>input_sequence_73189
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-------------------------------------------------------------AGATCCCAGCGAACTCGTA
AACACGTCTGTGCATAGTGCTAT----------------------------------TACGTATACTCCCCCACTCACCC
CCGAGAAGTCAGGAGGCATGGCGAGGAAGGCAGCGGCAGCGGC------CATGGACGGCAAGAGCTCCGAGCTCGCGAGG
GCCGTGGCGGAGGCGGAGGCGCGGGAGGAGCGGCTGCAGCGGGAGCTGGAGGCGGCGCTGGCGCGGGTGGCCGTGGCGGA
GGAGGCCGAGGAGCGGCTGTGCGTGCAGCTCGGCGAGCTGGAGGCGGAGGCCATGACGCAGGCCATGGAGTACCAGCAGC
ACGTCAGGGCGCTCTCCGAGAGGCTCGCCCTCATGGACGGCCTGCTCAGGTCCTCCGGCCTCCACGGCGCCGTCGTGCAG
CCCGGCCTTCACTGACGAACCGAATCTCATCATGCGTTCCCTTGCCTGT------TATTATGTGTGATCATGCAAGGCTG
TAGTGGTTGTTAAATTTTTCTCCTTTCCGCCGGCGTGTGTTTGATGCCAACTCGTGCGTGCTGGTGGCGT---GTAGTGT
AGGATGTACATTTCTTTTCTTTTCTTTTTGAGATGTACT----GTATATAACGTCGTTTGTGTAGTTCTACATATCTCTT
--GAGAACATCTTAATGTTGCCCCCGATCTGTTGC---------------------------------------------
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>chr1A_1_TraesCS1A01G179400
CATCATCCTCTTTGACACCTCCGACGATGACGACGACCATGGCTCCTTG-----------------TCCGACACCAGCTG
TCGATGCCTACAGCTGCGTCGGCGACCGGAAGGGCAAAGAGCCGGTGAGGAAGTGGTGAATCTCCGTCGTCTCTGTCTTC
AATTTCAAG-TTTTAGTAATCTAGTTTAAACTTGTCCGTCGTTTATGTGAATTATGTGAACTTTAGCGATCTTTTGGACA
TCAATCGATAATCTTTGGGTGATCCGAATGTGCATTTCTATGCCCAGATTATATGTTTGTGTGATGACCTACGTTGTTTT
TATCTATGTTGCATGCTAGTATGGATATGATGGACCGAATATGAGATACACGGATGTGGCCGACAAGATTTGAGAAGTGC
TCATTCAGTGCCCACGGCCGCGCCCAGGCGCGTCCGCGGGCGTTTGAGGGCCCGAATTTGCAGGTCGTTGATGTAGATGC
TCTTATAAACTCTATTGATGATGGGTTTTTCTCTCTATGTGTGCTTCGAATT-TGGATCTGAATTATTTATGAGTTATAA
ACACACGTGTTGTGAATATTTACAAACAAACAGAAATATTTAAATTTAACCATTCTTTTAAGTTTTATCATGG-AGCAGG
TAAGCAATGGTATCGCCCGATATTCACCCTCGTCTGTCTCTCCAATCCCCACTCTCCGACGCTCGATCGAACGGCCAGAA
TGTGCTAGACAAATCAGGCAAAAGTTGTGGTTGCTGGTGTTTGACTATCCATCCGCCCACCACGTTCACCTCTCAACCAG
GAGGAAATGCAATAAGAGAGAGACGTACGGGCAAAGCATTGAATTATCAACG-ATGATGACCTCACCTTATATGTAGCAG
CTCTGTAGGCGTACGCCGACACCTAACGTGCCCGATTGGTTCATTGAACCTGGACACATTCCCGCTTTCCCTCCGCGGCG
GCAGCCGGCCCGAGCGGCCCGGCCTATATAAAAGGCGCCACAACCTGATCAAGAGAGATCCAGATCCCAGCGAACTCGTA
AACACGTCTGTGCATAGTGCTAT----------------------------------TACGTATACTCCCCCACTCACCC
CCGAGAAGTCAGGAGGCATGGCGAGGAAGGCAGCGGCAGCGGC------CATGGACGGCAAGAGCTCCGAGCTCGCGAGG
GCCGTGGCGGAGGCGGAGGCGCGGGAGGAGCGGCTGCAGCGGGAGCTGGAGGCGGCGCTGGCGCGGGTGGCCGTGGCGGA
GGAGGCCGAGGAGCGGCTGTGCGTGCAGCTCGGCGAGCTGGAGGCGGAGGCCATGACGCAGGCCATGGAGTACCAGCAGC
ACGTCAGGGCGCTCTCCGAGAGGCTCGCCCTCATGGACGGCCTGCTCAGGTCCTCCGGCCTCCACGGCGCCGTCGTGCAG
CCCGGCCTTCACTGACGAACCGAATCTCATCATGCGTTCCCTTGCCTGT------TATTATGTGTGATCATGCAAGGCTG
TAGTGGTTGTTAAATTTTTCTCCTTTCCGCCGGCGTGTGTTTGATGCCAACTCGTGCGTGCTGGTGGCGT---GTAGTGT
AGGATGTACATTTCTTTTCTTTTCTTTTTGAGATGTACT----GTATATAACGTCGTTTGTGTAGTTCTACATATCTCTT
--GAGAACATCTTAATGTTGCCCCCGATCTGTTGCAAACTTGAGCTGACGTATGCATTCACCTAATATCACACGCAACGG
ATTCCTTGACAACGATCGAGCGCATGTGCATATATACATGAGGAGCACACGCAAATGAGGTTCTTGATATGAAGACATAA
AGAAATGAACTGGTCCCACATATAAATTCGAAAAATTACCAGTGCTATCCCAAGTTCTCAACTCCATTAA----------
----------------------------------------------------------TCTTTCCTTCCCGCGAA-----
-AAAATAACTCCATTAATCTTGCTTCAACTCCGTAACAAAGCATAAAGCATATGCATTACGAGTAAAATTCCTTGACAAG
CTATAATTGTTGGCGGCACACCGCGTGGCAACTGGTCATCAATCTCCCGACCAAAACTAATAATGTTGGCAACAAAGGCG
GCAAGGAAAAACCATGAACCAGTCAAAAACACCGAAAACATCCGTTTCACCTCGGAAATTTCGGCCGAAACTGACTTCTC
GTAAGGATGATGAAACTTGGAAGTCTGAACAATTC-AATCAATTTGAATCACCTAGACAGCACTACTAGAAACA-AGACG
TGTGACACCACGCAGAAAACGACCGCACCAGCTGCTCAATTAAAAAAGAAATATATAGGAAACTTCGGACCTCGGCTATT
TGACAGCACAAAGTTGACTGGTTTAATGCAATTGGAAATTGCAATGGCAAATCAGGGACCTCGGACATTTGACAGTAGCA
TGCATGGA--------------------------CATGGAACTTTTCATCCTGAAAT-TTGTCAATCTTCCAGATAGCTG
ACTGGAGGTGTGAAATGGCCATGCTCCCCAGAAACCAAGACAATTCCACGGAATTACCGTGAACGCGGAAGTGTACAGAC
AAGAGGTACAGAAATTGATGA------------GACTTGTCTCCAATAGGGTGACTTGATCTTTAATCAGGAGTACTGCG
TTCAGATACGCGCCTGGAATCCAGGCTGGAAGCAGAAAAACGTCCTGTCTACA---TCCATGGAAGTTGGATTAAATCAA
TCAGTAAATCTTCTAGAGGACTAACAAAATCTT
>chr1D_1
CATCATCCTCTTCGACACCTCCGACGATCACGACGATCGCGAGTCCACGTCCGACGACTCAGACGATCCGCCACCAGC--
----------------CGCCGGCGATCGGAAGGGCAAAAGGCCAGCGAGAAAGTGGTGAATCTCCGCCATCTCTGTCTTC
AATTTCAAGTTTTTAGTAATCTAGTTTAAACTTGTCCGTCGTTTATGTGAATTATGTGAACTTTAGCGATCTTTTGGACA
TTAGTCGGTAATCTTTCGGTGACCGGAATGTGCATTTCTATGCTC-GATTCTATATTTGTGTGATGATCTACGTTGTTTT
TATCTATGTTGCATGCTAGTATGGATATGAGGGGCCAGATATGAGATACACGGATGTGGACGACATGATTTGGGGAGTGC
CCGGTCAATGCCCACGGACGCGCCCGGGCGCGTCCGCGGGCGTTTCATGGCCCGGATCTGCAGGTCACGGCTGTAGATGC
TCTTATAAACACTATTGATGAT-----TTTTTTTCTATGTGTGCTTCGAATTTTGGATATGAATTATTTGGGAGTTA---
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>chr1D_536
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--------------------------------------------------------------------------TTATAA
ACACACGTGTTGTGAATATTTATAAACAAACAGAAATATTTAAATTCAACCCTTTTTATAAGTTGTATCATGGGAGCATT
TAAGCGATGGTATCACTCAATATTCACCCTCATATATCTCTCCAATCTCCACCCTCCGGCGCTCGATCGAACGGCCAGAA
TGTGCTAGACAAATCAAGCAAAAGTTGTGGTTGCTGGTGTTTGACTATCCAGCCGCCCACCACGTTCACCTCTCAGCCAG
GAGGAAATGCAATAAGAGAGAGACGTACGGGCAAAGCATCGAATTATCAACG-ATGATGACCTCACCTTATATGTAGCAG
CGCTGTAGACGTACGCCGACACCTAACGTGCCCGATTGGTTCATTGAACCTGGACACATTCCCGCTTTCCCTCCGCAGCT
GCAGC---------CGGCCCGGCCTATATAAAAGGCGCCACAACCTGA----GAGGGATCCAGAT-CCAACGAACTCGTG
AACACGTCTGTCTATAGTGTACGCATCCTCCTCAAAGAAA-AAAAAGGTCTATAGTGTACGCATACTCTCCCACTCACAC
CCGAGAAGTTAGGAGGCATGGCGAGGAAGGCAGCGGCAGCGGCAGCGGCCATGGACGGCAAGAGCTCCGAGCTCGCGAGG
GCCGTGGCGGAGGCGGAGGCGCGGGAGGAGCGGCTGCGGCGGGAGCTGGAGGCGGCGCTGGCGCGGGTGGCCGTGGCGGA
GGAGGCCGAGGAGCGGCTGTGCGTGCAGCTCGGCGAGCTGGAGGCGGAGGCCATGACGCAGGCCATGGAGTACCAGCAGC
ACGTCAGGGCGCTCTCCGAGAGGCTCGCCCTCATGGACGGCCTGCTCAGGTCCTCCGGCCTCCACAGCGCCGTCGTGCAG
TCCGGCCTTCACTGACGAACCGAATCTCACCATCCGTTTCCTTGCTTATTACTACTATTATGTGCGATCATGCAAGGCTG
TACCTGTACGGGTTCCTAAAT--TTTCCGCCGGCGTGTGTTTGATGCCAACTCGTGCGTGGTGGTGGTGGAGCGTAGCGT
AGGATGTACTGTACATTTTTCTTCTTCTTGATGAGATGTAGGAGTATATAATGTCGTTTGTGTGGTACTACGAATATCTT
GGGAGGACATCGAAATGTTGCCCCCGATCTGATGCAAACTTGAGCTGACGCATGCATTCATCTAATATCACACGCAGCGG
ATTCCTTGACAACGATCGAGCTTATGTGCATATAAAACGAGATGATCACGAGCCAGATCCATTGGCGCAGAGTGCGTCGC
GCTGGAGGACGACCCACAGGACGTTCGTTCTCTAAATTTTCCTTCGATTGAATTGTTCGACTTTCAGGTTTCACCATCCT
TACGAGCAGCCAGTTCCCAGGGGAAGCCGATGTTTCGGTGTTCTTGACAAGTTCCTGGTTTCTCCTTGCCGCCAA-----
-CATATTCTGGTCGAGAGATTGCTGACCACGTTGCCAAGCTGTGTGCTGCCAACAGTTATACTATAGCAAGGAATTCTAC
TCGCAACGCGTATGCCCTGCTACGGAGTTC--------------------------------------------------
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--------------------------------TTCAAATCAATTTGGATCGATTAGATGGCACTACTGGAAAACGAGACG
TCTGACGCCACACAGAAAACGACCGCACGAGCTGCTCAATTAAGCAACAAAAATA-AGGAAACTTCGGACCAACATCAT-
--ACAGCGCAAAGTTGACTGATATAATGCAATTGGAAATAGTAATGGCAAATCAGGGACCTCGGATATTTGACAGCAGCA
CGCATGTAATGAAAAAGAGAGGTATGAAATGGAGCATGGAACTTTTGACCCTGAAAAATTGTCAATCTTCCAGATAGCTG
ACTGGAGGTGTGAAATGGCCATACTCTCCAGAAACGAAAACAATTCCACGGAATTACCATGGACGCGGAAGTGTGCAGAC
AAGAGGTACAGAAATTGATGGAGCATATGACCTGACTTGTCTCAAATAGGGTGACCTGATCTTTAATCAGGAGTACTGCG
TTCAGATACGCACCTGGAATCCAGGCTGGAAGGAGGAAAACGTCCTGTCTGCATTCTCCATGAAACTTGGGTAAAATCAA
TCAGTAAATCTTCTA------------------
>chr1B_630
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---------GTATCACCCGATATTCACCCTCGTATGTCTCTCCAACCTCTACCCTCCGACGCTCGATCGAACGGCCAGAA
TGTGCTAGACAAATCAAGCAAAAGTTGTGGTTGCTGGTGTTTGACTATCCATCCGCCCACCACGTTCACCTCTCAACCAG
GAGGAAATGCAATAAGAGAGAGACGTACGGGCAAAGCATCGAATTATCAACGAATGATGACCTCACCTTATATGTAGCAG
CGCTGTACACGTACGCCGACACCTAACGTGCCCGATTGGTTCATTGAACCTGGACACATTCCCGCTTTCCCTCGGCAGCT
GCAGC---------CGGCCCGGCCTATATAAAAGGCGCCACAACCTGA----GAGGCATCCAGAT-CCAACGAACTCGTA
AACACGTCTGTCTATAGTGTACGCATTCTCCTCAAAGAAAAAAAAAGGTCTATAGTGTACACATATTCTCCCACTCATCC
CCGAGAAGTTAGGAGGCATGGCGAGGAAGGCAGC---------AGCGGCCATGGACGGCAAGAGCTCCGAGCTCGCGAGG
GCCGTGGCGGAGGCGGAGGCGAGGGAGGAACGGCTGAGGCGGGAGCTGGAGGCAGCGCTGGCGCGGGTGGCCGTGGCGGA
GGAGGCCGAGGAGCGGCTGTGCGTGCAGCTCGGCGAGCTGGAGGCCGAGGCCATGACGCAGGCCATGGAGTACCAGCAGC
ACGTCAGGGCGCTCTCCGAGAGGCTCGCCCTCATGGACGGCCTGCTCAGGTCCTCCGGCCTCCACAGCGGCGTCGTGCAA
TCCGGCCTTCACTGACGAACCGAATCTCATCATGCGTTTCCTTGCTTATTACTACTATTATGTGCGATTATGCAAGGCTG
TACCTGTACGGGTTTCTAAAT--TTTCCGCCGGCGTGTGTTTGATGCCAACTCGTCCGTGGTGGTGGAGC---GTAGTTT
AGGATGTACTGTACATTTTTCTTCTTCTTGATGAGATGT------ATATAATGTTGTTTGTGTAGTACTACGAATCTCTT
-GGAGGACATCTAAATGTTGCCCCCGATCTGATGCAAACTTGAGCTGACGCATGCATTCATCTAATATCACACGCAACGG
ATTCCTTGACAACGATCGAGCTTATGTGCATATAAAACGAGATGATCACGAGCCATATCCATTGGCGCAGAGTGCGTCGC
GCTGGAGGACGACCCACAGGACGTTCGTTCTCTAAATTTTCCCTCGATTGAATTGTTCGACTTTCAGGTTTCACCATCCT
TACGAGCAGTCAGTTCCCAGGGGAAGCCGATGTTTCGGTGTTCTTGACAAGTTCCTGGTTTCTTCTTGCGGGTGCGGCCA
GCATATTCTGGTCGAGAGATTGCTGACCACGTTGCCAAGCTGTGAGCTGCCAACAGTTATACTATAGCAAGGAATTCTAC
TTGCAATGCATACGCTCTGTTACGGAATTC--------------------------------------------------
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--------------------------------TTC-AAACAATTTGAATCGACTAGATGACACTGCTAGAAAACGAGACG
TGTGACGCCACACAGAAAACGACCGCACCAGCTGCTCAATTAAGCAACAAAAGTA-AGGAAACTTCGGACCAACACCAT-
--ACAGCACAAAGTTGACTGATATAATGCAATTGGAAATAGTAATGGCAAATCAGGGACCTCGGATATTTGACAGCAGCA
CGCATGTAATGAAAAAGAGAGGTATGAAATGGGGCATGGAACTTTTCATCCTGAAAAAATGTCAATCTTCCAGATAGCTG
ACTGGAGGTGTGAAATGGTCATGCTCCTCAGAAACCAAGACAATTCCACGGAATAACCATGAACGCGGAAGTGTGCAGAC
AAGAGGTACAAAAATTGATGGAGCATATGACCTGACTTGTCTCCAATAGGGTGACCTGATCTTTAATCAGGAGTACTGCG
TTCAGATACGCACCTGGAATCCAGGCTGGAAGGAGGAAAACGTCTTGTCTGCATTCTCCATGAAACTTGGGTAAAATCAA
TCAGTAAATCTTCTA------------------
>SNPs
------------S---------------S-------S-SS-SS---SS----------------------S-------SS
SSSSSSSSSSSSSSSS--S------S------------SS---S-S---S----------------S-S-----------
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-S-S---S--------S-----S-S------------------S-S----S---S------------S------------
------------------------------S--S--SS---------------------S-----S------S-S-----
S-SS---S---------S-------S-------------------S-S------S--S--------SSS-S---------
----------S-----------SSSSS---S-S-------------------------S----------SS---------
----------------------S-----------------------S----S--S--S------S-------------SS
-----S--------S------------------S-------------S----S---------------------------
----------------S---------------------------------------------------------------
---------------------------------------S----------------------------------------
-S------S-------------------------------------------------------------------S--S
-----SSSSSSSSS----------------------------------SSSS---S---------S---S----------
-----------SS------SSSS--------------------------------------S------S-----------
---------S----------------------------------------------------------------------
-------------------------------------S------------------------------------------
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-----------------------------------------------------------------S--------------
S-------------------------------------S------S-S----------------S---------------
--SSS--SSSSSSS-S-SSS-SS-------------------------------------S------S-S----------
---------SS-S-S---S-S-----S----SSS-SSS-------------S--------------S----SS-------
-----S------S------------------S------------------S---------S-------------------
---------------------SS-----------S-SSSSSSSSSSSSSSSSSS--SSSSS-SSSSSS-SSSS-SSSSSS
SSSSSS-S--SSSS-S--SSSSSSSSS-SSSSS--S-SSSSS-S-S--SSS-SSS-SSS-SS-S--SSSS----------
-----------------------------------------------------------S-S-----S----S-------
-S-S--SSSSSSSSSS-SS-----SSSSSSSSSSSSS-SSSSSS-SSSSSS-SSSS---SSSSSS-SSSSSSSSSS-S-S
S-SS---SSS-SSSSS-SSSSSSS-S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------------SS-----SS-------------SS------
------S----S-------------------------------SS--S---S---S---------------SSSS-S--S
SS------------------S-S----------------S-S-----------------------S---------S----
S-----S-------------------------------------------------S-----------------------
----------------------------------------------------------S---------------S-----
--------------------S----------------------------------S------------------------
-----------S--------------------S--S--------------S-----------S--S----S-S-------
---------------SSSSSSSSSSSSSSSSSS
>forward_674
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--------------GCCCGATATTCACCCTCGTC----------------------------------------------
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>reverse_2221
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------------------------------------------------------------TCGGCCGAAACTGACTTCTC
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