changeset 0:6647bc2c663a draft

Imported from capsule None
author devteam
date Tue, 01 Apr 2014 09:12:41 -0400
parents
children 7e217827b520
files maf_cpg_filter.py maf_cpg_filter.xml test-data/6.maf test-data/6_mask_cpg.maf test-data/6_mask_noncpg.maf tool_dependencies.xml
diffstat 6 files changed, 320 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maf_cpg_filter.py	Tue Apr 01 09:12:41 2014 -0400
@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+#Guruprasad Ananda
+#Adapted from bx/scripts/maf_mask_cpg.py
+"""
+Mask out potential CpG sites from a maf. Restricted or inclusive definition
+of CpG sites can be used. The total fraction masked is printed to stderr.
+
+usage: %prog < input > output restricted
+    -m, --mask=N: Character to use as mask ('?' is default)
+"""
+
+import bx.align
+import bx.align.maf
+from bx.cookbook import doc_optparse
+import sys
+import bx.align.sitemask.cpg
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def main():
+    options, args = doc_optparse.parse( __doc__ )
+    try:
+        inp_file, out_file, sitetype, definition = args
+        if options.mask:
+            mask = int(options.mask)
+        else:
+            mask = 0
+    except:
+        print >> sys.stderr, "Tool initialization error."
+        sys.exit()
+
+    reader = bx.align.maf.Reader( open(inp_file, 'r') )
+    writer = bx.align.maf.Writer( open(out_file,'w') )
+    
+    mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?', 5:'N'}
+    mask = mask_chr_dict[mask]
+    
+    if sitetype == "CpG":
+        if int(definition) == 1:
+            cpgfilter = bx.align.sitemask.cpg.Restricted( mask=mask )
+            defn = "CpG-Restricted"
+        else:
+            cpgfilter = bx.align.sitemask.cpg.Inclusive( mask=mask )
+            defn = "CpG-Inclusive"
+    else:
+        cpgfilter = bx.align.sitemask.cpg.nonCpG( mask=mask )
+        defn = "non-CpG"
+    cpgfilter.run( reader, writer.write )
+    
+    print "%2.2f percent bases masked; Mask character = %s, Definition = %s" % ( float(cpgfilter.masked)/float(cpgfilter.total) * 100, mask, defn )
+
+if __name__ == "__main__":
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maf_cpg_filter.xml	Tue Apr 01 09:12:41 2014 -0400
@@ -0,0 +1,90 @@
+<tool id="cpgFilter" name="Mask CpG/non-CpG sites" version="1.0.0">
+  <description> from MAF file</description>
+  <requirements>
+    <requirement type="package" version="0.7.1">bx-python</requirement>
+  </requirements>
+  <command interpreter="python">
+  	maf_cpg_filter.py 
+    $input 
+    $out_file1 
+    $masksite.type
+    #if $masksite.type == "CpG":
+     $masksite.definition
+    #else:
+     "NA"
+   #end if
+    -m $mask_char
+  </command>
+  <inputs>
+    <page>
+    	<param format="maf" name="input" type="data" label="Select data"/>
+   		<param name="mask_char" size="5" type="select" label="Mask character">
+    		<option value="0" selected="true">#</option>
+          	<option value="1">$</option>
+          	<option value="2">^</option>
+          	<option value="3">*</option>
+          	<option value="4">?</option>
+          	<option value="5">N</option>
+        </param>
+        <conditional name="masksite">
+            <param name="type" size="5" type="select" label="Sites to be masked">
+                <option value="CpG" selected="true">CpG sites</option>
+                <option value="nonCpG">non-CpG sites</option>
+             </param>
+            <when value="CpG">
+                <param name="definition" size="5" type="select" label="Definition">
+                    <option value="0" selected="true">Inclusive</option>
+                    <option value="1">Restricted</option>
+                 </param>
+            </when>
+            <when value="nonCpG" />
+        </conditional>
+    </page>
+  </inputs>
+  <outputs>
+    <data format="maf" name="out_file1" metadata_source="input"/>
+  </outputs>
+  <requirements>
+    <requirement type="python-module">numpy</requirement>
+  </requirements>
+  <tests>
+    <test>
+      <param name="input" value="6.maf"/>
+      <param name="mask_char" value="0"/>
+      <param name="type" value="CpG" />
+      <param name="definition" value="0" />
+      <output name="out_file1" file="6_mask_cpg.maf"/>
+    </test>
+    <test>
+      <param name="input" value="6.maf"/>
+      <param name="mask_char" value="0"/>
+      <param name="type" value="nonCpG" />
+      <output name="out_file1" file="6_mask_noncpg.maf"/>
+    </test>
+  </tests>
+ <help> 
+
+.. class:: infomark
+
+**What it does**
+
+This tool takes a MAF file as input and masks CpG sites in every alignment block of the MAF file. 
+
+-----
+
+.. class:: warningmark
+
+**Note**
+
+*Inclusive definition* defines CpG sites as those sites that are CG in at least one of the species.
+
+*Restricted definition* considers sites to be CpG if they are CG in at least one of the species, however, sites that are part of overlapping CpGs are excluded.
+
+For more information on CpG site definitions, please refer this article_.
+
+.. _article: http://mbe.oxfordjournals.org/cgi/content/full/23/3/565
+
+  </help>  
+
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/6.maf	Tue Apr 01 09:12:41 2014 -0400
@@ -0,0 +1,57 @@
+##maf version=1
+a score=356676.0
+s hg18.chr1      2817 1438 + 247249719 GTCATCCCCTTCACTCCCAGCTCAGAGCCCAGGCCAGGGGCCCCCAAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCCTGGCTGCCTCCAGCTGGGTCGACAGACAGGGGCTGGAGAAGGGGAGAAGAGGAAAGTGAGGTTGCCTGCCCTGTCTCCTACCTGAGGCTGAGGAAGGAGAAGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCTTAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGTTGGCCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCACTCCTGCCTTTTCCTTTCCCTAGAGCCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGAATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTGCGTGGCCGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATT--TGTCCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCCATCTGCTACTGCCCTTTCTATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCCTCTCAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTTGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGGACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGATCCTTTATTAAAAG 
+s panTro2.chr15 16051 1440 - 100063422 GTCATCCCCTTCACTCCCAGCTCTGAGCCCAGGCCAGGGGCCCCCAAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCCTGGCTGCCTCCAGCTGGGTGGACAGACAGGCGCTGGAGAAGGGGAGAAGAGGAAAGGGGGGCTGCCTGCCCTGTCTCCCACCTGAGGCTGAGGAAGGAGAGGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCCTAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAATGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACAAGCTGTTGGCCTGGATCTGAGCCCTCGTGGAGCTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCAGTCCTGCCTTTTCCTTTCCCGAGAGGCTCCACCACCCCGAGATCGCACTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGCGCCCTTCCTTTGCTCTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGAATCCCAAAGAAATGGTGAGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTGCGTGGCAGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTCTGTCCTGCCCACCTTCTAAGAAGCGAGACGGAGGACACCCATCTGCTTCTGCCCTTTCCATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCTATTTAAAAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCACTTCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCCTCTCAACTACTTGAGCAAACTTGAAGACATCTTCAACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTCGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGCACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGGTCCTTAATTAAAAG 
+
+a score=33380.0
+s hg18.chr1      4393 135 + 247249719 GTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTG 
+s panTro2.chr15 17634 135 - 100063422 GTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAGGGAAGCAGGTCTCAGCAGCTTGTCCTGGCTGTGTCCGTGTCAGAGCAACGGCCCAAGTCTG 
+
+a score=364526.0
+s hg18.chr1      4528 1436 + 247249719 GGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGCAGGACAGAATTACAAGGTGCTGGCCCAGGGCGGGCAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATGCGACCGGTGACTCCCTGTCCCCACCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGTCGATCCCTGACCCAGCACCGGGCACTGATGAGACAGCGGCTGTTTGAGGAGCCACCTCCCAGCCACCTCGGGGCCAGGGCCAGGGTGTGCAGCAccactgtacaatggggaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcagcgctgggtacaagctcaAAACCATAGTGCCCAGGGCACTGCCGCTGCAGGCGCAGGCATCGCATCACA-----CCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACCGCTCTTGGCAGTCGAAGAAGATTCTCCTGTCA--GTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCCACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGGTGGCGGCCCAGGGCTTCCAGCATGTGCCCTAGGGGAAGCAGGGGCCAGCTGGCAAGAGCAGGGGGTGGGCAGAAAGCACCCGGTGGACTCAGGGCTGGAGGGGAGGAGGCGATCTTGCCCAAGGCCCTCCGACTGCAAGCTCCAGGGCCCGCTCACCTTGCTCCTGCTCCTTCTGCTGCTGCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCC-AGCCACCGGAGGGGTCAACCACTTCCCTGGGAGCTCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGGGCTGGGGAAGCTTACTGTGTCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAACGAGGAGCCCTGCGCTGGGGAGGCCGGACCTTTGGAGACTGTGT 
+s panTro2.chr15 18013 1444 - 100063422 GGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTAGGATTCCCAGTCGTCCTCATCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGCTTCCCCCAGCCCCCAGAGACTTAAATACAGGAAGAAAAAGGCAGGACACAATTACAATGTGCCGGCCCAGGGCGGGCAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTCCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATGTGACCGGTGGCTCCCTGTCCCCAGCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGTCGATCCCTGACCCAGCACCGGGCGCTGATGAGAAAGCGGCTGTTTGAGGAGCCACCTCCCAGCCACCTTGGGGACAGGGCCAGGGTGTGCAGCACcactgtacaatggggaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcagcgctgTGTACAAGCTCAAAACCATAGTGCCCAGGGCATTGCCACTGCAGGCGCAGGCATCGCATCACATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCAAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACCGCTCTTGGCAGTCGAAGAAGATTCTCCTGTCACAGTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCCACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGGTGGCGGCCCAGGGATTCCAGCATGTGCCCTAGGAGAAGCAGGGGCCAGCTGCCAAGAGCAGGGGGTGGGCAGAAAGCACCCAGTGGACTCAGGGCTGGAGGGAAGGAGGCGATCTTGCCCAAGGCCCTCCGACCGCAGGCTCCAGGGCCCGCtcaccttgctcctgctccttctgcttcttcttctccagctttcgctccttcACGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGATTCTAGCAGAGTGGCCCGGCCACCGGAGGGGTCGACCACTTCCCTGGGAGCTCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGGGCTGGGGAAGCTTATTGTATCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAACGAGGAGCCCCGCGCTGGGGAGGCCGGACCTTTGGAGACTGTGT 
+
+a score=521291.0
+s hg18.chr1      5995 1988 + 247249719 CCTGAGCGCGGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTAGCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTTGCACACACGAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTACACTGGGAGACACAGCAGTGAAGCTGAAATGAAAAATGTGTTGCTGTAGTTT-----GTTATTAGACCCCTTCTTTCCATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCTAGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAACAAGATATTTGAAATGGAAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACCCACAGAAAATCCACCCGAGTGCACTGAGCACGCCAGAAATCAGGTGGCCTCAAAGAGCTGCTCCCACCTGAAGGAGACGCGCTGCTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACAGGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggtggtggtgggggcggtgggggtggtg---------ttagtACCCCATCTTGTAGGTCTGAAACACAAAGTGTGGGGTGTCTAGGGAAGAAGGTGTGTGACCAGGGAGGTCCCCGGCCCAGCTCCCATCCCAGAACCCAGCTCACCTACCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGTGAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGTGGAATAAGGGGCCCAACAGCCTTGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTGCACCTGTCTCCACCTCTGTCCCACCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCCTCTGGCCATACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAGAGGGCCAGGATGGCCAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGCTGCCATCCCATCCCAGTCAGCCTCCTCTGGGGGACAGAACCCTATGGTGGCCCCGGCTCCTCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGC-----TATATGCGCGGCCAGCAGACCTGCAGGGCCCGCTCGTCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCAGGCCAGGGTCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCCCTGGAGCAGGGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAGGCTCAGAGGGCTAGGATTGCT 
+s panTro2.chr15 19485 2006 - 100063422 CCTGAGTGCAGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTAGCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTGGCACACATGAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTAGACTGGGAGATACAACAGTGAAGCTGAGAAGAAAAATGTGTTGCTGTAGTTTAGTTGGTTATTAGACCCCTTCTTTCCATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCTAGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAACAAGATATTTGAAATGGGAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACCCACAGAAAATACACCCGAGTGCACTGAGCACGCCAGAAATGAGGTGGCCTCAAAGAGCTGCTCCCACCTGAAGGAGACGCGCTGCTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACAGGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggaggtggtgggggcggtgggggtggtgggggtgctgttagtACCCCATCTTGTAGGTCTGAAACACAAAGTGTGGGGTGTCTAGGGAAGAAGGTGTGTGAGCAGGGAGGTCCCCAGCCCAGCTCCCATCCCAGAGCCCAGCTCACCTGCCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCACTGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGTGAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGTGGAATAAGGGGCTCAACAGCCTGGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTGCACCTGTCTCCACCTCTGTCCCGCCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTGTACCTACAGGGGCGACATGGGGGTCAGGCAAGCTGACACCTGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGTGTGCACCGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCTTCTGGCCATACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGGGCCCCGGCTTGGTGCTCACGCACACAGGAAAGTACTTCAGCTTCTCCTGGGAGGGCCAGAATGGCCAAGGGATGGTGAATATTTAGTGCCGGGCCTAATCAGCTGCCACCCCATCCCGGTCAGCCTCCTCTGGGGGACAGAACCCT-TGGTGGCCCCGGCTCCTCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGCTAAGTTATGTGCGCGGCCAGCAGACCTGCAGGGCCCGCTCATCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCAGGCCAGGGTCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCTCTGGAGCAGGGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAGGCTCAGAGGGCTAGGATTGCT 
+
+a score=311095.0
+s hg18.chr1      7983 1272 + 247249719 TGGCAGGAGAGGGTGGAGTTGGAAGCCTGGGCGAGAAGAAAGCTCAAGGTACAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCACGGGGAAATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGTATGGGGACTACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCTGCCATGGAGAAGATCACAGAGGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGGTGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGTCGAGGAGTTGACGGTGCTGAGTTCCCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCTGAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTACTGATGGGGCAAGCACTTCACAACCCCTCATGATCACGTGCAGCAGACAATGTGGCCTCTGCAGAGGGGGAACGGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTCGTCACCTAAATTCAGACGGGGAACTGCCCCTGCACATACTGAACGGCTCACTGAGCAAACCCCGAGTCCCGACCACCGCCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtgcggggtgggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttgtgtgcttgcatctcatggaacgccatttccccagacatccctgtggctggctcctGATGCCCGAGGCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGGCCGCAGCAAGGCCGCTCTCACTGCAAAGTTAACTCTGATGCGTGTGTAACACAACATCCTCCTCCCAGTCGCCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCCACACTCCACGTGCAGAGCAGCCTCAGCACTCACCGGGCACGAGCGAGCCTGTGTGGTGCGCAGGGATGAGAAGGCAGAGGCGCGACTGGGGTTCATGAGGAAGGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGTTTGAGAAGGCAGAGGCGC 
+s panTro2.chr15 21491 1270 - 100063422 TGGCAGGAGAGGGTGGAGTTGGGAGCCTGGGCGAGAAGAAAGCCCAAGGTAGAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCACGGGGAAATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGCATGGGGACTACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCCGCTGGGAGATCCTGCCATGGAGAAGATCACAGAGGCTGGGCTGCTCCCCACCCCCTGCACACCTCCTGCTCCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTTAAGTCAGGGTCACCTGCTTGCCAGGGCTGATCTTGGTGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGTCGAGGAGTTGATGGTACTGAGTTCCCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCTGAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTATTGATGGGGCAAGCATTTCACAACCCCTCATGATCACGTGCAGCAGACAAAGTAGCCTCTGCAGAGGGGGAATGGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTCATCACCTAAATTCAGACGGGGAACTGCCCCCGCACATAGTGAACGGCTCACTGAGCAAACCCTGAGTCCCAACCACCGCCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtgcggggtgggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttatgtgcttgcatctcatggaacaccatttccccagacatgcctgtggctggctcctGGTGCCCGAGGCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGGCCGCAGCAAGGCCGCTCTCACTGCAAAGTTAACTCTGATGCGTGTGTA--ACAACATCCTCCTCCCAGTCGCCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCCACACTCCACGTGCAGAGCAGCCTCAGCACTCACCGGGCACGAGCGAGCCTGTGTGGTGCGCAGGGATGAGAAGGCAGAGGCGCGACTGGGGTTCGTGAGGAAAGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGTTTGAGAAGGCAGAGGCGC 
+
+a score=268744.0
+s hg18.chr1      9255 1055 + 247249719 GACTGGGGTTCATGAGGAAAGGGAGGGGGAGGATGTGGGATGGTGGAGGGGCTGCAGACTCTGGGCTAGGGAAAGCTGGGATGTCTCTAAAGGTTGGAATGAATGGCCTAGAATCCGACCCAATAAGCCAAAGCCACTTCCACCAACGTTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGAAGTCCCCGTGCCCTAAAGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCTGGGAGTACCAGCAGGCACTCAAGCGGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAGCGGGACCACCACCCAGCGTGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGGTCCTCCAGCACAAGCTGTCTTAATTGACCCTAGTTCCCAGGGCAGCCTCGTTCTGCCTTGGGTGCTGACACGACCTTCGGTAGGTGCATAAGCTCTGCATTCGAGGTCcacaggggcagtgggagggaactgagactggggagggacaaaggctgctctgtcctggtgctcccacaaagg--agaagggctgatcactcaaagttgcgaacaccaagctcaacaatgagccctggaaaatttctggaatggattattaaacagagagtctgtaagcacttagaaaaggccgcggtgagtcccaggggccagcactgctcgaaatgtacagcatttctctttgtaacaggattattagcctgctgtgcccggggaaaacatgcagcacagtgcatctcgagtcagcaggattttgacggcttctaacaaaatcttgtagacaagatggagctatgggggttggaggagagaacatataggaaaaatcagagccaaatgaaccacagccccaaagggcacagttgaacaatggactgattccagccttgcacggagggatctggcagagtccatccagttcattcaacacctggttagaaaactggggccag 
+s panTro2.chr15 22901 1056 - 100063422 GACTGGGGTTCATGAGGAAAGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGCTGCAGACTCTGGGCTTGGGAAAGCTGGGGTGTCTCTAAAGGTTGGAATGAATGGCCTAGAATCGGACCCAATAAGCCAAAGCCACTTCCACCAACGTTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGGAGTCCCCGTGCCCTAATGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCTGGGAGTACCAGCAGGCACTCAAGCGGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAGCGGGGCCACCACCCAGCGTGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGGTCCTCCAGCACAAGCTGTTTTAATTTACCCTAGTTCCCAAGGCAGCCTCATTCTGCCTTGGGTGCTGACACGACCTTCGGTAGGTGCATAAGCTCTGCATTCGAGGTCcacaggggcagtgggagggaactgagactggggagggacaaaggctgctctgtcctggtgctcccacaaaggacagaagggctgatcactcaaagttgcgaacaccaagctcaacaatgagccctggaaaatttctggaatggattattacacagagagtctgtaagcacttagaaaaggccgcggtgagtcccaggggccagcactgctcgaagtgtacagcatttctctttgtaacaggattagtagcttgctgtgcccggggagaacatgcagcacagcgcatctcgagtcagcaggatttcgacggcttctaacaaaatcctgtagacaagatggagctatgggggttggaggagagaacatatagg-aaaatcagagccaaatgaaccacagccccaaagggcacagttgaacaatggactgattccagccttgcacggagggatctggcagagtccatccggttcATTCAACACCTGGTTAGAAAACTGGGGCCAG 
+
+a score=95099.0
+s hg18.chr1             10310 371 + 247249719 cacacaggggaagggtaagctggtttcatgatcgaatcaaggctcagacaatttttaaaggccagagggtagactgcaatcaccaagatgaaatttacaaggaacaaatgtgaagcccaacatttaggttttaaaaatcaagcgtataaatacagaaggtggagggaacttgctttagacacagttcaggtgaagaaagacctggaaacttctgttaactataagctcagtaggggctaaaagcatgttaatcggcataaaaaggcaatgagatcttaggGCACACAGCTCCCCGCCCCTCTTCTGCCCTTCATCCTTCTTTCAATCAGCAGGGACCGTGCACTCTCTTGGAGCCACCACAGAAAACAGAG 
+s panTro2.chr9_random 4675776 371 +   7733331 cacacaggggaagggtaagttggtttcatgatcgaatcaaggctcagacaattttcaaaggccagagggtagactgcaatcacccagatgaaatttacaaggaacaaatgtgaagcccaacatttaggttttaaaaatcaagcgtataaatatagaaggtggagggaacttgttttagacacagttcaggtgaagaaagacctggaaacttctgttaactataagctcagtaggggctaaaagcatgttaatcggcataaaaaggcaatgagatcttaggGCACACAGCTCCCCGCCCCTCTTCTGCCCTTCATCCTTCTTTCAATCAGCAGGGACGGTGCACTCTCTTGGAGCCACCACAGAAAACAGAG 
+
+a score=33853.0
+s hg18.chr1        10770 227 + 247249719 CAGAGCAGGAGGAGAGAGCACAGCCTGCAATGCTAATTTGCCAGGAGCTCACCTGCCTGCGTCACTGGGCACAGACGCCAGTGAGGCCAGAGGCCGGGCTGTGCTGGGGCCTGAG-CCGGGTGGTGGGGAG-------AGAGTCTCTCCCCTGCCC--CTGTCTCTTCCGTGCAGGAGG---------------AGCATGTTTAAGGGGACGGGTTCAAAGCTGGTCACATCCCCACCGAAAAAGCCCATGG 
+s panTro2.chr12 77693524 219 - 135371336 CAGAGCAGGAGGAGAGAGCATGGCCAGGAATGCTAATTTGCCAGGAGCTCACCTGCCTGCGTCACAAGGCACAGGTGCCAATGAGGCCAGGGTCCAGTCTG-----GGGCATGAGATGGGGTGGTGGGGAGGAGAGAGACAGTCTCTCCTCTACCCACCTGTCTCTTCTGTGCAGGTGGTTTCCGAGCAGGTGAAGCACATTTAAAGGGGGAGGTTCTAAACTG---------------------------- 
+
+a score=83473.0
+s hg18.chr1             10997 329 + 247249719 ACAACGAAAAGCCCACTAGCTTGTCCAGTGCCACAGGAGGGGCAAGTGGAGGAGGAGAGGTGGCGGTGCTCCCCACTCCACTGCCAGTCGTCACTGGCTCTCCCTTCCCTTCATCCTCGTTCCCTATCTGTCACCATTTCCTGTCGTCGTTTCCTCTGAATGTCTCACCCTGCCCTCCCTGCTTGCAAGTCCCCTGTCTGTAGCCTCACCCCTGTCGTATCCTGACTACAATAACAGCTTCTGGGTGTCCCTGGCATCCACTCTCTCTCCCTTCTTGTCCCTTCCGTGACGGATGCCTGAGGAACCTTCCCCAAACTCTTCTGTCCCAT 
+s panTro2.chr9_random 4677170 329 +   7733331 ACAACGAAAAGCCCACTTGCTTGTCCAGTGCCACAGGAGGGGCAAGTGGAGGAGGAGAGGTGGCGGTGCTCCCCACTCCACTGCCAGTCATCACTGGCTCTCCCTTCCCTTCATCCTCGTTCCCTATCTGTCACCATTTCCTGTCGTCGTTTCCTCTGAATGTCTCACCCTGCCCTCCCTGCTTGCAAGTCCCCTGTCTGTAGCCTCACCCCTGTCACATCCTGACTACAATAACAGCTTCTGGGTGTCCCCAGCATCCACTCTCTCTCCCTTCTTGTCCCTTCCGTGATGGATGCTTGAGGAACCTTCCCCAAACTCTTCCGTCCCAT 
+
+a score=1716519.0
+s hg18.chr1     11326 6774 + 247249719 CCCTGCCCTGCTCAAAATCCAATCACAGCTCCCTAACACGCCTGAATCAACTTGAAGTCCTGTCTTGAGTAATCCGTGGGCCCTAACTCACTCATCCCAACTCTTCACTCACTGCCCTGCCCCACACCCTGCCAGGGAGCCTCCCGTGGCACCGTGGGGACACAAAGGAACCAGGGCAAAGCTCCCTCAGCCCCATTCAAAGAGGCCTGGCCCACAGGCTCACGGAAAGTCAGCCTCTCATGCCCCGAGAGCTGAGTGCAAGGGAGAGGCAGCGCTGTCTGTGCTTCCCATGCAGAAGCACCCCCCTCCCACCCCTGTGCAGGCCGGCCTTCGCGGCAGACCACCATACACCACGTTCCAAGCCACACTGAGGCCTCCCTCCAAGCCTGCAGCCCCCATTTCCAGACCCTGCCAGGGCAACCTGCATATCCACCTCCCTACCCTGCCCCCCTCTTCCAGGAGTCTGCCCTATGTGGAGTAAGCACgtggttttcctcttcagcaactatttcctttttactcaagcaatggccccatttcccttggggaatccatctctctcgcaggcttagtcccagagcttcaggtggggctgcccacagagctcctcagtctaagccaagtggtgtgtcatagtcccctggccccattaatggattctgggatagacatgaggaccaagccaggTGGGATGAGTGAGTGTGGCTTCTGGAGGAAGTGGGGACACAGGACAGCATTCTTTCCTGCTGGACCTGACCCTGTGTCATGTCACCTTGCTACCACGAGAGCATGGCCTGTCTGGGAATGCAGCCAGACCCAAAGAAGCAAACTGACATGGAAGGAAAGCAAAACCAGGCCCTGAGGACATCATTTTAGCCCTTACTCCGAAGGCTGCTCTACTGATTGGTTAATTTTTGCTTAGCTTGGTCTGGGGAGTTCTGACAGGCGTGCCACCAATTCTTACCGATTTCTCTCCACTCTAGACCCTGAGAAGCCCACGCGGTTCATGCTAGCAATTAACAATCAATCTCGCCCTATGTGTTCCCATTCCAGCCTCTAGGACACAGTGGCAGCCACATAATTGGTATCTCTTAAGGTCCAGCACGAGGTGGAGCACATGGTGGAGAGACAGATGCAGTGACCTGGAACCCAGGAGTGAGGGAGCCAGGACTCAGGCCCAAGGCTCCTGAGAGGCATCTGGCCCTCCCTGCGCTGTGCCAGCAGCTTGGAGAACCCACACTCAATGAACGCAGCACTCCACTACCCAGGAAATGCCTTCCTGCCCTCTCCTCATCCCATCCCTGGGCAGGGGACATGCAACTGTCTACAAGGTGCCAAGTACCAGGACAGGAAAGGAAAGACGCCAAAAATCCAGCGCTGCCCTCAGAGAAGGGCAACCACGCAGTCCCCATCTTGGCAAGGAAACACAATTTCCGAGGGAATGGTTTTGGCCTCCATTCTAAGTGCTGGACATGGGGTGGCCATAATCTGGAGCTGATGGCTCTTAAAGACCTGCATCCTCTTCCCTAGGTGTCCCTCGGGCACATTTAGCACAAAGATAAGCACAAAAGGTGCATCCAGCACTTT--GTTACTATTGGTGGCAGGTTTATGAATGGCAACCAAAGGCAGTGTACGGGTCAAGATTATCAACAGGGAAGAGATagcatttcctgaaggcttcctaggtgccaggcactgttccattcctttgcatgttttgattaatttaatatttaaaataattctaccaggaag--------------ctaccattattaccacaacttcacaaatgagaacaccgaggcttagaggggttgggttgcccaaggttacagaggaagaaaacaggggagctggatctgagccaaggcatcaactccaaggtAACCCCTCAGTCACTTCACTGTGTGTCCCCTGGTTACTGGGACATTCTTGACAAACTCGGGGCAAGCCGGTGAGTCAGTGGGGGAGGACTTTCAGGAAGAGGTGGGTTCCCAGTTGGTGACAGAAGAGGAGGCTGCAAAGTGAAGGAGCAGGGGCTCCAGGTCTGGCGACAACCAGGGAAGGGACAGGGCAGGGATGGCTTGGACCACGAGAGGCACCTGAGTCAGGCAGTCACATACTTCCCACTGGGGTCTACCATGTGAGGCATGGTGTGGGATCCTGGGAAGGAGACCAAGCCTCATTTCAGTTTGCTTATGGCCAAAGACAGGACCTGTGTACCCGACAACCCCTGGGACCTTTACCAAAAAAAGAGCAAACACCATTCACTCACTCATGTTAGATAAACACTGAGTGAAGTCACTGGAGCCCAAGGACTGTGCGAGGTCAGCACTGCCAATACAAGAAGCTGCAGCCCTCCAGCTCGCctccctcaatggccactccgtgctccagccatgctggcttccttttaggtcctccacctccaggctgtagttcatgtgcttctttctggaatgttcttcccaacctacccactcaaccctcagactttaccataaatgtcatttcctcacgtctgccttccctgacctgagaccaagccaggCTTCCCATGACGAGCCTCACAGTACCCCATCTCCCCTGAACAGATGCAGTAATAACCTACATAACccggggccatgatctatggctttgaatcctggctctgtcactaggccaggtctctcagcccttctgtgcctcagtttcctcatctataaaatgagatgacggcagtgcctgctcatgaagtgtgagttaatgcactcaaatcaatggttgtgcacggtttatatgaatattagtgattaCAAAATATTATCAatagaccttgtcacaactgttattgaagaactaatcatctattgcttatttaggtctttctctcctgccagaatgtgcgctccaggtggagaggtatgttgccttatccgtggctggatatatagagattcccacactgccttgcacacgagcactgctgggtaaatatttgttggctgcaggaaAACGTGAAGGAATAGGCCCTCCAATGGGAGGAAAAGCATGAGTTGTGAGAGCAGAGCCACCACAGGAAACCAGGAGGCTAAGTGGGGTGGAAGGGAGTGAGCTCTCGGACTCCCAGGAGTAAAAGCTTCCAAGTTGGGCTCTCACTTCAGCCCCTCCCACACAGGGAAGCCAGATGGGTTCCCCAGGACCGGGATTCCCCAAGGGGGCTGCTCCCAGAGGGTGTGTTGCTGGGATTGCCCAGGACAGGGATGGCCCTCTCATCAGGTGGGGGTGAGTGGCAGCACCCACCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCGCCGCAGGTCTGGCTGGATGAAGGGCACGGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCCTGTGGGTCGGAGCCGGAGCGTCAGAGCCACCCACGACCACCGGCACGCCCCCACCACAGGGCAGCGTGGTGTTGAGACAACACAGCCCTCATCCCAACTATGCACATAGCTTCAGCCTGCACAGATAGGGGAGTAGGGGACAGAGCATTTGCTGAGAGGCCAGGAGCGCATAGATGGGACTCTGCTGATGCCTGCTGAGTGAATGAGGGAAAGGGCAGGGCCCGGGACTGGGGAATCTGTAGGGTCAATGGAGGAGTTCAGAGAAGGTGCAACATTTCTGACCCCCTACAAGGTGCTTGCTACCTGCCAGGCACCCTTTCCATACCTTGTCTCAGTTCAGCTCCCCACCTTGGATAAACAAGAAACCTTGGTTGCAGAGGAAAAAAGAGGCTGGAAACAAAGGGGTAGAAATGGGGTAGCAGGGGAGATTGCCTGATCAACTGCCAAATGGTACACAGTTCTGGAAAAGCACAAAAAATGTGCACACACGGGTTCTTCCCACTTTAACCCCTGAGGAATCTGAGGCCTGCTCCTGAAACAGACTGGGCAGTGGCTAGTGACTCTAGGTATAGGAGTATCCAGCCCTGCTCACCCAGGCTAGAGCTTAGGGGGACAAGAGGAAAGAGGTGCCTGTGGGGGTGGAGGACAGGAAGGAAAAACACTCCTGGAATTGCAAAGTGAGGGCAGAGTCTATTTATATTGGGTTTAATTAACTCCTCTCCCTGGTGCCACTAAAGCAGCAATCACACTGCAGACAGCACTGATTTGATTGGCAAGAGATGCACCAGGCAGAATATTAAGGGACCAGGCCCCTATAAATAGGCCTAATCACAGCCCCTCACTGGAAAATGGTAAGGAAGACATTAATCAGGCCTGGCACTGTGCCCTAGACCTGCTCCCCTAGGCACTACAGTGGGGCCCTTGGTTGCAACACAAGTAGGTAGGGATGGATGAGTGTGGCATGAAGGGCCTAGGAGATTTCACTTGGGTTTAAAATGCTGTGACCTTGAGTAAGTTGCCGTCTCTGAATCTGATCCTTTCGATTTCCCATTCTCCAAACTGAGAACTAGCACTGCTGAGACGTGGTTATTTCCAATAATAATTTGTATATTTTACATAACGCACCACACCAACATCTTCACCCAGTTGGAGCCTACTCCTTTGCTCCCGCTGCTGGCTTCCCCAGCCCTCCCTTCTGCCCTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTTTGCATACAGGCTTTCCAGATCTGTACTTGCCTTGAATACTCATCAGAGCCCAGGAGTTACTCCTCACCTCCCACTTATTTTTCCTCCCATCAAATAACTAAAGCATGGCCAGCTGATGCCCAGCCAACTGAGAAACCCAACCCTCTGAGACCAGCACACCCCTTTCAAGCATGTTCCTCCCTCCCCTTCTTTGTATTTATACTGATGCAAGTTTGCTGGCTGTcctaacttatttctgtgcctcagttctcccatatgtaagatcacaaagggggtaaagaTGCAAGATATTTCCTGTGCACATCTTCAGATGAATTTCTTGTTAGTGTGTGTGTGTTTGCTCACACATATGCGTGAAAGAAGAGTACATACACAGATCTCCTCAAAAAGGAGGCAGCAAGCCCGTTCAAGAATGGGACTGAATACACCTGATGAGTGGTTTACTTTCTGTCTGCAAACATCTACTGATCATCTGTTAGGTGCAGGCCATGATCACAACAAAGACGAATAAGACACTACACTAGCCAGGGAGAGTCTCAAAAACAACTAAACTCAAATTAAATTCATTCTACTCCAGTCATGGGTACAAAGCTAAGGAGTGACAAATCCCTCTTGGAGTTAGGGGAGTCAGGAAAAAGCTCTTAGCAGAATGTGTGCCTCTCggccgggcgcagcggctcacgcctgtaatcccagcactttgggaggcgaaggcaggcagatcacctgaggtcgggagttcgagaccagtctgaccaacatggtgaaactccatctctactaaaaatacaaaattagccaggcgtggtggtgcatgcctgtaatccccgctactcgggaggctgaggaaggagaatcacttgaaccaggaaggtggaggttgcagtgtgccaagatcgcgccatggcactccagcctaggcaacgagggtgaaCCAGGTCCAGGAAGAAGGTGCAAAGACAGCATTCCAGGTAAAAGAAACAGCTTGAACAAAAAGTGTGTAGGGGAACCGCAAGCGGTCTTGAGTGCTGAGGGTACAATCATCCTTGGGGAAGTACTAGAAGAAAGAATGATAAACAGAGGCCAGTTTGTTAAAAACACTCAAAATTAAAGCTAGGAGTTTGGACTTGTGGCAGGAATgaaatccttagacctgtgctgtccaatatggtagccaccaggcacatgcagccactgagcacttgaaatgtggatagtctgaattgagatgtgccataagtgtaaaatatgcaccaaatttcaaaggctagaaaaaaagaatgtaaaatatcttattattttatattgattacgtgctaaaataaccatatttgggatatactggattttaaaaatatatcactaatttcatctgtttctttttacttttAGAAATCACATATGTGACTTAAATATTTCTTTTCTTTTTCTTTCCTCTCACTCAGCGTCCTGTGATTCCAAAGAAATGAGTCTCTGCTGTTTTTGGGCAGCAGATATCCTAGAATGGACTCTGACCTAAGCATCAAAATTAATCATCATAACGTTATCATTTTATGGCCCCTTCTTCCTATATCTGGTAGCTTTTAAATGATGACCATGTAGATAATCTTTATTGTCCCTCTTTCAGCAGACGGTATTTTCTTATGCTACAGTATGACTGCTAATAATACCTACACATGTTAGAACCATTCTGACTCCTCAAGAatctcatttaactcttattatcagtgaatttatcatcatcccctattttacataaggaaatggggttagaaagaccaaataacattttttcaacatcaaaacactagcttgagatcaagcccagacttggatctgtcgtctgaattccaagctttttgttatttattgatatgttttgttgtTTTCATGCAATAATGCAAATCTTAGCCCAAACATTTTGTTAGTAGTACCAACTGTAAGTCACCTTATCTTCATACTTTGTCTTTATGTAAACCTAAATTAGATCTGTTTTTGATACTGAGGGAAAAACAAGGGAATctaacactaaccagcccgtagtgtgtggtcaacactttcgttactttagtatacatcaccccaattgtttgtcttcaccacacactt 
+s panTro2.chr15 23957 6770 - 100063422 CCCTGCCCTGCTTAAAATCCAATCACAGCTCCCTAACACTCCTGAATCAACTTGAAGTCCTGTCTTGAGTAATCCGTGGGCCCTAACTCACTCACCCCAACTCTTCACTCACTGCCTTGCCCCACACCCTGCCAGGGAGCCTCCCGTGGCACCGTGGGGACACAAAGGAACCAGGGCAAAGCTCCCTCAGCCCCATTCAAAGAGGCCTGGCCCACAGGCTCACGGAAAGTCAGCCTCTCATGCCCCGAGAGATGAGTGCAAGGGAGAGGCAGCGCTGTCTGTGCTTCCCATGCAGAAGCACCCTCCTCCCACCCCTGTGCAGGCCGGCCTTCATGGCAGACCACCATACACCACGTTCCAAGCCACACTGAGGCCTCTCTCCAAGCCCGCGGCCCCCATTTCCAGACCCCACCAGGGCAACCTGCATATCCACCTCCCTACCCTGCCCCCCTCTTCCAGGAGTCTGCCCTATGTGGAGTAAGCACgtggttttcctcttcagcaactatttcctttttactcaagcaatggccccatttcccttggggaatccatctctctcgcaggcttagtcccagagcttcaggtggggctgcccacagagttcctcagtctaagccaagtggtgtgtcatagtcccctggccccagtaatggattctgggatagacatgaggaccaagccaggtgggatgggtaagtgtggcttctggaggaagtggggacacaggagagcattctttcctgctggACCTGACCCTGTGTCATGTCACCTTGCTACCACGACAGCATGGCCTGTCTGGGAATGCAGCCAGACCCAAAGAAGCAAACTGACATGGAAGGAAAGCAAAACCAGGCCCTGAGGACATCATTTTAGCCCTTACTCCGAAGGCTGCTCTACTGATTGTTTAATTTTTGCTTAGCTTGGTTTGGGGAGTTCTGACAGGCGTGCCACCAATTCTTACCGATTTCTCTCCACTCTAGACCCTGAGAAGCCCACGCGGTTCATGCTAGCAATTAACAATCAATCTCGCCCTATGTGTTCCCATTCCAGCCTCTAGGACACAGTGTCAGCCACATAATTGGTATCTCTTAAGGTCCAGCACGAGGTGGAGCACATGGTGGAGAGACAGATGCAGTGACCTGGAACCCAGGAGTGAGGGAGCCAGGACTCAGGCCCAAGGCTCCTGAGAGGCATCCGGCCCTCCCTGGGCTGTGCCAGCAGCTTGGAGAACCCACACTCAATGAACGCAGCACTCCACTACCCAGGAAATGCCTTCCTGCCCTCTCCTCATCCCATCCCTGGGCAGGGGACATGCAACTGTCTACAAGGTGCCAAGTACCAGGACAGGAAAGGAAAGATGCCAAAAATCCAGGGCTGCCCTCAGAGAAGGGCAACCATGCAGTCCCCATCTTGGCAAGGAAACACAATTTCCGAGGGAATGGTTTTGGCCTCCATTCTAAGTGCTGGACATGGGGTGGCCACAATCTGGAGCTGATGGCTCTTAAAGACCTGCGTCCTCTTCCCTAGGCGTCCCTTGGGCACATCTAGCACAACGATAAGCACAAAAGGTGCATCCAGCACTTTCTGTTACTATTGGTGGCAGGTTCATGAATGGCAACCAAAGGCAGTGTACGGGTCAAGATCATCAACGGGGAAGAGATagcatttcctgaaggcttcctaggtgccaggcactgttccattcctttgcatgttttgattaatttaatatttacaataattctaccaggaagaattattaccattattaccattattaccacaacttcacaaatgagaacactgaggcttagaggggttgggttgtccaaggttacagaggaagaaaacaggggagctggatctgagccaaggcatcaactccaaggtAACCCCTCAGTCACTTCAGTGCGTGTGCCCTGGTTACTGGGACATTCTTGACAAGCTTGGGGCAAGCCGGTGAGTCAGTGGGGGAGGACTTTCAGGAAGAGGTGGGTTCCCAGTTGGTGACAGAAGAGGAGGCTGCAAAGTGAAGGAGCAGGGGCTCCAGGTCTGGCGACAACCAGGGAAGGGACAGGGCAGGGATGGCTTGGACCACGAGAGGCACCCGAGTCAGGCAGTCACATACTTCCCGCTGGGGTCTACCATGTGAGGCATGGTGTGGGATCCTGGGAAGGAGACCAAGCCTCATTTCAGTTTGCTTATGGCCAAAGACAGGACCTGTGTACCCGACAACCCCTGGGACCTTTGCCAAAAAAACAGCAAACACCATTCACTCACTCATGTTAGATAAACACTGAGTGAAGACACTGGAGCCCAAGGACTGTGCGAGGTCAGCGCTGCCAATACAAGAAGCTGCACCCCTCCAGCTCGCctccctcaatggccactctgtgctccagccatgctggcttccttttaggtcctccacctccaggctgtagttcatgtgcttctttctggaatgttcttcccaacctacccactcaaccctcagactttaccataaatgtcatttcctcacatctgccttccctgacctgagaccaagccaggcttcccatgacgagcctcacagtacccCATCTCCGCTGAACAGATGCAGTAATAACCTACATAACccggggccatgatctatggctttgaatcctggctctgtcacttggccaggtctctcagcctttctgtgcctcagtttcctcatctataaaatgagatgacggcagtgcctgctcatgaagtgtgagTTAATGCACTCAAATCAATGGTGGTGCACGGTTTATATGAATATTAGTGATTACAAAATATTATCAATAGACCTTGTCACAACTGTTATTGAAGAATTAATCATGTAttggttatttaggtctctctctcctgccagaatgtgcgctcca--tggagaggtatgttgccttatccgtggctggatatatagagattcccacactgccttgcacaccagcactgctgggtaaatatttgctggctgcaggaaAACGTGAAGGAATAGGCCCTCCAGTGGGAGGAAAAGCACGAGTTGTGAGAGCAGAGCCACCACAGGAAACCAGGAGGCTAAGTGGGGTGGAAGGGACTGAGCTCTCGGACTCCCAGGAGTAAAAGCTTCCAAGTTGGGCTCTCACTTCAGCCCCTCCCACACAGGGAAGCCAGATGGGTTCCCCAGGACCAGGATTCCCCAAGGGGGCTGCTCCCAGAGGGTGTGTTGCTGGGATATCCCAGGACAGGGATGGCCCTCTCATCAGGTGGGGGTGGGTGGCAGCACCCACCTGCCGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCGCCGCAGGTCTGGCTGGATGAGGGGCACGGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCCTGTGGGTGGGAGCCGGAGCATCAGAGCCACCCACGACCACCTGCACCCACCCACCACAGGGCAGCGTGGTGTTGAGACAACACAGCCCTCATCCCAACTATGCACATAGCTTCAGCCTGCACAGATAGGGGAGTAGGGGACAGAGCATTTGGTGAGAGGCCAGGAGCGCATAGATGGGACTCTGCTGATGCCTGCTGAGTGAATGAGGTAAAGGGCAGGACCAGGGACTGGGGAATCTGTAGGGTCAATGGAGGAGTTCAGAGAAGGTGCAACATTTCTGACCCCCTACAAGTTGCTTGCTACCTGCCAGGTACCCTTTCCATACATTGTCTCAGTTCAGCTCCCTACCTTGGATAAACAAGAAACCTTGGTTGCGGAGGAAAAAAGAGGCTGGAAACAAAGGGGTAGAAATGGGGTAGTGGGGGAGATTGCCTGATCAACTGCCAAATGGTACCCAGTTCTGGAAAAGCACAAAAAATGTGCACACACGGGTTCTTCCCACTTTAACCCCTGAGGAATTTGAGGCCTGCTCCTGAAACAGACTGGGCAGTGGCTAGTGACTCTAGGTATAGGAGTATCCAGCCCTGCTCACCCAGGCTAGAGCTTAGGGGGCCAAGAGGAAAGAGGTGCCTGTGGGGGTGGAGGACAGGAAGGAAAAACACTCCTGGAATTGCAAAGTGAGGGCAGAGTCTATTTATATTGGGTTTAATTAACTCCTCTCCCTGGTGCCACTAAAGCAGCAATCACACTGCAGACAGCACTGATTTGATTGGCAAGAGATGCACCAGGCAGAATATTAAGGGACCAGGCCCCTATAAATAGGCCTAATCACAGCCCCTCGCTGGAAAATGCTAAGGAAGACATTAATCAGGCCTGGCACTGTGCCCTAGACCTGCTCCCCTAGGCACTACAGTGGGGCCCTTGGTTGCAACACAAGTAGGTAAGGATGGATGAGTCTGGTATGAAGGGCCTAGGAGATTTCATTTGGGTTTAAAATGCTGTGACCCTGAGTAAGTTGCTGTCTCTGAATCTGATCCTTTCCATTTCCCATTCTCCAAACTGAGAACTAGCACTGCTGAGACGTGGTTATTCCCAATAATAATTTGTATATTTTACATAACGTACCACACCAACATCTTCACCCAGCTGGAGCCTACTCCTTTGCTCCCCCTGCTGGCTTCCCCAGCCCTCCCTTCTGCCCTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTTTGCATACAGGCTTTCCAGATCTGTACTTGCCTTGAATACTCATCAGAGCCCAGGAGTTACTCCTCACCTCCCACTTATTTTTCCTCCCATCAAATAACTAAAGCATGGCCAGCTGATGCCCAGCCAACTGAGAAACCTAACCCTCTGAGACCACCACACCCCTTTCAAGCATGTTCCTCCCTCCCCTTCTTTGTATTTATACTGACGCAAGTTTGCTGGCTGTcctaacttatttctgtgcctcagttctcccatatgtaagatcacaaagggggtaaagatgcaagATATTTCCTGTGCACATCTTCAGATGAATTTCT------TGTGTGTGTGTTTGCTCACACATATGCGTGAAAGAAGAGTACATACACAAAT---CTCAAAAAGGAGGCAGCAAGCCCGTTCAAGAATGGGACTGAATACACCTGATGAGTGGTTTACTTTCTGTCTGCAAACATCTACTGATCATCTGTTAGGTGCAGGCCATGATCACAACAAAGACGAATAAGACACTACACTAGCCAGGGAGAGTCTCAAAAACAACTAAACTCAAATTAAATTCATTCTAATCCAGTCATGAGTACAAAGCTAAGGAGTGACAAATCCCTTTTGGAGTTAGGGGAGTCAGGAAAAAGCTCTTAGCAGAATGTGTGCCTCTCggctgggcacagcggctcacgcctgtaatcccagcactttgggaggcgaaggcaggcagatcacctgaggtcaggagttcgagaccagtctgaccaacatggtgaaactccatctctactaaaaatacaaaattagccaggcgtggtggtgcatgcctgtaatcccagctactcgggaggctgaggaaggagaatcacttgaaccggggaggtcgaggttgcagtgtgccgagatcgcgccattgcactccagcctgggcaacaaaagtgaaCCAGGTCCAGGAAGAAGGTGCAAAGACAGCATTCCAGGTAAAAGAAACAGCTTGAACAAAAAGTGTGTAGGGGAACAGCAAGCGGTCTTGAGTGCTGAGGGTACAATCATCCTTGGGGAAGTACTAGAAGAAAGAATGATAAACAGAGGCCAGTTTGTTAAAAACACTCAAAATTAAAGCTAGGAGTTTGGACTTGTGGCAGGAATgaaatccttagacctgtgctgtccaatatggtagccaccaggcacatgcagccactgagcacttgatatgtggatagtctgaattgagatgtgccataagtgtaaactatgcaccaaatttcaaagactagaaaaaaagaatgtaaaatata-----attttatattgattacatgctaaaataaccatatttgggatatactggattttaaaaatatattgctaatttcatctgtttctttttacttttAGAAATCACATATGTGACTTAAATATTTCTTTTCTTTTTCTTTCCTCTCACTCAGCGTCCTGTGATTCCAAAGAAATGAGTCTCTGCTCTTTTTGGGCAGGAGATATCCTAGAATGGACTCTGACCTAAGAATCAAAATTAATAATCATAACGTTATCATTTTATGGCCCCTTCTTCCTATATCTGGTAGCTTTTAAATGATGACCATGTAGATAATCTTTATTATCCCTCTTTCAGCAGACGGTATTTTCTTATGCTACAGTATGACTGCTAATAATACCTACATACGTTAGAACCATTCTGACTCCTCAAGAatctcatttaactcttattatcagtgaatttatcatcatccccaattttagataaggaaatggggttagaaagaccaaataacattttttcaacatcaaaacactagcttgagatcaagcccaaacttggatctgttgtctgaattccaagctttttg----ttattgatatgttttgttgtTTTCATGCAATAATGCAAATCTTAGCCCAAACATTTTGTTAGTAGTACCAACTGTAAGTCACCTTATCTTGATACTTTGTCTTTATGTAAACCTAAATTAGATCTGTTTTTGATACTGAGGGAAAAACAAGGGAATCTAACACTAACCagcccgtagtgtgtggtcaacactttcgttactttagtatacatcaccccaattgtttgtcttcaccacacactt 
+
+a score=407272.0
+s hg18.chr1     18260 1630 + 247249719 GATTTTGTTGGCGGAAAAAAAAATTTATCAAAAGTCGTCTTCTATCAGGGAGTTTTATGAGAAACCCTAGCTCCTCAGTTCCACAGTGGGTAACTGTAATTCATTCTAGGTCTGCGATATTTCCTGCCTATCCATTTTGTTAACTCTTCAATGCATTCCACAAATACCTAAGTATTCTTTAATAATGGTGGTTTTTTTTTTTTTTTGCATCTATGAAGTTTTTTCAAATTCTTTTTAAGTGACAAAACTTGTACATGTGTATCGCTCAATATTTCTAGTCGACAGCACTGCTTTCGAGAATGTAAACCGTGCACTCCCAGGAAAATGCAGACACAGCACGCCTCTTTGGGACCGCGGTTTATACTTTCGAAGTGCTCGGAGCCCTTCCTCCAGACCGTTCTCCCACACCCCGCTCCAGGGTCTCTCCCGGAGTTACAAGCCTCGCTGTAGGCCCCGGGAACCCAACGCGGTGTCAGAGAAGTGGGGTCCCCTACGAGGGACCAGGAGCTCCGGGCGGGCAGCAGCTGCGGAAGAGCCGCGCGAGGCTTCCCAGAACCCGGCAGGGGCGGGAAGACGCAGGAGTGGGGAGGCGGAACCGGGACCCCGCAGAGCCCGGGTCCCTGCGCCCCACAAGCCTTGGCTTCCCTGCTAGGGCCGGGCAAGGCCGGGTGCAGGGCGCGGCTCCAGGGAGGAAGCTCCGGGGCGAGCCCAAGACGCCTCCCGGGCGGTCGGGGCCCAGCGGCGGCGTTCGCAGTGGAGCCGGGCACCGGGCAGCGGCCGCGGAACACCAGCTTGGCGCAGGCTTCTCGGTCAGGAACGGTCCCGGGCCTCCCGCCCGCCTCCCTCCAGCCCCTCCGGGTCCCCTACTTCGCCCCGCCAGGCCCCCACGACCCTACTTCCCGCGGCCCCGGACGCCTCCTCACCTGCGAGCCGCCCTCCCGGAAGCTCCCGCCGCCGCTTCCGCTCTGCCGGAGCCGCTGGGTCCTAGCCCCGCCGCCCCCAGTCCGCCCGCGCCTCCGGGTCCTAACGCCGCCGCTCGCCCTCCACTGCGCCCTCCCCGAGCGCGGCTCCAGGACCCCGTCGACCCGGAGCGCTGTCCTGTCGGGCCGAGTCGCGGGCCTGGGCACGGAACTCACGCTCACTCCGAGCTCCCGACGTGCACACGGCTCCCATGCGTTGTCTTCCGAGCGTCAGGCCGCCCCTACCCGTGCTTTCTGCTCTGCAGACCCTCTTCCTAGACCTCCGTCCTTTGTCCCATCGCTGCCTTCCCCTCAAGCTCAGGGCCAAGCTGTCCGCCAACCTCGGCTCCTCCGGGCAGCCCTCGCCCGGGGTGCGCCCCGGGGCAGGACCCCCAGCCCACGCCCAGGGCCCGCCCCTGCCCTCCAGCCCTACGCCTTGACCCGCTTTCCTGCGTCTCTCAGCCTACCTGACCTTGTCTTTACCTCTGTGGGCAGCTCCCTTGTGATCTGCTTAGTTCCCACCCCCCTTTAAGAATTCAATAGAGaagccagacgcaaaactacagatatcgtatgagtccagttttgtgaagtgcctagaatagtcaaaattcacagagacagaagcagtggtcgccaggaatggggaagcaaggcggagttgggcagct 
+s panTro2.chr15 30886 1625 - 100063422 GATTTTGTTGGCGGAAAAAAAAATTTATCAAAAGTCGTCTTCTATC--GGAGTTTTATGAGAAACCCTAGCTCCTCAGTTCCACAGTGGGTAACTGCAATTCATTCTAGGTCTGCGATATTTCCAGCCTATCCATTTCGTTAACTCTTCAATGCATTCCATAAATGCCTAAGTATTCTTTAATAATGGTGG--TTTTTTTTTTTTTGCATCTATGAAGTTTTTTCAAATTCTTTTTAAGTGACAAAACTTGTACATGTGTATCGCACAATATTTCTAGTCGACAGCACTGCTTTCGAGAATGTAAACCGTGCACTCCCAGGAACATGCAGACACAGCGCGCCTCTTTGGGACCACGGTTCATAATTTGGGAGTGCTCGGAGCCCTTCCTCCAGACCGTTCTCCCACACCCCGCTCCAGGGTCTCTCCCGGAGTTACAGGCCTCGCTGTAGGTCCCGGGAACCCAACGCGGTGTCAGAGAAGTGGGGTCCCCTACGAGGGACCAGGAGCTCCGGGCGGGCAGCAGCTGCGGAAGAGCCGCGCGAGGCTTCCCAGAACCCGGCCGGGGCGGGAAGACGCAGGAGTGGGGAGGCGGAACCGGGACCCCGCAGAGCCCGGGTCCCTGCGCCCCACAAGCCTTGGCTTCCCTGCTAGGGCCGGGCAAGGCCGGGTGCAGGGCGCGGCTCCAGGGAGGAAGCTCCGGGGCGAGCCCAAGACGCCTCCCGGGCGATCGGGGCCCAGCGGCGGCGTTCGCAGTGGAGCCGGGCACCGGGCAGCGGCCGCGGAACACCAGCTTGGCGCAGGCTTCTCGGTCAGGAACGGTCCCGGGCCTCCCGCCCGCCTCCCTCCAGCCCCTCCGGGTCCCCTACTTCGCCCCGCCAGGCCCCCACGACCCTACTTCCCGCGGCCCCGGACGCCTCCTCACCTGCGAGCCGCCCTCCCGGAAGCTCCCGCCGCCGCTTCCGCTCTGCCGGAGCCGCTGGGTCCTAGCCCCGCCGCTCACAGTCCGCCCGCGCCTCCGGGTCCTAACGCCGCCGTTCACCCTCCGCTGCGCCCTCCCCGAGCGCGGCTCCAGGACCCCGTCGACCCGGAGCGCTGTCCTGGCGGGCCGAGTCGCGGGCCTGGGCACGGAACTCACGCTCACTCCGAGCTCCCGACGTGCACACGGCTCCCATCCGTTGTCTTCCGAGCGCAGGGCCTCCCCTACCCGTGCTTTCTGCTCTGCAGACCCTCTTCCCAGACCTCCGTCCTTTGTCCCATCGCTGCCTTCCCCTCAAGCTCAGGGCCAAGCTGTCCGCCAGCCTCGGCTCCTCCGGGCAGTCCTCGCCCTGGGTGCGCCCCGGGGCAGGACCCCCAGCCCAGGCCCAGGGCCCGCCCCTGCCCTCCAGCCCTACACCTTGACCCGCTTTCCTGCCTCTCTCAGCCTACCTGACCTTGTCTTTACCTCTGTGGGCAGCTCCCTTGTGATCTGCTTAGTTCCCA-CACCCTTTAAGAATTAAATAGAGaagccagacgcaaaactacagatatcgtatgagtccacttttgtgaagtgcctagaatagtcaaaattcacagagacagaagcagtggtcgccaggaatggggaagcaaggcggagatgggcagct 
+
+a score=458960.0
+s hg18.chr1        19890 1848 + 247249719 cgtgttcaatgggtagagtttcaggctggggtgatggaagggtgctggaaatgagtggtagtgatggcggcacaacagtgtgaatctacttaatcccactgaactgtatgctgaaaaatggtttagacggtgaattttaggttatgtatgttttaccacaatttttaaaaaGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTTTAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCCGTTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTtagggttgccagattaaaagacaggatgcccagctagtttgaattttagataaacaacgaataatttcgtagcataaatatgtcccaagcttagtttgggacatacttatgctaaaaaacattattggttgtttatctgagattcagaattaagcattttatattttatttgctgcctctggccaccctaCTCTCTTCCTAACACTCTCTCCCTCTCCCAGTTTTGTCCGCCTTCCCTGCCTCCTCTTCTGGGGGAGTTAGATCGAGTTGTAACAAGAACATGCCACTGTCTCGCTGGCTGCAGCGTGTGGTCCCCTTACCAGAGGTAAAGAAGAGATGGATCTCCACTCAtgttgtagacagaatgtttatgtcctctccaaatgcttatgttgaaaccctaacccctaatgtgatggtatgtggagatgggcctttggtaggtaattacggttagatgaggtcatggggtggggccctcattatagatctggtaagaaaagagaGCATTGtctctgtgtctccctctctctctctctctctctctctcatttctctctatctcatttctctctctctcgctatctcatttttctctctctctctttctctcctctgtcttttcccaccaagtgaggatgcgaagagaaggtggctgtctgcaaaccaggaagagagccctcaccgggaacccgtccagctgccaccttgaacttggacttccaagcctccagaactgtgagggataaatgtatgattttaaagtcgcccagtgtgtggtattttgttttgactaatacaaCCTGAAAACATTTTCCCCTCACTCCACCTGAGCAATATCTGAGTGGCTTAAGGTACTCAGGACACAACAAAGGAGAAATGTCCCATGCACAAGGTGCACCCATGCCTGGGTAAAGCAGCCTGGCACAGAGGGAAGCACACAGGCTCAGggatctgctattcattctttgtgtgaccctgggcaagccatgaatggagcttcagtcaccccatttgtaatgggatttaattgtgcttgccctgcctccttttgagggctgtagagaaaagatgtcaaagtattttgtaATCTggctgggcgtggtggctcatgcctgtaatcctagcactttggtaggctgacgcgagaggactgcttgagcccaagagtttgagatcagcctgggcaatattgtgagattccatctctacaaaaataaaataaaatagccagtcatggtgtcacacacctgtagtcccagctacatgggaggctgaggcgggaggatcacttgagcttgggagatcgaggctgcagtgagctatgattgtaccactgcactccaggctgggcgacagagagagaccctgtctcagaaaaaaaaaaaaaaGTACTTTGTAATCTGTAAGGTTTATTTCAACACACACAAAAAAAGTGTATATGCTCCACGATGCCTGTGAATATACACACACACCACATCATATACCAAGCCTGGCTGTGTCTTCTCACAAATGCACTGCTAGGCACCACCC 
+s panTro2.chrUn 57103829 1814 -  58616431 tgtgttcaatgggtagagtttcaggctggggtgatggaagggtgctggaaatgagtggtagcgatggcggcgcaacagtgtgaatctacttaatcccactgaactgtatgcttaaaaatggtttagacggtgaattttaggttatgtatgttttaccacaatttttaaaaaGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTTTAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCCGTTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTtagggttgccagattaaaatacaggatgcccagttagtttgaattttagataaacaacgaataatttcgtagcataaatatgtcccaagcttagtttgggacatacttatgctaaaaaacattattggttgtttatctgagattcaaaattaagcattttatattttatttgctgcctctggccaccctaCTCTCTTCCTGACACTCTCTCCCTCTCCCAGTTTTGTCCGCCTTCCTTGCCTCCTCTTCTGGGGGAGTTAGATCGAGTTGTAACAAGAACATGCCACTGTCTCACTGGCTGCAGCGTGTGGTCCCCTTACCAGAGGTAAGGAAGAGATGGATCTCCACTCAtgttgtagacagaatgtttatgtcctctccaaattcttatgttgaaaccctaacccctaatgtgatggtatgtggagatgggcctttggtaggtaattacggttagatgaggtcatggggtggggccctcattatagatctggtaagaaaagagagcattgtctctctgtctccctctc-----------------------tctctctatgtcatttctctctct----ctatctca--tttctctctctctctctctctcctctgtcttttcccaccaagtgaggatgcgaagagaaggtggctgtctgcaaaccaggaagagagccctcaccaggaacccgtccagctgccaccttgaacttggacttccaagcctccagaactgtgagggataaatgtatgattttaaagtcgcccagtgtgtggtattttgttttgactaatacaaCCTGAAAACATTTTCCCCTCACTCCACCTGAGGAATATCTGAGTGGCTTAATGTACTCAGGACACAACAA---AGAAATGTCCCATGCACAAGGTGCACCCATGCCtgggtaaagcagcctggcacagagggaagcacacaggctcagggctctgctattcattctttgtgtgaccctgggcaagccatgaatggagcttcagtcaccccatttgtaatgggatttaattgagcttgccctgcctccttctgagggctgtagagaaaagatgtcaaagtattttgtaatctggctgggcgtggtggctcatgcctgtaatcccagcactttggtaggctgacgcgagaggactgcttgagcccaagagtttgagatcagcctgggcaatattgtgagattccatctctacaaaaataaaataaaatagccagtcatggtgtcacacacctgtagtcccagctacatgggaggctgaggcgggaggatcacttgagcttgggagatcgaggctgcagtgagctatgattgtaccactgcactccaggctgggcgacagagagagaccctgtctcag--aaaaaagaaaaagtactttgtaatctgtaaggtttatttcaacacACACAAAAAAAGTGTATATGCTCCACGATGCCTGTGAATATACACACACACCACATCATATACCAAGCCTGGCTGTGTCTTCTCACAAATGCGCTGCTGGGCACCACCC 
+
+a score=97796.0
+s hg18.chr1        21738 409 + 247249719 CCAGTTCTAGAATCACACCAGCCAGTTCACCCTCCAGATGGTTCACCCTCAACTTCATAAAAGTTCCCTACCTAATCTACT---GACAGGCTCATCCCCGACCTAATTTTAAAGATTTCCTAGGA----------------------------------GCTGCAGTGGGAATCCTGGACCTCAGCCTGGACAAAGAACAGCTGCAGGTCATTCTCATGTGTGGACACAGAAGCTCTGCCTGCCTTTGCTGGCCAGCTGGGCTGAGCGGGCCTGGGAA-TTAAGGCTGCAGGGTTGGTCCCAGGCAGTCTTGCTGAAGCTTGCCACATCCCCCAGCCTCCTGGATTTGCCAGGATCCAAGAGCATGGACTTTAGGAATTCCTGGTGGAGGAGTGAAGAAAATGTGACAGGGTGTCCTAAGCCCCGATCTACAGGAAGAAAACTGGAA 
+s panTro2.chrUn 57107006 446 -  58616431 CCAGTTCTAGAACCAGACCAGACAGTTCACCCTCCAGACGGTTCACCCTCAACTGTATAAAAGTTCTCTACCTAATCTACTACTGACAGACTCATCTCAGACCTAATTTTAAAGATTTCCTAGGAACTGAATTGCAAAAACTTTTACCCTCACCCTAGAGCTGCAATGGGAATCCTG-ACCTCAGCGTAGACAAAGAAAAGCTGCAGGTCATTCTCATGTGTGGACACGGAAGCCCTGCCTGCCTTTGCTGGCCAGCTGGGCTGAGTGGGCCTGGGAAATTAAGGCTGCAGGGTTGGTCCCAGGCAGTCTTGCTGAAGCTTGCCACATCCCCCAGCCTCCTGGATTTGCCAGGATCCAAGAGCATGGACTTTAGGAATTCCTGGTGGAGGAGTGAAGAAAATGTGACAGGGTGTCCTAGGCCCCAATCTACAGGAAGAAAACTGGAA 
+
+a score=7233.0
+s hg18.chr1        22147 35 + 247249719 ATAAGACTGAGGACTTAGTTTAAGATGTTCCTACT 
+s panTro2.chrUn 57107452 35 -  58616431 ATAAGACTGAGGACTTAGTTTAAGATGTTCCTACT 
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/6_mask_cpg.maf	Tue Apr 01 09:12:41 2014 -0400
@@ -0,0 +1,57 @@
+##maf version=1
+a score=356676.0
+s hg18.chr1      2817 1438 + 247249719 GTCATCCCCTTCACTCCCAGCTCAGAGCCCAGGCCAGGGGCCCCCAAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCCTGGCTGCCTCCAGCTGGGT#GACAGACAGG#GCTGGAGAAGGGGAGAAGAGGAAAGTGAGGTTGCCTGCCCTGTCTCCTACCTGAGGCTGAGGAAGGAGAAGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCTTAGCCTCTGTTCCCA##AAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACA#GCTGTTGGCCTGGATCTGAGCCCT#GTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCACTCCTGCCTTTTCCTTTCCC#AGAGCCTCCACCACCCC#AGATC#CATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGG##CTG#GCCCTTCCTTTGCTCTGCCC#CTGGAGA#GGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCC#TTGGAGAAAACAGGGGAATCCC#AAGAAATGGTGGGTCCTGGCCATCC#TGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTG##TGGCCGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATT--TGTCCTGCCCACCTTCTTAGAAG##AGA#GGAGCAGACCCATCTGCTACTGCCCTTTCTATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGT##ATGGCACCTCCCTCCCTCTCAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCC#TGTCTGTCACTGAAACCTTTTT#GTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGGACCAACAGGGGCAGGAGGCAGTCACTGACCCC#AGA##TTTGCATCCTGCACAGCTAGAGATCCTTTATTAAAAG 
+s panTro2.chr15 16051 1440 - 100063422 GTCATCCCCTTCACTCCCAGCTCTGAGCCCAGGCCAGGGGCCCCCAAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCCTGGCTGCCTCCAGCTGGGT#GACAGACAGG#GCTGGAGAAGGGGAGAAGAGGAAAGGGGGGCTGCCTGCCCTGTCTCCCACCTGAGGCTGAGGAAGGAGAGGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCCTAGCCTCTGTTCCCA##AAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAATGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACA#GCTGTTGGCCTGGATCTGAGCCCT#GTGGAGCTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCAGTCCTGCCTTTTCCTTTCCC#AGAGGCTCCACCACCCC#AGATC#CACTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGG##CTG#GCCCTTCCTTTGCTCTGCCC#CTGGAGA#GGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCC#TTGGAGAAAACAGGGGAATCCC#AAGAAATGGTGAGTCCTGGCCATCC#TGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTG##TGGCAGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTCTGTCCTGCCCACCTTCTAAGAAG##AGA#GGAGGACACCCATCTGCTTCTGCCCTTTCCATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCTATTTAAAAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCACTTCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGT##ATGGCACCTCCCTCCCTCTCAACTACTTGAGCAAACTTGAAGACATCTTCAACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCC#TGTCTGTCACTGAAACCTTTTT#GTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGCACCAACAGGGGCAGGAGGCAGTCACTGACCCC#AGA##TTTGCATCCTGCACAGCTAGAGGTCCTTAATTAAAAG 
+
+a score=33380.0
+s hg18.chr1      4393 135 + 247249719 GTGTGGCCTCAAGCCAGCCTTCC#CTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCC#TCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCC#TGTCAGAGCAA#GGCCCAAGTCTG 
+s panTro2.chr15 17634 135 - 100063422 GTGTGGCCTCAAGCCAGCCTTCC#CTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCC#TCACCCCCTCCCAGGGAAGCAGGTCTCAGCAGCTTGTCCTGGCTGTGTCC#TGTCAGAGCAA#GGCCCAAGTCTG 
+
+a score=364526.0
+s hg18.chr1      4528 1436 + 247249719 GGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTA#GATTCCCAGT##TCCTC#TCCTCCTCTGCCTGTGGCTGCTG#GGTGG#GGCAGAGGAGGGATGGAGTCTGACA###GGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGCAGGACAGAATTACAAGGTGCTGGCCCAGGG#GGGCAG#GGCCCTGCCTCCTACCCTTG##CCTCATGACCAGCTTGTTGAAGAGATCC#ACATCAAGTGCCCACCTTGGCT##TGGCTCTCACTGCAA#GGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATG#GACCGGTGACTCCCTGTCCCCACCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGT##ATCCCTGACCCAGCACCGGGC#CTGATGAGACAG#GGCTGTTTGAGGAGCCACCTCCCAGCCACCT#GGGGCCAGGGCCAGGGTGTGCAGCAccactgtacaatggggaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcag##ctgggtacaagctcaAAACCATAGTGCCCAGGGCACTGCC#CTGCAGG##CAGGCAT##CATCACA-----CCAGTGTCTG##TTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACC#CTCTTGGCAGT##AAGAAGATTCTCCTGTCA--GTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCCACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGGTGG#GGCCCAGGGCTTCCAGCATGTGCCCTAGGGGAAGCAGGGGCCAGCTGGCAAGAGCAGGGGGTGGGCAGAAAGCACCCGGTGGACTCAGGGCTGGAGGGGAGGAGG##ATCTTGCCCAAGGCCCTCC#ACTGCAAGCTCCAGGGCCC#CTCACCTTGCTCCTGCTCCTTCTGCTGCTGCTTCTCCAGCTTT##CTCCTTCA#GCTG##CAGCTTGGCCTTGCC#ATGCCCCCAGCTTGG#GGATGGACTCTAGCAGAGTGGCC-AGCCACCGGAGGGGTC#ACCACTTCCCTGGGAGCTCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGGGCTGGGGAAGCTTACTGTGTCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAA##AGGAGCCCTG##CTGGGGAGGCCGGACCTTTGGAGACTGTGT 
+s panTro2.chr15 18013 1444 - 100063422 GGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTA#GATTCCCAGT##TCCTC#TCCTCCTCTGCCTGTGGCTGCTG#GGTGG#GGCAGAGGAGGGATGGAGTCTGACA###GGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGCTTCCCCCAGCCCCCAGAGACTTAAATACAGGAAGAAAAAGGCAGGACACAATTACAATGTGCCGGCCCAGGG#GGGCAG#GGCCCTGCCTCCTACCCTTG##CCTCATGACCAGCTTGTTGAAGAGATCC#ACATCAAGTCCCCACCTTGGCT##TGGCTCTCACTGCAA#GGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATG#GACCGGTGGCTCCCTGTCCCCAGCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGT##ATCCCTGACCCAGCACCGGGC#CTGATGAGAAAG#GGCTGTTTGAGGAGCCACCTCCCAGCCACCT#GGGGACAGGGCCAGGGTGTGCAGCACcactgtacaatggggaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcag##ctgTGTACAAGCTCAAAACCATAGTGCCCAGGGCATTGCC#CTGCAGG##CAGGCAT##CATCACATCACACCAGTGTCTG##TTCACAGCAGGCATCATCAGTAGCCTCAAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACC#CTCTTGGCAGT##AAGAAGATTCTCCTGTCACAGTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCCACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGGTGG#GGCCCAGGGATTCCAGCATGTGCCCTAGGAGAAGCAGGGGCCAGCTGCCAAGAGCAGGGGGTGGGCAGAAAGCACCCAGTGGACTCAGGGCTGGAGGGAAGGAGG##ATCTTGCCCAAGGCCCTCC#ACCGCAGGCTCCAGGGCCC#Ctcaccttgctcctgctccttctgcttcttcttctccagcttt##ctccttcA#GCTG##CAGCTTGGCCTTGCC#ATGCCCCCAGCTTGG#GGATGGATTCTAGCAGAGTGGCCCGGCCACCGGAGGGGTC#ACCACTTCCCTGGGAGCTCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGGGCTGGGGAAGCTTATTGTATCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAA##AGGAGCCCCG##CTGGGGAGGCCGGACCTTTGGAGACTGTGT 
+
+a score=521291.0
+s hg18.chr1      5995 1988 + 247249719 CCTGAG#GCGGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTAGCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTTGCACACA#GAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTACACTGGGAGACACAGCAGTGAAGCTGAAATGAAAAATGTGTTGCTGTAGTTT-----GTTATTAGACCCCTTCTTTCCATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCTAGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAACAAGATATTTGAAATGGAAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACCCACAGAAAATCCACCC#AGTGCACTGAGCA##CCAGAAATCAGGTGGCCTCAAAGAGCTGCTCCCACCTGAAGGAGA####CTGCTGCTGCTGT##TCCTGCCTGG##CCTTGGCCTACAGGGGCC##GGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggtggtggtggggg#ggtgggggtggtg---------ttagtACCCCATCTTGTAGGTCTGAAACACAAAGTGTGGGGTGTCTAGGGAAGAAGGTGTGTGACCAGGGAGGTCCCCGGCCCAGCTCCCATCCCAGAACCCAGCTCACCTACCTTGAGAGGCT#GGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGT#GGCAATGTACATGAGGT##TTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGTGAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGTGGAATAAGGGGCCCAACAGCCTTGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTGCACCTGTCTCCACCTCTGTCCC#CCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGG##ACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAG#GTGCACTGTGGGGTCCCAGGCCTCCC#AGCC#AGCCACCC#TCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCC#CCCACACCCCT#GGCCCTGCCCTCTGGCCATACAGGTTCT#GGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCAT##TCCT#GGGCTCCGGCTTGGTGCTCA##CACACAGGAAAGTCCTTCAGCTTCTCCTGAGAGGGCCAGGATGGCCAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGCTGCCATCCCATCCCAGTCAGCCTCCTCTGGGGGACAGAACCCTATGGTGGCCCCGGCTCCTCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGC-----TATATG###GGCCAGCAGACCTGCAGGGCCC#CTC#TCCAGGGGG#GGTGCTTGCTCTGGATCCTGTGG#GGGGG##TCTCTGCAGGCCAGGGTCCTGGG##CCC#TGAAGATGGAGCCATATTCCTGCAGG##CCCTGGAGCAGGGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAGGCTCAGAGGGCTAGGATTGCT 
+s panTro2.chr15 19485 2006 - 100063422 CCTGAG#GCAGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTAGCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTGGCACACA#GAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTAGACTGGGAGATACAACAGTGAAGCTGAGAAGAAAAATGTGTTGCTGTAGTTTAGTTGGTTATTAGACCCCTTCTTTCCATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCTAGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAACAAGATATTTGAAATGGGAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACCCACAGAAAATACACCC#AGTGCACTGAGCA##CCAGAAATGAGGTGGCCTCAAAGAGCTGCTCCCACCTGAAGGAGA####CTGCTGCTGCTGT##TCCTGCCTGG##CCTTGGCCTACAGGGGCC##GGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggaggtggtggggg#ggtgggggtggtgggggtgctgttagtACCCCATCTTGTAGGTCTGAAACACAAAGTGTGGGGTGTCTAGGGAAGAAGGTGTGTGAGCAGGGAGGTCCCCAGCCCAGCTCCCATCCCAGAGCCCAGCTCACCTGCCTTGAGAGGCT#GGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGT#GGCACTGTACATGAGGT##TTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGTGAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGTGGAATAAGGGGCTCAACAGCCTGGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTGCACCTGTCTCCACCTCTGTCCC#CCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTGTACCTACAGGGG##ACATGGGGGTCAGGCAAGCTGACACCTGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAG#GTGCACCGTGGGGTCCCAGGCCTCCC#AGCC#AGCCACCC#TCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCC#CCCACACCCCT#GGCCCTGCCTTCTGGCCATACAGGTTCT#GGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCAT##TCCT#GGGCCCCGGCTTGGTGCTCA##CACACAGGAAAGTACTTCAGCTTCTCCTGGGAGGGCCAGAATGGCCAAGGGATGGTGAATATTTAGTGCCGGGCCTAATCAGCTGCCACCCCATCCCGGTCAGCCTCCTCTGGGGGACAGAACCCT-TGGTGGCCCCGGCTCCTCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGCTAAGTTATGTG###GGCCAGCAGACCTGCAGGGCCC#CTC#TCCAGGGGG#GGTGCTTGCTCTGGATCCTGTGG#GGGGG##TCTCTGCAGGCCAGGGTCCTGGG##CCC#TGAAGATGGAGCCATATTCCTGCAGG##CTCTGGAGCAGGGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAGGCTCAGAGGGCTAGGATTGCT 
+
+a score=311095.0
+s hg18.chr1      7983 1272 + 247249719 TGGCAGGAGAGGGTGGAGTTGGAAGCCTGGG##AGAAGAAAGCTCAAGGTACAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCA#GGGGAAATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGTATGGGGACTACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCTGCCATGGAGAAGATCACAGAGGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGGTGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGT##AGGAGTTGA#GGTGCTGAGTTCCCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCTGAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTACTGATGGGGCAAGCACTTCACAACCCCTCATGATCA##TGCAGCAGACAATGTGGCCTCTGCAGAGGGGGAA#GGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTC#TCACCTAAATTCAGA#GGGGAACTGCCCCTGCACATACTGAA#GGCTCACTGAGCAAACCCCGAGTCCC#ACCACC#CCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtg#ggggtgggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttgtgtgcttgcatctcatggaac#ccatttccccagacatccctgtggctggctcctGATGCCC#AGGCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGGCC#CAGCAAGGCC#CTCTCACTGCAAAGTTAACTCTGATG##TGTGTAACACAACATCCTCCTCCCAGT##CCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCCACACTCCA##TGCAGAGCAGCCTCAGCACTCACCGGGCA##AG##AGCCTGTGTGGTG##CAGGGATGAGAAGGCAGAGG####ACTGGGGTTC#TGAGGAAGGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGTTTGAGAAGGCAGAGG##C 
+s panTro2.chr15 21491 1270 - 100063422 TGGCAGGAGAGGGTGGAGTTGGGAGCCTGGG##AGAAGAAAGCCCAAGGTAGAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCA#GGGGAAATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGCATGGGGACTACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCCGCTGGGAGATCCTGCCATGGAGAAGATCACAGAGGCTGGGCTGCTCCCCACCCCCTGCACACCTCCTGCTCCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTTAAGTCAGGGTCACCTGCTTGCCAGGGCTGATCTTGGTGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGT##AGGAGTTGA#GGTACTGAGTTCCCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCTGAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTATTGATGGGGCAAGCATTTCACAACCCCTCATGATCA##TGCAGCAGACAAAGTAGCCTCTGCAGAGGGGGAA#GGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTC#TCACCTAAATTCAGA#GGGGAACTGCCCCCGCACATAGTGAA#GGCTCACTGAGCAAACCCTGAGTCCC#ACCACC#CCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtg#ggggtgggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttatgtgcttgcatctcatggaac#ccatttccccagacatgcctgtggctggctcctGGTGCCC#AGGCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGGCC#CAGCAAGGCC#CTCTCACTGCAAAGTTAACTCTGATG##TGTGTA--ACAACATCCTCCTCCCAGT##CCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCCACACTCCA##TGCAGAGCAGCCTCAGCACTCACCGGGCA##AG##AGCCTGTGTGGTG##CAGGGATGAGAAGGCAGAGG####ACTGGGGTTC#TGAGGAAAGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGTTTGAGAAGGCAGAGG##C 
+
+a score=268744.0
+s hg18.chr1      9255 1055 + 247249719 GACTGGGGTTCATGAGGAAAGGGAGGGGGAGGATGTGGGATGGTGGAGGGGCTGCAGACTCTGGGCTAGGGAAAGCTGGGATGTCTCTAAAGGTTGGAATGAATGGCCTAGAATCCGACCCAATAAGCCAAAGCCACTTCCACCAA##TTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGAAGTCCCC#TGCCCTAAAGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCTGGGAGTACCAGCAGGCACTCAAG#GGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAG#GGGACCACCACCCAG##TGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGGTCCTCCAGCACAAGCTGTCTTAATTGACCCTAGTTCCCAGGGCAGCCTC#TTCTGCCTTGGGTGCTGACA##ACCTT#GGTAGGTGCATAAGCTCTGCATT##AGGTCcacaggggcagtgggagggaactgagactggggagggacaaaggctgctctgtcctggtgctcccacaaagg--agaagggctgatcactcaaagttg##aacaccaagctcaacaatgagccctggaaaatttctggaatggattattaaacagagagtctgtaagcacttagaaaaggcc##ggtgagtcccaggggccagcactgct##aaatgtacagcatttctctttgtaacaggattattagcctgctgtgcccggggaaaacatgcagcacag#gcatct##agtcagcaggattt#ga#ggcttctaacaaaatcttgtagacaagatggagctatgggggttggaggagagaacatataggaaaaatcagagccaaatgaaccacagccccaaagggcacagttgaacaatggactgattccagccttgca#ggagggatctggcagagtccatccagttcattcaacacctggttagaaaactggggccag 
+s panTro2.chr15 22901 1056 - 100063422 GACTGGGGTTCATGAGGAAAGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGCTGCAGACTCTGGGCTTGGGAAAGCTGGGGTGTCTCTAAAGGTTGGAATGAATGGCCTAGAATCGGACCCAATAAGCCAAAGCCACTTCCACCAA##TTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGGAGTCCCC#TGCCCTAATGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCTGGGAGTACCAGCAGGCACTCAAG#GGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAG#GGGGCCACCACCCAG##TGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGGTCCTCCAGCACAAGCTGTTTTAATTTACCCTAGTTCCCAAGGCAGCCTC#TTCTGCCTTGGGTGCTGACA##ACCTT#GGTAGGTGCATAAGCTCTGCATT##AGGTCcacaggggcagtgggagggaactgagactggggagggacaaaggctgctctgtcctggtgctcccacaaaggacagaagggctgatcactcaaagttg##aacaccaagctcaacaatgagccctggaaaatttctggaatggattattacacagagagtctgtaagcacttagaaaaggcc##ggtgagtcccaggggccagcactgct##aagtgtacagcatttctctttgtaacaggattagtagcttgctgtgcccggggagaacatgcagcacag#gcatct##agtcagcaggattt#ga#ggcttctaacaaaatcctgtagacaagatggagctatgggggttggaggagagaacatatagg-aaaatcagagccaaatgaaccacagccccaaagggcacagttgaacaatggactgattccagccttgca#ggagggatctggcagagtccatccggttcATTCAACACCTGGTTAGAAAACTGGGGCCAG 
+
+a score=95099.0
+s hg18.chr1             10310 371 + 247249719 cacacaggggaagggtaagctggtttcatgat##aatcaaggctcagacaatttttaaaggccagagggtagactgcaatcaccaagatgaaatttacaaggaacaaatgtgaagcccaacatttaggttttaaaaatcaag##tataaatacagaaggtggagggaacttgctttagacacagttcaggtgaagaaagacctggaaacttctgttaactataagctcagtaggggctaaaagcatgttaat#ggcataaaaaggcaatgagatcttaggGCACACAGCTCCCC#CCCCTCTTCTGCCCTTCATCCTTCTTTCAATCAGCAGGGACCGTGCACTCTCTTGGAGCCACCACAGAAAACAGAG 
+s panTro2.chr9_random 4675776 371 +   7733331 cacacaggggaagggtaagttggtttcatgat##aatcaaggctcagacaattttcaaaggccagagggtagactgcaatcacccagatgaaatttacaaggaacaaatgtgaagcccaacatttaggttttaaaaatcaag##tataaatatagaaggtggagggaacttgttttagacacagttcaggtgaagaaagacctggaaacttctgttaactataagctcagtaggggctaaaagcatgttaat#ggcataaaaaggcaatgagatcttaggGCACACAGCTCCCC#CCCCTCTTCTGCCCTTCATCCTTCTTTCAATCAGCAGGGACGGTGCACTCTCTTGGAGCCACCACAGAAAACAGAG 
+
+a score=33853.0
+s hg18.chr1        10770 227 + 247249719 CAGAGCAGGAGGAGAGAGCACAGCCTGCAATGCTAATTTGCCAGGAGCTCACCTGCCTG##TCACTGGGCACAGA#GCCAGTGAGGCCAGAGGCCGGGCTGTGCTGGGGCCTGAG-CCGGGTGGTGGGGAG-------AGAGTCTCTCCCCTGCCC--CTGTCTCTTCCGTGCAGGAGG---------------AGCATGTTTAAGGGGACGGGTTCAAAGCTGGTCACATCCCCACCGAAAAAGCCCATGG 
+s panTro2.chr12 77693524 219 - 135371336 CAGAGCAGGAGGAGAGAGCATGGCCAGGAATGCTAATTTGCCAGGAGCTCACCTGCCTG##TCACAAGGCACAGG#GCCAATGAGGCCAGGGTCCAGTCTG-----GGGCATGAGATGGGGTGGTGGGGAGGAGAGAGACAGTCTCTCCTCTACCCACCTGTCTCTTCTGTGCAGGTGGTTTCCGAGCAGGTGAAGCACATTTAAAGGGGGAGGTTCTAAACTG---------------------------- 
+
+a score=83473.0
+s hg18.chr1             10997 329 + 247249719 ACAA##AAAAGCCCACTAGCTTGTCCAGTGCCACAGGAGGGGCAAGTGGAGGAGGAGAGGTGG#GGTGCTCCCCACTCCACTGCCAGTC#TCACTGGCTCTCCCTTCCCTTCATCCT##TTCCCTATCTGTCACCATTTCCTGT##T##TTTCCTCTGAATGTCTCACCCTGCCCTCCCTGCTTGCAAGTCCCCTGTCTGTAGCCTCACCCCTGTC#TATCCTGACTACAATAACAGCTTCTGGGTGTCCCTGGCATCCACTCTCTCTCCCTTCTTGTCCCTTCC#TGA#GGATGCCTGAGGAACCTTCCCCAAACTCTTCTGTCCCAT 
+s panTro2.chr9_random 4677170 329 +   7733331 ACAA##AAAAGCCCACTTGCTTGTCCAGTGCCACAGGAGGGGCAAGTGGAGGAGGAGAGGTGG#GGTGCTCCCCACTCCACTGCCAGTC#TCACTGGCTCTCCCTTCCCTTCATCCT##TTCCCTATCTGTCACCATTTCCTGT##T##TTTCCTCTGAATGTCTCACCCTGCCCTCCCTGCTTGCAAGTCCCCTGTCTGTAGCCTCACCCCTGTC#CATCCTGACTACAATAACAGCTTCTGGGTGTCCCCAGCATCCACTCTCTCTCCCTTCTTGTCCCTTCC#TGA#GGATGCTTGAGGAACCTTCCCCAAACTCTTCCGTCCCAT 
+
+a score=1716519.0
+s hg18.chr1     11326 6774 + 247249719 CCCTGCCCTGCTCAAAATCCAATCACAGCTCCCTAACAC#CCTGAATCAACTTGAAGTCCTGTCTTGAGTAATCC#TGGGCCCTAACTCACTCATCCCAACTCTTCACTCACTGCCCTGCCCCACACCCTGCCAGGGAGCCTCCC#TGGCACC#TGGGGACACAAAGGAACCAGGGCAAAGCTCCCTCAGCCCCATTCAAAGAGGCCTGGCCCACAGGCTCA#GGAAAGTCAGCCTCTCATGCCCC#AGAGCTGAGTGCAAGGGAGAGGCAG##CTGTCTGTGCTTCCCATGCAGAAGCACCCCCCTCCCACCCCTGTGCAGGCCGGCCTTC##GGCAGACCACCATACACCA##TTCCAAGCCACACTGAGGCCTCCCTCCAAGCCTGCAGCCCCCATTTCCAGACCCTGCCAGGGCAACCTGCATATCCACCTCCCTACCCTGCCCCCCTCTTCCAGGAGTCTGCCCTATGTGGAGTAAGCA##tggttttcctcttcagcaactatttcctttttactcaagcaatggccccatttcccttggggaatccatctctct##caggcttagtcccagagcttcaggtggggctgcccacagagctcctcagtctaagccaagtggtgtgtcatagtcccctggccccattaatggattctgggatagacatgaggaccaagccaggTGGGATGAGTGAGTGTGGCTTCTGGAGGAAGTGGGGACACAGGACAGCATTCTTTCCTGCTGGACCTGACCCTGTGTCATGTCACCTTGCTACCA##AGAGCATGGCCTGTCTGGGAATGCAGCCAGACCCAAAGAAGCAAACTGACATGGAAGGAAAGCAAAACCAGGCCCTGAGGACATCATTTTAGCCCTTACTCC#AAGGCTGCTCTACTGATTGGTTAATTTTTGCTTAGCTTGGTCTGGGGAGTTCTGACAGG##TGCCACCAATTCTTACC#ATTTCTCTCCACTCTAGACCCTGAGAAGCCCA###GGTTCATGCTAGCAATTAACAATCAATCT##CCCTATGTGTTCCCATTCCAGCCTCTAGGACACAGTGGCAGCCACATAATTGGTATCTCTTAAGGTCCAGCA##AGGTGGAGCACATGGTGGAGAGACAGATGCAGTGACCTGGAACCCAGGAGTGAGGGAGCCAGGACTCAGGCCCAAGGCTCCTGAGAGGCATCTGGCCCTCCCTG#GCTGTGCCAGCAGCTTGGAGAACCCACACTCAATGAA##CAGCACTCCACTACCCAGGAAATGCCTTCCTGCCCTCTCCTCATCCCATCCCTGGGCAGGGGACATGCAACTGTCTACAAGGTGCCAAGTACCAGGACAGGAAAGGAAAGA#GCCAAAAATCCAG#GCTGCCCTCAGAGAAGGGCAACCA#GCAGTCCCCATCTTGGCAAGGAAACACAATTTCC#AGGGAATGGTTTTGGCCTCCATTCTAAGTGCTGGACATGGGGTGGCCATAATCTGGAGCTGATGGCTCTTAAAGACCTGC#TCCTCTTCCCTAGG#GTCCCT#GGGCACATTTAGCACAA#GATAAGCACAAAAGGTGCATCCAGCACTTT--GTTACTATTGGTGGCAGGTTTATGAATGGCAACCAAAGGCAGTGTA#GGGTCAAGATTATCAACAGGGAAGAGATagcatttcctgaaggcttcctaggtgccaggcactgttccattcctttgcatgttttgattaatttaatatttaaaataattctaccaggaag--------------ctaccattattaccacaacttcacaaatgagaacaccgaggcttagaggggttgggttgcccaaggttacagaggaagaaaacaggggagctggatctgagccaaggcatcaactccaaggtAACCCCTCAGTCACTTCACTG#GTGTCCCCTGGTTACTGGGACATTCTTGACAAACT#GGGGCAAGCCGGTGAGTCAGTGGGGGAGGACTTTCAGGAAGAGGTGGGTTCCCAGTTGGTGACAGAAGAGGAGGCTGCAAAGTGAAGGAGCAGGGGCTCCAGGTCTGG##ACAACCAGGGAAGGGACAGGGCAGGGATGGCTTGGACCA##AGAGGCACCTGAGTCAGGCAGTCACATACTTCCC#CTGGGGTCTACCATGTGAGGCATGGTGTGGGATCCTGGGAAGGAGACCAAGCCTCATTTCAGTTTGCTTATGGCCAAAGACAGGACCTGTGTACCC#ACAACCCCTGGGACCTTTACCAAAAAAAGAGCAAACACCATTCACTCACTCATGTTAGATAAACACTGAGTGAAGTCACTGGAGCCCAAGGACTGTG##AGGTCAGC#CTGCCAATACAAGAAGCTGCAGCCCTCCAGCT##Cctccctcaatggccactccgtgctccagccatgctggcttccttttaggtcctccacctccaggctgtagttcatgtgcttctttctggaatgttcttcccaacctacccactcaaccctcagactttaccataaatgtcatttcctcac#tctgccttccctgacctgagaccaagccaggCTTCCCATGA##AGCCTCACAGTACCCCATCTCC#CTGAACAGATGCAGTAATAACCTACATAACccggggccatgatctatggctttgaatcctggctctgtcactaggccaggtctctcagcccttctgtgcctcagtttcctcatctataaaatgagatga#ggcagtgcctgctcatgaagtgtgagttaatgcactcaaatcaatggttgtgca#ggtttatatgaatattagtgattaCAAAATATTATCAatagaccttgtcacaactgttattgaagaactaatcatctattgcttatttaggtctttctctcctgccagaatgtg##ctccaggtggagaggtatgttgccttatcc#tggctggatatatagagattcccacactgccttgcacac#agcactgctgggtaaatatttgttggctgcaggaaAA##TGAAGGAATAGGCCCTCCAATGGGAGGAAAAGCA#GAGTTGTGAGAGCAGAGCCACCACAGGAAACCAGGAGGCTAAGTGGGGTGGAAGGGAGTGAGCTCT#GGACTCCCAGGAGTAAAAGCTTCCAAGTTGGGCTCTCACTTCAGCCCCTCCCACACAGGGAAGCCAGATGGGTTCCCCAGGACCGGGATTCCCCAAGGGGGCTGCTCCCAGAGGGTGTGTTGCTGGGATTGCCCAGGACAGGGATGGCCCTCTCATCAGGTGGGGGTGAGTGGCAGCACCCACCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCC#CCATCTGCTGGA#GGCCTCCTCT##CC#CAGGTCTGGCTGGATGAAGGGCA#GGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCCTGTGGGT#GGAGCCGGAGC#TCAGAGCCACCCA##ACCACCGGCAC#CCCCCACCACAGGGCAG##TGGTGTTGAGACAACACAGCCCTCATCCCAACTATGCACATAGCTTCAGCCTGCACAGATAGGGGAGTAGGGGACAGAGCATTTGCTGAGAGGCCAGGAG##CATAGATGGGACTCTGCTGATGCCTGCTGAGTGAATGAGGGAAAGGGCAGGGCCCGGGACTGGGGAATCTGTAGGGTCAATGGAGGAGTTCAGAGAAGGTGCAACATTTCTGACCCCCTACAAGGTGCTTGCTACCTGCCAGGCACCCTTTCCATACCTTGTCTCAGTTCAGCTCCCCACCTTGGATAAACAAGAAACCTTGGTTGCAGAGGAAAAAAGAGGCTGGAAACAAAGGGGTAGAAATGGGGTAGCAGGGGAGATTGCCTGATCAACTGCCAAATGGTACACAGTTCTGGAAAAGCACAAAAAATGTGCACACA#GGGTTCTTCCCACTTTAACCCCTGAGGAATCTGAGGCCTGCTCCTGAAACAGACTGGGCAGTGGCTAGTGACTCTAGGTATAGGAGTATCCAGCCCTGCTCACCCAGGCTAGAGCTTAGGGGGACAAGAGGAAAGAGGTGCCTGTGGGGGTGGAGGACAGGAAGGAAAAACACTCCTGGAATTGCAAAGTGAGGGCAGAGTCTATTTATATTGGGTTTAATTAACTCCTCTCCCTGGTGCCACTAAAGCAGCAATCACACTGCAGACAGCACTGATTTGATTGGCAAGAGATGCACCAGGCAGAATATTAAGGGACCAGGCCCCTATAAATAGGCCTAATCACAGCCCCTC#CTGGAAAATGGTAAGGAAGACATTAATCAGGCCTGGCACTGTGCCCTAGACCTGCTCCCCTAGGCACTACAGTGGGGCCCTTGGTTGCAACACAAGTAGGTAGGGATGGATGAGTGTGGCATGAAGGGCCTAGGAGATTTCACTTGGGTTTAAAATGCTGTGACCTTGAGTAAGTTGCCGTCTCTGAATCTGATCCTTTC#ATTTCCCATTCTCCAAACTGAGAACTAGCACTGCTGAGA##TGGTTATTTCCAATAATAATTTGTATATTTTACATAA##CACCACACCAACATCTTCACCCAGTTGGAGCCTACTCCTTTGCTCCC#CTGCTGGCTTCCCCAGCCCTCCCTTCTGCCCTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTTTGCATACAGGCTTTCCAGATCTGTACTTGCCTTGAATACTCATCAGAGCCCAGGAGTTACTCCTCACCTCCCACTTATTTTTCCTCCCATCAAATAACTAAAGCATGGCCAGCTGATGCCCAGCCAACTGAGAAACCCAACCCTCTGAGACCAGCACACCCCTTTCAAGCATGTTCCTCCCTCCCCTTCTTTGTATTTATACTGA#GCAAGTTTGCTGGCTGTcctaacttatttctgtgcctcagttctcccatatgtaagatcacaaagggggtaaagaTGCAAGATATTTCCTGTGCACATCTTCAGATGAATTTCTTGTTAGTGTGTGTGTGTTTGCTCACACATATG##TGAAAGAAGAGTACATACACAGATCTCCTCAAAAAGGAGGCAGCAAGCCC#TTCAAGAATGGGACTGAATACACCTGATGAGTGGTTTACTTTCTGTCTGCAAACATCTACTGATCATCTGTTAGGTGCAGGCCATGATCACAACAAAGA##AATAAGACACTACACTAGCCAGGGAGAGTCTCAAAAACAACTAAACTCAAATTAAATTCATTCTACTCCAGTCATGGGTACAAAGCTAAGGAGTGACAAATCCCTCTTGGAGTTAGGGGAGTCAGGAAAAAGCTCTTAGCAGAATGTGTGCCTCT#ggccgggc#cag#ggctca##cctgtaatcccagcactttgggagg##aaggcaggcagatcacctgaggtcgggagtt##agaccagtctgaccaacatggtgaaactccatctctactaaaaatacaaaattagccagg##tggtggtgcatgcctgtaatccccgctact#gggaggctgaggaaggagaatcacttgaaccaggaaggt#gaggttgcagtgtgcc#agat####ccatggcactccagcctaggcaac#agggtgaaCCAGGTCCAGGAAGAAGGTGCAAAGACAGCATTCCAGGTAAAAGAAACAGCTTGAACAAAAAGTGTGTAGGGGAACCGCAAG#GGTCTTGAGTGCTGAGGGTACAATCATCCTTGGGGAAGTACTAGAAGAAAGAATGATAAACAGAGGCCAGTTTGTTAAAAACACTCAAAATTAAAGCTAGGAGTTTGGACTTGTGGCAGGAATgaaatccttagacctgtgctgtccaatatggtagccaccaggcacatgcagccactgagcacttgaaatgtggatagtctgaattgagatgtgccataagtgtaaaatatgcaccaaatttcaaaggctagaaaaaaagaatgtaaaatatcttattattttatattgattac#tgctaaaataaccatatttgggatatactggattttaaaaatatatcactaatttcatctgtttctttttacttttAGAAATCACATATGTGACTTAAATATTTCTTTTCTTTTTCTTTCCTCTCACTCAG##TCCTGTGATTCCAAAGAAATGAGTCTCTGCTGTTTTTGGGCAGCAGATATCCTAGAATGGACTCTGACCTAAGCATCAAAATTAATCATCATAA##TTATCATTTTATGGCCCCTTCTTCCTATATCTGGTAGCTTTTAAATGATGACCATGTAGATAATCTTTATTGTCCCTCTTTCAGCAGA#GGTATTTTCTTATGCTACAGTATGACTGCTAATAATACCTACACA#GTTAGAACCATTCTGACTCCTCAAGAatctcatttaactcttattatcagtgaatttatcatcatcccctattttacataaggaaatggggttagaaagaccaaataacattttttcaacatcaaaacactagcttgagatcaagcccagacttggatctgt#gtctgaattccaagctttttgttatttattgatatgttttgttgtTTTCATGCAATAATGCAAATCTTAGCCCAAACATTTTGTTAGTAGTACCAACTGTAAGTCACCTTATCTTCATACTTTGTCTTTATGTAAACCTAAATTAGATCTGTTTTTGATACTGAGGGAAAAACAAGGGAATctaacactaaccagccc#tagtgtgtggtcaacacttt##ttactttagtatacatcaccccaattgtttgtcttcaccacacactt 
+s panTro2.chr15 23957 6770 - 100063422 CCCTGCCCTGCTTAAAATCCAATCACAGCTCCCTAACAC#CCTGAATCAACTTGAAGTCCTGTCTTGAGTAATCC#TGGGCCCTAACTCACTCACCCCAACTCTTCACTCACTGCCTTGCCCCACACCCTGCCAGGGAGCCTCCC#TGGCACC#TGGGGACACAAAGGAACCAGGGCAAAGCTCCCTCAGCCCCATTCAAAGAGGCCTGGCCCACAGGCTCA#GGAAAGTCAGCCTCTCATGCCCC#AGAGATGAGTGCAAGGGAGAGGCAG##CTGTCTGTGCTTCCCATGCAGAAGCACCCTCCTCCCACCCCTGTGCAGGCCGGCCTTC##GGCAGACCACCATACACCA##TTCCAAGCCACACTGAGGCCTCTCTCCAAGCCCGCGGCCCCCATTTCCAGACCCCACCAGGGCAACCTGCATATCCACCTCCCTACCCTGCCCCCCTCTTCCAGGAGTCTGCCCTATGTGGAGTAAGCA##tggttttcctcttcagcaactatttcctttttactcaagcaatggccccatttcccttggggaatccatctctct##caggcttagtcccagagcttcaggtggggctgcccacagagttcctcagtctaagccaagtggtgtgtcatagtcccctggccccagtaatggattctgggatagacatgaggaccaagccaggtgggatgggtaagtgtggcttctggaggaagtggggacacaggagagcattctttcctgctggACCTGACCCTGTGTCATGTCACCTTGCTACCA##ACAGCATGGCCTGTCTGGGAATGCAGCCAGACCCAAAGAAGCAAACTGACATGGAAGGAAAGCAAAACCAGGCCCTGAGGACATCATTTTAGCCCTTACTCC#AAGGCTGCTCTACTGATTGTTTAATTTTTGCTTAGCTTGGTTTGGGGAGTTCTGACAGG##TGCCACCAATTCTTACC#ATTTCTCTCCACTCTAGACCCTGAGAAGCCCA###GGTTCATGCTAGCAATTAACAATCAATCT##CCCTATGTGTTCCCATTCCAGCCTCTAGGACACAGTGTCAGCCACATAATTGGTATCTCTTAAGGTCCAGCA##AGGTGGAGCACATGGTGGAGAGACAGATGCAGTGACCTGGAACCCAGGAGTGAGGGAGCCAGGACTCAGGCCCAAGGCTCCTGAGAGGCATCCGGCCCTCCCTG#GCTGTGCCAGCAGCTTGGAGAACCCACACTCAATGAA##CAGCACTCCACTACCCAGGAAATGCCTTCCTGCCCTCTCCTCATCCCATCCCTGGGCAGGGGACATGCAACTGTCTACAAGGTGCCAAGTACCAGGACAGGAAAGGAAAGA#GCCAAAAATCCAG#GCTGCCCTCAGAGAAGGGCAACCA#GCAGTCCCCATCTTGGCAAGGAAACACAATTTCC#AGGGAATGGTTTTGGCCTCCATTCTAAGTGCTGGACATGGGGTGGCCACAATCTGGAGCTGATGGCTCTTAAAGACCTGC#TCCTCTTCCCTAGG#GTCCCT#GGGCACATCTAGCACAA#GATAAGCACAAAAGGTGCATCCAGCACTTTCTGTTACTATTGGTGGCAGGTTCATGAATGGCAACCAAAGGCAGTGTA#GGGTCAAGATCATCAACGGGGAAGAGATagcatttcctgaaggcttcctaggtgccaggcactgttccattcctttgcatgttttgattaatttaatatttacaataattctaccaggaagaattattaccattattaccattattaccacaacttcacaaatgagaacactgaggcttagaggggttgggttgtccaaggttacagaggaagaaaacaggggagctggatctgagccaaggcatcaactccaaggtAACCCCTCAGTCACTTCAGTG#GTGTGCCCTGGTTACTGGGACATTCTTGACAAGCT#GGGGCAAGCCGGTGAGTCAGTGGGGGAGGACTTTCAGGAAGAGGTGGGTTCCCAGTTGGTGACAGAAGAGGAGGCTGCAAAGTGAAGGAGCAGGGGCTCCAGGTCTGG##ACAACCAGGGAAGGGACAGGGCAGGGATGGCTTGGACCA##AGAGGCACCCGAGTCAGGCAGTCACATACTTCCC#CTGGGGTCTACCATGTGAGGCATGGTGTGGGATCCTGGGAAGGAGACCAAGCCTCATTTCAGTTTGCTTATGGCCAAAGACAGGACCTGTGTACCC#ACAACCCCTGGGACCTTTGCCAAAAAAACAGCAAACACCATTCACTCACTCATGTTAGATAAACACTGAGTGAAGACACTGGAGCCCAAGGACTGTG##AGGTCAGC#CTGCCAATACAAGAAGCTGCACCCCTCCAGCT##Cctccctcaatggccactctgtgctccagccatgctggcttccttttaggtcctccacctccaggctgtagttcatgtgcttctttctggaatgttcttcccaacctacccactcaaccctcagactttaccataaatgtcatttcctcac#tctgccttccctgacctgagaccaagccaggcttcccatga##agcctcacagtacccCATCTCC#CTGAACAGATGCAGTAATAACCTACATAACccggggccatgatctatggctttgaatcctggctctgtcacttggccaggtctctcagcctttctgtgcctcagtttcctcatctataaaatgagatga#ggcagtgcctgctcatgaagtgtgagTTAATGCACTCAAATCAATGGTGGTGCA#GGTTTATATGAATATTAGTGATTACAAAATATTATCAATAGACCTTGTCACAACTGTTATTGAAGAATTAATCATGTAttggttatttaggtctctctctcctgccagaatgtg##ctcca--tggagaggtatgttgccttatcc#tggctggatatatagagattcccacactgccttgcacac#agcactgctgggtaaatatttgctggctgcaggaaAA##TGAAGGAATAGGCCCTCCAGTGGGAGGAAAAGCA#GAGTTGTGAGAGCAGAGCCACCACAGGAAACCAGGAGGCTAAGTGGGGTGGAAGGGACTGAGCTCT#GGACTCCCAGGAGTAAAAGCTTCCAAGTTGGGCTCTCACTTCAGCCCCTCCCACACAGGGAAGCCAGATGGGTTCCCCAGGACCAGGATTCCCCAAGGGGGCTGCTCCCAGAGGGTGTGTTGCTGGGATATCCCAGGACAGGGATGGCCCTCTCATCAGGTGGGGGTGGGTGGCAGCACCCACCTGCCGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCC#CCATCTGCTGGA#GGCCTCCTCT##CC#CAGGTCTGGCTGGATGAGGGGCA#GGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCCTGTGGGT#GGAGCCGGAGC#TCAGAGCCACCCA##ACCACCTGCAC#CACCCACCACAGGGCAG##TGGTGTTGAGACAACACAGCCCTCATCCCAACTATGCACATAGCTTCAGCCTGCACAGATAGGGGAGTAGGGGACAGAGCATTTGGTGAGAGGCCAGGAG##CATAGATGGGACTCTGCTGATGCCTGCTGAGTGAATGAGGTAAAGGGCAGGACCAGGGACTGGGGAATCTGTAGGGTCAATGGAGGAGTTCAGAGAAGGTGCAACATTTCTGACCCCCTACAAGTTGCTTGCTACCTGCCAGGTACCCTTTCCATACATTGTCTCAGTTCAGCTCCCTACCTTGGATAAACAAGAAACCTTGGTTGCGGAGGAAAAAAGAGGCTGGAAACAAAGGGGTAGAAATGGGGTAGTGGGGGAGATTGCCTGATCAACTGCCAAATGGTACCCAGTTCTGGAAAAGCACAAAAAATGTGCACACA#GGGTTCTTCCCACTTTAACCCCTGAGGAATTTGAGGCCTGCTCCTGAAACAGACTGGGCAGTGGCTAGTGACTCTAGGTATAGGAGTATCCAGCCCTGCTCACCCAGGCTAGAGCTTAGGGGGCCAAGAGGAAAGAGGTGCCTGTGGGGGTGGAGGACAGGAAGGAAAAACACTCCTGGAATTGCAAAGTGAGGGCAGAGTCTATTTATATTGGGTTTAATTAACTCCTCTCCCTGGTGCCACTAAAGCAGCAATCACACTGCAGACAGCACTGATTTGATTGGCAAGAGATGCACCAGGCAGAATATTAAGGGACCAGGCCCCTATAAATAGGCCTAATCACAGCCCCTC#CTGGAAAATGCTAAGGAAGACATTAATCAGGCCTGGCACTGTGCCCTAGACCTGCTCCCCTAGGCACTACAGTGGGGCCCTTGGTTGCAACACAAGTAGGTAAGGATGGATGAGTCTGGTATGAAGGGCCTAGGAGATTTCATTTGGGTTTAAAATGCTGTGACCCTGAGTAAGTTGCTGTCTCTGAATCTGATCCTTTC#ATTTCCCATTCTCCAAACTGAGAACTAGCACTGCTGAGA##TGGTTATTCCCAATAATAATTTGTATATTTTACATAA##TACCACACCAACATCTTCACCCAGCTGGAGCCTACTCCTTTGCTCCC#CTGCTGGCTTCCCCAGCCCTCCCTTCTGCCCTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTTTGCATACAGGCTTTCCAGATCTGTACTTGCCTTGAATACTCATCAGAGCCCAGGAGTTACTCCTCACCTCCCACTTATTTTTCCTCCCATCAAATAACTAAAGCATGGCCAGCTGATGCCCAGCCAACTGAGAAACCTAACCCTCTGAGACCACCACACCCCTTTCAAGCATGTTCCTCCCTCCCCTTCTTTGTATTTATACTGA#GCAAGTTTGCTGGCTGTcctaacttatttctgtgcctcagttctcccatatgtaagatcacaaagggggtaaagatgcaagATATTTCCTGTGCACATCTTCAGATGAATTTCT------TGTGTGTGTGTTTGCTCACACATATG##TGAAAGAAGAGTACATACACAAAT---CTCAAAAAGGAGGCAGCAAGCCC#TTCAAGAATGGGACTGAATACACCTGATGAGTGGTTTACTTTCTGTCTGCAAACATCTACTGATCATCTGTTAGGTGCAGGCCATGATCACAACAAAGA##AATAAGACACTACACTAGCCAGGGAGAGTCTCAAAAACAACTAAACTCAAATTAAATTCATTCTAATCCAGTCATGAGTACAAAGCTAAGGAGTGACAAATCCCTTTTGGAGTTAGGGGAGTCAGGAAAAAGCTCTTAGCAGAATGTGTGCCTCT#ggctgggc#cag#ggctca##cctgtaatcccagcactttgggagg##aaggcaggcagatcacctgaggtcaggagtt##agaccagtctgaccaacatggtgaaactccatctctactaaaaatacaaaattagccagg##tggtggtgcatgcctgtaatcccagctact#gggaggctgaggaaggagaatcacttgaaccggggaggt#gaggttgcagtgtgcc#agat####ccattgcactccagcctgggcaac#aaagtgaaCCAGGTCCAGGAAGAAGGTGCAAAGACAGCATTCCAGGTAAAAGAAACAGCTTGAACAAAAAGTGTGTAGGGGAACAGCAAG#GGTCTTGAGTGCTGAGGGTACAATCATCCTTGGGGAAGTACTAGAAGAAAGAATGATAAACAGAGGCCAGTTTGTTAAAAACACTCAAAATTAAAGCTAGGAGTTTGGACTTGTGGCAGGAATgaaatccttagacctgtgctgtccaatatggtagccaccaggcacatgcagccactgagcacttgatatgtggatagtctgaattgagatgtgccataagtgtaaactatgcaccaaatttcaaagactagaaaaaaagaatgtaaaatata-----attttatattgattac#tgctaaaataaccatatttgggatatactggattttaaaaatatattgctaatttcatctgtttctttttacttttAGAAATCACATATGTGACTTAAATATTTCTTTTCTTTTTCTTTCCTCTCACTCAG##TCCTGTGATTCCAAAGAAATGAGTCTCTGCTCTTTTTGGGCAGGAGATATCCTAGAATGGACTCTGACCTAAGAATCAAAATTAATAATCATAA##TTATCATTTTATGGCCCCTTCTTCCTATATCTGGTAGCTTTTAAATGATGACCATGTAGATAATCTTTATTATCCCTCTTTCAGCAGA#GGTATTTTCTTATGCTACAGTATGACTGCTAATAATACCTACATA#GTTAGAACCATTCTGACTCCTCAAGAatctcatttaactcttattatcagtgaatttatcatcatccccaattttagataaggaaatggggttagaaagaccaaataacattttttcaacatcaaaacactagcttgagatcaagcccaaacttggatctgt#gtctgaattccaagctttttg----ttattgatatgttttgttgtTTTCATGCAATAATGCAAATCTTAGCCCAAACATTTTGTTAGTAGTACCAACTGTAAGTCACCTTATCTTGATACTTTGTCTTTATGTAAACCTAAATTAGATCTGTTTTTGATACTGAGGGAAAAACAAGGGAATCTAACACTAACCagccc#tagtgtgtggtcaacacttt##ttactttagtatacatcaccccaattgtttgtcttcaccacacactt 
+
+a score=407272.0
+s hg18.chr1     18260 1630 + 247249719 GATTTTGTTGG#GGAAAAAAAAATTTATCAAAAGT##TCTTCTATCAGGGAGTTTTATGAGAAACCCTAGCTCCTCAGTTCCACAGTGGGTAACTGTAATTCATTCTAGGTCTG##ATATTTCCTGCCTATCCATTT#GTTAACTCTTCAATGCATTCCACAAATACCTAAGTATTCTTTAATAATGGTGGTTTTTTTTTTTTTTTGCATCTATGAAGTTTTTTCAAATTCTTTTTAAGTGACAAAACTTGTACATGTGTAT##CTCAATATTTCTAGT##ACAGCACTGCTTT##AGAATGTAAACC#TGCACTCCCAGGAAAATGCAGACACAGC###CCTCTTTGGGACC##GGTTTATACTTT#GAAGTGCT#GGAGCCCTTCCTCCAGACC#TTCTCCCACACCCC#CTCCAGGGTCTCTCCCGGAGTTACAAGCCT##CTGTAGGCCCCGGGAACCCAA###GGTGTCAGAGAAGTGGGGTCCCCTA##AGGGACCAGGAGCTCCGGG#GGGCAGCAGCTG#GGAAGAGCC#####AGGCTTCCCAGAACCCGGCAGGGG#GGGAAGA##CAGGAGTGGGGAGG#GGAACCGGGACCCC#CAGAGCCCGGGTCCCTG##CCCCACAAGCCTTGGCTTCCCTGCTAGGGCCGGGCAAGGCCGGGTGCAGGG###GGCTCCAGGGAGGAAGCTCCGGGG##AGCCCAAGA##CCTCCCGGG#GGT#GGGGCCCAG#GG#GG##TT##CAGTGGAGCCGGGCACCGGGCAG#GGCC##GGAACACCAGCTTGG##CAGGCTTCT#GGTCAGGAA#GGTCCCGGGCCTCCC#CCC#CCTCCCTCCAGCCCCTCCGGGTCCCCTACTT##CCCC#CCAGGCCCCCA##ACCCTACTTCCC##GGCCCCGGA##CCTCCTCACCTG##AGCC#CCCTCCCGGAAGCTCCC#CC#CC#CTTCC#CTCTGCCGGAGCC#CTGGGTCCTAGCCCC#CC#CCCCCAGTCC#CCC###CCTCCGGGTCCTAA##CC#CC#CTC#CCCTCC#CTG##CCCTCCCC#AG###GGCTCCAGGACCCC#T##ACCCGGAG##CTGTCCTGT#GGGCC#AGT###GGGCCTGGGCA#GGAACTCA##CTCACTCC#AGCTCCC#A##TGCACA#GGCTCCCATGC#TTGTCTTCC#AG##TCAGGCC#CCCCTACCC#TGCTTTCTGCTCTGCAGACCCTCTTCCTAGACCTCC#TCCTTTGTCCCAT##CTGCCTTCCCCTCAAGCTCAGGGCCAAGCTGTCC#CCAACCT#GGCTCCTCCGGGCAGCCCT##CCCGGGGTG##CCCCGGGGCAGGACCCCCAGCCCA#GCCCAGGGCCC#CCCCTGCCCTCCAGCCCTAC#CCTTGACCC#CTTTCCTGC#TCTCTCAGCCTACCTGACCTTGTCTTTACCTCTGTGGGCAGCTCCCTTGTGATCTGCTTAGTTCCCACCCCCCTTTAAGAATTCAATAGAGaagccaga##caaaactacagatat##tatgagtccagttttgtgaagtgcctagaatagtcaaaattcacagagacagaagcagtggt##ccaggaatggggaagcaagg#ggagttgggcagct 
+s panTro2.chr15 30886 1625 - 100063422 GATTTTGTTGG#GGAAAAAAAAATTTATCAAAAGT##TCTTCTATC--GGAGTTTTATGAGAAACCCTAGCTCCTCAGTTCCACAGTGGGTAACTGCAATTCATTCTAGGTCTG##ATATTTCCAGCCTATCCATTT#GTTAACTCTTCAATGCATTCCATAAATGCCTAAGTATTCTTTAATAATGGTGG--TTTTTTTTTTTTTGCATCTATGAAGTTTTTTCAAATTCTTTTTAAGTGACAAAACTTGTACATGTGTAT##CACAATATTTCTAGT##ACAGCACTGCTTT##AGAATGTAAACC#TGCACTCCCAGGAACATGCAGACACAGC###CCTCTTTGGGACC##GGTTCATAATTT#GGAGTGCT#GGAGCCCTTCCTCCAGACC#TTCTCCCACACCCC#CTCCAGGGTCTCTCCCGGAGTTACAGGCCT##CTGTAGGTCCCGGGAACCCAA###GGTGTCAGAGAAGTGGGGTCCCCTA##AGGGACCAGGAGCTCCGGG#GGGCAGCAGCTG#GGAAGAGCC#####AGGCTTCCCAGAACCCGGCCGGGG#GGGAAGA##CAGGAGTGGGGAGG#GGAACCGGGACCCC#CAGAGCCCGGGTCCCTG##CCCCACAAGCCTTGGCTTCCCTGCTAGGGCCGGGCAAGGCCGGGTGCAGGG###GGCTCCAGGGAGGAAGCTCCGGGG##AGCCCAAGA##CCTCCCGGG#GAT#GGGGCCCAG#GG#GG##TT##CAGTGGAGCCGGGCACCGGGCAG#GGCC##GGAACACCAGCTTGG##CAGGCTTCT#GGTCAGGAA#GGTCCCGGGCCTCCC#CCC#CCTCCCTCCAGCCCCTCCGGGTCCCCTACTT##CCCC#CCAGGCCCCCA##ACCCTACTTCCC##GGCCCCGGA##CCTCCTCACCTG##AGCC#CCCTCCCGGAAGCTCCC#CC#CC#CTTCC#CTCTGCCGGAGCC#CTGGGTCCTAGCCCC#CC#CTCACAGTCC#CCC###CCTCCGGGTCCTAA##CC#CC#TTC#CCCTCC#CTG##CCCTCCCC#AG###GGCTCCAGGACCCC#T##ACCCGGAG##CTGTCCTGG#GGGCC#AGT###GGGCCTGGGCA#GGAACTCA##CTCACTCC#AGCTCCC#A##TGCACA#GGCTCCCATCC#TTGTCTTCC#AG##CAGGGCC#CCCCTACCC#TGCTTTCTGCTCTGCAGACCCTCTTCCCAGACCTCC#TCCTTTGTCCCAT##CTGCCTTCCCCTCAAGCTCAGGGCCAAGCTGTCC#CCAGCCT#GGCTCCTCCGGGCAGTCCT##CCCTGGGTG##CCCCGGGGCAGGACCCCCAGCCCA#GCCCAGGGCCC#CCCCTGCCCTCCAGCCCTAC#CCTTGACCC#CTTTCCTGC#TCTCTCAGCCTACCTGACCTTGTCTTTACCTCTGTGGGCAGCTCCCTTGTGATCTGCTTAGTTCCCA-CACCCTTTAAGAATTAAATAGAGaagccaga##caaaactacagatat##tatgagtccacttttgtgaagtgcctagaatagtcaaaattcacagagacagaagcagtggt##ccaggaatggggaagcaagg#ggagatgggcagct 
+
+a score=458960.0
+s hg18.chr1        19890 1848 + 247249719 cgtgttcaatgggtagagtttcaggctggggtgatggaagggtgctggaaatgagtggtag#gatgg#ggc#caacagtgtgaatctacttaatcccactgaactgtatgctgaaaaatggtttaga#ggtgaattttaggttatgtatgttttaccacaatttttaaaaaGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTTTAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCC#TTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTtagggttgccagattaaaagacaggatgcccagctagtttgaattttagataaacaa##aataattt##tagcataaatatgtcccaagcttagtttgggacatacttatgctaaaaaacattattggttgtttatctgagattcagaattaagcattttatattttatttgctgcctctggccaccctaCTCTCTTCCTAACACTCTCTCCCTCTCCCAGTTTTGTCC#CCTTCCCTGCCTCCTCTTCTGGGGGAGTTAGAT##AGTTGTAACAAGAACATGCCACTGTCTC#CTGGCTGCAG##TGTGGTCCCCTTACCAGAGGTAAAGAAGAGATGGATCTCCACTCAtgttgtagacagaatgtttatgtcctctccaaatgcttatgttgaaaccctaacccctaatgtgatggtatgtggagatgggcctttggtaggtaatta#ggttagatgaggtcatggggtggggccctcattatagatctggtaagaaaagagaGCATTGtctctgtgtctccctctctctctctctctctctctctcatttctctctatctcatttctctctctctcgctatctcatttttctctctctctctttctctcctctgtcttttcccaccaagtgaggatg##aagagaaggtggctgtctgcaaaccaggaagagagccctcaccgggaaccc#tccagctgccaccttgaacttggacttccaagcctccagaactgtgagggataaatgtatgattttaaagt##cccagtgtgtggtattttgttttgactaatacaaCCTGAAAACATTTTCCCCTCACTCCACCTGAGCAATATCTGAGTGGCTTAAGGTACTCAGGACACAACAAAGGAGAAATGTCCCATGCACAAGGTGCACCCATGCCTGGGTAAAGCAGCCTGGCACAGAGGGAAGCACACAGGCTCAGggatctgctattcattctttgtgtgaccctgggcaagccatgaatggagcttcagtcaccccatttgtaatgggatttaattgtgcttgccctgcctccttttgagggctgtagagaaaagatgtcaaagtattttgtaATCTggctggg##tggtggctcatgcctgtaatcctagcactttggtaggctga####agaggactgcttgagcccaagagtttgagatcagcctgggcaatattgtgagattccatctctacaaaaataaaataaaatagccagtcatggtgtcacacacctgtagtcccagctacatgggaggctgagg#gggaggatcacttgagcttgggagat##aggctgcagtgagctatgattgtaccactgcactccaggctggg##acagagagagaccctgtctcagaaaaaaaaaaaaaaGTACTTTGTAATCTGTAAGGTTTATTTCAACACACACAAAAAAAGTGTATATGCTCCA##ATGCCTGTGAATATACACACACACCACATCATATACCAAGCCTGGCTGTGTCTTCTCACAAATGC#CTGCTAGGCACCACCC 
+s panTro2.chrUn 57103829 1814 -  58616431 tgtgttcaatgggtagagtttcaggctggggtgatggaagggtgctggaaatgagtggtag#gatgg#ggc#caacagtgtgaatctacttaatcccactgaactgtatgcttaaaaatggtttaga#ggtgaattttaggttatgtatgttttaccacaatttttaaaaaGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTTTAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCC#TTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTtagggttgccagattaaaatacaggatgcccagttagtttgaattttagataaacaa##aataattt##tagcataaatatgtcccaagcttagtttgggacatacttatgctaaaaaacattattggttgtttatctgagattcaaaattaagcattttatattttatttgctgcctctggccaccctaCTCTCTTCCTGACACTCTCTCCCTCTCCCAGTTTTGTCC#CCTTCCTTGCCTCCTCTTCTGGGGGAGTTAGAT##AGTTGTAACAAGAACATGCCACTGTCTC#CTGGCTGCAG##TGTGGTCCCCTTACCAGAGGTAAGGAAGAGATGGATCTCCACTCAtgttgtagacagaatgtttatgtcctctccaaattcttatgttgaaaccctaacccctaatgtgatggtatgtggagatgggcctttggtaggtaatta#ggttagatgaggtcatggggtggggccctcattatagatctggtaagaaaagagagcattgtctctctgtctccctctc-----------------------tctctctatgtcatttctctctct----ctatctca--tttctctctctctctctctctcctctgtcttttcccaccaagtgaggatg##aagagaaggtggctgtctgcaaaccaggaagagagccctcaccaggaaccc#tccagctgccaccttgaacttggacttccaagcctccagaactgtgagggataaatgtatgattttaaagt##cccagtgtgtggtattttgttttgactaatacaaCCTGAAAACATTTTCCCCTCACTCCACCTGAGGAATATCTGAGTGGCTTAATGTACTCAGGACACAACAA---AGAAATGTCCCATGCACAAGGTGCACCCATGCCtgggtaaagcagcctggcacagagggaagcacacaggctcagggctctgctattcattctttgtgtgaccctgggcaagccatgaatggagcttcagtcaccccatttgtaatgggatttaattgagcttgccctgcctccttctgagggctgtagagaaaagatgtcaaagtattttgtaatctggctggg##tggtggctcatgcctgtaatcccagcactttggtaggctga####agaggactgcttgagcccaagagtttgagatcagcctgggcaatattgtgagattccatctctacaaaaataaaataaaatagccagtcatggtgtcacacacctgtagtcccagctacatgggaggctgagg#gggaggatcacttgagcttgggagat##aggctgcagtgagctatgattgtaccactgcactccaggctggg##acagagagagaccctgtctcag--aaaaaagaaaaagtactttgtaatctgtaaggtttatttcaacacACACAAAAAAAGTGTATATGCTCCA##ATGCCTGTGAATATACACACACACCACATCATATACCAAGCCTGGCTGTGTCTTCTCACAAATGC#CTGCTGGGCACCACCC 
+
+a score=97796.0
+s hg18.chr1        21738 409 + 247249719 CCAGTTCTAGAATCACACCAGCCAGTTCACCCTCCAGA#GGTTCACCCTCAACTTCATAAAAGTTCCCTACCTAATCTACT---GACAGGCTCATCCCCGACCTAATTTTAAAGATTTCCTAGGA----------------------------------GCTGCAGTGGGAATCCTGGACCTCAGC#TGGACAAAGAACAGCTGCAGGTCATTCTCATGTGTGGACACAGAAGCTCTGCCTGCCTTTGCTGGCCAGCTGGGCTGAG#GGGCCTGGGAA-TTAAGGCTGCAGGGTTGGTCCCAGGCAGTCTTGCTGAAGCTTGCCACATCCCCCAGCCTCCTGGATTTGCCAGGATCCAAGAGCATGGACTTTAGGAATTCCTGGTGGAGGAGTGAAGAAAATGTGACAGGGTGTCCTAAGCCCC#ATCTACAGGAAGAAAACTGGAA 
+s panTro2.chrUn 57107006 446 -  58616431 CCAGTTCTAGAACCAGACCAGACAGTTCACCCTCCAGA#GGTTCACCCTCAACTGTATAAAAGTTCTCTACCTAATCTACTACTGACAGACTCATCTCAGACCTAATTTTAAAGATTTCCTAGGAACTGAATTGCAAAAACTTTTACCCTCACCCTAGAGCTGCAATGGGAATCCTG-ACCTCAGC#TAGACAAAGAAAAGCTGCAGGTCATTCTCATGTGTGGACACGGAAGCCCTGCCTGCCTTTGCTGGCCAGCTGGGCTGAG#GGGCCTGGGAAATTAAGGCTGCAGGGTTGGTCCCAGGCAGTCTTGCTGAAGCTTGCCACATCCCCCAGCCTCCTGGATTTGCCAGGATCCAAGAGCATGGACTTTAGGAATTCCTGGTGGAGGAGTGAAGAAAATGTGACAGGGTGTCCTAGGCCCC#ATCTACAGGAAGAAAACTGGAA 
+
+a score=7233.0
+s hg18.chr1        22147 35 + 247249719 ATAAGACTGAGGACTTAGTTTAAGATGTTCCTACT 
+s panTro2.chrUn 57107452 35 -  58616431 ATAAGACTGAGGACTTAGTTTAAGATGTTCCTACT 
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/6_mask_noncpg.maf	Tue Apr 01 09:12:41 2014 -0400
@@ -0,0 +1,57 @@
+##maf version=1
+a score=356676.0
+s hg18.chr1      2817 1438 + 247249719 ###A##CCCT##A#T#CCA##T#A#A##CCAG##CAGGG##CCCCAA###AG##T#TG#TG#A####CT#T##AT##AG##T###A##CA###CA#AG##AA##CTG##T##CT#CA##TGG#TCG##A###AGGGG#TG#A##AGGG#A##A#AG###AGTGAG##T##CT##CCT###T#CTA#CT#AG##T#AG##AG#A#AAGGG##T##A#T##TGGG#AG##A##T#####T#A#A##CTTA##CT#T####CCACG#AG##AGG##CA##AG##A#CA#AGG#####T##CA##A#A#T##T#CTG###CA#T#####A#CCG##A#CCT###CTG###ACG#T##TG##CTG####T#A##CCTGGTG#AG#T#A#A##CA#CT#TG####T##CA#T##T##T#T#TG##A####A#T#CT##CT####CT###CCTA#AG#CT#CA#CA#CCCGA###CA#A#T##T#A#T##CT##T###T##CCA#####A#CA##A##AG##CT#T##CT###AG##A##T##A#CA#T##CTG#CG#T#TG#CCT##CT#T##T#T##CCG#TG#A##CG#T###T###ATGG##CTG###T##AGG####CT##T##A#AG#T#####CCAG#A#A#T#TG#A###CA#A#T##T##CAG###CCAG##A#AG##A##A#T##CCG#TG#A######AGGG#####CCG#A####TG#TGG###CTG##CA##CGT#A####T##CCAGG##A##T#CCCT#T#TG#####CA###T###T##CA##CT#CGTG##CGAGG##CAG##T##T#A#TGG##CT#T##AG#AG##T##CA##--T###CT##CCA#CT##T#A##A#CGA##CG#AG#A#A#CCA##T##T##T##CCT###TA#######T##A###A##T##CCTG###T####A#CCCCTA###T#A#####A##A####CCCATG##CA#AGG##CCCT##CTGGGG##TT###A#CT#CCCCA#CT##T##CT#A###A#T#CT##A##CTT##T#CCT###CT##CCCA#A##CTT##CTG######T###T#CCTG##TTG#T##CA####CT#CAA##CG#TG##A#CT#CCT#CCT#T#A##CA#TT#A##A###TCCAA###A##T##T##CCCA##A#CA##A##T#T##CAAGG##CA##AG##T#T#A##AT###T######A#A###CCCGT###T###A#T#####CT####TGTGG#A###T####CT#CCA##T##A##A##T##CCCT##T###T##CCT##T#T#CT#CCT#T#A##CCA#A#####AG###A##TGG#A##T##T##CCCCA#T##CTAGG#A#CA##AGGG##AG#AG##A###A#T###CCCGA##CG##T##A##CT##A#A##TA#AG###CT########AG 
+s panTro2.chr15 16051 1440 - 100063422 ###A##CCCT##A#T#CCA##T#T#A##CCAG##CAGGG##CCCCAA###AG##T#TG#TG#A####CT#T##AT##AG##T###A##CA###CA#AG##AA##CTG##T##CT#CA##TGG#TGG##A###AGGCG#TG#A##AGGG#A##A#AG###AGGGGG##T##CT##CCT###T#CCA#CT#AG##T#AG##AG#A#AGGGG##T##A#T##TGGG#AG##A##T#####T#A#A##CCTA##CT#T####CCACG#AG##AGG##CA##AG##A#CA#AGG#####T##CA##A#A#T##T#CTG###CA#T#####A#CCG##A#CCT###CTG###AAG#T##TG##CTG####T#A##CCTCGTG#AG#T#A#A##CA#CT#TG####T##CA#T##T##T#T#TG##A####A#T#CT##CT####CT###CCGA#AG#CT#CA#CA#CCCGA###CG#A#T##T#A#T##CT##T###T##CCA#####A#CA##A##AG##CT#T##CT###AG##A##T##A#CA#T##CTG#CG#T#CG#CCT##CT#T##T#T##CCG#TG#A##CG#T###T###ATGG##CTG###T##AGG####CT##T##A#AG#T#####CCAG#A#A#T#TG#A###CA#A#T##T##CAG###CCAG##A#AG##A##A#T##CCG#TG#A######AGGG#####CCA#A####TG#TGA###CTG##CA##CGT#A####T##CCAGG##A##T#CCCT#T#TG#####CA###T###T##CA##CT#CGTG##AGAGG##CAG##T##T#A#TGG##CT#T##AG#AG##T##CA####T###CT##CCA#CT##T#A##A#CGA##CG#AG#A#A#CCA##T##T##T##CCT###CA#######T##A###A##T##CCTG###T####A#CCCCTA###T#T#####A##A####CCCATG##CA#AGG##CCCT##CTGGGG##TT###A#CT#CCCCA#CT##T##CT#A###A#T#CT##A##CTT##T#CCT###CT##CCCA#A##CTT##CTG######T###T#CCTG##TTG#T##CA####CT#CAA##CG#TG##A#CT#CCT#CCT#T#A##TA#TT#A##A###TTGAA###A##T##A##CCCA##A#CA##A##T#T##CAAGG##CA##AG##T#T#A##AT###T######A#A###CCCGT###T###A#T#####CT####CGTGG#A###T####CT#CCA##T##A##A##T##CCCT##T###T##CCT##T#T#CT#CCT#T#A##CCA#A#####AG###A##TGG#A##T##T##CCCCA#T##CTAGG#A#CA##AGGG##AG#AG##A###A#T###CCCGA##CG##T##A##CT##A#A##TA#AG###CT########AG 
+
+a score=33380.0
+s hg18.chr1      4393 135 + 247249719 #T#TG##CT#AA##CA##CT##CG#T#CTT##A##TG###T#CA#A#A#T##TG####CG##A#CCCCT#CCAAG##A##AG###T#A##A##TT###CTG##T#T###CAT###A#A##A#CG##CCAA###TG 
+s panTro2.chr15 17634 135 - 100063422 #T#TG##CT#AA##CA##CT##CG#T#CTT##A##TG###T#CA#A#A#T##TG####CG##A#CCCCT#CCAGG##A##AG###T#A##A##TT###CTG##T#T###CGT###A#A##A#CG##CCAA###TG 
+
+a score=364526.0
+s hg18.chr1      4528 1436 + 247249719 ####TGGGGGG##AG#T###ATG#A##CCCCTACG####CCA##CG##CTCG##CT#CT#T##CT#TG##T##T#CG#TG#CG##A#AG#AGG##TG#A###T###ACGCGG##A#AG##T#CT#CGG##CCCT#A#CA##CCCAG###CT###CCA#A##T##CTG#AGG####AG##T#A#T#AGG#TG##TG#TGG#####CCTG#T##CCCCA##CCCCG#A###T#######AG##A#####AG##AG###A#A#####AAG#T##TG##CCAGG#CGG##A#CG##CCT##CT#CT##CCTT#CG#CT#AT###CA##TT##T##A#A####CG##A##AA#T#CCCA#CTTG##TCGTG##T#T#A#T##A#CGG###A##CA#A###TGGG#T##A#A####A###A#AT#CG##CG#TG##T#CCT###CCCA#CCCCAT###A#T#CCCA##CCT#CAAG##CA#T#T#####CCA###A##T#A#A##CT#A##CG###CCT###CCA##A#CGG#CA#T##T#A###A#CG##T###T#AG#A##CA#CT#CCA##CA#CTCGGG##CAGG##CAGG#T#T##A##A#ca#t####a#tggg#####tg##cca#a#ag#t#ag##a##tt##ctggg###a#a#a##aag##a##a##a#cg#tgg####aa##t#a####CA#A#T##CCAGG##A#T##CG#T##AG#CG#AG##A#CG#A##A#A-----#CA#T###T#CG###A#A##AG##A##A##A##A##CT#CA#AG##CT#AG###CA###T#T#########T#AG#AG##T##A#TG##T###CA#T##CTTG###CG#T#TTG##A##CG#A##A#####T#CT###A--###T#A##TGG#T#A##T#A#A#AG###A##T#CA#T#TG##T#CCA###CAG##AG#A##CA#A##CCAG##AG#AGG##T#AG###CT#TG#TG#CG##CCAGG##T##CA##AT#T##CCTAGGG##A##AGGG##CA##TG#CAA#A##AGGGG#TGG##A###A##A#CCG#TG###T#AGG##TG#AGGG#AG#AG#CG###TT##CCAAG##CCT#CG##TG#AA##T#CAGG##CCG#T#A#CTT##T#CT##T#CT##T##T##T##T##T#CA##T##CG#T#CT##ATG#T#CG#A##TTG##CTT##CG#T##CCCCA##TTG#CG##TG###T#TA##A#A#TG##C-A##CA#CG#AGGG##CA##CA#T##CCTGG#A##T#CCTG###TG#A##CGG#AG#TGGG####AGG##AAG#AG###AG##T##T#AG##AGG##TGGG##A##T###T#T###CAA#A##CT##TGG#AGG##A###A#CT#CCCT#A##CGAG#A##CCTGCG#TGGG#AG##CG###CT#TG#A###T#T#T 
+s panTro2.chr15 18013 1444 - 100063422 ####TGGGGGG##AG#T###ATG#A##CCCCTAGG####CCA##CG##CTCA##CT#CT#T##CT#TG##T##T#CG#TG#CG##A#AG#AGG##TG#A###T###ACGCGG##A#AG##T#CT#CGG##CCCT#A#CA##CCCAG###CT###CCA#A##T##CTG#AGG####AG##T#A#T#AGG#TG##TG#TGG#####CCTG#T##CCCCA##CCCCA#A###T#######AG##A#####AG##AG###A#A#####AAT#T##CG##CCAGG#CGG##A#CG##CCT##CT#CT##CCTT#CG#CT#AT###CA##TT##T##A#A####CG##A##AA#T#CCCA#CTTG##TCGTG##T#T#A#T##A#CGG###A##CA#A###TGGG#T##A#A####A###A#AT#TG##CG#TG##T#CCT###CCCA#CCCCAT###A#T#CCCA##CCT#CAAG##CA#T#T#####CCA###A##T#A#A##CT#A##CG###CCT###CCA##A#CGG#CG#T##T#A###A#CG##T###T#AG#A##CA#CT#CCA##CA#CTTGGG##CAGG##CAGG#T#T##A##A#ca#t####a#tggg#####tg##cca#a#ag#t#ag##a##tt##ctggg###a#a#a##aag##a##a##a#cg#tgT####AA##T#A####CA#A#T##CCAGG##A#T##CA#T##AG#CG#AG##A#CG#A##A#A##A#A#CA#T###T#CG###A#A##AG##A##A##A##A##CT#AA#AG##CT#AG###CA###T#T#########T#AG#AG##T##A#TG##T###CA#T##CTTG###CG#T#TTG##A##CG#A##A#####T#CT###A#A###T#A##TGG#T#A##T#A#A#AG###A##T#CA#T#TG##T#CCA###CAG##AG#A##CA#A##CCAG##AG#AGG##T#AG###CT#TG#TG#CG##CCAGG##T##CA##AT#T##CCTAGGA##A##AGGG##CA##TG#CAA#A##AGGGG#TGG##A###A##A#CCA#TG###T#AGG##TG#AGGG#AG#AG#CG###TT##CCAAG##CCT#CG##CG#AG##T#CAGG##CCG#t#a#ctt##t#ct##t#ct##t##t##t##t##t#ca##t##cg#t#ct##ACG#T#CG#A##TTG##CTT##CG#T##CCCCA##TTG#CG##TG###T#TA##A#A#TG##CCG##CA#CG#AGGG##CG##CA#T##CCTGG#A##T#CCTG###TG#A##CGG#AG#TGGG####AGG##AAG#AG###AG##T##T#AG##AGG##TGGG##A##T###T#T###CAA#A##CT##TGG#AGG##A###A#CT#CCCT#A##CGAG#A##CCCGCG#TGGG#AG##CG###CT#TG#A###T#T#T 
+
+a score=521291.0
+s hg18.chr1      5995 1988 + 247249719 #CT#A#CGCGG##A##CT#T#T##A#####T#CCT##T##CT#T#TA##CCCCA#CCT##A#A##TG###CCCT#A##TA##CAT##T#T###A###T#A#TT##A#A#ACGA##CA##A#AGGG####T#T##CA#T##TG##T##TAGG###A#A#TGG#A###A#A##A#T##A##T#A##T######T#T##T##T##A####-----######A###CCCT##T###CA#TG########AG###TGGG####CCA#A##CT#A#TT####AG##T#CCT#T##CCTA##A#T#A##A###CA#A##T#T##A###T######CA#T######T####CAA##A####AA######T####TGG####T####A######T#A#######T###CA#T####A###CCA#A#######CA#CCGA#T##A#T#A##ACG#CA####T#AG#TG##CT#A#A#A##T##T#CCA#CT##AG#A##CGCG#T##T##T##T##CG##CT##CTG#CG#CTTG##CT##AGGG##CGCG##T#AGG#TGG#A#TGGGG#T##A#TG##CA##A#CT#AG#A##tgggg#tg#tg#tgggg#cg#tgggg#tg#tg---------##a####CCCA##TT##AG###T#####A#A#A#T#TGGG#T###TAGG##A##AG#T#T#T#A#CAGG#AG###CCCG##CCA##T#CCA##CCA#A##CCA##T#A#CT##CTT#A#AG##TCG##T##CT#A#T#TG##AG#TGG##A####TG###TG#T##CAGGG##A#AGGGG##A#T##CGGG##CCAG##CG##A#T####AT#AG##CG#TG##A#T##CGG##AG###AG##AG##AG##TG####A##A###T#AG##A#CTG##CCAG###TG##A#A#A##A##A####T#TGG###CT##AA####AG##AGG###AT#T#A#AG#T###AGG###CT##AGGG##A##CA##AA###CTT#T#T##A#CT#CCATGG#TG#####AGGG##CCA##A##CTT###TG#A#AG#A##T#TG##AAG##CCTGG##CA#T##A#CT###T#CA#CT#T###CCA#CCCT#CCA#CT##T####CA##T##T#T#T#TT##T##TG###AAGGGG##A##A###A##T##T#CT#T###T#T##CCCCA##A##A#ATGG###T#T#####A##A#CA##CAGGGG###CAG##A###A###T##TT#T##CT##AGAG#CG##ATGGGG###AG##AA##T###A#CCG#T###CT#A##CCAT####CT#T#CCA#A##A##AGGG##A#A#CGT##A#TGTGGG###CCAG##CT#CCGA##CGA##CA#CCG##A#CCCCTG##T#CTG##CT#T#T##T####CT#T###T##T##CCTGG###CCCA#T#A##CAG##CGG##CT#CCG#CCA#A#CCCTCG##CCT##CCT#TG##CA###AG####TCG#TG#T##T##A#A##A##AAG#A##T###A#A##T##T##T##TGG##A###CCCCAA###CCT#T##T##A#CG##CTCGG##TCCG##TTG#T##T#ACG#A#A#AG###A###CT##A##T##T#CTGA#AGG##CAG##TG##CAAGG##TG#T#######TG#T##TGG##CT####A##T##CA#CCCA##CCA###A##CT#CT#TGGGG###A####CCT#TG#TG##CCCG##T#CT#CCCA#####CA###CT#CTG#T#T#T###AG##-----##T#T#CGCG##CA##A###CT##AGG##CCG#TCG##CAGGGG#CG#T##TT##T#TG####CT#TG#CGGGG#CG##T#T##AG##CAGG###CTGG#CG#CCGT##A##TG#A##CA#####CT##AG#CG#CCTG#A##AGG####TTG##A#TG#A####A#CT#TG###A#AGG###AA###T#AGGGG##CCCAA#AG##T#A#AGG##TAG###T##T 
+s panTro2.chr15 19485 2006 - 100063422 #CT#A#TGCAG##A##CT#T#T##A#####T#CCT##T##CT#T#TA##CCCCA#CCT##A#A##TG###CCCT#A##TA##CAT##T#T###A###T#A#TG##A#A#ATGA##CA##A#AGGG####T#T##CA#T##TG##T##TAGG###A#A#TGG#A###A#A##A#T##A##T#A##A######T#T##T##T##A####A##TG######A###CCCT##T###CA#TG########AG###TGGG####CCA#A##CT#A#TT####AG##T#CCT#T##CCTA##A#T#A##A###CA#A##T#T##A###T######CA#T######T####CAA##A####AA######T####TGG####T####A######T#A#######T###CA#T####A###CCA#A#######CA#CCGA#T##A#T#A##ACG#CA####T#AG#TG##CT#A#A#A##T##T#CCA#CT##AG#A##CGCG#T##T##T##T##CG##CT##CTG#CG#CTTG##CT##AGGG##CGCG##T#AGG#TGG#A#TGGGG#T##A#TG##CA##A#CT#AG#A##tgggg#ag#tg#tgggg#cg#tgggg#tg#tgggg#t##t###a####CCCA##TT##AG###T#####A#A#A#T#TGGG#T###TAGG##A##AG#T#T#T#A#CAGG#AG###CCCA##CCA##T#CCA##CCA#A##CCA##T#A#CT##CTT#A#AG##TCG##T##CT#A#T#TG##AG#TGG##A####TG###TG#T##CAGGG##A#AGGGG##A#T##CGGG##CCAG##CG##A#T####AT#AG##CG#TG##A#T##CGG##AG###AG##AG##AG##TG####A##A###T#AG##A#CTG##CCAG###TG##A#A#A##A##A####T#TGG###CT##AA####AG##AGG###AT#T#A#AG#T###AGG###CT##AGGG##A##CA##AA###CTT#T#T##A#CT#CCATGG#TG#####AGGG##TCA##A##CTG###TG#A#AG#A##T#TG##AAG##CCTGG##CA#T##A#CT###T#CA#CT#T###CCG#CCCT#CCA#CT##T####CA##T##T#T#T#TT##T##TG###AAGGGG##A##A###A##T##T#CT#T###T#T##CCCCA##A##A#ATGG###T#T#####A##A#CA##CAGGGG###CAG##A###A###T##TT#T##CT##AGGG#CG##ATGGGG###AG##AA##T###A#CTG#T###CT#A##CCAT####CT#T#CCA#A##A##AGGG##A#A#TGT##A#CGTGGG###CCAG##CT#CCGA##CGA##CA#CCG##A#CCCCTG##T#CTG##CT#T#T##T####CT#T###T##T##CCTGG###CCCA#T#A##CAG##CGG##CT#CCG#CCA#A#CCCTCG##CCT##CTT#TG##CA###AG####TCG#TG#T##T##A#A##A##AAG#A##T###A#A##T##T##T##TGG##A###CCCCAA###CCT#T##T##A#CG##CTCGG##CCCG##TTG#T##T#ACG#A#A#AG###A###CT##A##T##T#CTGG#AGG##CAG##TG##CAAGG##TG#T#######TA#T##CGG##CT####A##T##CA#CCCA##CCG###A##CT#CT#TGGGG###A####CCT-TG#TG##CCCG##T#CT#CCCA#####CA###CT#CTG#T#T#T###AG##T#A####T#T#CGCG##CA##A###CT##AGG##CCG#TCA##CAGGGG#CG#T##TT##T#TG####CT#TG#CGGGG#CG##T#T##AG##CAGG###CTGG#CG#CCGT##A##TG#A##CA#####CT##AG#CG#TCTG#A##AGG####TTG##A#TG#A####A#CT#TG###A#AGG###AA###T#AGGGG##CCCAA#AG##T#A#AGG##TAG###T##T 
+
+a score=311095.0
+s hg18.chr1      7983 1272 + 247249719 #G##AG#A#AGG#TG#A##TGG#A##CTGG#CGA##A###A##TCAAG##A#AG#TGG##A##AGG##A#A###TGG##A##CT#A#AG##ACGGG####TG#AGG###T##CCA##A##CT#AG###A#AGGG##ATGGG###T##CTT##TG##CT##TT##T##CCTT####T##T#A###TTG##CTGG##CAAG#A###CT##T#T#CA#TG##CT##A#CTG##T#CG##T#T##T#T##CTG#TGG#A####CT##CATG#A##A####A#A#AG##TGG##T##T#CCCA#CCTCT##A#A#CT#CT##T#CT###A##A#A##T##CAG##CAG##CCT#AG##AAGG##T#T##A###AGG###A#CT##TT##CAGG##CG###TTG#T##CA##CAGGGG##CT#T##AAG#######T###CT##AGG##CGAG#A##T##CG#T##T#A####CCT##A#T#T#A##AGG###AG##CCT#T##T##CA#CT####AT##T###T##AG###A##CT#CAGG##A#A#A#AG##TG########A#AT##A#A#ATG##T##T##TGGG##AA##A#T##A#A##CCCT#AT####ACGT##A##A###A#T#TG##CT#T##A#AGGGG###CG#A###CG#AG##T#A###TG##AAG##TG###CT#A#T##CG##A#CT######A##CGGG####T##CCCTG#A#A#A#T###CG##T#A#T#A##A###CCCGA###CCG##CA#CG#CT#A#T#TG###TA##T#ct#a#ct##t##ca##ct#cctg#t#cggg#tgg##cca#t######a##t##ct##t####ccca##t#t##caa#t##a###tt#t#t##tt##a##t#atg###cg#ca####ccca###at#cct#tg##tg##t#ctG#T##CCGAG##CCAA#T###T##T##T###AG##A#A##A#CCCA#T#AT##T####CAT####T#TG##CG#A##AAG##CG#T#T#A#T##A#A######T#T##T#CGT#T#####A#A##A##CT#CT#CCA##CG#CCCT##A##T#CCCT##CT#CAA#A##CCA##CCTT##CCA#AGG##CA#A#T#CACGT##A#A##A##CT#A##A#T#A#CGG##ACGA#CGA##CT#T#TG#T#CG#AGG##T#A##AG##A#AG#CGCG##TGGG###CAT#AG##AGG##AG#AG#AGG#T#TGG##TG#TG#AGGG###T#A##AG##A#AG#CGC 
+s panTro2.chr15 21491 1270 - 100063422 #G##AG#A#AGG#TG#A##TGG#A##CTGG#CGA##A###A##CCAAG##A#AG#TGG##A##AGG##A#A###TGG##A##CT#A#AG##ACGGG####TG#AGG###T##CCA##A##CT#AG###A#AGGG##ATGGG###T##CTT##TG##CT##TT##T##CCTT####T##T#A###TTG##CTGG##CAAG#A###CT##T#T#CA#TG##CT##A#CTG##T#CG##T#T##T#T##CCG#TGG#A####CT##CATG#A##A####A#A#AG##TGG##T##T#CCCA#CCCCT##A#A#CT#CT##T#CT###A##A#A##T##CAG##CAG##CCT#AG##AAGG##T#T##A###AGG###A#CT##TT##CAGG##TG###TTG#T##CA##CAGGGG##CT#T##AAG#######T###CT##AGG##CGAG#A##T##TG#T##T#A####CCT##A#T#T#A##AGG###AG##CCT#T##T##CA#CT####AT##T###T##AG###A##CT#CAGG##A#A#A#AG##TG########A#AT##A#A#ATG##T##T##TGGG##AA##A#T##A#A##CCCT#AT####ACGT##A##A###A#A#TA##CT#T##A#AGGGG###TG#A###CG#AG##T#A###TG##AAG##TG###CT#A#T##CA##A#CT######A##CGGG####T##CCCCG#A#A#A#T###CG##T#A#T#A##A###CCTGA###CCA##CA#CG#CT#A#T#TG###TA##T#ct#a#ct##t##ca##ct#cctg#t#cggg#tgg##cca#t######a##t##ct##t####ccca##t#t##caa#t##a###tt#t#t##tt##a##t#atg###ca#ca####ccca###at#cct#tg##tg##t#ctG#T##CCGAG##CCAA#T###T##T##T###AG##A#A##A#CCCA#T#AT##T####CAT####T#TG##CG#A##AAG##CG#T#T#A#T##A#A######T#T##T#CGT#T###--A#A##A##CT#CT#CCA##CG#CCCT##A##T#CCCT##CT#CAA#A##CCA##CCTT##CCA#AGG##CA#A#T#CACGT##A#A##A##CT#A##A#T#A#CGG##ACGA#CGA##CT#T#TG#T#CG#AGG##T#A##AG##A#AG#CGCG##TGGG###CGT#AG##AAG##AG#AG#AGG#T#TGG##TG#TG#AGGG###T#A##AG##A#AG#CGC 
+
+a score=268744.0
+s hg18.chr1      9255 1055 + 247249719 ###TGGG####AT#AG###AGG#AGGGG#AGG#T#TGG##TG#TG#AGGG##T##A###T#TGG##TAGG###A##TGGG#T###T#T##AG##TG###T###TG##CTA####CCG##CCA###A##CA#A##CA#T##CA#CA#CG##A##AG##CTTG##CCCCA#A#A##CA#####A#A###CAG#A###CCCGT##CCT##AGG###T##CCT######T#CTG##T#CTT#T#T##AGGGG##T#AG##ATG##AGG##TGG#A####CA##AG##A#T#AA#CG##T##A#T####CAT###A###TG###T##AG#TG##CA#A####A###A######A##A#A##A#CA##T#CT##CA#T#AG##A#CGGG##CA#CA#CCA#CGT#T##T#CA##T####TG##TGGG#A#AG##CT##A##T##T####AGG###CT#CA##A#AA##T###T####T###CCTA####CCAGG##A##CTCG###T##CTTGG#T##T###ACG##CT#CG##AG#T##A##A##T#T##A##CGAG###ca#aggg##a#tgg#agg####t#a###tggg#agg###a#ag##t##t#t###ctg#t##t#cca#a#ag#--a##agg##t####a#t#a#a##t#cg###a#caa##t#a##a#t#a##cctg#########tg###tg#########a#a#a#a###t###a##a#t#a####ag##cgcg#t#a###ccaggg##ca##a#t##tcg#a#t####a##a####t#t#t#####ag####a##a##ct##t#t##ccggg#a####at##a##a#a#tg#a##tcga###a##ag#####tg#cg##t##t###a#####tt##a###aa##tg#a##t#tgggg##tg#ag#a#a####a###ag########a#a##ca##t####ca#a##ccca#agg##a#a##t####a#tg###t#####ca##ctt##acg#agg####tg##a#a###ca##ca####a###a##a#ctg###a######tggg##cag 
+s panTro2.chr15 22901 1056 - 100063422 ###TGGG####AT#AG###AGG#AGGAG#AGG#T#TGG##TG#TG#AGGG##T##A###T#TGG##TTGG###A##TGGG#T###T#T##AG##TG###T###TG##CTA####CGG##CCA###A##CA#A##CA#T##CA#CA#CG##A##AG##CTTG##CCCCA#A#A##CA#####A#A###CAG#A###CCCGT##CCT##TGG###T##CCT######T#CTG##T#CTT#T#T##AGGGG##T#AG##ATG##AGG##TGG#A####CA##AG##A#T#AA#CG##T##A#T####CAT###A###TG###T##AG#TG##CA#A####A###A######A##A#A##A#CA##T#CT##CA#T#AG##A#CGGG##CA#CA#CCA#CGT#T##T#CA##T####TG##TGGG#A#AG##CT##A##T##T####AGG###CT#CA##A#AA##T###T####T###CCTA####CCAAG##A##CTCA###T##CTTGG#T##T###ACG##CT#CG##AG#T##A##A##T#T##A##CGAG###ca#aggg##a#tgg#agg####t#a###tggg#agg###a#ag##t##t#t###ctg#t##t#cca#a#ag###a##agg##t####a#t#a#a##t#cg###a#caa##t#a##a#t#a##cctg#########tg###tg#########a#a#a#a###t###a##a#t#a####ag##cgcg#t#a###ccaggg##ca##a#t##tcg#a#t####a##a####t#t#t#####ag####a##a##tt##t#t##ccggg#a####at##a##a#a#cg#a##tcga###a##ag#####cg#cg##t##t###a#####ct##a###aa##tg#a##t#tgggg##tg#ag#a#a####a###ag#-######a#a##ca##t####ca#a##ccca#agg##a#a##t####a#tg###t#####ca##ctt##acg#agg####tg##a#a###ca##cg####A###A##A#CTG###A######TGGG##CAG 
+
+a score=95099.0
+s hg18.chr1             10310 371 + 247249719 #a#a#aggg##agg###a##tg#####at###cg####aag##t#a###a######a#ag##ca#agg##a###t##a###a#caa##t#########aag####a##t#t##a##cca##a###ag############aa#cg#########a##ag#tg#agg####tt##t##a###a#a####ag#t##a###a###ctg#####t##t######t###a##t#a##aggg##t###a##at######cg##a#####ag##a#t#a####t#agg##A#A#A##T#CCCG#CCCT#T##T##CCT##A##CT##T###A###A##AGG##CCGT##A#T#T#TTG#A##CA#CA#A######A#AG 
+s panTro2.chr9_random 4675776 371 +   7733331 #a#a#aggg##agg###a##tg#####at###cg####aag##t#a###a######a#ag##ca#agg##a###t##a###a#cca##t#########aag####a##t#t##a##cca##a###ag############aa#cg#########a##ag#tg#agg####tt##t##a###a#a####ag#t##a###a###ctg#####t##t######t###a##t#a##aggg##t###a##at######cg##a#####ag##a#t#a####t#agg##A#A#A##T#CCCG#CCCT#T##T##CCT##A##CT##T###A###A##AGG##CGGT##A#T#T#TTG#A##CA#CA#A######A#AG 
+
+a score=33853.0
+s hg18.chr1        10770 227 + 247249719 #A#A##AG#AG#A#A#A##ACA##CTG#A#T##T####T##CAG#A##T#A#CT##CT#CG##A#TGG##A#AG#CG#CA#T#AG##CAGAG##CGG##T#T##TGGG##CT#A#-CCGG#TG#TGGG#AG-------A#A###T#T#CCCT##CC--CT###T#T##CGT##AG#AG#---------------A##ATG####AGGGGACGG####A#A##TG###A#A##CCCA#CG####A##CCATGG 
+s panTro2.chr12 77693524 219 - 135371336 #A#A##AG#AG#A#A#A##ATG##CAG#A#T##T####T##CAG#A##T#A#CT##CT#CG##A#AAG##A#AG#TG#CA#T#AG##CAGGG##CAG##T#-----GG##AT#A##TGGG#TG#TGGG#AG#A#A#A#A#A###T#T#CTCT##CCA#CT###T#T##TGT##AG#TG#####CGA##AG#T##A##ACA####AAGGGGGAG####T#A##TG---------------------------- 
+
+a score=83473.0
+s hg18.chr1             10997 329 + 247249719 ##A#CG###A##CCA#TA##TT###CA#T##CA#AG#AGGG##AA#TG#AG#AG#A#AG#TG#CG#T##T#CCCA#T#CA#T##CA##CG##A#TG##T#T#CCT##CCT##A##CTCG###CCT###T###A#CA####CT##CG#CG####CT#T###T###T#A#CCT##CCT#CCT##TT##AA###CCCT###T##A##CT#A#CCCT##CG#A##CT###T##A#####A##T##TGG#T###CCTG##A##CA#T#T#T#T#CCT##TT###CCT##CGT##CG##T##CT#AG####CT##CCCA###T#T##TG##CCAT 
+s panTro2.chr9_random 4677170 329 +   7733331 ##A#CG###A##CCA#TT##TT###CA#T##CA#AG#AGGG##AA#TG#AG#AG#A#AG#TG#CG#T##T#CCCA#T#CA#T##CA##CA##A#TG##T#T#CCT##CCT##A##CTCG###CCT###T###A#CA####CT##CG#CG####CT#T###T###T#A#CCT##CCT#CCT##TT##AA###CCCT###T##A##CT#A#CCCT##CA#A##CT###T##A#####A##T##TGG#T###CCCA##A##CA#T#T#T#T#CCT##TT###CCT##CGT##TG##T##TT#AG####CT##CCCA###T#T##CG##CCAT 
+
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+s panTro2.chr15 30886 1625 - 100063422 #####T##TG#CG################A##A##CG##T##T###--G#A######T#A#####CCTA##T#CT#A####CA#A#TGG#####T##A####A###TAG###T#CG#######CA##CT###CA###CG#####T#T##A#T##A###CA#A##T##CT#A######T#######TG#TG#--############T##A##T#T##A########A#####T#####A#T###A####TT####AT#T####CG#A#A#######TA##CG##A##A#T##T##CGA###T######CGT##A#T#CCAG####AT##A###A#A#CGCG#CT#T#TGG###CACG####A###T#TGG#A#T##TCG#A##CCT##CT#CA###CG###T#CCA#A#CCCG#T#CAGG###T#T#CCG#A#####AG##CTCG#T##AG##CCCGG####CCA#CGCG#T###A#A##A#TGGG###CCCT#CGAGG###CAG#A##T#CGG#CGG##A##A##T#CG##A#A##CGCGCGAG##T##CCA####CCG##CGGG#CGG##A##CG#AG#A#TGGG#AG#CG####CGG###CCCG#A#A##CCGG###CCT#CG#CCCA#AA##CTTG##T##CCT##TAGG##CGG##AAG##CGG#T##AGG#CGCG##T#CAGG#AG##A##T#CGGG#CGA##CCAA##CG#CT#CCGG#CG##CGGG##CCA#CG#CG#CG##CG#A#TG#A##CGG##A#CGG##A#CG##CGCG####A#CA##TTG#CG#AG##T##TCG###AG###CG###CCGG##CT#CCG#CCG#CT#CCT#CA##CCCT#CGG###CCCT##T#CG#CCCG#CAG##CCCCACG##CCT##T##CCGCG##CCCG##CG#CT#CT#A#CT#CGA##CG#CCT#CCG##A##T#CCG#CG#CG#T##CG#T#T##CG#A##CG#TGG###CTA##CCCG#CG#TCACA###CG#CCGCG#CT#CGG###CT##CG#CG#CG#TCA#CCT#CG#T#CG#CCT#CCCGA#CGCG##T#CAG###CCCG#CG##CCG#A#CG#T###CTG#CGG##CGA##CGCGG##CTGG##ACG####T#ACG#T#A#T#CGA##T#CCG#CGT##A#ACG##T#CCAT#CG#T###T##CGA#CG#AGG##CT#CCCT##CCGT##T###T##T#T##A###CCT#T##CCA###CT#CG##CT#T###CCA#CG#T##CT##CCCT#AA##T#AGG##CAA##T###CG#CA##CTCG##T#CT#CGG##A##CCTCG#CCTGG#T#CG#CCCGGG##AG###CCCCA##CCAGG#CCAGG##CCG#CCCT##CCT#CA##CCT#CA#CTT###CCG#T###CT#CCT#T#T#A##CT##CT###CTT###T####CT#T#TGG##A##T#CCTT#T####T##T#A####CCA-CACCCT###A######A##A#A##a##ca##cg#a####t##a#####cg##t#a###ca#t##t#t##a#t##cta####a###a######a#a#a###a##a##a#tg##cg#cag###tggg##a##aag#cg#a##tgg##a##t 
+
+a score=458960.0
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+s panTro2.chrUn 57103829 1814 -  58616431 #gt####a#tgg##a#a#####ag##tggg#t##tg##agg#t##tg####t#a#tg##a#cg#tg#cg#cg#a##a#t#t#####t##t#####cca#t####t###t##t######tg####a##cg#t#######ag####t###t#######ca#a##########a##TA#T####A##TG######A###A####A#AG##T#########A###############A#A##A##A##A###CA#A###CA##A##T###CCT#CTG#####CG#TG##TT##CT#CG##A####TG##CCTT##CT###agg##t##ca#######a###ag##t##cca##ta###t#######a#######a#cg########cg#a##a######t###ccaa##t#a###tgg###a###t##t##t#######a####tg##t#######t#a#####a######a##a##############t##t##ct#tg##ca#cct##T#T#T##CT###A#T#T#T#CCT#T#CCA####T###CG#CT##CTT##CT#CT#T##TGGGG#A###A###CGA##T#####AA####AT##CA#T###TCA#TG##T##A#CGT#TG###CCCT###CA#AG###AG##A#A##TG####T#CA#T#At##t##a###a###t#####t###ct#t#ca##t##t##t##t#####cct###ccct##t#t##tg###t#tg#a##tgg##ct#tg##ag#######cg###a##t#ag###atggg#tggg##cct#a####a####tg###a####a#a#a##a#t###t#t#t###t#cct#t#-----------------------##t#t#t#t#t#a####t#t#t#t----#t###t#a--####t#t#t#t#t#t#t#t#t#ct#t###t####cca#caa#t#ag##t#cg#a#a##ag#tg##t###t##a###cag##a#a#a##cct#a#cag####ccg##ca##t##ca#ctt####ttg###t##caa##ct#ca####t#t#agg######t###t########a##cg#cca#t#t#tg######t####t###t#####a##CT######A#####CCCT#A#T#CA#CT#AG#A#####T#A#TG##T##AT####T#AG###A#A##A#---A####T###CCAT##A#AAG#T##A#CCAT##Ctgg####a##a##ctg##a#a#agg##a##a#a#ag##t#agg##t#t##t####a###t#t#t#t###cctgg##aa##cat###tg#a##t##a###a#ccca##t####tgg########t#a##tt##cct##ct#ct##t#agg##t##a#a####a##t###a#a######t######tg##tgg#cgtg#tg##t#at##ct######cca##a#t#tg##ag##t##cgcga#ag###t##tt#a##ccaa#a###t#a####a##ctgg##a####t#t#a#####ca##t#t##a###############a##ca###atg#t###a#a#a#ct##a###cca##t##atgg#ag##t#ag#cgg#ag####a#tt#a##ttgg#a###cgag##t##a#t#a##t#t###t####ca#t##a#t#cag##tgg#cg##a#a#a#a###cct###t#a#--#####a#####a####t#t######t###ag#########a##a#A#A#A#####A#T#####T##T#CACG#T##CT#T########A#A#A#A#CA#A##A#####CAA##CTG##T#T###T##T#A#A##T#CG#T##TGG##A#CA#CC 
+
+a score=97796.0
+s hg18.chr1        21738 409 + 247249719 #CA####TA####CA#A#CA##CA####A#CCT#CA##TG####A#CCT#A##T##A####A####CCT##CT####T##T---###AG##T#A##CCCG##CT########A######CTAG##----------------------------------##T##A#TGG#####CTG###CT#A#CCTG###A#A####A##T##AG###A###T#AT#T#TG###ACA##A##TCT##CT##CT#T##TG##CA##TGG##T#A#CGG##CTGG###-###AG##T##AGG##TG###CCAG##A###TT##T##A##TT##CA#A##CCCCA##CT#CTG####T##CAG####CAA#A##ATG###T##AG######CTG#TG#AG#A#T##A#####T#T###AGG#T###CTAA##CCCG###T##AG##A######TG##A 
+s panTro2.chrUn 57107006 446 -  58616431 #CA####TA####CA#A#CA##CA####A#CCT#CA##CG####A#CCT#A##T##A####A####TCT##CT####T##T##T###AG##T#A##TCAG##CT########A######CTAG####T####T##A#####T#####CCT#A#CCTA#A##T##A#TGG#####CTG-##CT#A#CGTA###A#A####A##T##AG###A###T#AT#T#TG###ACG##A##CCT##CT##CT#T##TG##CA##TGG##T#A#TGG##CTGG#######AG##T##AGG##TG###CCAG##A###TT##T##A##TT##CA#A##CCCCA##CT#CTG####T##CAG####CAA#A##ATG###T##AG######CTG#TG#AG#A#T##A#####T#T###AGG#T###CTAG##CCCA###T##AG##A######TG##A 
+
+a score=7233.0
+s hg18.chr1        22147 35 + 247249719 ###A###T#AG###T#A#####A##T####CT##T 
+s panTro2.chrUn 57107452 35 -  58616431 ###A###T#AG###T#A#####A##T####CT##T 
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Apr 01 09:12:41 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="bx-python" version="0.7.1">
+      <repository changeset_revision="cdb5991f9790" name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>