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Merge pull request #6366 from martenson/ucsc-updates
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update UCSC axtToMaf
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@martenson
martenson authored Sep 26, 2024
2 parents 490c050 + e3b506e commit 27e5f08
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Showing 5 changed files with 126 additions and 9 deletions.
27 changes: 19 additions & 8 deletions tools/ucsc_tools/ucsc_axtchain/axtchain.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -72,17 +72,28 @@
`axtChain`_ is a tool to chain together alignments in `axt`_ format. The `chain`_ format describes a pairwise alignment that allow gaps in both sequences simultaneously.
For implementation details see axtChain's `source code`_.
sample linearGap file (loose)::
linearGap defaults:
tablesize 11
smallSize 111
position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
loose::
tablesize 11
smallSize 111
position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
medium::
tableSize 11
smallSize 111
position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300
For implementation details see axtChain's `source code`_.
.. _axtChain: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
.. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html
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44 changes: 43 additions & 1 deletion tools/ucsc_tools/ucsc_axttomaf/axttomaf.xml
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@@ -1,9 +1,21 @@
<tool id="ucsc_axtomaf" name="axtToMaf" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
<tool id="ucsc_axtomaf" name="axtToMaf" version="@TOOL_VERSION@+galaxy1" profile="21.05" license="MIT">
<description>
Convert dataset from axt to MAF format
</description>
<macros>
<token name="@TOOL_VERSION@">469</token>
<xml name="sanitize_query">
<sanitizer>
<valid initial="string.printable">
<remove value=" "/>
<remove value="&apos;" />
</valid>
<mapping initial="none">
<add source=" " target=""/>
<add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
</mapping>
</sanitizer>
</xml>
</macros>
<xrefs>
<xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
Expand All @@ -25,6 +37,14 @@
#else:
'$query_reference_index_source.que_ref_index_file.fields.path'
#end if
#if str($t_prefix)
-tPrefix='$t_prefix'
#end if
#if str($q_prefix)
-qPrefix='$q_prefix'
#end if
$score
$scoreZero
'$out'
]]></command>
<inputs>
Expand Down Expand Up @@ -60,6 +80,14 @@
</when>
</conditional>

<param name="t_prefix" type="text" optional="true" label="add this to start of TARGET sequence name in maf" help="Typically organism name and a dot (hg38.) is used">
<expand macro="sanitize_query"/>
</param>
<param name="q_prefix" type="text" optional="true" label="add this to start of QUERY sequence name in maf" help="Typically organism name and a dot (mm10.) is used">
<expand macro="sanitize_query"/>
</param>
<param argument="-score" type="boolean" truevalue="-score" falsevalue="" label="Recalculate score" />
<param argument="-scoreZero" type="boolean" truevalue="-scoreZero" falsevalue="" label="Recalculate score if zero" />
</inputs>
<outputs>
<data name="out" format="maf" />
Expand All @@ -77,6 +105,20 @@
</conditional>
<output name="out" file="1.maf"/>
</test>
<test>
<param name="in_axt" value="2.axt"/>
<conditional name="target_reference_index_source">
<param name="target_reference_index_source_selector" value="history" />
<param name="in_tar_ref_index" value="hg38.noprefix.fasta.fai"/>
</conditional>
<conditional name="query_reference_index_source">
<param name="query_reference_index_source_selector" value="history" />
<param name="in_que_ref_index" value="mm39.noprefix.fasta.fai"/>
</conditional>
<param name="t_prefix" value="hg38." />
<param name="q_prefix" value="mm39." />
<output name="out" file="1.maf"/>
</test>
<test>
<param name="in_axt" value="1.axt"/>
<conditional name="target_reference_index_source">
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19 changes: 19 additions & 0 deletions tools/ucsc_tools/ucsc_axttomaf/test-data/2.axt
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@@ -0,0 +1,19 @@
0 chr1 52448 53340 chr2 111209343 111210259 + 33103
GCCAATGGATAGAGTAAATAATTCTGCGGTATCTAAATTTGTATTGATTGGACTTTCAAGCTCTTGGGAGATGCATCTTTTTCTTTTTTGGTTCTTCTCTGTGTTCTACATGGGAATTATCCTGGAAAATCTCTTCATTGTGTTCACAGTAATTATTGACTCTCATTTA-AATTCCCCAGGTACTGCCTACTGGCCAACATTTATCTTCTTGATCTGGG----TCTTCTCCTACAGT-------------TCTGACTTTTTCACTAACTGCAGCATCATTTCTTTTCCAAGATGCATCATACAGATATTTTTCATTTGTGTCATGCGTAAAAATTGAGATGGTGCTGCTCATAACCATGGCATAGAGCAGGTACACTGCCAATCTGTAAGCCTCCCCATTACCTGACCACAATGAACCCCAAAATGTGTGTTTCCTTTGT---TGGAGGCATCCTGGATAGTCAGGATAATCCATGCTGTATCTCAGTTTGTTTTTGCCATAAACTTGCCTTTTTGTGGCCCTAATAGAGTAGGTAGTTTTCACTGTGATTTTCCTTATGTCATGAAACTTGCTTGTGTAGACACTTACAAACTAGAGGTTGTAGTCACTGCTAACAGTGGGCTTATATCCATAGCTACCTGTTTCTTATTAATAATATCCTATATTTTCATTTCGGTAACCGTCTAGAATCCTTCTTCAGGAGACTTATCTAAAGCATTTGT-GTCATGTTAGATCACATCACAGTAGGGATTTTGTTTTTTATGCCATGTATATTTCTGTATGTGTAGCCTTTGCCTAAAACAACACATGATTAATATTTGTTCATTGTTCCTTTTGCTATCACCCCTG--------TCTAGGATCTACACATTAAGAAACAAAGACATGAACGTCTCCATGGAAAGACTGGGAAAATGGA
GTCAATGGATCAAATAAATGAAACTGTAGCTTTTGAATTTGTGTTGTTGGGACTCTCCAGTTCTTGGAAAAATACAATTTTTCTCATGTCCACCTTCTCTTTGCTCTATGTAAGCATCATCGTGGGAAACCTTTTCATTGTCTTTTTGGTAATTAATGACTCCCGTTTACAGTCTCCTATGTATTTTCTTTTGGCCAATCTGTCCCTCATTGATGTTGGACTTTCCTCTACCACAGTGCCCAAGATGATCTCAGATCTTCTGAAAGAGCACAAAGTAATATCTTTCCACAGTTGCATGACTCAGATCTGCTCCATCCACATTATG-GGAGGAGTGGAGATGGTGCTGCTCATAGCCATGGCGTTTGACAGGTACACGGCCA-TCTGTAAGCCTCTGCACTACATGAGCATCATGAGCCCTAGAATATGCATTTCATTTGTAATTGCTGGC----TGGGTCACTGGAGTGGTCCATGCCATGTCACAGTTCTCTTTTGTTGTGAACCTGCCTTTTTGTGGTCCTAACAAAGTGGACAGCTTTTACTGCGACTTCCCTCGAATCATACAACTGGCATGCACGGATAGAGACACATTTGAGTTTGTTGTTGCTGCCAACAGTGGCTTCATGACCTTGGGGACCTTCTTCTTGCTTCTCCTCTCCTATGTCTTCATTTTGGTCACAGTCTGGCAAAGGTCTTCAGGGGACTTGTCAAAGGCGCTTGTCACTCTGTCAGCTCACATCACTGTGGTTGTTCTGTTTTTTACTCCATGCATGTTTCTCTATGTGTGGCCTTTCCCCACATCATCGACTGACAAATACCTGTTCATTGTTGACTTTGCTGTCACCCCTGCTCTTAATCCTGTCATCTATACTTTAAGGAACAAAGATATGAAGGAAGCCATAAAAAAGCTGAGCAAGCAGA

1 chr1 56555 58924 chr2 111303515 111305845 + 43395
CACATTATTCTGCAGTTTTTATCTTGCTTACGTATTTTTGGAATGTTACTATTTTTCAAAAATTAATTTGGGATCAACCAACACTTCTTATTCTGCTGCTGTTCTAGAGAAAATCATTTTCCTCATTTCTGAACAAGAGAAAATGAAAT-----------------ACAGCTCTAAACAAATGCCACTGTAAACCAAGGTGGAGCCTTTGCACTTTCAGGCCACCATGATAACCT---GGAGATTAGATTTTTCTGTGTCTTTATATCAATAATAAAGCCAAGCTTCTCCAGGGGTATCCACTAGGCTTGTCTCAATGGCTCAATACAGGTCCTTTTGTGAATGATTACCTCACCCTCATGGAAACACACTCTT-GTTACAGAAACTCAGAATGATTCTATTTTTTCTTTTATATTTGTATATGTTTTTCCAATACCTCTGAAAAAACTGATCCAAAAAAAATACAAATTTTAATTGTAGCCAGTCAATTCAGGAAGGATAAAGGTCAAAAACTTTCAAAGAAACCTTCAGCCCCAACACACTAAACTTTGGGAGCACAGGTTGGCATCCAGAGGTAAACATTTGCTATAACTGATAACAGGAGAAGGATCCATTTATTCACCTGTTATCAATTACAGGCATTGTATTTAAAGATCAGATGTTTTATATTTATTTCTTCAAATTTCATTCATGGTGCCATAAGTGAAGGTATCTCTGTCCACCCTGAATATATTTTCACTCCCTCATCTCAGTCATTCCGAACAATTCACACACTAAGATTACCCATGCTAAATGGGGATTCTTTTTTACTAGCCAATGTAGTACCTCAAATCCTTCCTTCCCTCCCCCTATTTCATCAGCAGGCAATTCTTTTGATACTTTTGTCAAGGGGAAATTGTGTGACTCAGAGATCTAGTCCCCAAGAGAAACTAATAATGGGCTGGGTATTGTCTGTCTCAGCAGCATCAGTGGGTCCCTCTCCTGTGCAGCTAATTAGCTTCCTTTCCAATATGAAGAATCTTATATATAGCTTTGTCTTT-GGGGTATTAC----ATAAATGAAGATTAAGCTATCTGAATTTCTCCTTCTCCTAAAAATGCACATCCTATGACTGAAAAGACAGGTAAAAGAGATGCTTTTAATTACAAAACTTTCCCTGTCGTGGTTGCTTCTCTCTATCCTTCTAAACTCCCTTTCAATTTCTTCTCTTCTGTAACATATTTGTGCCCAAAATCTTCTGCTTTCTGAAATATTTT--ATCTTTTTCTTCCACACTATCTC----TTATTTTCCAATTTTAATCATTAAATTATATTATGTCTTATAAAACTAATCCCACATATAAACCCCTATGATA--ATTTCAGTTTG--TCCCTAGTATGAAG-TTCTTTAAAGATGTGTAGTTTTCTAACTTTCATGCTCTCCAATTAATTATAAACTTCATTTTCCACTCTGAAAAGGAGATGTCTGATCTCAGCTATTTCCATCCTATTTGAAAACCAGATTTAGTTTTAAACCAGAGGAAGGGAATCTCAAGTCTTTACCTCCCACAGTCTGGTGTGATTCTCTCTCTTTTGGTATTACCTTCCTCCACATTGGAACACTCCAGCCAATGCATAGGCTGAGAGGCTATCTC-AGATTCAGAAAGATTTGGCCTCATCCCAGGGGAGGGTACAGAGGAGCTGATGACTATGAATTC--TGAAATGGAACTGTTCCAG-------------GTTGAAGAAATAAGAAAGGGAATTGGGAAGAGCAAT-----GCCCAGTGAAAAAGAAGAAATAA-TATTTTAGGAAGT-GAATGC-TAATTTTATTTTAAACAAAATAAGAACTCAAGGAATAAGAGGGTTCTTCCAATAGGTTAGAGTGATCCTGTCAAACATATATGCTTCT-AGATTTTTTTAAAGACTGTTTCTACTAAGAAAGCATAGACCGCTATTGAGAAAGATCATTAAACTGGAATTTAGGAGGTCTGCCTTCTGATTCTGACTTCTTGAATGTATTGTTAGCCAT----TTAACCACACTGTGTTGTTTC--------TCA--TTCTACCTGTAGAATCTCAAAGTTCTTTCCCACTTCTATACAAAACTATAATTCTGAACATCCTTTTTGTTTAATATAAGTCTGCATTTCCTGTTTGAA--GATATGTGTCCC-AGACCCTAAATGACTGACAAATTTTAAATCTCC---AATAGGAAAGATGACAAACTCTATGGAAACTTGGCTTCTGAAGAACTCCTAGAAGCTTTCCAAAGTCATCAGTGTTTCCTAAGAAGGCAGAGAAATCAAACAC-----------------------------------ATGG----------------------------TCTTTTCCTCCAGACAAGCTCCTTTGGGTCATCAGGATTTCTTCAACAATA---AAATGTAATAATTCCAAATGTTTGTAACAGAATGGGTAGGACTTTCTTCACTTATTTAAATACTCCCTTTTT
cacattgtattgta--ctctattatgttt-tattgtattatattatTGTTGTTTTTCAAAAATT----TTGGTTAAACTAGCATCCCTTCTTTTTCTGTTGACCTAAGAAGAAACCCTTTCCTTCTTT-TGAACAAGATAAAATGAAGTGCAGATTTCTAAACAACACAGCTTTAAAGAAGCACACTTATAAACAAAGGTAGAGCTTTCACTGTTTCA-------ATGA-AACCTCAGTGAGATCAGATT-----ATGACTCTACATAAATGACAAAG------------------ACCCACCGAGACTGGTACCATGTTTTCATTCATATGGTGTTA--AATGATGGTCTC---CTCGGGTATCCAGACCCTTCATTTAAGTAACTCAAAACAACT----------------ATCTATAT-----CTTCCAAAATTTCTAAACAAATTGACCCGATGACT-TACAAGTTTAACTTATAATAGATCAACTCA--AATGATAAAA--TAGTGATTTTCAGATATACCTATATCCTCTGG---------TTTTGTAGAGCATTCAGGCTTTCTTGGACAAACATTTGTCA-AAATGA-AACAATAAGAACTTTTATCTTTTTCCATACTAACAAGTGAAG----TGTATTTTCAGATAATTAGTTTTAGACT-ATTTTT---AATTTGATATATGAATCCA-GAGTAAAAATACAGCTATCCACTTTTGGAATATTTTTTATTCT-----------ATTTCAAGCAATTCATAAAAAAAGATTATAACTCCTCAA-GGAGGTTATTTTAAATT---TAATACATTACACAGAATATTTTTATTTTTTCCCTT-TTATATAACCAGACAATTCTTTTGATACTTCTCTCTTGGGGAAACCA-ACAGCTCAT-GATCCAATTCCCAATAGAAACTATTAATGAACTGGGTATTGGACACCTTCACAGTGCCAATGGGTCACTCTCCTGAGCAAATAATTGGCTTCTTTGCCACTATAAACAGTCATACATATATCTTTGTCTTCAGGGGCATTGCTTATAGAAATGAATGATAACCTACTTAAATTT-TCTTTTTCTTCAAAGCGTACCTGCTGTTACTTTAGAGA-AGGT--AAGGGGTGGTTTACATTTAAAACCTG--CCGATTATAGTTG----TTTCAATCTTGCTAA------CTCTAAT---CTCCCATCTGTAAAATAATTATGTCAGACAT-GTCACCTTTCAAGAGTATTTTTACCCTTTTAATTTTAAACTATCACAGAATCGTTTTGTGATTTTATTTA--AAAATAT----TGCTTTATATAATTAATCTCGTGCTCACAACCTTTTGATATTTTTTTAATTTGCTTCTTTGGTATGAAGATTTTTCAAGAACGTGTG--TTTCTGCTTTTTGTAGCCCTCAGACAATTGTGCAATTCATTTCCAACTATGCCAAGCAGATGTCTGGTCTCAGATATTTCCTGCATA-TTAAAGATCATATTACAATCTCAAT-----------AATCTCAAGCCTTGTCTGCCAATACTCTGGAGTAATTCTTACCTTT----TATT-------TCAATATTTGAATACTGTAAGCAGTGAATACACTGAGAGACTATTCCAAGACTTAGATATATT-----CTAGCCCACAGGATTCTAAAAAAGTGC-ATTAAATAGAAATTCTTTTTATTGCAACTGTTCAAGTAGTGGTCTAGATGTTTGAAAAA-AAGAAAAAAAATTGGCAAAGTCTATTAAGGGCACAGGGTAGGGAAAGGACTAGTTTTTTTACGAAGTAGGATGTGTAGTTTTATGCCAAACTGAGTATGAGTTCAAAGACTAACACAATCCTTTCAGTAAAGCAAAGTGATCATATCAAATATATAGTATTCTGAGATTTT----ACAACTGTTTCTCCTAATCATTTGTAGAGTAATACTGACGAA---CAGTACACTAGAGTTTAGGACACCTACCCTCTGA-TCTGTAGTTCTGTATGTTTTGCTCTTGATGCTGTTAA--ACACTAGGCTGTTTTATGCAGAATCAAGTGTTAAATGCGTTTTCTCACAGTTGTTCCCAGTTTTCATGTAAATCTACGATTCCATTAGTATGCTTTGTTTAACACATGTCTATGTATCTTGTTTGAAGTGATACTTATCCCTAGACCTTGAATAATAGACAAATTTTAAGTCACCACAACCAGGAAAACCATCAAACACTATGGGGACTTGGTTTCTGATGCACTCCTTGAAGCTCCATGCTGTTATCAACAGCTCT---GAAGGGAAAGGAATAAAGCACTATattttgcttttgttttgattttatattttgaGATGGAGCTGAGAAGTTGTTTTGTTGTATTTTTACTATTTTTACACATAAATTCTCTAGAAACATGTGGATTtaat-aataatatataaaaataataaCCCAAAATGCTTGTAA-------GATAAAAAGACCTTCATTTATTTAAGTTCTCATTCTTT

2 chr1 60917 61125 chr2 111306441 111306644 + 8501
TTAATATTTCCCACTTCATCATTACTAACCTCACTCACTCTGAACTTGATGAGAGCACCTGAGCATTAATTTTTCTTATAATTATTTAATGATTACCAGAATTCGTTCAGTATGGCCAGCTCTGGTCAAAGTGAGGCAGGCAAGATGCTTTGTCAACTGCCTGGATGGAATGTCTCAAAAGGTTTCCATTTCATGGTAGCATTATGCAA
ttAATAT--CCCAGTGCACC-TCACTACTCTGGCTCACGCTGAGCCTGATGAGGTCATA-GGGCATCCATTTTTCTTGTAGTTATTTTATTATTACCAGAATTCATTCAGAATGGCCACCTCTAGTCAACACAAAATAAGCAGCGTGCTTTGTC-ACTATTTGAGTAGACTTCCTTAGGAAGTTTTCATCTTAGGGTAGTTTTACATAA

3 chr1 61126 61836 chr2 111307411 111308031 + 9500
AGTTCAAGACGTTTAATCAAGACCCTTCACTTACTTAACTATACCTCCTTGAGA-ATCCCATCTATGAAAAAATTCTAGTCATTATAAAAATGATTGATTAAATGAGGGAAGTAGTAGAGTTCTTCATTTCTTTAGTTGGTTTAGTCTCCTATGAGTCAATCCTA-TTTTCAAA-ATTCTTAATAAACCATTTATTCCTTCAACTTTCTATGCCATTTGATGTTTTGTAAAAAAAAAAATATAA------TATGTATACAAAAAGATATTTCAAAATCTAGAAAGAGAGCTTTAGAGCTTTGTAAAGCTCTTTTAAAAATCAAAAACAACTACTGTTAATTAACATGTTGTACTATGC-AATTTGTTTACCATTATTACTCTTGGTATTTTTAAGAAAAGTCTT----TCCATTGTTATTATAAATGCTTCTATTGATATTTATTTTAATAACTGTTATTACAGTCCGTCATGTACATACACTATACTTAAAcctaatgtttggtatttaaatcgtttcaagattttatc----actgtcaacaaagtatgatgaatattttta--tgctgaaaacttctgtaaaaatagaattccaagagtattattgcaccaaaaggcatggacttaaaattcttgatacatgatttcaaaatattttctttaaggtttgaatcagtctatattccctccagcagcgtataaaagtgccaatttctctgatccttagcc
aGCCCAAGAAAATTAAACAAATCCCTTTACTAATTTAAATGTATCTTGCTACTAGATATCATTTGTGA---------------CATAAATATTTGCAATAAAAT--------CACTAACATTATTTATTTCATCAGTG-------------ATGGGTTAACCCTAGTTTTCAAACAGCTTTGATAAATCTGTCATCTCTTTAGATCACTAGATAATTTGATATTTGAGGGGAAAATAGATATGAATGCACTATGTGCATTAAAATATCCCTTAAA-TCTAAAAATAGAA-TTAGAAGCTCTG------------AAACCTGAAATGCTATCATTGTAACCGGGAATGATGGGATATGCTAATTACTTTACAACAAT----------GTTTTAAGCAAGAATCTTAAAGTCCA------------------------ACATCTAGTTT------TGTTATTATAGCCAACTGTGTATATTTGATATATTTATACCTAATTGCTTTCATTTAAACTGCCTTAAAGCTTTACTTAAAACTATCAATAAAGTCTTGCTAGTATTTGTGACTGGAGATATTATCTGTACAAGTAGTTATTTCAGAGAAGTACTTTACAACAAGGTATGGAGATAAAATTATTGACATAT---------------TGTTTAAGGGTTAAA-----ATATCTTCCCTCTTGTGAATTATAAATAAACCAATTTCATTGAGCTTTTGCT

4 chr1 61944 64435 chr2 111308032 111310602 + 69061
ctccgcctcccggggtcaagctattctcctgcctcagcctcccaagtagctgggactacaggcatgcaccaccatgcccagctaatttttgttatttttagtagagatggagtttccccatgttggacaggatggtctcgatctcttgacctcgtgatccaccctcctcggcctcccaaagtgctgggataacaggcgtgaacaaccatgcccggcctgtaaaactttttcctaatttaacagaaaaataatagtattatattttatcatatttctttgatttctaAGacacacatacacacaca---cacacacatatctgtatatacaaatacacgtatagc---------------------------------------------ttacaTTTT--AATTCTTCATTTCATTTGTTCATTTATTAGGTCTTGGAGATTTTGTGAAAC---------TGTTTAAATTCTTTTTTATACTATGAAGATATCAACCTT-TTGTCTCTACAGCATTTCAAATTCAAGTATGAT----TCACGTGTTGGTTTGGGGTAGATCATTATAGGCACATGTAGGAAACAGCTTT-----------------------------------------------------------------------CAGAGA----------------TGC----------CTTAACCGT-----------------------------------AATTATGCATTTGTATTC--------------TAATTTTTATTTAATGTTATTATT----GATTGCATTTTTAAAG--ATTCTGT--ATTTTTTAAACCATTTATTTGTATATGTTGGTATACAATCTTGCCATTTTCTGGGATTTCATATTTCCTTATTTTTGTTTTT--TACCTTTTTTGGCTTGAATT---TTTTGAGTTTTTATGCATTCTTTTCCAGTTTCTTAAGATGCTAATAAGTTCATGTATTTGAGCAATTGAGAACATTTAAAGCAATAGACTGCCTCTGAGCACAGCTTTGTCCATATTACATTAACCTTTTATACCCTGGGTTCCCACTAGTTTTTAAATAATCTACTATCAAATAAAAG-ATTTGTTAATAATAA-------------------------------------------------------ATTTTAAATCATTAACACTTAACGCATTATTTTCAGTCACACTAAGTTGATTCCTTCGTTTCTTTCAGGTTGCTTCAGAGTCTTCCCTTCTATCTGATTCAGTGGACCAAGTAAATGACTCTCTGGTAACAGAATTTGTATTACTTGGACTTGCACAATCCTTGGAAATGCAGTTTTTCCTTTTTCTCTTCTTCTCTTTATTCTATGTGGGAATTATCCTGGGAAAACTCTTCATTGTGTTCACAGTGATCTTTGATCCTCACTTACACTCCCCCATGTATATTCTGCTGGCCAACCTATCGCTCATTGACTTGAGCCTTTCATCTACCACAGTTCCTAGGTTGATCTACGATCTTTTTACTGATTGTAAAGTTATTTCCTTCCATAATTGCATGATACAAAAGTTCTTTATCCATGTTATGGGAGGAGTTGAAATGGTGCTGCTGATAGTCATGGCATATGATAGGTACACTGCGATCTGCAAGCCTCTCCACTATCCAACTATTATGAATCCCAAAATGTGCATGTTTTTGGTAGCAGCAGCTTGGGTCATTGGGGTGATTCATGCTATGTCTCAGTTTGTTTTTGTCATAAATTTACCCTTCTGTGGCCCTAATAATGTGGGGAGCTTTTATTGTGATTTTCCTCGGGTTATTAAACTTGCATGCATGGACACTTATGGGCTAGAATTTGTGGTCACTGCCAACAGTGGATTCATATCGATGGGCACCTTCTTTTTCTTAATTGTATCATACATTTTTATTCTGGTCACTGTCCAACGACATTCCTCAAATGATTTATCCAAAGCATTCTTCACTTCGTCGGCTCACATCACCGTAGTGGTTTTGTTTTTTGCTCCATGCATGTTTCTCTACGTGTGGCCTTTCCCTACTAAGTCATTGGATAAATTTTTTGCCATCATGAACTTTGTTGTCACCCCTGTCGTAAATCCTGCCATCTATACTTTAAGGAACAAAGATATGAAGTTTGCAATGAGAAGGCTGAATCAACATATTTTAAATTCTATGGAGACGACATAACACATTTGGTTGATGAGAGCACAGGATAAATGCCATGGACCATCAAGACTCCTGTGATCACCATGATCACTATGGAACGCGCACATTTTTAGTATTGCCTGAAAAAACTGAAAAATCTGCAAAAAGGATGCATTAAATCTAAGAATTGTATTTCAGATAAAGTTGCAACATTTTTTGTTAATCATA----AAAAGTA-----------------------------------------TATATTTCTATCT--------AATGTGTGTATCTAATTAA-----------CAGCAATGACTAC-------------CTTT----------------AATTTTGATGTAGTTAT-TTTATATCTGTATATAAGCACATACACATATATATGACCTAGGTTTATTTATCAGTATTTTTATGCTGATAATAAGCATCACTGGAAATTAAT-----TTTCTTATGGAAATTATGTGGATCCAATGGATAAAATATGAGTTTATATAAATTAGTAAATGCCAAAATCAAGGAAGAAACAATTTTTATTTTAATTGTACTTTAAGTTAGATAAATGGTAAGGTCAACAGCTTGTTACAACCCTTAAGTATTATTTTCAGGCTGATTGTCAATATGTTTTGTACAatgttctcac
CTCTGCTTTGTGTGGAGAAG-TATTGTCC--------ACTCTGAATGATTTGGTAATA-------ATAATAATATATTTTGCTAATT--------------------------------ATATT---------------------------------------------------------------------------------------------TGTAA----TTTTTCTTATTTAACA-AGAAATGAGA-------ATTTTCTTATATTTCACTGATTTCTAacacacacacatatacacatcacatacacacaaagagagagacagagacacagagagacacagagagacagacagacagacagacagacagacagatacacagtcaCATTTCTCAATTCTCTATATCATT-GTTCACTT----TGCCTGATGGGTTTTTAGTAGCAATCATGTATATTTTAAT-CATTTTAATATTATAAAGATATCAGCTTTATTCTCTCTA-AACATTG-AAATTCAAGTACAAGATAAGCATGAGTTAGTTTTGTG---------ACAAGCATGTGTAAGAAATAATTCTTtctctctctctctctctctctctctctctctctctctctctctctccatttttctttctttctttTGGTACAGAGGATGAAAGTTCCACATGTGCTCTTAAAGCACTTTATCATTGAGTCTATTTTTTCAGTTGGCATAAGTAAAAATAAGTTAAGTGTTTTGACTCACCATTCTAATGCTTGATATTCACTTAATTTTATTAGTTTTAAATTTCAGTTTTAAAATAATTTTTTTAAGTTTTGAAAACAAT-----GTTAATGTCCTTACAGAGTCTTTTCATTTTCTGGACTACTGCATTCATTTAGGATTGTTCCCAATATCTCTTTTTATTTCACCTGCACTTGAGAATTTAATACATTTTATCCTACTACAT--AAATCGTGTCATGTTTATGT-TTTTATCAATTGCTATAATTTAATGCAGTATATCAT-TCTGAGTAGAGCTTTTTTCAAACTCCATAAATCTTATATACACTGGATTCCTCACATTTTGTAAATTGTCTAC-ACCAATTAAAAATACTTGTTAATAGAAATTGTTTTGATAAACAAATTGTCTAGTGTTAAACAATATCTCTGGTACAGTGACTGATTTTAAATGACTAACATTTAAT--CTTACTTT--GATGCCTTAAAATAATTCAT-CTTGTCTTTCAGGATTTTTATGTATTTTCCCAACTTTCTGATCCAATGGACCAAGTTAATGCTTCTGCTCTACCTGAATTTGTTTTGCTGGGACTTGCACAATCGTTTGGAACACAGATTTTCTTTGGCCTCTTCTTCTCCTTATTTTATGTGGGGATTCTTTTTGGAAACCTCTTCATTGTGTTCATAGTGATTGTTGATTCTCATTTACACTTCCCCATGTATATTCTATTGGCCAACCTTTCGCTCATTGACTTGGGCCTTTCATCTACAACAATTCCTAGGACAATATCTGATCTTTTTACTGGCTGTAAAGTCATTTCTTTCCACAGCTGCATGACACAAATGTTCTTCATTCATGTGATGGGTGGAGTTGAGATGGTACTGCTCATAGCCATGGCATATGACAGATATATAGCAATCTGCAAGCCTCTTCACTACCTGATGATCATGAATCCCAAAAAATGTATAATTTTGGTAATAGCAGCTTGGGTCATAGGGATGATTCATGCAGTGTCTCAGTTTCTGTTTGTTGTAAATTTACCCTTCTGTGGTCCCTACAATGTAGGAAGTTTTTATTGTGATTTTCCAAGGGTCATTAAACTTGCATGCATGGACACTTATAAACTAGAATTTGTGGTCTCTGCCAACAGTGGCTTTATTTCTATGTGTACCTTCTTTTTTCTGATTACATCATACATTTTTATCCTGGCCAGTGTACGACAACATTCTTCAACTGATTTATCCAAAGCATTTGTCACCTTGTCAGCTCACATCACTGTAGTGGTTTTGTTTTTCATACCATGCATGTTTCTGTATGTATGGCCATTTCCGACCAAGTCACTTGATAATTTCTTTGCTATTGTTGACTTTGTTCTCACTCCTGTCTTAAATCCTACTATCTATACTTTAAGGAATAAAGATATGAGGTTGGCCATCAGAAGGCTAAGTAGACAGGTTTTAAGTTCTAGGGAATTTATATAGTAAATTTTATTAGTATCAACACTGA--AAATGTGATAAACTATCAA---------------TATTAACACTATAGAATAAAAACATTATT-TTATTGGGTTTAGAAACATAAGAATGTAC--------------CTATCAAAGAGTTTCAATTAATAAGGAGTTACAATAACTTCTGCTGGTTACAAAATAAAAGTGTTATATGTTTTCAAATCAACATAACTAAATCTTGTTGGTTTTATATTTTTGTATTGAATTGAAGTATTCATATTTATTTAAGTTATTATAACCAGCAATTATTGCACAAATGTTCATGCTTTTTGGTTTGTATAAATAAATGTGCatatatatatatatatatatatatatatatatatatatatatatataAAATGAACC--TTTATCAGCATCTATATGCAGATAATA--CAACACTGGTTACTAATATATATTTCTTGTGGAAATTATGTGGATCCAATGGATAAA-----GGTTTATGTAAACCAATA------------------------------ATTTTAA------TTTAAGACTTATAAGTAGGA------------------------TAACCATCACTATTAAGAT-------------TTTTGTGTCCTTCTCTTAC
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