>input_sequence_87159
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-------------------------------------------------------------------------ATGTCGG
ACACGGAGAGGTCCGTGGCGAGCTGCGTGGCGTACGTCGGCATGGAATTGAGGCAGAGGAGCGTGGCCAGGAATGGGAGG
GTGGTGTCGATTGTGGAGGACACGGTCAGCAGCTGCGGAAACAGCTCGCGTGAAAGCGCT------GCGGCTGACGCCAC
GGTGCGGGTT----------CGGCCCGGCGGCCTGAGTTGA---------------------------------------
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>chr3A_1_TraesCS3A01G263100
GTTATCAATTCTCTATCTAGATACTTGTGCATGTTTTTTCTTCCTTTTTGTTTGATCAAATTGGTTTAGCTTCGCTACAT
GTTGTCCTTTCGCTAGGCATAAATAATCTGGACCATGGAGGTGATGGCTGGCTATACTCTGCATCTTCACTACTAGGGAA
AGGAGAGGTGGTAGTGGCAGATTAATTTTAATATTTTATTTATTTATCATCGTGTTGTTATTGCTTTGATAGAGATCTTT
TCTCACTAAGCTCAATTGTTGTACATTCTCTGCATGGCTAAATTATGTGCTTTGTGCTGCACATTTTGTCAGCAAAATGC
AATTTTCCTGTTTTTTTTTAATTCTCGCTAAAAAAACATCCAAGTAACTGTTATAGACTTATTGTTGTCACAATATTAGT
GATGGCTATAGATAGAGGGACTGTCTGAAATACTGACAACTGATTGTTATTGTATCATCACATGATCAAACACAATAAGG
CGCTAGGCAAGGGCGCTCACTCGCGCTATCCACCTGTCCAAATATTGTGCTGATTTTACTGTACAGGACGAGAAAGAAAA
AAACGAGCACGCAACTCCCTTCGTACGCAGCGTTCTTTTCCCTTTTCCTCCCATCTAAGCTTACTGCCGCTGCCGTCGCC
ACCCTCTCCATCTTCTGCCTGAGCTCCACCTCTCAAGCCTCTACTTGCGATGACCACGAGGCCCCGCCCACGCCTAGGGT
TCGCGAGGGAGCTCTCCCGCCTCCGCCTCC---GCCGGCCATGTCATTCCGATCCGGCGGCTGCAC-CTCTTGTTCGAGC
TCCTCTCCAGCGGCCTCACCAC---------CGCCGCCGATGACAACACATCCCTTCACTTCCTCCCGAGACCT------
-------AGCGCCGCCGCAACA----CTGCAAGCGCAAGCAGAGGTTCTG---GAGCCCCTCGATTGTGGAGGAGGAGCC
GCGTGTGGACGTCCATGCGCCCGCCGTGCTCAGGGCAACGGATCTGAGGCCTGTGGCGGAGAAGGCCTGCCAGATGTCGG
ACACGGAGAGGTCCGTGGCGAGCTGCGTGGCGTACGTCGGCATGGAATTGAGGCAGAGGAGCGTGGCCAGGAATGGGAGG
GTGGTGTCGATTGTGGAGGACACGGTCAGCAGCTGCGGAAACAGCTCGCGTGAAAGCGCT------GCGGCTGACGCCAC
GGTGCGGGTT----------CGGCCCGGCGGCCTGAGTTGAACGA-----TGAAGAAACTGCAGAAGGATGAGTCGCTGG
GCTGGGACAAGTACATCAAGGAGAACAGCAACATTCTCGGAGGTATAGATTTCTGTTCATTTGGATTTCAGTACATATTT
TAGTTTTTTGCACACC--TCTTTCATGGTGTGA---TGTTTCATTGCTGTTGGTAAGAACATTCGCATTGAACTGAAATT
CTGTAGAGTGCGGCATTTGTGAATTTCATACCAGCTACGC----AGTCTATGAACATTGTGACATAAA--------CGAA
ACAGTCGGAAGTAGAAATTAGGAATTAATCTTGTGTTACACTGAAGTGGTTCCCTTATGGGTTTTG-TGCGTCCTGCTAA
ATTTGGAGGATCATGAGAAATAAAGTGTATTGTAGTTTAGAAAGAACACTGGCATCATGGTTTTAGTTGGGGTATAT-AA
AAATTTATCAGAAAAGCTGCAGATAATCATATCATAACCTGCATTTTCTAAGTAAGAAAATAAGGATGCACTGATTCTCT
ACAAGCTCG----------------------TGAAAAA--------------------------TGAAAATAGTA--ACT
-CAGAAAGTTGAACCAAATAATTTAAACCAGCGAGGTACT----------------------------------------
---------------------------------------------------------------------CTGTTCATGTT
TTTTTTATGAAAACCTTTAAAAG-ATATCATTACCAGTCTCTGGATTTGCATTTCTTTTTAACTGCCCAGCTCCTAACCA
TTGTTGCTTTGTAGTGGCCATAGATGGGAACAACTTTTAGTCAGATTTCCTATCGCACACTGAATTAGTCCAATGTATGC
GTTTACACCTCTTTTCAACTATGATATACTGCAAAAGTCGAGCGCCGTGACAATTCACCTTTCAGATACTTCGTTGGAGA
AATGTATAGCGGCAATTCACTTAGGAGTACAATTGCAGTGGGTAATGACAAGAAGCGACAGCGGGTCTACAACACTATGT
TTCATGTGCCTTGGAGATGTGAATGGGTATATATTTCACTTGCAAATATGTTCCCTTCT-TGTACCCTATATATTAGATA
TATTT---GTTGGAATTTTAGGGCCATCCT
>chr4B_697
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--------------------------------------------------------CGAGGCCCGGCCCGCGCCTAGGGT
TCGCGAGGGGACTCTCCCGCCGCCGCCACCCACGCCGCCCATGTCACTCCGATCCGGCGGCCGCAAGCTCTCGTTCGAGC
TCCTCTCCAGCGGCCTCACCGCCGCCAACGACGCCGCCGACGACGACGCGTCCCCGCGCTCCCTCCCCGAGACCTCCTCC
GATGGCCAGCGCCGCCGCAAGAGGCGCTCCAAACGCAAGCGGGGGGCGCTCCAGAGCCCCCCGATCGCGGAGGAGGAGCC
GCGCGTGGACGCCCACCCGCCCGCCGCGCTCAGGGTAGCGGATCTGATGCCCGTGGTGGAGAAGGTCTGCCAGGCCTCGG
ACGCGGAGCGGTCCGCGGCGAGCTGCGTGGCCTACGTCGGCGTGGAGCTGAGGCAGAGGAACGTGGCCGGGAATGGGAGG
GCGGTGACGTTCGCCGAGGACGCGGCCAGCAGCTGCGGAAGCAGCTCGCGTGAAAGTGCCGCCGCCGCCGCT---GCCGC
GGTGCCGGATGCGATTGACCCGGCCCGGCGGCCCGAGGCGAACGGTGTCGTGAAGAAACTGGAGAAGGATGAGTCGCTGG
ACTGGGAAAAGTACATCAAGGAGAACAGCAACGTTCTCGGAGGTACAGATTTCTCTTCGTCTGGATTTCAGCACATATTT
TGGTTTTTCTTGTACCTTTCTTTCATGTTGTGACGTTGTTTCGATGGTGCTGGTTATAACATTCGCATT-----------
---TAGAGTGTGTCATTTGTGAATTTCGTATCAGCAACCAGCAGGGTCTATGAACATTGTGACATATA--------CGAA
ACAGCCTGAGGTACAAATTAGGAATTACTTTTGGGGTACACTGAAGTGGTTCACTTATGGGTTTTGGTATGCCCTGCTAA
AGTTGGAGGATCATTAGAAATAAAGTGTACCGTGGTTTAGAAAGAACACTGGCATCATGTTTTTAGTTGGAATATGTCAA
AAAATTATCAGGAAACCTGCAGATAATCGTATCATAACCTGCATTTTCTAAGTAAGAAAATAAGGATGCACTGATTTTCT
ATAAGCTCG----------------------TCAAACGGACTTGTGCAATGAGATACAAATGGGTGAAAATAGTA--ACT
ACAGAAAGTTGAACCAAATAATTTAAACCAGTGAGCTACC----------------------------------------
---------------------------------------------------------------------CTGTTCATGC-
TTTTTTATGGAAACCTTTAAAAAAATATCATTACCAGTCTGTGGATTTGCATTTCTTTTTAACTGTCAAGTTTCTAATGG
TTGTTGCTTTGTAGTGGCCGTAGATGAGAACAACTTTTAGTCAGATTTCCTATTGCACACTG-ATTAGTCCAATGTATGC
ATTTACACCTCTTTTCAACTATGTGATACTGCAGAAGTCGAGCGCCGTGACAATTCACCATTCAGATACTTCATTGGAGA
AATGTATAGCGGCAATTCGCTTAGGAGTACAATTGCAGTGGGTAATGACAAAAAGCGACAGCGGGTCTACAACACTATGT
TTCATGTGCCTTGGAGATGTGAACGGGTATATATCTCGCTTGCAAATATGCCCCCTTCTTTGTACTCTGTATAT------
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>chr4D_746
CCTCC---------------------------------------------------------------------------
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--------------------------------CGCCGCCCATGTCACTCCGATCCGGCGGCCGCAAGCTCTCGTTCGAGC
TCCTCTCCAGCGGTCTCACC------------GCCGCCGACGACGACGCGTCCCCGCGCTCCCTCCCCGAGACCTCCTCC
GATGGCCAGCGCCGCCGCAAGAGGCGCTCCAAGCGCAAGCGGGGGGCGCTCCAGAGCCCCCCGATCGCGGAGGAGGAGCC
GCGCGTGGACGCCCACCCGCCCGCCGCGCTCAGGGTAGCGGATCTGATGCCCGTGGTGGAGAAGGTCTGCCAGACCTCGG
ACGCGGAGCGGTCCGCGGCGGGCTGCGTGGCGTACGTCGGCGTGGAGCTGAGGCAGAGGAACGTGGCCGGGAATGGGAGG
GCGGTGACGTTCGCGGAGGACGCGGCCAGCAGCTGCGGGAGCAGCTCGCGTGAAAGCGCCGCCGCCGCCGCCGCCGCCGC
GGTGCCGGATGTGATTGACCCGGCCCGGCGGCCTGAGGCGAATGGCGTTGTGAAGAAACTGGAGAAGGATGAGTCTCTGG
ACTGGGAAAAGTACATCAAGGAGAACAGCAACGTTCTCGGAGGTACAGATTTCTGTTTGTTTGGATTTCAGCACATATTT
TGGTTTTTCTTGTATCTTTCTTTCATGTTGTGACGTTGTTTCGATGGTGCTGGTTATAACATTGGCATT-----------
---TAGAGCGTGTCATTTGTGAATTTCGTATCAGCAACCAGCAGGGTCTATGAACATTGT-ACATATA--------CGAA
ACAGCCTGAGGTACAAATTAGGAATTACTTTTGGGGTACACTGAAGTGGTTCACTTATGGGTTTTG-TATGCCCTGCTAA
AGTTGGAGGATCATTAGAAATAAAGTGTACCGTGGTTTAGAAAGAACACTGGCACCATGTTTTTAGTTGGAATATGT-AA
AAATTCACCAGAAAACCTGCAGATAATCATATCATAACCTGCATTTTCTAAGTAAGGAAATAAGGAGGCACTGATTTTCT
ATAAGCTCG----------------------TTAAACGGACTTGTGCAATACGATAAAAATGGGTGAAAATAGTA--ACT
ACAGAAAGTTGGTCCAAATAATTTAAACCAGTGAGGTACT----------------------------------------
---------------------------------------------------------------------CTGTTCATGTT
TTTTTTATGGAAACCTCTAAAAA-CTATCATTACCAGTCTGTGGATTTGCATTTCTTTTTGACTGTCCAGCTCCTAATCA
TCGTTGCTTTGTAGTGGTCCTAGATGAGAACAACTTTTAGTCAGATTTCCTATTGCACACTGAATTAGTCCAATGTATGC
ATTTACACCTCTTTTCAACTATGTGATACTGCAGAAGTCGAGCGCCGGGACAATTCACCATTCAGATACTTCATTGGAGA
AATGTATAGCGGCAATTCACTTAGGAGTACAATTGCAGTGGGTAATGACAAGAAGCGACAGCGGGTCTACAACACTATGT
TTCATGTGCCTTGGAGATGTGAACGGGTATATATCTCGCTTGCAAATATGCCCCCTTCTTTGTACCCTATATATTG--TT
T-TTT---TTTTGAATTATAGGGCCATCCT
>chr4A_1385
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---TAGAGTGTGTCACTTGTGAATTTCGTACCAGCAACCAGCAGAGTCTATGAACATTGTGACATAAACGAAACAGCGAA
ACAGCCCGAGGTACAAATTAGGAATTACTTTTGGGGCACACTGAAGTGGCTCCCTTATGGGTTTTGCCT-GTCCTGCTAA
AGTTGGAGGATCCTGAGAAATAAAGTGTACC-TGGTTTAGAAAGAACACTGGCATCATGTTTTTAGTTGGAATATGT-AA
AAATTCACCAGAAAACCTGCAGATAATCATATCATAACCTGCATTTTCTAAGTAAGAAAATAAGGATGCACTGATTTTCT
ATAAGCTCG----------------------TCAAACGGACTTGTGCAATACGATACAAATGGGTGAAAATAGTATAACT
ACAGAAAGTTGAAGCAAATAATTTAAACTAGTGAGGTACT----------------------------------------
---------------------------------------------------------------------CTGTTCATGTT
TTTTTAATGGAAACCTCTAAAAA-CTATCATTACTAGTCTGGGGATTTGCATTTCTTTTTGACTGTC-------TAATCG
TTGTTGCTTTGTATTGGCCATATATGAGAACAACTTTTAGTCAGATTTCCTATTGCACACTGAATTAGTCCAATGTATGC
ATTTACACCTCTTTTCAACTATGTGATACTGCAGAAGTCGAGCGCCGTGACAATTCACCATTCAGATACTTCATTGGAGA
AATGTATAGCGGCAATTCGCTTAGGAGTACAATTGCAGTGGGTAATGACAAGAAGCGACAGCGGGTCTACAACACTATGT
TTCATGTGCCTTGGAGATGTGAACGGGTATATATCTCACTTGCAAATATGCCCCCTTCTTTGTACCCTATATATTGGATT
T-TTT---TTTGGAATTATAGGGCCATCCT
>chr4A_1576
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-----------------------------------------------ACTGGCACCATGGTTTTAGTTGGAACATAT-AA
AAGATTGTTAGAAAACCTGAAGATAATCATATCATAACCTGCATTTTCTAAGTAAGAAAATAAGGATGCACTGATTCTCC
ATAAGCTCA----------------------TCAAAC-GACTTGTGCAAGACGATACAAATGGGTGGAAATAGTA--ACT
-TAGAAAGTCGAACCAAATAATTAAAACCAGTGAGGTACTTTGCTCATTTTTGTATGGAAACTTTTAAAAGATATCATAA
CCAGCATACAAATGGGTGGAAATAGTAGGTCAGAAAGTCGAACCAAATAATTAAAACCGCTAAGGTACTCTGTTCATTTA
TTTTTTATGAAAACCTTTAAAAG-ATACCATTACCAGCATGTGGATTTGCATTTCTTTTTAACTGTCCAGCTCCTAACAA
TTGTTGTTTTGTAGTGGCCATAGATGAAAACCACTTTTAGTCAGATTTCCTATTGCACACTAAATTAGTTCAATGTATGC
GTTTACACCTCTTTTCAACTATGTGATACTGTAGAAATCGAGCATCATAACAATTCACCATTTAGATACTTC--------
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>chr2D_1576
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-----------------------------------------------ACTGGCACCATGGTTTTAGTTGGAACATAT-AA
AAGATTGTCAGAAAACCTAAAGATAATCATATCATAACCTGCATTTTCTAAGTAAGAAAATAAGGATGCACTGATTCTCC
ATAAGCTCA----------------------TCAAAC-GACTTGTGCAAGACGATACAAATGGGTGGAAATAGTA--ACT
-CAGAAAGTCGAACCAAATAATTAAAACCAGTGAGGTACTTTGTTCATTTTTGTATGGAAACTTTTAAAAGATATCATAA
CCAGCATAC-AATGGGTGGAAATAGTAGGTCAGAAAGCCAAACCAAATAATTAAAACCGGTGAGGTACTCTGTTCATGT-
TTTTTTATGAAAACCTTTAAAAG-ATGCCATTACCAGCATGTGGATTTGCATTTCTTTTTAACTGTCCAGCTCTTAACAA
TTGTTGCTTTGTAGTGGCCATAGATGAAAACTACTTTTAGTCAGATTTCCTATTGCACACTGAATTAGTTCCATGTATGC
GTTTACACCTCTTTTCAACTATGTGATACTGTAGAAATCAAGAACCGTAACAATTCACCATTTAGATACTTC--------
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>chr5A_1653
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---------------------------------------------TTCTAAGTAAGAAAATAAGGATGCACTGATTCTCT
ATAAGCTTGTCAAACATTCTCTATAAGCTTGTCAAAC-GACTTGTGGAAGACGATGCAAATGGGTGAAAATAGTA--ACT
-CGGAAAGTTGAGCCAAATAATTTAAACCAGTGAGGTATT----------------------------------------
---------------------------------------------------------------------ATG--------
TTTTCAATGGAATCCTTTAAAAG-ATATTATTACCAGTATGTGGACTTGCATTTGTTTTTAACTGTCCAGCTCCTAACCA
TTGTTGCTTTGTAGTGGCCGTTGATGAGAACCACTTTTAGTCAGATTTCCTATCGCACACTGAATTAGTACAATGTATGC
GTTTACACCTCATCTCAACTATGTGATACCGCAAAAGTTGAGCGTCGTGATAATTCACCATTCAGATACTTCATTGGAGA
AATGTATAGA--CAATTCACTTAGGAGTACAATTGCAGTA-GTAATGACAAGAAGCGACAGTGGGTCTACAACACTATGT
TTCATGT--------GATGTGAATGGGTATATATCTTACTTGCAAATATGCTCCCTTCTTTGTACCCTATACATTAGATA
T-TTTGTTTTTTGAATTTTTGGGCCAT---
>SNPs
SS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------S----S----------
---------SS----------S-----S---------S--------S--------------S---S-----S--------
--------------------S-------------------S---S--S-S----SS-S--S------SSSSS-S------
--------------------S-------S-----------S-S--SSSSS----------S----S-S------------
---S-------S---SS---------S--------S-S---------S---S----S--------S--------SS----
--S-----S------S-------------------------S----SS------------S-------S-----------
-S----S--S-S-S-------S---S--------------S------------------S--------S----S----S-
-----S--S----------------------------SS-----S----------------S------------------
S------S------------------------S------------S------------S------------S--------
-S------SSSSS--------------S--------------SS--S--S----S-S------------SSSSSSSSSSS
SSS-------S-S--------------S-------S--SS----------------------------------------
----S-S--S---S-------------S-S---S-S--------------------------------SS----------
-S---------------------------SS--S------------------------------------SS--------
---------------S----------------------------------------------------------------
-S------------------------------S---SS------------------------------------------
-------------------------------S------------------------------------------------
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----------------------------------------S------------------------S--------------
--------------------------S-----------------------------------------------------
-----------------------SS----------------------------------S------------S-------
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----------------------------------S---------------S-----------------------------
-S------S---------------------
>forward_578
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------------------------------------------------------------------------------AA
AAACGAGCACGCAACTCC--------------------------------------------------------------
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>reverse_1440
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-------------------------------------------------------------------------------T
CTGTAGAGTGCGGCATTTGT------------------------------------------------------------
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