClass "LTR"; repEnd "2543"; repFamily "ERVK"; repLeft "-4993"; repStart "1";
+chr1	rmsk	exon	75380582	75380780	1643	+	.	gene_id "HML2_1p31.1"; transcript_id "HML2_1p31.1"; locus "HML2_1p31.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0007"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "-2002"; repStart "5336";
+chr1	rmsk	exon	75380780	75382395	14607	+	.	gene_id "HML2_1p31.1"; transcript_id "HML2_1p31.1"; locus "HML2_1p31.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0007"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "-95"; repStart "5826";
+chr1	rmsk	exon	75382491	75383458	8811	+	.	gene_id "HML2_1p31.1"; transcript_id "HML2_1p31.1"; locus "HML2_1p31.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0007"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_1q21.3 ###								
+chr1	rmsk	gene	150632886	150634662	.	-	.	gene_id "HML2_1q21.3"; transcript_id "HML2_1q21.3"; locus "HML2_1q21.3"; category "internal"; intModel "HERVK-int"; locid "HERVK-int_0009"; model_cov "1783"; model_pct "23.7";
+chr1	rmsk	exon	150632886	150634662	15187	-	.	gene_id "HML2_1q21.3"; transcript_id "HML2_1q21.3"; locus "HML2_1q21.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0009"; repClass "LTR"; repEnd "5563"; repFamily "ERVK"; repLeft "3780"; repStart "-1973";
+### HML2_1q22 ###								
+chr1	rmsk	gene	155626666	155635845	.	-	.	gene_id "HML2_1q22"; transcript_id "HML2_1q22"; locus "HML2_1q22"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0011"; model_cov "7148"; model_pct "94.9";
+chr1	rmsk	exon	155626666	155627633	8978	-	.	gene_id "HML2_1q22"; transcript_id "HML2_1q22"; locus "HML2_1q22"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0011"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr1	rmsk	exon	155627729	155629344	14971	-	.	gene_id "HML2_1q22"; transcript_id "HML2_1q22"; locus "HML2_1q22"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0011"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "5826"; repStart "-95";
+chr1	rmsk	exon	155629344	155634877	50700	-	.	gene_id "HML2_1q22"; transcript_id "HML2_1q22"; locus "HML2_1q22"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0011"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "1"; repStart "-2002";
+chr1	rmsk	exon	155634878	155635845	8978	-	.	gene_id "HML2_1q22"; transcript_id "HML2_1q22"; locus "HML2_1q22"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0011"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_1q23.3 ###								
+chr1	rmsk	gene	160690785	160700016	.	+	.	gene_id "HML2_1q23.3"; transcript_id "HML2_1q23.3"; locus "HML2_1q23.3"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0012"; model_cov "7209"; model_pct "95.7";
+chr1	rmsk	exon	160690785	160691753	8986	+	.	gene_id "HML2_1q23.3"; transcript_id "HML2_1q23.3"; locus "HML2_1q23.3"; repName "LTR5"; geneRegion "ltr"; locid "HERVK-int_0012"; repClass "LTR"; repEnd "969"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr1	rmsk	exon	160691754	160697338	32110	+	.	gene_id "HML2_1q23.3"; transcript_id "HML2_1q23.3"; locus "HML2_1q23.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0012"; repClass "LTR"; repEnd "5178"; repFamily "ERVK"; repLeft "-2358"; repStart "-416";
+chr1	rmsk	exon	160697338	160698953	14352	+	.	gene_id "HML2_1q23.3"; transcript_id "HML2_1q23.3"; locus "HML2_1q23.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0012"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "-95"; repStart "5826";
+chr1	rmsk	exon	160699048	160700016	8448	+	.	gene_id "HML2_1q23.3"; transcript_id "HML2_1q23.3"; locus "HML2_1q23.3"; repName "LTR5"; geneRegion "ltr"; locid "HERVK-int_0012"; repClass "LTR"; repEnd "969"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_1q24.1 ###								
+chr1	rmsk	gene	166605366	166611021	.	-	.	gene_id "HML2_1q24.1"; transcript_id "HML2_1q24.1"; locus "HML2_1q24.1"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0013"; model_cov "3660"; model_pct "48.6";
+chr1	rmsk	exon	166605366	166606355	7845	-	.	gene_id "HML2_1q24.1"; transcript_id "HML2_1q24.1"; locus "HML2_1q24.1"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0013"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr1	rmsk	exon	166606445	166609934	20727	-	.	gene_id "HML2_1q24.1"; transcript_id "HML2_1q24.1"; locus "HML2_1q24.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0013"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "3882"; repStart "-89";
+chr1	rmsk	exon	166609929	166610025	470	-	.	gene_id "HML2_1q24.1"; transcript_id "HML2_1q24.1"; locus "HML2_1q24.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0013"; repClass "LTR"; repEnd "102"; repFamily "ERVK"; repLeft "7"; repStart "-7434";
+chr1	rmsk	exon	166610032	166611021	7616	-	.	gene_id "HML2_1q24.1"; transcript_id "HML2_1q24.1"; locus "HML2_1q24.1"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0013"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_1q32.2 ###								
+chr1	rmsk	gene	207635112	207639291	.	-	.	gene_id "HML2_1q32.2"; transcript_id "HML2_1q32.2"; locus "HML2_1q32.2"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0014"; model_cov "3184"; model_pct "42.3";
+chr1	rmsk	exon	207635112	207636074	7708	-	.	gene_id "HML2_1q32.2"; transcript_id "HML2_1q32.2"; locus "HML2_1q32.2"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0014"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr1	rmsk	exon	207636165	207637777	13912	-	.	gene_id "HML2_1q32.2"; transcript_id "HML2_1q32.2"; locus "HML2_1q32.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0014"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "5826"; repStart "-95";
+chr1	rmsk	exon	207637777	207638358	4802	-	.	gene_id "HML2_1q32.2"; transcript_id "HML2_1q32.2"; locus "HML2_1q32.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0014"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "4952"; repStart "-2002";
+chr1	rmsk	exon	207638337	207639291	7029	-	.	gene_id "HML2_1q32.2"; transcript_id "HML2_1q32.2"; locus "HML2_1q32.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0014"; repClass "LTR"; repEnd "2716"; repFamily "ERVK"; repLeft "1729"; repStart "-4820";
+### HML2_1q43 ###								
+chr1	rmsk	gene	238762295	238764473	.	-	.	gene_id "HML2_1q43"; transcript_id "HML2_1q43"; locus "HML2_1q43"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0015"; model_cov "1101"; model_pct "14.6";
+chr1	rmsk	exon	238762295	238763288	7387	-	.	gene_id "HML2_1q43"; transcript_id "HML2_1q43"; locus "HML2_1q43"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0015"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr1	rmsk	exon	238763378	238764473	7000	-	.	gene_id "HML2_1q43"; transcript_id "HML2_1q43"; locus "HML2_1q43"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0015"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "6346"; repStart "-89";
+### HML2_2q21.1 ###								
+chr2	rmsk	gene	129961965	129965044	.	-	.	gene_id "HML2_2q21.1"; transcript_id "HML2_2q21.1"; locus "HML2_2q21.1"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0016"; model_cov "2023"; model_pct "26.8";
+chr2	rmsk	exon	129961965	129962925	8380	-	.	gene_id "HML2_2q21.1"; transcript_id "HML2_2q21.1"; locus "HML2_2q21.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0016"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr2	rmsk	exon	129963021	129964636	14541	-	.	gene_id "HML2_2q21.1"; transcript_id "HML2_2q21.1"; locus "HML2_2q21.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0016"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "5826"; repStart "-95";
+chr2	rmsk	exon	129964636	129965044	3589	-	.	gene_id "HML2_2q21.1"; transcript_id "HML2_2q21.1"; locus "HML2_2q21.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0016"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "5126"; repStart "-2002";
+### HML2_3p25.3 ###								
+chr3	rmsk	gene	9847662	9854552	.	-	.	gene_id "HML2_3p25.3"; transcript_id "HML2_3p25.3"; locus "HML2_3p25.3"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0020"; model_cov "4918"; model_pct "65.3";
+chr3	rmsk	exon	9847662	9848644	7459	-	.	gene_id "HML2_3p25.3"; transcript_id "HML2_3p25.3"; locus "HML2_3p25.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0020"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr3	rmsk	exon	9848734	9850354	13139	-	.	gene_id "HML2_3p25.3"; transcript_id "HML2_3p25.3"; locus "HML2_3p25.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0020"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "5826"; repStart "-89";
+chr3	rmsk	exon	9850354	9850938	4633	-	.	gene_id "HML2_3p25.3"; transcript_id "HML2_3p25.3"; locus "HML2_3p25.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0020"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "4952"; repStart "-2002";
+chr3	rmsk	exon	9850917	9853634	21518	-	.	gene_id "HML2_3p25.3"; transcript_id "HML2_3p25.3"; locus "HML2_3p25.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0020"; repClass "LTR"; repEnd "2716"; repFamily "ERVK"; repLeft "1"; repStart "-4820";
+chr3	rmsk	exon	9853635	9854552	6737	-	.	gene_id "HML2_3p25.3"; transcript_id "HML2_3p25.3"; locus "HML2_3p25.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0020"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_3p12.3 ###								
+chr3	rmsk	gene	75551314	75559999	.	+	.	gene_id "HML2_3p12.3"; transcript_id "HML2_3p12.3"; locus "HML2_3p12.3"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0022"; model_cov "7535"; model_pct "100.0";
+chr3	rmsk	exon	75551314	75551382	580	+	.	gene_id "HML2_3p12.3"; transcript_id "HML2_3p12.3"; locus "HML2_3p12.3"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0022"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "0"; repStart "965";
+chr3	rmsk	exon	75551383	75558968	37160	+	.	gene_id "HML2_3p12.3"; transcript_id "HML2_3p12.3"; locus "HML2_3p12.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0022"; repClass "LTR"; repEnd "7536"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr3	rmsk	exon	75558969	75559999	8382	+	.	gene_id "HML2_3p12.3"; transcript_id "HML2_3p12.3"; locus "HML2_3p12.3"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0022"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_3q12.3 ###								
+chr3	rmsk	gene	101691893	101701015	.	+	.	gene_id "HML2_3q12.3"; transcript_id "HML2_3q12.3"; locus "HML2_3q12.3"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0023"; model_cov "7148"; model_pct "94.9";
+chr3	rmsk	exon	101691893	101692861	8050	+	.	gene_id "HML2_3q12.3"; transcript_id "HML2_3q12.3"; locus "HML2_3q12.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0023"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr3	rmsk	exon	101692862	101698340	22220	+	.	gene_id "HML2_3q12.3"; transcript_id "HML2_3q12.3"; locus "HML2_3q12.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0023"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "-2002"; repStart "1";
+chr3	rmsk	exon	101698340	101699951	14507	+	.	gene_id "HML2_3q12.3"; transcript_id "HML2_3q12.3"; locus "HML2_3q12.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0023"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "-95"; repStart "5826";
+chr3	rmsk	exon	101700047	101701015	8320	+	.	gene_id "HML2_3q12.3"; transcript_id "HML2_3q12.3"; locus "HML2_3q12.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0023"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_3q13.2 ###								
+chr3	rmsk	gene	113024277	113033435	.	-	.	gene_id "HML2_3q13.2"; transcript_id "HML2_3q13.2"; locus "HML2_3q13.2"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0024"; model_cov "7148"; model_pct "94.9";
+chr3	rmsk	exon	113024277	113025236	9337	-	.	gene_id "HML2_3q13.2"; transcript_id "HML2_3q13.2"; locus "HML2_3q13.2"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0024"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr3	rmsk	exon	113025332	113026948	14772	-	.	gene_id "HML2_3q13.2"; transcript_id "HML2_3q13.2"; locus "HML2_3q13.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0024"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "5826"; repStart "-95";
+chr3	rmsk	exon	113026948	113032475	50828	-	.	gene_id "HML2_3q13.2"; transcript_id "HML2_3q13.2"; locus "HML2_3q13.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0024"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "1"; repStart "-2002";
+chr3	rmsk	exon	113032476	113033435	9337	-	.	gene_id "HML2_3q13.2"; transcript_id "HML2_3q13.2"; locus "HML2_3q13.2"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0024"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_3q21.2 ###								
+chr3	rmsk	gene	125890459	125899596	.	+	.	gene_id "HML2_3q21.2"; transcript_id "HML2_3q21.2"; locus "HML2_3q21.2"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0026"; model_cov "7446"; model_pct "98.8";
+chr3	rmsk	exon	125890459	125891239	6706	+	.	gene_id "HML2_3q21.2"; transcript_id "HML2_3q21.2"; locus "HML2_3q21.2"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0026"; repClass "LTR"; repEnd "789"; repFamily "ERVK"; repLeft "-179"; repStart "1";
+chr3	rmsk	exon	125891209	125891262	317	+	.	gene_id "HML2_3q21.2"; transcript_id "HML2_3q21.2"; locus "HML2_3q21.2"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0026"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "915";
+chr3	rmsk	exon	125891263	125898703	63114	+	.	gene_id "HML2_3q21.2"; transcript_id "HML2_3q21.2"; locus "HML2_3q21.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0026"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "-89"; repStart "1";
+chr3	rmsk	exon	125898793	125899573	6625	+	.	gene_id "HML2_3q21.2"; transcript_id "HML2_3q21.2"; locus "HML2_3q21.2"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0026"; repClass "LTR"; repEnd "789"; repFamily "ERVK"; repLeft "-179"; repStart "1";
+chr3	rmsk	exon	125899543	125899596	290	+	.	gene_id "HML2_3q21.2"; transcript_id "HML2_3q21.2"; locus "HML2_3q21.2"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0026"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "915";
+### HML2_3q24 ###								
+chr3	rmsk	gene	148563690	148567609	.	-	.	gene_id "HML2_3q24"; transcript_id "HML2_3q24"; locus "HML2_3q24"; category "internal"; intModel "HERVK-int"; locid "HERVK-int_0028"; model_cov "3918"; model_pct "52.0";
+chr3	rmsk	exon	148563690	148567609	35394	-	.	gene_id "HML2_3q24"; transcript_id "HML2_3q24"; locus "HML2_3q24"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0028"; repClass "LTR"; repEnd "3919"; repFamily "ERVK"; repLeft "1"; repStart "-3617";
+### HML2_3q27.2 ###								
+chr3	rmsk	gene	185562548	185571727	.	-	.	gene_id "HML2_3q27.2"; transcript_id "HML2_3q27.2"; locus "HML2_3q27.2"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0029"; model_cov "7148"; model_pct "94.9";
+chr3	rmsk	exon	185562548	185563515	8924	-	.	gene_id "HML2_3q27.2"; transcript_id "HML2_3q27.2"; locus "HML2_3q27.2"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0029"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr3	rmsk	exon	185563611	185565226	14815	-	.	gene_id "HML2_3q27.2"; transcript_id "HML2_3q27.2"; locus "HML2_3q27.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0029"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "5826"; repStart "-95";
+chr3	rmsk	exon	185565226	185570759	50470	-	.	gene_id "HML2_3q27.2"; transcript_id "HML2_3q27.2"; locus "HML2_3q27.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0029"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "1"; repStart "-2002";
+chr3	rmsk	exon	185570760	185571727	8884	-	.	gene_id "HML2_3q27.2"; transcript_id "HML2_3q27.2"; locus "HML2_3q27.2"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0029"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_4p16.3a ###								
+chr4	rmsk	gene	241200	245565	.	+	.	gene_id "HML2_4p16.3a"; transcript_id "HML2_4p16.3a"; locus "HML2_4p16.3a"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0030"; model_cov "3299"; model_pct "43.8";
+chr4	rmsk	exon	241200	242201	7488	+	.	gene_id "HML2_4p16.3a"; transcript_id "HML2_4p16.3a"; locus "HML2_4p16.3a"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0030"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "4";
+chr4	rmsk	exon	242202	242389	1073	+	.	gene_id "HML2_4p16.3a"; transcript_id "HML2_4p16.3a"; locus "HML2_4p16.3a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0030"; repClass "LTR"; repEnd "198"; repFamily "ERVK"; repLeft "-7338"; repStart "1";
+chr4	rmsk	exon	242385	245212	15829	+	.	gene_id "HML2_4p16.3a"; transcript_id "HML2_4p16.3a"; locus "HML2_4p16.3a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0030"; repClass "LTR"; repEnd "3715"; repFamily "ERVK"; repLeft "-3821"; repStart "873";
+chr4	rmsk	exon	245308	245565	1656	+	.	gene_id "HML2_4p16.3a"; transcript_id "HML2_4p16.3a"; locus "HML2_4p16.3a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0030"; repClass "LTR"; repEnd "3958"; repFamily "ERVK"; repLeft "-3578"; repStart "3698";
+### HML2_4p16.3b ###								
+chr4	rmsk	gene	3977324	3986912	.	-	.	gene_id "HML2_4p16.3b"; transcript_id "HML2_4p16.3b"; locus "HML2_4p16.3b"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0031"; model_cov "7535"; model_pct "100.0";
+chr4	rmsk	exon	3977324	3978367	8576	-	.	gene_id "HML2_4p16.3b"; transcript_id "HML2_4p16.3b"; locus "HML2_4p16.3b"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0031"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr4	rmsk	exon	3978368	3985909	45400	-	.	gene_id "HML2_4p16.3b"; transcript_id "HML2_4p16.3b"; locus "HML2_4p16.3b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0031"; repClass "LTR"; repEnd "7536"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr4	rmsk	exon	3985910	3986912	8316	-	.	gene_id "HML2_4p16.3b"; transcript_id "HML2_4p16.3b"; locus "HML2_4p16.3b"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0031"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_4p16.1a ###								
+chr4	rmsk	gene	9121786	9131367	.	+	.	gene_id "HML2_4p16.1a"; transcript_id "HML2_4p16.1a"; locus "HML2_4p16.1a"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0034"; model_cov "7446"; model_pct "98.8";
+chr4	rmsk	exon	9121786	9122809	8752	+	.	gene_id "HML2_4p16.1a"; transcript_id "HML2_4p16.1a"; locus "HML2_4p16.1a"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0034"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr4	rmsk	exon	9122810	9130255	44130	+	.	gene_id "HML2_4p16.1a"; transcript_id "HML2_4p16.1a"; locus "HML2_4p16.1a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0034"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "-89"; repStart "1";
+chr4	rmsk	exon	9130345	9131367	8342	+	.	gene_id "HML2_4p16.1a"; transcript_id "HML2_4p16.1a"; locus "HML2_4p16.1a"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0034"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_4p16.1b ###								
+chr4	rmsk	gene	9657956	9667550	.	+	.	gene_id "HML2_4p16.1b"; transcript_id "HML2_4p16.1b"; locus "HML2_4p16.1b"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0036"; model_cov "7447"; model_pct "98.8";
+chr4	rmsk	exon	9657956	9658973	8450	+	.	gene_id "HML2_4p16.1b"; transcript_id "HML2_4p16.1b"; locus "HML2_4p16.1b"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0036"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr4	rmsk	exon	9658974	9666434	46859	+	.	gene_id "HML2_4p16.1b"; transcript_id "HML2_4p16.1b"; locus "HML2_4p16.1b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0036"; repClass "LTR"; repEnd "7448"; repFamily "ERVK"; repLeft "-88"; repStart "1";
+chr4	rmsk	exon	9666525	9667550	8382	+	.	gene_id "HML2_4p16.1b"; transcript_id "HML2_4p16.1b"; locus "HML2_4p16.1b"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0036"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_4q13.2 ###								
+chr4	rmsk	gene	68597991	68603505	.	+	.	gene_id "HML2_4q13.2"; transcript_id "HML2_4q13.2"; locus "HML2_4q13.2"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0037"; model_cov "3562"; model_pct "47.3";
+chr4	rmsk	exon	68597991	68598948	6942	+	.	gene_id "HML2_4q13.2"; transcript_id "HML2_4q13.2"; locus "HML2_4q13.2"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0037"; repClass "LTR"; repEnd "955"; repFamily "ERVK"; repLeft "-78"; repStart "1";
+chr4	rmsk	exon	68598949	68602490	20320	+	.	gene_id "HML2_4q13.2"; transcript_id "HML2_4q13.2"; locus "HML2_4q13.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0037"; repClass "LTR"; repEnd "7511"; repFamily "ERVK"; repLeft "-25"; repStart "3949";
+chr4	rmsk	exon	68602500	68603505	7736	+	.	gene_id "HML2_4q13.2"; transcript_id "HML2_4q13.2"; locus "HML2_4q13.2"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0037"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_4q32.1 ###								
+chr4	rmsk	gene	160658786	160660924	.	+	.	gene_id "HML2_4q32.1"; transcript_id "HML2_4q32.1"; locus "HML2_4q32.1"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0038"; model_cov "1186"; model_pct "15.7";
+chr4	rmsk	exon	160658786	160659753	8801	+	.	gene_id "HML2_4q32.1"; transcript_id "HML2_4q32.1"; locus "HML2_4q32.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0038"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr4	rmsk	exon	160659754	160660025	2390	+	.	gene_id "HML2_4q32.1"; transcript_id "HML2_4q32.1"; locus "HML2_4q32.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0038"; repClass "LTR"; repEnd "272"; repFamily "ERVK"; repLeft "-7264"; repStart "1";
+chr4	rmsk	exon	160660008	160660924	8165	+	.	gene_id "HML2_4q32.1"; transcript_id "HML2_4q32.1"; locus "HML2_4q32.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0038"; repClass "LTR"; repEnd "1338"; repFamily "ERVK"; repLeft "-6198"; repStart "423";
+### HML2_4q32.3 ###								
+chr4	rmsk	gene	164995688	165002916	.	+	.	gene_id "HML2_4q32.3"; transcript_id "HML2_4q32.3"; locus "HML2_4q32.3"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0040"; model_cov "4910"; model_pct "65.2";
+chr4	rmsk	exon	164995688	164996655	7694	+	.	gene_id "HML2_4q32.3"; transcript_id "HML2_4q32.3"; locus "HML2_4q32.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0040"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr4	rmsk	exon	164996656	164999353	21428	+	.	gene_id "HML2_4q32.3"; transcript_id "HML2_4q32.3"; locus "HML2_4q32.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0040"; repClass "LTR"; repEnd "2716"; repFamily "ERVK"; repLeft "-4820"; repStart "1";
+chr4	rmsk	exon	164999332	164999426	2771	+	.	gene_id "HML2_4q32.3"; transcript_id "HML2_4q32.3"; locus "HML2_4q32.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0040"; repClass "LTR"; repEnd "5043"; repFamily "ERVK"; repLeft "-2493"; repStart "4952";
+chr4	rmsk	exon	164999735	165000000	2771	+	.	gene_id "HML2_4q32.3"; transcript_id "HML2_4q32.3"; locus "HML2_4q32.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0040"; repClass "LTR"; repEnd "5301"; repFamily "ERVK"; repLeft "-2235"; repStart "5044";
+chr4	rmsk	exon	165000001	165000233	1948	+	.	gene_id "HML2_4q32.3"; transcript_id "HML2_4q32.3"; locus "HML2_4q32.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0040"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "-2002"; repStart "5302";
+chr4	rmsk	exon	165000233	165001857	13233	+	.	gene_id "HML2_4q32.3"; transcript_id "HML2_4q32.3"; locus "HML2_4q32.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0040"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "-95"; repStart "5826";
+chr4	rmsk	exon	165001953	165002916	7826	+	.	gene_id "HML2_4q32.3"; transcript_id "HML2_4q32.3"; locus "HML2_4q32.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0040"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_4q35.2 ###								
+chr4	rmsk	gene	190106259	190113546	.	-	.	gene_id "HML2_4q35.2"; transcript_id "HML2_4q35.2"; locus "HML2_4q35.2"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0041"; model_cov "4984"; model_pct "66.1";
+chr4	rmsk	exon	190106259	190107263	7790	-	.	gene_id "HML2_4q35.2"; transcript_id "HML2_4q35.2"; locus "HML2_4q35.2"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0041"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr4	rmsk	exon	190107266	190108168	5549	-	.	gene_id "HML2_4q35.2"; transcript_id "HML2_4q35.2"; locus "HML2_4q35.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0041"; repClass "LTR"; repEnd "7534"; repFamily "ERVK"; repLeft "6626"; repStart "-2";
+chr4	rmsk	exon	190108264	190111540	23124	-	.	gene_id "HML2_4q35.2"; transcript_id "HML2_4q35.2"; locus "HML2_4q35.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0041"; repClass "LTR"; repEnd "6328"; repFamily "ERVK"; repLeft "3007"; repStart "-1208";
+chr4	rmsk	exon	190111624	190111683	261	-	.	gene_id "HML2_4q35.2"; transcript_id "HML2_4q35.2"; locus "HML2_4q35.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0041"; repClass "LTR"; repEnd "820"; repFamily "ERVK"; repLeft "761"; repStart "-6716";
+chr4	rmsk	exon	190111667	190111959	1729	-	.	gene_id "HML2_4q35.2"; transcript_id "HML2_4q35.2"; locus "HML2_4q35.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0041"; repClass "LTR"; repEnd "696"; repFamily "ERVK"; repLeft "401"; repStart "-6840";
+chr4	rmsk	exon	190112160	190112541	2323	-	.	gene_id "HML2_4q35.2"; transcript_id "HML2_4q35.2"; locus "HML2_4q35.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0041"; repClass "LTR"; repEnd "402"; repFamily "ERVK"; repLeft "1"; repStart "-7134";
+chr4	rmsk	exon	190112542	190113546	7805	-	.	gene_id "HML2_4q35.2"; transcript_id "HML2_4q35.2"; locus "HML2_4q35.2"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0041"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "6"; repStart "0";
+### HML2_5p13.3 ###								
+chr5	rmsk	gene	30486653	30496098	.	-	.	gene_id "HML2_5p13.3"; transcript_id "HML2_5p13.3"; locus "HML2_5p13.3"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0042"; model_cov "7440"; model_pct "98.7";
+chr5	rmsk	exon	30486653	30487612	8378	-	.	gene_id "HML2_5p13.3"; transcript_id "HML2_5p13.3"; locus "HML2_5p13.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0042"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr5	rmsk	exon	30487708	30495147	66061	-	.	gene_id "HML2_5p13.3"; transcript_id "HML2_5p13.3"; locus "HML2_5p13.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0042"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "1"; repStart "-95";
+chr5	rmsk	exon	30495148	30496098	8198	-	.	gene_id "HML2_5p13.3"; transcript_id "HML2_5p13.3"; locus "HML2_5p13.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0042"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_5p12 ###								
+chr5	rmsk	gene	46000057	46009900	.	-	.	gene_id "HML2_5p12"; transcript_id "HML2_5p12"; locus "HML2_5p12"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0043"; model_cov "7241"; model_pct "96.1";
+chr5	rmsk	exon	46000057	46001004	6385	-	.	gene_id "HML2_5p12"; transcript_id "HML2_5p12"; locus "HML2_5p12"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0043"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr5	rmsk	exon	46001005	46002716	13121	-	.	gene_id "HML2_5p12"; transcript_id "HML2_5p12"; locus "HML2_5p12"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0043"; repClass "LTR"; repEnd "7536"; repFamily "ERVK"; repLeft "5826"; repStart "0";
+chr5	rmsk	exon	46002716	46008021	41714	-	.	gene_id "HML2_5p12"; transcript_id "HML2_5p12"; locus "HML2_5p12"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0043"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "217"; repStart "-2002";
+chr5	rmsk	exon	46008729	46008936	41714	-	.	gene_id "HML2_5p12"; transcript_id "HML2_5p12"; locus "HML2_5p12"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0043"; repClass "LTR"; repEnd "216"; repFamily "ERVK"; repLeft "2"; repStart "-7320";
+chr5	rmsk	exon	46008940	46009900	6205	-	.	gene_id "HML2_5p12"; transcript_id "HML2_5p12"; locus "HML2_5p12"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0043"; repClass "LTR"; repEnd "965"; repFamily "ERVK"; repLeft "1"; repStart "-3";
+### HML2_5q33.2 ###								
+chr5	rmsk	gene	154635953	154644655	.	-	.	gene_id "HML2_5q33.2"; transcript_id "HML2_5q33.2"; locus "HML2_5q33.2"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0046"; model_cov "6623"; model_pct "87.9";
+chr5	rmsk	exon	154635953	154636977	7881	-	.	gene_id "HML2_5q33.2"; transcript_id "HML2_5q33.2"; locus "HML2_5q33.2"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0046"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "-30"; repStart "0";
+chr5	rmsk	exon	154636980	154640034	20165	-	.	gene_id "HML2_5q33.2"; transcript_id "HML2_5q33.2"; locus "HML2_5q33.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0046"; repClass "LTR"; repEnd "7534"; repFamily "ERVK"; repLeft "4466"; repStart "-2";
+chr5	rmsk	exon	154640032	154642817	16400	-	.	gene_id "HML2_5q33.2"; transcript_id "HML2_5q33.2"; locus "HML2_5q33.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0046"; repClass "LTR"; repEnd "3553"; repFamily "ERVK"; repLeft "743"; repStart "-3983";
+chr5	rmsk	exon	154642910	154643647	4615	-	.	gene_id "HML2_5q33.2"; transcript_id "HML2_5q33.2"; locus "HML2_5q33.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0046"; repClass "LTR"; repEnd "746"; repFamily "ERVK"; repLeft "1"; repStart "-6790";
+chr5	rmsk	exon	154643648	154644655	7899	-	.	gene_id "HML2_5q33.2"; transcript_id "HML2_5q33.2"; locus "HML2_5q33.2"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0046"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "3"; repStart "0";
+### HML2_5q33.3 ###								
+chr5	rmsk	gene	156657706	156666885	.	-	.	gene_id "HML2_5q33.3"; transcript_id "HML2_5q33.3"; locus "HML2_5q33.3"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0047"; model_cov "7148"; model_pct "94.9";
+chr5	rmsk	exon	156657706	156658673	8851	-	.	gene_id "HML2_5q33.3"; transcript_id "HML2_5q33.3"; locus "HML2_5q33.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0047"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr5	rmsk	exon	156658769	156660384	14111	-	.	gene_id "HML2_5q33.3"; transcript_id "HML2_5q33.3"; locus "HML2_5q33.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0047"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "5826"; repStart "-95";
+chr5	rmsk	exon	156660384	156665917	47612	-	.	gene_id "HML2_5q33.3"; transcript_id "HML2_5q33.3"; locus "HML2_5q33.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0047"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "1"; repStart "-2002";
+chr5	rmsk	exon	156665918	156666885	8861	-	.	gene_id "HML2_5q33.3"; transcript_id "HML2_5q33.3"; locus "HML2_5q33.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0047"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_6p22.1 ###								
+chr6	rmsk	gene	28682591	28692958	.	+	.	gene_id "HML2_6p22.1"; transcript_id "HML2_6p22.1"; locus "HML2_6p22.1"; category "unknown"; intModel "HERVK-int"; locid "HERVK-int_0049"; model_cov "7588"; model_pct "100.0";
+chr6	rmsk	exon	28682591	28683408	3942	+	.	gene_id "HML2_6p22.1"; transcript_id "HML2_6p22.1"; locus "HML2_6p22.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0049"; repClass "LTR"; repEnd "965"; repFamily "ERVK"; repLeft "-3"; repStart "189";
+chr6	rmsk	exon	28683412	28684170	5291	+	.	gene_id "HML2_6p22.1"; transcript_id "HML2_6p22.1"; locus "HML2_6p22.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0049"; repClass "LTR"; repEnd "776"; repFamily "ERVK"; repLeft "-6760"; repStart "1";
+chr6	rmsk	exon	28684224	28687381	53735	+	.	gene_id "HML2_6p22.1"; transcript_id "HML2_6p22.1"; locus "HML2_6p22.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0049"; repClass "LTR"; repEnd "3909"; repFamily "ERVK"; repLeft "-3627"; repStart "722";
+chr6	rmsk	exon	28687382	28688356	6122	+	.	gene_id "HML2_6p22.1"; transcript_id "HML2_6p22.1"; locus "HML2_6p22.1"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0049"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr6	rmsk	exon	28688357	28692010	53735	+	.	gene_id "HML2_6p22.1"; transcript_id "HML2_6p22.1"; locus "HML2_6p22.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0049"; repClass "LTR"; repEnd "7536"; repFamily "ERVK"; repLeft "0"; repStart "3910";
+chr6	rmsk	exon	28692011	28692958	5830	+	.	gene_id "HML2_6p22.1"; transcript_id "HML2_6p22.1"; locus "HML2_6p22.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0049"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_6p21.1 ###								
+chr6	rmsk	gene	42893671	42903629	.	-	.	gene_id "HML2_6p21.1"; transcript_id "HML2_6p21.1"; locus "HML2_6p21.1"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0050"; model_cov "7529"; model_pct "99.9";
+chr6	rmsk	exon	42893671	42894666	7663	-	.	gene_id "HML2_6p21.1"; transcript_id "HML2_6p21.1"; locus "HML2_6p21.1"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0050"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr6	rmsk	exon	42894674	42900373	42072	-	.	gene_id "HML2_6p21.1"; transcript_id "HML2_6p21.1"; locus "HML2_6p21.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0050"; repClass "LTR"; repEnd "7524"; repFamily "ERVK"; repLeft "1856"; repStart "-12";
+chr6	rmsk	exon	42900685	42901811	42072	-	.	gene_id "HML2_6p21.1"; transcript_id "HML2_6p21.1"; locus "HML2_6p21.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0050"; repClass "LTR"; repEnd "1855"; repFamily "ERVK"; repLeft "743"; repStart "-5681";
+chr6	rmsk	exon	42901891	42902625	4270	-	.	gene_id "HML2_6p21.1"; transcript_id "HML2_6p21.1"; locus "HML2_6p21.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0050"; repClass "LTR"; repEnd "758"; repFamily "ERVK"; repLeft "9"; repStart "-6778";
+chr6	rmsk	exon	42902633	42903629	7599	-	.	gene_id "HML2_6p21.1"; transcript_id "HML2_6p21.1"; locus "HML2_6p21.1"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0050"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_6q11.1 ###								
+chr6	rmsk	gene	60654987	60660975	.	+	.	gene_id "HML2_6q11.1"; transcript_id "HML2_6q11.1"; locus "HML2_6q11.1"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0051"; model_cov "3472"; model_pct "46.1";
+chr6	rmsk	exon	60654987	60656012	8037	+	.	gene_id "HML2_6q11.1"; transcript_id "HML2_6q11.1"; locus "HML2_6q11.1"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0051"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr6	rmsk	exon	60656013	60656707	3744	+	.	gene_id "HML2_6q11.1"; transcript_id "HML2_6q11.1"; locus "HML2_6q11.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0051"; repClass "LTR"; repEnd "696"; repFamily "ERVK"; repLeft "-6840"; repStart "1";
+chr6	rmsk	exon	60656834	60659432	16583	+	.	gene_id "HML2_6q11.1"; transcript_id "HML2_6q11.1"; locus "HML2_6q11.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0051"; repClass "LTR"; repEnd "5613"; repFamily "ERVK"; repLeft "-1923"; repStart "3007";
+chr6	rmsk	exon	60659770	60659941	1027	+	.	gene_id "HML2_6q11.1"; transcript_id "HML2_6q11.1"; locus "HML2_6q11.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0051"; repClass "LTR"; repEnd "7528"; repFamily "ERVK"; repLeft "-8"; repStart "7357";
+chr6	rmsk	exon	60659956	60660975	7824	+	.	gene_id "HML2_6q11.1"; transcript_id "HML2_6q11.1"; locus "HML2_6q11.1"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0051"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_6q14.1 ###								
+chr6	rmsk	gene	77716945	77726366	.	-	.	gene_id "HML2_6q14.1"; transcript_id "HML2_6q14.1"; locus "HML2_6q14.1"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0053"; model_cov "7440"; model_pct "98.7";
+chr6	rmsk	exon	77716945	77717904	8674	-	.	gene_id "HML2_6q14.1"; transcript_id "HML2_6q14.1"; locus "HML2_6q14.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0053"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr6	rmsk	exon	77718000	77725406	48157	-	.	gene_id "HML2_6q14.1"; transcript_id "HML2_6q14.1"; locus "HML2_6q14.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0053"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "1"; repStart "-95";
+chr6	rmsk	exon	77725407	77726366	8726	-	.	gene_id "HML2_6q14.1"; transcript_id "HML2_6q14.1"; locus "HML2_6q14.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0053"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_6q25.1 ###								
+chr6	rmsk	gene	150859613	150862438	.	+	.	gene_id "HML2_6q25.1"; transcript_id "HML2_6q25.1"; locus "HML2_6q25.1"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0054"; model_cov "1757"; model_pct "23.3";
+chr6	rmsk	exon	150859613	150861371	13136	+	.	gene_id "HML2_6q25.1"; transcript_id "HML2_6q25.1"; locus "HML2_6q25.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0054"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "-95"; repStart "5684";
+chr6	rmsk	exon	150861466	150862438	6300	+	.	gene_id "HML2_6q25.1"; transcript_id "HML2_6q25.1"; locus "HML2_6q25.1"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0054"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_7p22.1 ###								
+chr7	rmsk	gene	4582426	4600400	.	-	.	gene_id "HML2_7p22.1"; transcript_id "HML2_7p22.1"; locus "HML2_7p22.1"; category "tandem*"; intModel "HERVK-int"; locid "HERVK-int_0055"; model_cov "7440"; model_pct "98.7";
+chr7	rmsk	exon	4582426	4583393	8941	-	.	gene_id "HML2_7p22.1"; transcript_id "HML2_7p22.1"; locus "HML2_7p22.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0055"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr7	rmsk	exon	4583489	4590929	68784	-	.	gene_id "HML2_7p22.1"; transcript_id "HML2_7p22.1"; locus "HML2_7p22.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0055"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "1"; repStart "-95";
+chr7	rmsk	exon	4590930	4591897	8936	-	.	gene_id "HML2_7p22.1"; transcript_id "HML2_7p22.1"; locus "HML2_7p22.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0055"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr7	rmsk	exon	4591993	4599432	68780	-	.	gene_id "HML2_7p22.1"; transcript_id "HML2_7p22.1"; locus "HML2_7p22.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0055"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "1"; repStart "-95";
+chr7	rmsk	exon	4599433	4600400	8980	-	.	gene_id "HML2_7p22.1"; transcript_id "HML2_7p22.1"; locus "HML2_7p22.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0055"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_7q11.21 ###								
+chr7	rmsk	gene	66004684	66007803	.	-	.	gene_id "HML2_7q11.21"; transcript_id "HML2_7q11.21"; locus "HML2_7q11.21"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0058"; model_cov "2029"; model_pct "26.9";
+chr7	rmsk	exon	66004684	66005676	8096	-	.	gene_id "HML2_7q11.21"; transcript_id "HML2_7q11.21"; locus "HML2_7q11.21"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0058"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr7	rmsk	exon	66005766	66007803	11693	-	.	gene_id "HML2_7q11.21"; transcript_id "HML2_7q11.21"; locus "HML2_7q11.21"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0058"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "5418"; repStart "-89";
+### HML2_7q22.2 ###								
+chr7	rmsk	gene	104748902	104752819	.	-	.	gene_id "HML2_7q22.2"; transcript_id "HML2_7q22.2"; locus "HML2_7q22.2"; category "internal"; intModel "HERVK-int"; locid "HERVK-int_0059"; model_cov "3915"; model_pct "52.0";
+chr7	rmsk	exon	104748902	104752819	33350	-	.	gene_id "HML2_7q22.2"; transcript_id "HML2_7q22.2"; locus "HML2_7q22.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0059"; repClass "LTR"; repEnd "3919"; repFamily "ERVK"; repLeft "4"; repStart "-3617";
+### HML2_7q34 ###								
+chr7	rmsk	gene	141752118	141756138	.	-	.	gene_id "HML2_7q34"; transcript_id "HML2_7q34"; locus "HML2_7q34"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0060"; model_cov "3914"; model_pct "51.9";
+chr7	rmsk	exon	141752118	141755274	25017	-	.	gene_id "HML2_7q34"; transcript_id "HML2_7q34"; locus "HML2_7q34"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0060"; repClass "LTR"; repEnd "3918"; repFamily "ERVK"; repLeft "743"; repStart "-3618";
+chr7	rmsk	exon	141755372	141756103	5407	-	.	gene_id "HML2_7q34"; transcript_id "HML2_7q34"; locus "HML2_7q34"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0060"; repClass "LTR"; repEnd "741"; repFamily "ERVK"; repLeft "2"; repStart "-6795";
+chr7	rmsk	exon	141756105	141756138	282	-	.	gene_id "HML2_7q34"; transcript_id "HML2_7q34"; locus "HML2_7q34"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0060"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "969"; repStart "0";
+### HML2_8p23.1a ###								
+chr8	rmsk	gene	7497875	7502767	.	-	.	gene_id "HML2_8p23.1a"; transcript_id "HML2_8p23.1a"; locus "HML2_8p23.1a"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0063"; model_cov "3854"; model_pct "51.1";
+chr8	rmsk	exon	7497875	7498842	8965	-	.	gene_id "HML2_8p23.1a"; transcript_id "HML2_8p23.1a"; locus "HML2_8p23.1a"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0063"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr8	rmsk	exon	7498938	7500000	9764	-	.	gene_id "HML2_8p23.1a"; transcript_id "HML2_8p23.1a"; locus "HML2_8p23.1a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0063"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "6379"; repStart "-95";
+chr8	rmsk	exon	7500001	7502767	56636	-	.	gene_id "HML2_8p23.1a"; transcript_id "HML2_8p23.1a"; locus "HML2_8p23.1a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0063"; repClass "LTR"; repEnd "6378"; repFamily "ERVK"; repLeft "3586"; repStart "-1158";
+### HML2_8p23.1b ###								
+chr8	rmsk	gene	7502828	7507337	.	-	.	gene_id "HML2_8p23.1b"; transcript_id "HML2_8p23.1b"; locus "HML2_8p23.1b"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0064"; model_cov "3584"; model_pct "47.6";
+chr8	rmsk	exon	7502828	7506377	56636	-	.	gene_id "HML2_8p23.1b"; transcript_id "HML2_8p23.1b"; locus "HML2_8p23.1b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0064"; repClass "LTR"; repEnd "6378"; repFamily "ERVK"; repLeft "2794"; repStart "-1158";
+chr8	rmsk	exon	7506378	7507337	8874	-	.	gene_id "HML2_8p23.1b"; transcript_id "HML2_8p23.1b"; locus "HML2_8p23.1b"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0064"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_8p23.1c ###								
+chr8	rmsk	gene	8197178	8206699	.	+	.	gene_id "HML2_8p23.1c"; transcript_id "HML2_8p23.1c"; locus "HML2_8p23.1c"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0066"; model_cov "7446"; model_pct "98.8";
+chr8	rmsk	exon	8197178	8198203	8731	+	.	gene_id "HML2_8p23.1c"; transcript_id "HML2_8p23.1c"; locus "HML2_8p23.1c"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0066"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr8	rmsk	exon	8198204	8205586	41196	+	.	gene_id "HML2_8p23.1c"; transcript_id "HML2_8p23.1c"; locus "HML2_8p23.1c"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0066"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "-89"; repStart "1";
+chr8	rmsk	exon	8205676	8206699	8476	+	.	gene_id "HML2_8p23.1c"; transcript_id "HML2_8p23.1c"; locus "HML2_8p23.1c"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0066"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_8p23.1d ###								
+chr8	rmsk	gene	12216461	12225988	.	-	.	gene_id "HML2_8p23.1d"; transcript_id "HML2_8p23.1d"; locus "HML2_8p23.1d"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0067"; model_cov "7365"; model_pct "97.7";
+chr8	rmsk	exon	12216461	12217484	8110	-	.	gene_id "HML2_8p23.1d"; transcript_id "HML2_8p23.1d"; locus "HML2_8p23.1d"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0067"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr8	rmsk	exon	12217574	12223144	35557	-	.	gene_id "HML2_8p23.1d"; transcript_id "HML2_8p23.1d"; locus "HML2_8p23.1d"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0067"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "1872"; repStart "-89";
+chr8	rmsk	exon	12223176	12224961	7773	-	.	gene_id "HML2_8p23.1d"; transcript_id "HML2_8p23.1d"; locus "HML2_8p23.1d"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0067"; repClass "LTR"; repEnd "1893"; repFamily "ERVK"; repLeft "103"; repStart "-5643";
+chr8	rmsk	exon	12224962	12225988	8788	-	.	gene_id "HML2_8p23.1d"; transcript_id "HML2_8p23.1d"; locus "HML2_8p23.1d"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0067"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_8p23.1e ###								
+chr8	rmsk	gene	12458983	12461064	.	-	.	gene_id "HML2_8p23.1e"; transcript_id "HML2_8p23.1e"; locus "HML2_8p23.1e"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0068"; model_cov "998"; model_pct "13.2";
+chr8	rmsk	exon	12458983	12460006	8570	-	.	gene_id "HML2_8p23.1e"; transcript_id "HML2_8p23.1e"; locus "HML2_8p23.1e"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0068"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr8	rmsk	exon	12460096	12461064	44166	-	.	gene_id "HML2_8p23.1e"; transcript_id "HML2_8p23.1e"; locus "HML2_8p23.1e"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0068"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "6449"; repStart "-89";
+### HML2_8p23.1f ###								
+chr8	rmsk	gene	12461223	12468498	.	-	.	gene_id "HML2_8p23.1f"; transcript_id "HML2_8p23.1f"; locus "HML2_8p23.1f"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0069"; model_cov "6447"; model_pct "85.5";
+chr8	rmsk	exon	12461223	12467471	44166	-	.	gene_id "HML2_8p23.1f"; transcript_id "HML2_8p23.1f"; locus "HML2_8p23.1f"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0069"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "1000"; repStart "-89";
+chr8	rmsk	exon	12467472	12468498	8725	-	.	gene_id "HML2_8p23.1f"; transcript_id "HML2_8p23.1f"; locus "HML2_8p23.1f"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0069"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_8p22 ###								
+chr8	rmsk	gene	17908096	17916431	.	-	.	gene_id "HML2_8p22"; transcript_id "HML2_8p22"; locus "HML2_8p22"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0072"; model_cov "7010"; model_pct "93.0";
+chr8	rmsk	exon	17908096	17912373	17248	-	.	gene_id "HML2_8p22"; transcript_id "HML2_8p22"; locus "HML2_8p22"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0072"; repClass "LTR"; repEnd "7536"; repFamily "ERVK"; repLeft "3280"; repStart "0";
+chr8	rmsk	exon	17912665	17914948	17248	-	.	gene_id "HML2_8p22"; transcript_id "HML2_8p22"; locus "HML2_8p22"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0072"; repClass "LTR"; repEnd "3279"; repFamily "ERVK"; repLeft "966"; repStart "-4257";
+chr8	rmsk	exon	17915408	17915839	970	-	.	gene_id "HML2_8p22"; transcript_id "HML2_8p22"; locus "HML2_8p22"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0072"; repClass "LTR"; repEnd "442"; repFamily "ERVK"; repLeft "1"; repStart "-7094";
+chr8	rmsk	exon	17916217	17916431	252	-	.	gene_id "HML2_8p22"; transcript_id "HML2_8p22"; locus "HML2_8p22"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0072"; repClass "LTR"; repEnd "510"; repFamily "ERVK"; repLeft "279"; repStart "-458";
+### HML2_8q11.1a ###								
+chr8	rmsk	gene	46264028	46267723	.	-	.	gene_id "HML2_8q11.1a"; transcript_id "HML2_8q11.1a"; locus "HML2_8q11.1a"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0073"; model_cov "2666"; model_pct "35.4";
+chr8	rmsk	exon	46264028	46265053	7799	-	.	gene_id "HML2_8q11.1a"; transcript_id "HML2_8q11.1a"; locus "HML2_8q11.1a"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0073"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr8	rmsk	exon	46265056	46267136	11384	-	.	gene_id "HML2_8q11.1a"; transcript_id "HML2_8q11.1a"; locus "HML2_8q11.1a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0073"; repClass "LTR"; repEnd "7534"; repFamily "ERVK"; repLeft "5462"; repStart "-2";
+chr8	rmsk	exon	46267142	46267723	3196	-	.	gene_id "HML2_8q11.1a"; transcript_id "HML2_8q11.1a"; locus "HML2_8q11.1a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0073"; repClass "LTR"; repEnd "652"; repFamily "ERVK"; repLeft "58"; repStart "-6884";
+### HML2_8q11.1b ###								
+chr8	rmsk	gene	46267760	46272039	.	-	.	gene_id "HML2_8q11.1b"; transcript_id "HML2_8q11.1b"; locus "HML2_8q11.1b"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0074"; model_cov "5442"; model_pct "72.2";
+chr8	rmsk	exon	46267760	46271002	15126	-	.	gene_id "HML2_8q11.1b"; transcript_id "HML2_8q11.1b"; locus "HML2_8q11.1b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0074"; repClass "LTR"; repEnd "5476"; repFamily "ERVK"; repLeft "34"; repStart "-2060";
+chr8	rmsk	exon	46271034	46272039	7285	-	.	gene_id "HML2_8q11.1b"; transcript_id "HML2_8q11.1b"; locus "HML2_8q11.1b"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0074"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_8q24.3a ###								
+chr8	rmsk	gene	139459906	139462993	.	-	.	gene_id "HML2_8q24.3a"; transcript_id "HML2_8q24.3a"; locus "HML2_8q24.3a"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0075"; model_cov "2025"; model_pct "26.9";
+chr8	rmsk	exon	139459906	139460873	8925	-	.	gene_id "HML2_8q24.3a"; transcript_id "HML2_8q24.3a"; locus "HML2_8q24.3a"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0075"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr8	rmsk	exon	139460969	139461717	6940	-	.	gene_id "HML2_8q24.3a"; transcript_id "HML2_8q24.3a"; locus "HML2_8q24.3a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0075"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "6693"; repStart "-95";
+chr8	rmsk	exon	139461716	139462993	11668	-	.	gene_id "HML2_8q24.3a"; transcript_id "HML2_8q24.3a"; locus "HML2_8q24.3a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0075"; repClass "LTR"; repEnd "1278"; repFamily "ERVK"; repLeft "1"; repStart "-6258";
+### HML2_8q24.3b ###								
+chr8	rmsk	gene	145021244	145028834	.	-	.	gene_id "HML2_8q24.3b"; transcript_id "HML2_8q24.3b"; locus "HML2_8q24.3b"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0076"; model_cov "5527"; model_pct "73.3";
+chr8	rmsk	exon	145021244	145022259	8134	-	.	gene_id "HML2_8q24.3b"; transcript_id "HML2_8q24.3b"; locus "HML2_8q24.3b"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0076"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr8	rmsk	exon	145022262	145026351	27966	-	.	gene_id "HML2_8q24.3b"; transcript_id "HML2_8q24.3b"; locus "HML2_8q24.3b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0076"; repClass "LTR"; repEnd "7534"; repFamily "ERVK"; repLeft "3452"; repStart "-2";
+chr8	rmsk	exon	145026350	145027823	7746	-	.	gene_id "HML2_8q24.3b"; transcript_id "HML2_8q24.3b"; locus "HML2_8q24.3b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0076"; repClass "LTR"; repEnd "1446"; repFamily "ERVK"; repLeft "1"; repStart "-6090";
+chr8	rmsk	exon	145027824	145028834	8116	-	.	gene_id "HML2_8q24.3b"; transcript_id "HML2_8q24.3b"; locus "HML2_8q24.3b"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0076"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "2"; repStart "0";
+### HML2_9q34.11 ###								
+chr9	rmsk	gene	128850236	128857457	.	+	.	gene_id "HML2_9q34.11"; transcript_id "HML2_9q34.11"; locus "HML2_9q34.11"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0077"; model_cov "7533"; model_pct "100.0";
+chr9	rmsk	exon	128850236	128851238	7849	+	.	gene_id "HML2_9q34.11"; transcript_id "HML2_9q34.11"; locus "HML2_9q34.11"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0077"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr9	rmsk	exon	128851239	128856449	16412	+	.	gene_id "HML2_9q34.11"; transcript_id "HML2_9q34.11"; locus "HML2_9q34.11"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0077"; repClass "LTR"; repEnd "7534"; repFamily "ERVK"; repLeft "-2"; repStart "1";
+chr9	rmsk	exon	128856452	128857457	7931	+	.	gene_id "HML2_9q34.11"; transcript_id "HML2_9q34.11"; locus "HML2_9q34.11"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0077"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_9q34.3 ###								
+chr9	rmsk	gene	136780314	136789776	.	-	.	gene_id "HML2_9q34.3"; transcript_id "HML2_9q34.3"; locus "HML2_9q34.3"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0078"; model_cov "5732"; model_pct "76.1";
+chr9	rmsk	exon	136780314	136781296	6274	-	.	gene_id "HML2_9q34.3"; transcript_id "HML2_9q34.3"; locus "HML2_9q34.3"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0078"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr9	rmsk	exon	136781297	136781482	1708	-	.	gene_id "HML2_9q34.3"; transcript_id "HML2_9q34.3"; locus "HML2_9q34.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0078"; repClass "LTR"; repEnd "7536"; repFamily "ERVK"; repLeft "7350"; repStart "0";
+chr9	rmsk	exon	136781788	136781880	1708	-	.	gene_id "HML2_9q34.3"; transcript_id "HML2_9q34.3"; locus "HML2_9q34.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0078"; repClass "LTR"; repEnd "7349"; repFamily "ERVK"; repLeft "7258"; repStart "-187";
+chr9	rmsk	exon	136781866	136783596	11943	-	.	gene_id "HML2_9q34.3"; transcript_id "HML2_9q34.3"; locus "HML2_9q34.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0078"; repClass "LTR"; repEnd "5592"; repFamily "ERVK"; repLeft "3860"; repStart "-1944";
+chr9	rmsk	exon	136783849	136785013	19279	-	.	gene_id "HML2_9q34.3"; transcript_id "HML2_9q34.3"; locus "HML2_9q34.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0078"; repClass "LTR"; repEnd "3710"; repFamily "ERVK"; repLeft "2565"; repStart "-3826";
+chr9	rmsk	exon	136786163	136787981	19279	-	.	gene_id "HML2_9q34.3"; transcript_id "HML2_9q34.3"; locus "HML2_9q34.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0078"; repClass "LTR"; repEnd "2564"; repFamily "ERVK"; repLeft "743"; repStart "-4972";
+chr9	rmsk	exon	136788061	136788797	4132	-	.	gene_id "HML2_9q34.3"; transcript_id "HML2_9q34.3"; locus "HML2_9q34.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0078"; repClass "LTR"; repEnd "758"; repFamily "ERVK"; repLeft "1"; repStart "-6778";
+chr9	rmsk	exon	136788798	136789776	6413	-	.	gene_id "HML2_9q34.3"; transcript_id "HML2_9q34.3"; locus "HML2_9q34.3"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0078"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_10p14 ###								
+chr10	rmsk	gene	6824179	6833641	.	-	.	gene_id "HML2_10p14"; transcript_id "HML2_10p14"; locus "HML2_10p14"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0079"; model_cov "7440"; model_pct "98.7";
+chr10	rmsk	exon	6824179	6825146	7814	-	.	gene_id "HML2_10p14"; transcript_id "HML2_10p14"; locus "HML2_10p14"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0079"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr10	rmsk	exon	6825242	6832673	63906	-	.	gene_id "HML2_10p14"; transcript_id "HML2_10p14"; locus "HML2_10p14"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0079"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "1"; repStart "-95";
+chr10	rmsk	exon	6832674	6833641	7901	-	.	gene_id "HML2_10p14"; transcript_id "HML2_10p14"; locus "HML2_10p14"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0079"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_10q24.2 ###								
+chr10	rmsk	gene	99820812	99827988	.	-	.	gene_id "HML2_10q24.2"; transcript_id "HML2_10q24.2"; locus "HML2_10q24.2"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0081"; model_cov "6068"; model_pct "80.5";
+chr10	rmsk	exon	99820812	99821797	8326	-	.	gene_id "HML2_10q24.2"; transcript_id "HML2_10q24.2"; locus "HML2_10q24.2"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0081"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr10	rmsk	exon	99821893	99827959	54777	-	.	gene_id "HML2_10q24.2"; transcript_id "HML2_10q24.2"; locus "HML2_10q24.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0081"; repClass "LTR"; repEnd "6069"; repFamily "ERVK"; repLeft "1"; repStart "-1467";
+chr10	rmsk	exon	99827960	99827988	254	-	.	gene_id "HML2_10q24.2"; transcript_id "HML2_10q24.2"; locus "HML2_10q24.2"; repName "LTR5"; geneRegion "ltr"; locid "HERVK-int_0081"; repClass "LTR"; repEnd "969"; repFamily "ERVK"; repLeft "941"; repStart "0";
+### HML2_11p15.4a ###								
+chr11	rmsk	gene	3447426	3456979	.	-	.	gene_id "HML2_11p15.4a"; transcript_id "HML2_11p15.4a"; locus "HML2_11p15.4a"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0082"; model_cov "7535"; model_pct "100.0";
+chr11	rmsk	exon	3447426	3448449	8563	-	.	gene_id "HML2_11p15.4a"; transcript_id "HML2_11p15.4a"; locus "HML2_11p15.4a"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0082"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr11	rmsk	exon	3448450	3455952	47463	-	.	gene_id "HML2_11p15.4a"; transcript_id "HML2_11p15.4a"; locus "HML2_11p15.4a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0082"; repClass "LTR"; repEnd "7536"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr11	rmsk	exon	3455953	3456979	8618	-	.	gene_id "HML2_11p15.4a"; transcript_id "HML2_11p15.4a"; locus "HML2_11p15.4a"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0082"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_11p15.4b ###								
+chr11	rmsk	gene	4459435	4461473	.	-	.	gene_id "HML2_11p15.4b"; transcript_id "HML2_11p15.4b"; locus "HML2_11p15.4b"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0084"; model_cov "817"; model_pct "10.8";
+chr11	rmsk	exon	4459435	4459640	1531	-	.	gene_id "HML2_11p15.4b"; transcript_id "HML2_11p15.4b"; locus "HML2_11p15.4b"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0084"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "789"; repStart "0";
+chr11	rmsk	exon	4459658	4459795	611	-	.	gene_id "HML2_11p15.4b"; transcript_id "HML2_11p15.4b"; locus "HML2_11p15.4b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0084"; repClass "LTR"; repEnd "3010"; repFamily "ERVK"; repLeft "2888"; repStart "-4526";
+chr11	rmsk	exon	4459781	4460462	4101	-	.	gene_id "HML2_11p15.4b"; transcript_id "HML2_11p15.4b"; locus "HML2_11p15.4b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0084"; repClass "LTR"; repEnd "696"; repFamily "ERVK"; repLeft "1"; repStart "-6840";
+chr11	rmsk	exon	4460468	4461473	8224	-	.	gene_id "HML2_11p15.4b"; transcript_id "HML2_11p15.4b"; locus "HML2_11p15.4b"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0084"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "4"; repStart "0";
+### HML2_11q12.1 ###								
+chr11	rmsk	gene	59000009	59005723	.	+	.	gene_id "HML2_11q12.1"; transcript_id "HML2_11q12.1"; locus "HML2_11q12.1"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0085"; model_cov "5004"; model_pct "66.4";
+chr11	rmsk	exon	59000009	59000147	654	+	.	gene_id "HML2_11q12.1"; transcript_id "HML2_11q12.1"; locus "HML2_11q12.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0085"; repClass "LTR"; repEnd "696"; repFamily "ERVK"; repLeft "-6840"; repStart "559";
+chr11	rmsk	exon	59000270	59002749	13680	+	.	gene_id "HML2_11q12.1"; transcript_id "HML2_11q12.1"; locus "HML2_11q12.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0085"; repClass "LTR"; repEnd "5434"; repFamily "ERVK"; repLeft "-2102"; repStart "2427";
+chr11	rmsk	exon	59002774	59004639	10154	+	.	gene_id "HML2_11q12.1"; transcript_id "HML2_11q12.1"; locus "HML2_11q12.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0085"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "-89"; repStart "5587";
+chr11	rmsk	exon	59004729	59005723	7568	+	.	gene_id "HML2_11q12.1"; transcript_id "HML2_11q12.1"; locus "HML2_11q12.1"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0085"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_11q12.3a ###								
+chr11	rmsk	gene	62368491	62370999	.	-	.	gene_id "HML2_11q12.3a"; transcript_id "HML2_11q12.3a"; locus "HML2_11q12.3a"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0086"; model_cov "1457"; model_pct "19.3";
+chr11	rmsk	exon	62368491	62369451	5940	-	.	gene_id "HML2_11q12.3a"; transcript_id "HML2_11q12.3a"; locus "HML2_11q12.3a"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0086"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr11	rmsk	exon	62369545	62370999	11630	-	.	gene_id "HML2_11q12.3a"; transcript_id "HML2_11q12.3a"; locus "HML2_11q12.3a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0086"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "5984"; repStart "-95";
+### HML2_11q12.3b ###								
+chr11	rmsk	gene	62375545	62383091	.	-	.	gene_id "HML2_11q12.3b"; transcript_id "HML2_11q12.3b"; locus "HML2_11q12.3b"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0087"; model_cov "6011"; model_pct "79.8";
+chr11	rmsk	exon	62375545	62375829	42079	-	.	gene_id "HML2_11q12.3b"; transcript_id "HML2_11q12.3b"; locus "HML2_11q12.3b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0087"; repClass "LTR"; repEnd "5998"; repFamily "ERVK"; repLeft "5718"; repStart "-1538";
+chr11	rmsk	exon	62376126	62381099	42079	-	.	gene_id "HML2_11q12.3b"; transcript_id "HML2_11q12.3b"; locus "HML2_11q12.3b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0087"; repClass "LTR"; repEnd "5717"; repFamily "ERVK"; repLeft "743"; repStart "-1819";
+chr11	rmsk	exon	62381171	62381929	5179	-	.	gene_id "HML2_11q12.3b"; transcript_id "HML2_11q12.3b"; locus "HML2_11q12.3b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0087"; repClass "LTR"; repEnd "758"; repFamily "ERVK"; repLeft "1"; repStart "-6778";
+chr11	rmsk	exon	62381930	62382006	5110	-	.	gene_id "HML2_11q12.3b"; transcript_id "HML2_11q12.3b"; locus "HML2_11q12.3b"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0087"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "892"; repStart "0";
+chr11	rmsk	exon	62382200	62383091	5294	-	.	gene_id "HML2_11q12.3b"; transcript_id "HML2_11q12.3b"; locus "HML2_11q12.3b"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0087"; repClass "LTR"; repEnd "891"; repFamily "ERVK"; repLeft "-33"; repStart "-77";
+### HML2_11q22.1 ###								
+chr11	rmsk	gene	101695063	101704528	.	+	.	gene_id "HML2_11q22.1"; transcript_id "HML2_11q22.1"; locus "HML2_11q22.1"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0091"; model_cov "7439"; model_pct "98.7";
+chr11	rmsk	exon	101695063	101696030	8870	+	.	gene_id "HML2_11q22.1"; transcript_id "HML2_11q22.1"; locus "HML2_11q22.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0091"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr11	rmsk	exon	101696031	101699581	62466	+	.	gene_id "HML2_11q22.1"; transcript_id "HML2_11q22.1"; locus "HML2_11q22.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0091"; repClass "LTR"; repEnd "3583"; repFamily "ERVK"; repLeft "-3953"; repStart "1";
+chr11	rmsk	exon	101699645	101703465	62466	+	.	gene_id "HML2_11q22.1"; transcript_id "HML2_11q22.1"; locus "HML2_11q22.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0091"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "-95"; repStart "3584";
+chr11	rmsk	exon	101703561	101704528	8897	+	.	gene_id "HML2_11q22.1"; transcript_id "HML2_11q22.1"; locus "HML2_11q22.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0091"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_11q23.3 ###								
+chr11	rmsk	gene	118721015	118730174	.	-	.	gene_id "HML2_11q23.3"; transcript_id "HML2_11q23.3"; locus "HML2_11q23.3"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0092"; model_cov "7243"; model_pct "96.1";
+chr11	rmsk	exon	118721015	118721981	8482	-	.	gene_id "HML2_11q23.3"; transcript_id "HML2_11q23.3"; locus "HML2_11q23.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0092"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr11	rmsk	exon	118721982	118723687	14138	-	.	gene_id "HML2_11q23.3"; transcript_id "HML2_11q23.3"; locus "HML2_11q23.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0092"; repClass "LTR"; repEnd "7536"; repFamily "ERVK"; repLeft "5826"; repStart "0";
+chr11	rmsk	exon	118723687	118729206	48710	-	.	gene_id "HML2_11q23.3"; transcript_id "HML2_11q23.3"; locus "HML2_11q23.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0092"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "1"; repStart "-2002";
+chr11	rmsk	exon	118729207	118730174	8460	-	.	gene_id "HML2_11q23.3"; transcript_id "HML2_11q23.3"; locus "HML2_11q23.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0092"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_12p11.1 ###								
+chr12	rmsk	gene	34619620	34629282	.	-	.	gene_id "HML2_12p11.1"; transcript_id "HML2_12p11.1"; locus "HML2_12p11.1"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0093"; model_cov "7199"; model_pct "95.5";
+chr12	rmsk	exon	34619620	34620533	4503	-	.	gene_id "HML2_12p11.1"; transcript_id "HML2_12p11.1"; locus "HML2_12p11.1"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0093"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr12	rmsk	exon	34620629	34621290	5119	-	.	gene_id "HML2_12p11.1"; transcript_id "HML2_12p11.1"; locus "HML2_12p11.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0093"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "6780"; repStart "-95";
+chr12	rmsk	exon	34621720	34627344	41180	-	.	gene_id "HML2_12p11.1"; transcript_id "HML2_12p11.1"; locus "HML2_12p11.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0093"; repClass "LTR"; repEnd "6777"; repFamily "ERVK"; repLeft "1130"; repStart "-759";
+chr12	rmsk	exon	34627339	34627473	876	-	.	gene_id "HML2_12p11.1"; transcript_id "HML2_12p11.1"; locus "HML2_12p11.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0093"; repClass "LTR"; repEnd "877"; repFamily "ERVK"; repLeft "743"; repStart "-6659";
+chr12	rmsk	exon	34627553	34628301	4435	-	.	gene_id "HML2_12p11.1"; transcript_id "HML2_12p11.1"; locus "HML2_12p11.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0093"; repClass "LTR"; repEnd "758"; repFamily "ERVK"; repLeft "1"; repStart "-6778";
+chr12	rmsk	exon	34628302	34629282	5536	-	.	gene_id "HML2_12p11.1"; transcript_id "HML2_12p11.1"; locus "HML2_12p11.1"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0093"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "6"; repStart "0";
+### HML2_12q14.1 ###								
+chr12	rmsk	gene	58327459	58336915	.	-	.	gene_id "HML2_12q14.1"; transcript_id "HML2_12q14.1"; locus "HML2_12q14.1"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0094"; model_cov "7440"; model_pct "98.7";
+chr12	rmsk	exon	58327459	58328426	8871	-	.	gene_id "HML2_12q14.1"; transcript_id "HML2_12q14.1"; locus "HML2_12q14.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0094"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr12	rmsk	exon	58328522	58335947	49293	-	.	gene_id "HML2_12q14.1"; transcript_id "HML2_12q14.1"; locus "HML2_12q14.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0094"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "1"; repStart "-95";
+chr12	rmsk	exon	58335948	58336915	8873	-	.	gene_id "HML2_12q14.1"; transcript_id "HML2_12q14.1"; locus "HML2_12q14.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0094"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_12q24.33 ###								
+chr12	rmsk	gene	133090536	133096478	.	-	.	gene_id "HML2_12q24.33"; transcript_id "HML2_12q24.33"; locus "HML2_12q24.33"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0097"; model_cov "2905"; model_pct "38.5";
+chr12	rmsk	exon	133090536	133091545	8594	-	.	gene_id "HML2_12q24.33"; transcript_id "HML2_12q24.33"; locus "HML2_12q24.33"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0097"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr12	rmsk	exon	133091560	133093500	12073	-	.	gene_id "HML2_12q24.33"; transcript_id "HML2_12q24.33"; locus "HML2_12q24.33"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0097"; repClass "LTR"; repEnd "7522"; repFamily "ERVK"; repLeft "5587"; repStart "-14";
+chr12	rmsk	exon	133093506	133093784	2003	-	.	gene_id "HML2_12q24.33"; transcript_id "HML2_12q24.33"; locus "HML2_12q24.33"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0097"; repClass "LTR"; repEnd "5462"; repFamily "ERVK"; repLeft "5187"; repStart "-2074";
+chr12	rmsk	exon	133093979	133095471	4356	-	.	gene_id "HML2_12q24.33"; transcript_id "HML2_12q24.33"; locus "HML2_12q24.33"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0097"; repClass "LTR"; repEnd "696"; repFamily "ERVK"; repLeft "1"; repStart "-6840";
+chr12	rmsk	exon	133095472	133096478	8541	-	.	gene_id "HML2_12q24.33"; transcript_id "HML2_12q24.33"; locus "HML2_12q24.33"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0097"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_14q11.2 ###								
+chr14	rmsk	gene	24009696	24015776	.	-	.	gene_id "HML2_14q11.2"; transcript_id "HML2_14q11.2"; locus "HML2_14q11.2"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0099"; model_cov "3838"; model_pct "50.9";
+chr14	rmsk	exon	24009696	24010720	8164	-	.	gene_id "HML2_14q11.2"; transcript_id "HML2_14q11.2"; locus "HML2_14q11.2"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0099"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr14	rmsk	exon	24010723	24010906	1116	-	.	gene_id "HML2_14q11.2"; transcript_id "HML2_14q11.2"; locus "HML2_14q11.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0099"; repClass "LTR"; repEnd "7534"; repFamily "ERVK"; repLeft "7351"; repStart "-2";
+chr14	rmsk	exon	24011391	24015051	21036	-	.	gene_id "HML2_14q11.2"; transcript_id "HML2_14q11.2"; locus "HML2_14q11.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0099"; repClass "LTR"; repEnd "3656"; repFamily "ERVK"; repLeft "1"; repStart "-3880";
+chr14	rmsk	exon	24015052	24015776	5820	-	.	gene_id "HML2_14q11.2"; transcript_id "HML2_14q11.2"; locus "HML2_14q11.2"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0099"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "308"; repStart "0";
+### HML2_14q32.33 ###								
+chr14	rmsk	gene	105673313	105676203	.	+	.	gene_id "HML2_14q32.33"; transcript_id "HML2_14q32.33"; locus "HML2_14q32.33"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0100"; model_cov "1886"; model_pct "25.0";
+chr14	rmsk	exon	105673313	105675001	11016	+	.	gene_id "HML2_14q32.33"; transcript_id "HML2_14q32.33"; locus "HML2_14q32.33"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0100"; repClass "LTR"; repEnd "5462"; repFamily "ERVK"; repLeft "-2074"; repStart "3766";
+chr14	rmsk	exon	105675007	105675106	414	+	.	gene_id "HML2_14q32.33"; transcript_id "HML2_14q32.33"; locus "HML2_14q32.33"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0100"; repClass "LTR"; repEnd "5686"; repFamily "ERVK"; repLeft "-1850"; repStart "5587";
+chr14	rmsk	exon	105675105	105675196	575	+	.	gene_id "HML2_14q32.33"; transcript_id "HML2_14q32.33"; locus "HML2_14q32.33"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0100"; repClass "LTR"; repEnd "7532"; repFamily "ERVK"; repLeft "-4"; repStart "7441";
+chr14	rmsk	exon	105675200	105676203	8253	+	.	gene_id "HML2_14q32.33"; transcript_id "HML2_14q32.33"; locus "HML2_14q32.33"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0100"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_15q25.2 ###								
+chr15	rmsk	gene	84160268	84163612	.	+	.	gene_id "HML2_15q25.2"; transcript_id "HML2_15q25.2"; locus "HML2_15q25.2"; category "internal"; intModel "HERVK-int"; locid "HERVK-int_0101"; model_cov "3522"; model_pct "46.7";
+chr15	rmsk	exon	84160268	84163612	11857	+	.	gene_id "HML2_15q25.2"; transcript_id "HML2_15q25.2"; locus "HML2_15q25.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0101"; repClass "LTR"; repEnd "6330"; repFamily "ERVK"; repLeft "-1206"; repStart "2808";
+### HML2_16p11.2a ###								
+chr16	rmsk	gene	34412057	34414804	.	-	.	gene_id "HML2_16p11.2a"; transcript_id "HML2_16p11.2a"; locus "HML2_16p11.2a"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0104"; model_cov "1692"; model_pct "22.5";
+chr16	rmsk	exon	34412057	34413016	8716	-	.	gene_id "HML2_16p11.2a"; transcript_id "HML2_16p11.2a"; locus "HML2_16p11.2a"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0104"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr16	rmsk	exon	34413112	34414727	14823	-	.	gene_id "HML2_16p11.2a"; transcript_id "HML2_16p11.2a"; locus "HML2_16p11.2a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0104"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "5826"; repStart "-95";
+chr16	rmsk	exon	34414727	34414804	602	-	.	gene_id "HML2_16p11.2a"; transcript_id "HML2_16p11.2a"; locus "HML2_16p11.2a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0104"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "5457"; repStart "-2002";
+### HML2_16p11.2b ###								
+chr16	rmsk	gene	34997026	34999771	.	+	.	gene_id "HML2_16p11.2b"; transcript_id "HML2_16p11.2b"; locus "HML2_16p11.2b"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0105"; model_cov "1692"; model_pct "22.5";
+chr16	rmsk	exon	34997026	34997103	600	+	.	gene_id "HML2_16p11.2b"; transcript_id "HML2_16p11.2b"; locus "HML2_16p11.2b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0105"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "-2002"; repStart "5457";
+chr16	rmsk	exon	34997103	34998718	14851	+	.	gene_id "HML2_16p11.2b"; transcript_id "HML2_16p11.2b"; locus "HML2_16p11.2b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0105"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "-95"; repStart "5826";
+chr16	rmsk	exon	34998814	34999771	9064	+	.	gene_id "HML2_16p11.2b"; transcript_id "HML2_16p11.2b"; locus "HML2_16p11.2b"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0105"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_17p13.1 ###								
+chr17	rmsk	gene	8056337	8063901	.	+	.	gene_id "HML2_17p13.1"; transcript_id "HML2_17p13.1"; locus "HML2_17p13.1"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0107"; model_cov "6060"; model_pct "80.4";
+chr17	rmsk	exon	8056337	8056551	407	+	.	gene_id "HML2_17p13.1"; transcript_id "HML2_17p13.1"; locus "HML2_17p13.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0107"; repClass "LTR"; repEnd "510"; repFamily "ERVK"; repLeft "-458"; repStart "279";
+chr17	rmsk	exon	8057039	8057470	1171	+	.	gene_id "HML2_17p13.1"; transcript_id "HML2_17p13.1"; locus "HML2_17p13.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0107"; repClass "LTR"; repEnd "442"; repFamily "ERVK"; repLeft "-7094"; repStart "1";
+chr17	rmsk	exon	8057909	8058482	11977	+	.	gene_id "HML2_17p13.1"; transcript_id "HML2_17p13.1"; locus "HML2_17p13.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0107"; repClass "LTR"; repEnd "1551"; repFamily "ERVK"; repLeft "-5985"; repStart "966";
+chr17	rmsk	exon	8058796	8061901	11977	+	.	gene_id "HML2_17p13.1"; transcript_id "HML2_17p13.1"; locus "HML2_17p13.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0107"; repClass "LTR"; repEnd "4676"; repFamily "ERVK"; repLeft "-2860"; repStart "1552";
+chr17	rmsk	exon	8062292	8063901	2161	+	.	gene_id "HML2_17p13.1"; transcript_id "HML2_17p13.1"; locus "HML2_17p13.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0107"; repClass "LTR"; repEnd "6588"; repFamily "ERVK"; repLeft "-948"; repStart "4678";
+### HML2_19p13.3 ###								
+chr19	rmsk	gene	385095	387637	.	+	.	gene_id "HML2_19p13.3"; transcript_id "HML2_19p13.3"; locus "HML2_19p13.3"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0109"; model_cov "1491"; model_pct "19.8";
+chr19	rmsk	exon	385095	386584	12032	+	.	gene_id "HML2_19p13.3"; transcript_id "HML2_19p13.3"; locus "HML2_19p13.3"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0109"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "-95"; repStart "5950";
+chr19	rmsk	exon	386680	387637	8361	+	.	gene_id "HML2_19p13.3"; transcript_id "HML2_19p13.3"; locus "HML2_19p13.3"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0109"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_19p12a ###								
+chr19	rmsk	gene	20276591	20286703	.	+	.	gene_id "HML2_19p12a"; transcript_id "HML2_19p12a"; locus "HML2_19p12a"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0110"; model_cov "7444"; model_pct "98.8";
+chr19	rmsk	exon	20276591	20277574	6327	+	.	gene_id "HML2_19p12a"; transcript_id "HML2_19p12a"; locus "HML2_19p12a"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0110"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr19	rmsk	exon	20277575	20278301	5156	+	.	gene_id "HML2_19p12a"; transcript_id "HML2_19p12a"; locus "HML2_19p12a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0110"; repClass "LTR"; repEnd "746"; repFamily "ERVK"; repLeft "-6790"; repStart "1";
+chr19	rmsk	exon	20278394	20282633	41844	+	.	gene_id "HML2_19p12a"; transcript_id "HML2_19p12a"; locus "HML2_19p12a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0110"; repClass "LTR"; repEnd "4994"; repFamily "ERVK"; repLeft "-2542"; repStart "743";
+chr19	rmsk	exon	20282931	20284402	41844	+	.	gene_id "HML2_19p12a"; transcript_id "HML2_19p12a"; locus "HML2_19p12a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0110"; repClass "LTR"; repEnd "6447"; repFamily "ERVK"; repLeft "-1089"; repStart "4995";
+chr19	rmsk	exon	20284741	20285656	3635	+	.	gene_id "HML2_19p12a"; transcript_id "HML2_19p12a"; locus "HML2_19p12a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0110"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "-95"; repStart "6445";
+chr19	rmsk	exon	20285752	20286703	5747	+	.	gene_id "HML2_19p12a"; transcript_id "HML2_19p12a"; locus "HML2_19p12a"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0110"; repClass "LTR"; repEnd "965"; repFamily "ERVK"; repLeft "-3"; repStart "1";
+### HML2_19p12b ###								
+chr19	rmsk	gene	22575022	22581759	.	+	.	gene_id "HML2_19p12b"; transcript_id "HML2_19p12b"; locus "HML2_19p12b"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0111"; model_cov "4920"; model_pct "65.3";
+chr19	rmsk	exon	22575022	22575897	6995	+	.	gene_id "HML2_19p12b"; transcript_id "HML2_19p12b"; locus "HML2_19p12b"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0111"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "83";
+chr19	rmsk	exon	22575898	22578608	22553	+	.	gene_id "HML2_19p12b"; transcript_id "HML2_19p12b"; locus "HML2_19p12b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0111"; repClass "LTR"; repEnd "2716"; repFamily "ERVK"; repLeft "-4820"; repStart "1";
+chr19	rmsk	exon	22578587	22579173	4900	+	.	gene_id "HML2_19p12b"; transcript_id "HML2_19p12b"; locus "HML2_19p12b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0111"; repClass "LTR"; repEnd "5536"; repFamily "ERVK"; repLeft "-2000"; repStart "4952";
+chr19	rmsk	exon	22579171	22580702	8329	+	.	gene_id "HML2_19p12b"; transcript_id "HML2_19p12b"; locus "HML2_19p12b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0111"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "-89"; repStart "5826";
+chr19	rmsk	exon	22580792	22581759	7910	+	.	gene_id "HML2_19p12b"; transcript_id "HML2_19p12b"; locus "HML2_19p12b"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0111"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_19q11 ###								
+chr19	rmsk	gene	27637590	27646453	.	-	.	gene_id "HML2_19q11"; transcript_id "HML2_19q11"; locus "HML2_19q11"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0112"; model_cov "7438"; model_pct "98.7";
+chr19	rmsk	exon	27637590	27638584	8676	-	.	gene_id "HML2_19q11"; transcript_id "HML2_19q11"; locus "HML2_19q11"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0112"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr19	rmsk	exon	27638680	27641547	63870	-	.	gene_id "HML2_19q11"; transcript_id "HML2_19q11"; locus "HML2_19q11"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0112"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "4584"; repStart "-95";
+chr19	rmsk	exon	27641861	27646453	63870	-	.	gene_id "HML2_19q11"; transcript_id "HML2_19q11"; locus "HML2_19q11"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0112"; repClass "LTR"; repEnd "4583"; repFamily "ERVK"; repLeft "2"; repStart "-2953";
+### HML2_19q13.12a ###								
+chr19	rmsk	gene	35572527	35576532	.	-	.	gene_id "HML2_19q13.12a"; transcript_id "HML2_19q13.12a"; locus "HML2_19q13.12a"; category "internal"; intModel "HERVK-int"; locid "HERVK-int_0113"; model_cov "3681"; model_pct "48.8";
+chr19	rmsk	exon	35572527	35575603	24890	-	.	gene_id "HML2_19q13.12a"; transcript_id "HML2_19q13.12a"; locus "HML2_19q13.12a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0113"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "4362"; repStart "-89";
+chr19	rmsk	exon	35575937	35576532	4594	-	.	gene_id "HML2_19q13.12a"; transcript_id "HML2_19q13.12a"; locus "HML2_19q13.12a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0113"; repClass "LTR"; repEnd "2957"; repFamily "ERVK"; repLeft "2361"; repStart "-4579";
+### HML2_19q13.12b ###								
+chr19	rmsk	gene	37106647	37116164	.	-	.	gene_id "HML2_19q13.12b"; transcript_id "HML2_19q13.12b"; locus "HML2_19q13.12b"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0114"; model_cov "7454"; model_pct "98.9";
+chr19	rmsk	exon	37106647	37107600	5785	-	.	gene_id "HML2_19q13.12b"; transcript_id "HML2_19q13.12b"; locus "HML2_19q13.12b"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0114"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "5"; repStart "0";
+chr19	rmsk	exon	37107697	37114371	40845	-	.	gene_id "HML2_19q13.12b"; transcript_id "HML2_19q13.12b"; locus "HML2_19q13.12b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0114"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "744"; repStart "-95";
+chr19	rmsk	exon	37114452	37115196	5138	-	.	gene_id "HML2_19q13.12b"; transcript_id "HML2_19q13.12b"; locus "HML2_19q13.12b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0114"; repClass "LTR"; repEnd "758"; repFamily "ERVK"; repLeft "1"; repStart "-6778";
+chr19	rmsk	exon	37115197	37116164	6571	-	.	gene_id "HML2_19q13.12b"; transcript_id "HML2_19q13.12b"; locus "HML2_19q13.12b"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0114"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_19q13.41a ###								
+chr19	rmsk	gene	52745023	52748339	.	-	.	gene_id "HML2_19q13.41a"; transcript_id "HML2_19q13.41a"; locus "HML2_19q13.41a"; category "internal"; intModel "HERVK-int"; locid "HERVK-int_0115"; model_cov "5405"; model_pct "71.7";
+chr19	rmsk	exon	52745023	52748339	26124	-	.	gene_id "HML2_19q13.41a"; transcript_id "HML2_19q13.41a"; locus "HML2_19q13.41a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0115"; repClass "LTR"; repEnd "6681"; repFamily "ERVK"; repLeft "1276"; repStart "-855";
+### HML2_19q13.41b ###								
+chr19	rmsk	gene	52748422	52750454	.	-	.	gene_id "HML2_19q13.41b"; transcript_id "HML2_19q13.41b"; locus "HML2_19q13.41b"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0116"; model_cov "1362"; model_pct "18.1";
+chr19	rmsk	exon	52748422	52748830	26124	-	.	gene_id "HML2_19q13.41b"; transcript_id "HML2_19q13.41b"; locus "HML2_19q13.41b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0116"; repClass "LTR"; repEnd "6681"; repFamily "ERVK"; repLeft "6013"; repStart "-855";
+chr19	rmsk	exon	52748809	52749491	4464	-	.	gene_id "HML2_19q13.41b"; transcript_id "HML2_19q13.41b"; locus "HML2_19q13.41b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0116"; repClass "LTR"; repEnd "696"; repFamily "ERVK"; repLeft "2"; repStart "-6840";
+chr19	rmsk	exon	52749493	52750454	5671	-	.	gene_id "HML2_19q13.41b"; transcript_id "HML2_19q13.41b"; locus "HML2_19q13.41b"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0116"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "5"; repStart "0";
+### HML2_19q13.42 ###								
+chr19	rmsk	gene	53359095	53364791	.	+	.	gene_id "HML2_19q13.42"; transcript_id "HML2_19q13.42"; locus "HML2_19q13.42"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0117"; model_cov "3616"; model_pct "48.0";
+chr19	rmsk	exon	53359095	53360013	28625	+	.	gene_id "HML2_19q13.42"; transcript_id "HML2_19q13.42"; locus "HML2_19q13.42"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0117"; repClass "LTR"; repEnd "4740"; repFamily "ERVK"; repLeft "-2796"; repStart "3824";
+chr19	rmsk	exon	53361020	53363705	28625	+	.	gene_id "HML2_19q13.42"; transcript_id "HML2_19q13.42"; locus "HML2_19q13.42"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0117"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "-95"; repStart "4741";
+chr19	rmsk	exon	53363801	53364791	6549	+	.	gene_id "HML2_19q13.42"; transcript_id "HML2_19q13.42"; locus "HML2_19q13.42"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0117"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_20q11.22 ###								
+chr20	rmsk	gene	34127754	34136578	.	+	.	gene_id "HML2_20q11.22"; transcript_id "HML2_20q11.22"; locus "HML2_20q11.22"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0120"; model_cov "4785"; model_pct "63.5";
+chr20	rmsk	exon	34127754	34128531	5764	+	.	gene_id "HML2_20q11.22"; transcript_id "HML2_20q11.22"; locus "HML2_20q11.22"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0120"; repClass "LTR"; repEnd "1001"; repFamily "ERVK"; repLeft "-1"; repStart "220";
+chr20	rmsk	exon	34128532	34129076	4425	+	.	gene_id "HML2_20q11.22"; transcript_id "HML2_20q11.22"; locus "HML2_20q11.22"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0120"; repClass "LTR"; repEnd "556"; repFamily "ERVK"; repLeft "-6980"; repStart "1";
+chr20	rmsk	exon	34129382	34129595	4425	+	.	gene_id "HML2_20q11.22"; transcript_id "HML2_20q11.22"; locus "HML2_20q11.22"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0120"; repClass "LTR"; repEnd "758"; repFamily "ERVK"; repLeft "-6778"; repStart "557";
+chr20	rmsk	exon	34129673	34130246	3702	+	.	gene_id "HML2_20q11.22"; transcript_id "HML2_20q11.22"; locus "HML2_20q11.22"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0120"; repClass "LTR"; repEnd "1325"; repFamily "ERVK"; repLeft "-6211"; repStart "743";
+chr20	rmsk	exon	34130235	34131782	12082	+	.	gene_id "HML2_20q11.22"; transcript_id "HML2_20q11.22"; locus "HML2_20q11.22"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0120"; repClass "LTR"; repEnd "5190"; repFamily "ERVK"; repLeft "-2346"; repStart "3636";
+chr20	rmsk	exon	34133703	34135592	14111	+	.	gene_id "HML2_20q11.22"; transcript_id "HML2_20q11.22"; locus "HML2_20q11.22"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0120"; repClass "LTR"; repEnd "7535"; repFamily "ERVK"; repLeft "-1"; repStart "5642";
+chr20	rmsk	exon	34135594	34136578	5656	+	.	gene_id "HML2_20q11.22"; transcript_id "HML2_20q11.22"; locus "HML2_20q11.22"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0120"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_21q21.1 ###								
+chr21	rmsk	gene	18561341	18569644	.	-	.	gene_id "HML2_21q21.1"; transcript_id "HML2_21q21.1"; locus "HML2_21q21.1"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0121"; model_cov "6986"; model_pct "92.7";
+chr21	rmsk	exon	18561341	18561597	2222	-	.	gene_id "HML2_21q21.1"; transcript_id "HML2_21q21.1"; locus "HML2_21q21.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0121"; repClass "LTR"; repEnd "257"; repFamily "ERVK"; repLeft "1"; repStart "-711";
+chr21	rmsk	exon	18561693	18563304	14060	-	.	gene_id "HML2_21q21.1"; transcript_id "HML2_21q21.1"; locus "HML2_21q21.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0121"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "5826"; repStart "-95";
+chr21	rmsk	exon	18563304	18568678	45482	-	.	gene_id "HML2_21q21.1"; transcript_id "HML2_21q21.1"; locus "HML2_21q21.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0121"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "163"; repStart "-2002";
+chr21	rmsk	exon	18568679	18569644	8533	-	.	gene_id "HML2_21q21.1"; transcript_id "HML2_21q21.1"; locus "HML2_21q21.1"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0121"; repClass "LTR"; repEnd "966"; repFamily "ERVK"; repLeft "1"; repStart "-2";
+### HML2_22q11.21 ###								
+chr22	rmsk	gene	18938674	18947848	.	+	.	gene_id "HML2_22q11.21"; transcript_id "HML2_22q11.21"; locus "HML2_22q11.21"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0122"; model_cov "7154"; model_pct "94.9";
+chr22	rmsk	exon	18938674	18939641	9026	+	.	gene_id "HML2_22q11.21"; transcript_id "HML2_22q11.21"; locus "HML2_22q11.21"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0122"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr22	rmsk	exon	18939642	18945174	43432	+	.	gene_id "HML2_22q11.21"; transcript_id "HML2_22q11.21"; locus "HML2_22q11.21"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0122"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "-2002"; repStart "1";
+chr22	rmsk	exon	18945174	18946795	13254	+	.	gene_id "HML2_22q11.21"; transcript_id "HML2_22q11.21"; locus "HML2_22q11.21"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0122"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "-89"; repStart "5826";
+chr22	rmsk	exon	18946885	18947848	8954	+	.	gene_id "HML2_22q11.21"; transcript_id "HML2_22q11.21"; locus "HML2_22q11.21"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0122"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_22q11.23 ###								
+chr22	rmsk	gene	23536062	23546900	.	+	.	gene_id "HML2_22q11.23"; transcript_id "HML2_22q11.23"; locus "HML2_22q11.23"; category "unknown"; intModel "HERVK-int"; locid "HERVK-int_0123"; model_cov "7693"; model_pct "100.0";
+chr22	rmsk	exon	23536062	23537026	6743	+	.	gene_id "HML2_22q11.23"; transcript_id "HML2_22q11.23"; locus "HML2_22q11.23"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0123"; repClass "LTR"; repEnd "964"; repFamily "ERVK"; repLeft "-4"; repStart "1";
+chr22	rmsk	exon	23537028	23537189	1108	+	.	gene_id "HML2_22q11.23"; transcript_id "HML2_22q11.23"; locus "HML2_22q11.23"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0123"; repClass "LTR"; repEnd "163"; repFamily "ERVK"; repLeft "-7373"; repStart "1";
+chr22	rmsk	exon	23537190	23537250	437	+	.	gene_id "HML2_22q11.23"; transcript_id "HML2_22q11.23"; locus "HML2_22q11.23"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0123"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "942";
+chr22	rmsk	exon	23537740	23538729	7295	+	.	gene_id "HML2_22q11.23"; transcript_id "HML2_22q11.23"; locus "HML2_22q11.23"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0123"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr22	rmsk	exon	23538730	23546008	30409	+	.	gene_id "HML2_22q11.23"; transcript_id "HML2_22q11.23"; locus "HML2_22q11.23"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0123"; repClass "LTR"; repEnd "7267"; repFamily "ERVK"; repLeft "-269"; repStart "1";
+chr22	rmsk	exon	23546306	23546576	30409	+	.	gene_id "HML2_22q11.23"; transcript_id "HML2_22q11.23"; locus "HML2_22q11.23"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0123"; repClass "LTR"; repEnd "7533"; repFamily "ERVK"; repLeft "-3"; repStart "7268";
+chr22	rmsk	exon	23546582	23546900	2050	+	.	gene_id "HML2_22q11.23"; transcript_id "HML2_22q11.23"; locus "HML2_22q11.23"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0123"; repClass "LTR"; repEnd "331"; repFamily "ERVK"; repLeft "-671"; repStart "1";
+### HML2_Xq11.1 ###								
+chrX	rmsk	gene	62740079	62742584	.	+	.	gene_id "HML2_Xq11.1"; transcript_id "HML2_Xq11.1"; locus "HML2_Xq11.1"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0125"; model_cov "2423"; model_pct "32.2";
+chrX	rmsk	exon	62740079	62740554	2893	+	.	gene_id "HML2_Xq11.1"; transcript_id "HML2_Xq11.1"; locus "HML2_Xq11.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0125"; repClass "LTR"; repEnd "5462"; repFamily "ERVK"; repLeft "-2074"; repStart "4986";
+chrX	rmsk	exon	62740560	62742508	10851	+	.	gene_id "HML2_Xq11.1"; transcript_id "HML2_Xq11.1"; locus "HML2_Xq11.1"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0125"; repClass "LTR"; repEnd "7534"; repFamily "ERVK"; repLeft "-2"; repStart "5587";
+chrX	rmsk	exon	62742511	62742584	630	+	.	gene_id "HML2_Xq11.1"; transcript_id "HML2_Xq11.1"; locus "HML2_Xq11.1"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0125"; repClass "LTR"; repEnd "74"; repFamily "ERVK"; repLeft "-928"; repStart "1";
+### HML2_Xq12 ###								
+chrX	rmsk	gene	66464290	66466342	.	-	.	gene_id "HML2_Xq12"; transcript_id "HML2_Xq12"; locus "HML2_Xq12"; category "internal"; intModel "HERVK-int"; locid "HERVK-int_0126"; model_cov "2058"; model_pct "27.3";
+chrX	rmsk	exon	66464290	66466342	13660	-	.	gene_id "HML2_Xq12"; transcript_id "HML2_Xq12"; locus "HML2_Xq12"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0126"; repClass "LTR"; repEnd "5139"; repFamily "ERVK"; repLeft "3081"; repStart "-2397";
+### HML2_Xq28a ###								
+chrX	rmsk	gene	154588662	154591282	.	+	.	gene_id "HML2_Xq28a"; transcript_id "HML2_Xq28a"; locus "HML2_Xq28a"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0127"; model_cov "805"; model_pct "10.7";
+chrX	rmsk	exon	154588662	154589649	8253	+	.	gene_id "HML2_Xq28a"; transcript_id "HML2_Xq28a"; locus "HML2_Xq28a"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0127"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chrX	rmsk	exon	154589650	154591282	4975	+	.	gene_id "HML2_Xq28a"; transcript_id "HML2_Xq28a"; locus "HML2_Xq28a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0127"; repClass "LTR"; repEnd "3812"; repFamily "ERVK"; repLeft "-3724"; repStart "3007";
+### HML2_Xq28b ###								
+chrX	rmsk	gene	154608423	154615762	.	-	.	gene_id "HML2_Xq28b"; transcript_id "HML2_Xq28b"; locus "HML2_Xq28b"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0128"; model_cov "7445"; model_pct "98.8";
+chrX	rmsk	exon	154608423	154609415	8174	-	.	gene_id "HML2_Xq28b"; transcript_id "HML2_Xq28b"; locus "HML2_Xq28b"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0128"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chrX	rmsk	exon	154609505	154614774	22434	-	.	gene_id "HML2_Xq28b"; transcript_id "HML2_Xq28b"; locus "HML2_Xq28b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0128"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "2"; repStart "-89";
+chrX	rmsk	exon	154614775	154615762	8243	-	.	gene_id "HML2_Xq28b"; transcript_id "HML2_Xq28b"; locus "HML2_Xq28b"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0128"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_Yp11.2 ###								
+chrY	rmsk	gene	6958400	6965343	.	-	.	gene_id "HML2_Yp11.2"; transcript_id "HML2_Yp11.2"; locus "HML2_Yp11.2"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0129"; model_cov "5908"; model_pct "78.4";
+chrY	rmsk	exon	6958400	6959413	7973	-	.	gene_id "HML2_Yp11.2"; transcript_id "HML2_Yp11.2"; locus "HML2_Yp11.2"; repName "LTR5A"; geneRegion "ltr"; locid "HERVK-int_0129"; repClass "LTR"; repEnd "1033"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chrY	rmsk	exon	6959419	6963041	24065	-	.	gene_id "HML2_Yp11.2"; transcript_id "HML2_Yp11.2"; locus "HML2_Yp11.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0129"; repClass "LTR"; repEnd "7531"; repFamily "ERVK"; repLeft "3912"; repStart "-5";
+chrY	rmsk	exon	6963034	6965343	11787	-	.	gene_id "HML2_Yp11.2"; transcript_id "HML2_Yp11.2"; locus "HML2_Yp11.2"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0129"; repClass "LTR"; repEnd "2820"; repFamily "ERVK"; repLeft "531"; repStart "-4716";
+### HML2_Yq11.23a ###								
+chrY	rmsk	gene	24251690	24254888	.	-	.	gene_id "HML2_Yq11.23a"; transcript_id "HML2_Yq11.23a"; locus "HML2_Yq11.23a"; category "internal"; intModel "HERVK-int"; locid "HERVK-int_0130"; model_cov "3385"; model_pct "44.9";
+chrY	rmsk	exon	24251690	24254888	11436	-	.	gene_id "HML2_Yq11.23a"; transcript_id "HML2_Yq11.23a"; locus "HML2_Yq11.23a"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0130"; repClass "LTR"; repEnd "6193"; repFamily "ERVK"; repLeft "2808"; repStart "-1343";
+### HML2_Yq11.23b ###								
+chrY	rmsk	gene	25415255	25418454	.	+	.	gene_id "HML2_Yq11.23b"; transcript_id "HML2_Yq11.23b"; locus "HML2_Yq11.23b"; category "internal"; intModel "HERVK-int"; locid "HERVK-int_0131"; model_cov "3385"; model_pct "44.9";
+chrY	rmsk	exon	25415255	25418454	11433	+	.	gene_id "HML2_Yq11.23b"; transcript_id "HML2_Yq11.23b"; locus "HML2_Yq11.23b"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0131"; repClass "LTR"; repEnd "6193"; repFamily "ERVK"; repLeft "-1343"; repStart "2808";
+### HML2_1_KI270766v1_alt ###								
+chr1_KI270766v1_alt	rmsk	gene	150436	159977	.	+	.	gene_id "HML2_1_KI270766v1_alt"; transcript_id "HML2_1_KI270766v1_alt"; locus "HML2_1_KI270766v1_alt"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0132"; model_cov "7448"; model_pct "98.8";
+chr1_KI270766v1_alt	rmsk	exon	150436	151426	7851	+	.	gene_id "HML2_1_KI270766v1_alt"; transcript_id "HML2_1_KI270766v1_alt"; locus "HML2_1_KI270766v1_alt"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0132"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr1_KI270766v1_alt	rmsk	exon	151428	152160	4512	+	.	gene_id "HML2_1_KI270766v1_alt"; transcript_id "HML2_1_KI270766v1_alt"; locus "HML2_1_KI270766v1_alt"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0132"; repClass "LTR"; repEnd "746"; repFamily "ERVK"; repLeft "-6790"; repStart "2";
+chr1_KI270766v1_alt	rmsk	exon	152253	158890	20253	+	.	gene_id "HML2_1_KI270766v1_alt"; transcript_id "HML2_1_KI270766v1_alt"; locus "HML2_1_KI270766v1_alt"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0132"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "-89"; repStart "743";
+chr1_KI270766v1_alt	rmsk	exon	158980	159977	8041	+	.	gene_id "HML2_1_KI270766v1_alt"; transcript_id "HML2_1_KI270766v1_alt"; locus "HML2_1_KI270766v1_alt"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0132"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_6_GL000251v2_alt ###								
+chr6_GL000251v2_alt	rmsk	gene	172412	182779	.	+	.	gene_id "HML2_6_GL000251v2_alt"; transcript_id "HML2_6_GL000251v2_alt"; locus "HML2_6_GL000251v2_alt"; category "unknown"; intModel "HERVK-int"; locid "HERVK-int_0134"; model_cov "7558"; model_pct "100.0";
+chr6_GL000251v2_alt	rmsk	exon	172412	173229	3560	+	.	gene_id "HML2_6_GL000251v2_alt"; transcript_id "HML2_6_GL000251v2_alt"; locus "HML2_6_GL000251v2_alt"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0134"; repClass "LTR"; repEnd "965"; repFamily "ERVK"; repLeft "-3"; repStart "189";
+chr6_GL000251v2_alt	rmsk	exon	173233	173967	4885	+	.	gene_id "HML2_6_GL000251v2_alt"; transcript_id "HML2_6_GL000251v2_alt"; locus "HML2_6_GL000251v2_alt"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0134"; repClass "LTR"; repEnd "746"; repFamily "ERVK"; repLeft "-6790"; repStart "1";
+chr6_GL000251v2_alt	rmsk	exon	174045	177202	50015	+	.	gene_id "HML2_6_GL000251v2_alt"; transcript_id "HML2_6_GL000251v2_alt"; locus "HML2_6_GL000251v2_alt"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0134"; repClass "LTR"; repEnd "3909"; repFamily "ERVK"; repLeft "-3627"; repStart "722";
+chr6_GL000251v2_alt	rmsk	exon	177203	178177	5650	+	.	gene_id "HML2_6_GL000251v2_alt"; transcript_id "HML2_6_GL000251v2_alt"; locus "HML2_6_GL000251v2_alt"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0134"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+chr6_GL000251v2_alt	rmsk	exon	178178	181831	50015	+	.	gene_id "HML2_6_GL000251v2_alt"; transcript_id "HML2_6_GL000251v2_alt"; locus "HML2_6_GL000251v2_alt"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0134"; repClass "LTR"; repEnd "7536"; repFamily "ERVK"; repLeft "0"; repStart "3910";
+chr6_GL000251v2_alt	rmsk	exon	181832	182779	5423	+	.	gene_id "HML2_6_GL000251v2_alt"; transcript_id "HML2_6_GL000251v2_alt"; locus "HML2_6_GL000251v2_alt"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0134"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_8_KI270813v1_alt(a) ###								
+chr8_KI270813v1_alt	rmsk	gene	180978	185867	.	-	.	gene_id "HML2_8_KI270813v1_alt(a)"; transcript_id "HML2_8_KI270813v1_alt(a)"; locus "HML2_8_KI270813v1_alt(a)"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0136"; model_cov "3848"; model_pct "51.1";
+chr8_KI270813v1_alt	rmsk	exon	180978	181945	8834	-	.	gene_id "HML2_8_KI270813v1_alt(a)"; transcript_id "HML2_8_KI270813v1_alt(a)"; locus "HML2_8_KI270813v1_alt(a)"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0136"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr8_KI270813v1_alt	rmsk	exon	182041	185867	63496	-	.	gene_id "HML2_8_KI270813v1_alt(a)"; transcript_id "HML2_8_KI270813v1_alt(a)"; locus "HML2_8_KI270813v1_alt(a)"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0136"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "3593"; repStart "-95";
+### HML2_8_KI270813v1_alt(b) ###								
+chr8_KI270813v1_alt	rmsk	gene	185912	190440	.	-	.	gene_id "HML2_8_KI270813v1_alt(b)"; transcript_id "HML2_8_KI270813v1_alt(b)"; locus "HML2_8_KI270813v1_alt(b)"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0137"; model_cov "3591"; model_pct "47.7";
+chr8_KI270813v1_alt	rmsk	exon	185912	189480	63496	-	.	gene_id "HML2_8_KI270813v1_alt(b)"; transcript_id "HML2_8_KI270813v1_alt(b)"; locus "HML2_8_KI270813v1_alt(b)"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0137"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "3850"; repStart "-95";
+chr8_KI270813v1_alt	rmsk	exon	189481	190440	8730	-	.	gene_id "HML2_8_KI270813v1_alt(b)"; transcript_id "HML2_8_KI270813v1_alt(b)"; locus "HML2_8_KI270813v1_alt(b)"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0137"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_14_KI270846v1_alt ###								
+chr14_KI270846v1_alt	rmsk	gene	141082	143972	.	+	.	gene_id "HML2_14_KI270846v1_alt"; transcript_id "HML2_14_KI270846v1_alt"; locus "HML2_14_KI270846v1_alt"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0138"; model_cov "1886"; model_pct "25.0";
+chr14_KI270846v1_alt	rmsk	exon	141082	142770	11016	+	.	gene_id "HML2_14_KI270846v1_alt"; transcript_id "HML2_14_KI270846v1_alt"; locus "HML2_14_KI270846v1_alt"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0138"; repClass "LTR"; repEnd "5462"; repFamily "ERVK"; repLeft "-2074"; repStart "3766";
+chr14_KI270846v1_alt	rmsk	exon	142776	142875	414	+	.	gene_id "HML2_14_KI270846v1_alt"; transcript_id "HML2_14_KI270846v1_alt"; locus "HML2_14_KI270846v1_alt"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0138"; repClass "LTR"; repEnd "5686"; repFamily "ERVK"; repLeft "-1850"; repStart "5587";
+chr14_KI270846v1_alt	rmsk	exon	142874	142965	575	+	.	gene_id "HML2_14_KI270846v1_alt"; transcript_id "HML2_14_KI270846v1_alt"; locus "HML2_14_KI270846v1_alt"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0138"; repClass "LTR"; repEnd "7532"; repFamily "ERVK"; repLeft "-4"; repStart "7441";
+chr14_KI270846v1_alt	rmsk	exon	142969	143972	8253	+	.	gene_id "HML2_14_KI270846v1_alt"; transcript_id "HML2_14_KI270846v1_alt"; locus "HML2_14_KI270846v1_alt"; repName "LTR5B"; geneRegion "ltr"; locid "HERVK-int_0138"; repClass "LTR"; repEnd "1002"; repFamily "ERVK"; repLeft "0"; repStart "1";
+### HML2_19_GL383575v2_alt ###								
+chr19_GL383575v2_alt	rmsk	gene	10454	19925	.	-	.	gene_id "HML2_19_GL383575v2_alt"; transcript_id "HML2_19_GL383575v2_alt"; locus "HML2_19_GL383575v2_alt"; category "prototype"; intModel "HERVK-int"; locid "HERVK-int_0139"; model_cov "7446"; model_pct "98.8";
+chr19_GL383575v2_alt	rmsk	exon	10454	11421	8772	-	.	gene_id "HML2_19_GL383575v2_alt"; transcript_id "HML2_19_GL383575v2_alt"; locus "HML2_19_GL383575v2_alt"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0139"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+chr19_GL383575v2_alt	rmsk	exon	11511	18957	64100	-	.	gene_id "HML2_19_GL383575v2_alt"; transcript_id "HML2_19_GL383575v2_alt"; locus "HML2_19_GL383575v2_alt"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0139"; repClass "LTR"; repEnd "7447"; repFamily "ERVK"; repLeft "1"; repStart "-89";
+chr19_GL383575v2_alt	rmsk	exon	18958	19925	8778	-	.	gene_id "HML2_19_GL383575v2_alt"; transcript_id "HML2_19_GL383575v2_alt"; locus "HML2_19_GL383575v2_alt"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0139"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "1"; repStart "0";
+### HML2_19_GL383576v1_alt ###								
+chr19_GL383576v1_alt	rmsk	gene	69114	77314	.	+	.	gene_id "HML2_19_GL383576v1_alt"; transcript_id "HML2_19_GL383576v1_alt"; locus "HML2_19_GL383576v1_alt"; category "oneside"; intModel "HERVK-int"; locid "HERVK-int_0140"; model_cov "7148"; model_pct "94.9";
+chr19_GL383576v1_alt	rmsk	exon	69114	74636	50491	+	.	gene_id "HML2_19_GL383576v1_alt"; transcript_id "HML2_19_GL383576v1_alt"; locus "HML2_19_GL383576v1_alt"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0140"; repClass "LTR"; repEnd "5534"; repFamily "ERVK"; repLeft "-2002"; repStart "1";
+chr19_GL383576v1_alt	rmsk	exon	74636	76251	14968	+	.	gene_id "HML2_19_GL383576v1_alt"; transcript_id "HML2_19_GL383576v1_alt"; locus "HML2_19_GL383576v1_alt"; repName "HERVK-int"; geneRegion "internal"; locid "HERVK-int_0140"; repClass "LTR"; repEnd "7441"; repFamily "ERVK"; repLeft "-95"; repStart "5826";
+chr19_GL383576v1_alt	rmsk	exon	76347	77314	9262	+	.	gene_id "HML2_19_GL383576v1_alt"; transcript_id "HML2_19_GL383576v1_alt"; locus "HML2_19_GL383576v1_alt"; repName "LTR5_Hs"; geneRegion "ltr"; locid "HERVK-int_0140"; repClass "LTR"; repEnd "968"; repFamily "ERVK"; repLeft "0"; repStart "1";
diff -r 000000000000 -r 66ff74923224 test-data/telescope-out1.bam
Binary file test-data/telescope-out1.bam has changed
diff -r 000000000000 -r 66ff74923224 test-data/telescope-out1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/telescope-out1.tabular	Tue Sep 03 18:12:09 2019 -0400
@@ -0,0 +1,48 @@
+## RunInfo	version:1.0.3	annotated_features:99	total_fragments:9088	pair_mapped:9088	pair_mixed:0	single_mapped:0	unmapped:0	unique:9060	ambig:28	overlap_unique:0	overlap_ambig:136
+transcript	transcript_length	final_count	final_conf	final_prop	init_aligned	unique_count	init_best	init_best_random	init_best_avg	init_prop
+HML2_1q22	9180	95	33.00	0.472	136	0	5	17	16.81	0.351
+HML2_10p14	9463	5	4.00	0.000241	39	0	4	4	4.14	0.000167
+HML2_19q13.12b	9518	5	5.00	0.000121	7	0	3	3	3.08	7.72e-05
+HML2_3p25.3	6891	4	4.00	0.0216	22	0	4	4	4.00	0.0216
+HML2_1q23.3	9232	4	4.00	6.51e-05	68	0	4	5	5.33	0.000101
+HML2_11q23.3	9160	3	3.00	0.000175	68	0	3	4	4.38	0.000421
+HML2_4q32.3	7229	3	3.00	5.58e-06	9	0	3	3	3.00	5.58e-06
+HML2_2q21.1	3080	2	2.00	0.253	29	0	2	2	2.70	0.259
+HML2_19p13.3	2543	2	1.00	0.000155	16	0	1	3	1.76	9.98e-05
+HML2_6q14.1	9422	1	1.00	0.242	120	0	1	2	6.31	0.162
+HML2_7p22.1	17975	1	1.00	0.00912	123	0	1	10	8.04	0.0231
+HML2_16p11.2a	2748	1	1.00	0.00192	34	0	1	1	1.95	0.0018
+HML2_22q11.21	9175	1	1.00	0.000329	122	0	1	7	4.97	0.0149
+HML2_3q12.3	9123	1	0.00	0.000119	46	0	1	3	2.36	0.000761
+HML2_3q21.2	9138	1	1.00	1.83e-05	75	0	1	2	1.65	0.000137
+HML2_1q32.2	4180	1	1.00	1.53e-05	12	0	1	1	1.25	1.6e-05
+HML2_16p11.2b	2746	1	1.00	1.21e-05	34	0	1	1	1.95	0.000129
+HML2_19q13.42	5697	1	1.00	2.5e-06	3	0	1	1	1.00	2.5e-06
+HML2_21q21.1	8304	1	1.00	1.38e-06	55	0	1	1	1.48	1.32e-05
+HML2_1q21.3	1777	1	1.00	3.23e-07	4	0	1	1	1.00	3.28e-06
+HML2_8q11.1b	4280	1	1.00	1.22e-07	2	0	1	1	1.00	1.22e-07
+HML2_7q34	4021	1	1.00	5.95e-09	2	0	1	1	1.00	1.02e-07
+HML2_10q24.2	7177	0	0.00	3.5e-05	62	0	0	3	1.90	0.0158
+HML2_6p22.1	10368	0	0.00	3.34e-18	8	0	1	1	1.00	3.34e-05
+HML2_1p31.1	6373	0	0.00	1.14e-40	78	0	0	1	3.31	0.0655
+HML2_19p12b	6738	0	0.00	8.65e-75	25	0	0	0	0.06	3.21e-05
+HML2_5q33.3	9180	0	0.00	5.1e-106	134	0	0	7	8.30	0.0313
+HML2_5p13.3	9446	0	0.00	1.77e-109	103	0	0	3	2.64	0.00129
+HML2_3q27.2	9180	0	0.00	3.12e-130	116	0	0	5	3.74	0.0193
+HML2_19p12a	10113	0	0.00	1.19e-134	4	0	1	1	1.00	2.85e-06
+HML2_8p23.1a	4893	0	0.00	3.34e-135	81	0	0	4	4.24	0.0144
+HML2_11q22.1	9466	0	0.00	3.34e-135	128	0	0	6	4.73	0.0144
+HML2_19q13.41a	3317	0	0.00	3.05e-142	1	0	1	1	1.00	1.08e-06
+HML2_3q13.2	9159	0	0.00	6.06e-212	121	0	0	4	4.65	0.00249
+HML2_19q13.12a	4006	0	0.00	4.67e-241	17	0	0	0	0.06	3.07e-07
+HML2_19q11	8864	0	0.00	1.19e-292	109	0	0	3	3.50	0.000384
+__no_feature	0	0	0.00	0	4	0	0	0	0.00	5.95e-33
+HML2_3q24	3920	0	0.00	0	50	0	0	7	3.41	8.35e-30
+HML2_4q32.1	2139	0	0.00	0	31	0	0	4	1.71	5.61e-30
+HML2_5p12	9844	0	0.00	0	2	0	0	0	0.00	2.69e-33
+HML2_7q22.2	3918	0	0.00	0	51	0	0	2	1.93	6.32e-30
+HML2_8p23.1b	4510	0	0.00	0	69	0	0	1	3.23	1.24e-29
+HML2_8q24.3a	3088	0	0.00	0	40	0	0	0	1.41	8.25e-30
+HML2_11q12.3a	2509	0	0.00	0	1	0	0	0	0.00	1.72e-08
+HML2_11q12.3b	7547	0	0.00	0	10	0	0	0	0.15	1.72e-30
+HML2_12q14.1	9457	0	0.00	0	130	0	0	6	4.86	3.06e-06