>input_sequence_82510
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-------------------------------------------------------------ATGGCGACTCCTGGGGATG
GCGAGGACGCGCCGCCGCCGCCGCCGGTGAGCGCGGCGGGGGCTGGAGGCAGCTTGATCGCGAAGCTGCGGGAGCAATGG
AGGAGCACGAAAGAGCACGCGGAGACGTACCCGTACGTGTGGGGCTCCTACATCCTCGTCTACGGCGGGCTCGGCGCGTA
CATCACCTGGCGATGGTGCAAGCTCCGCCGCACCGAGGACCGCGTCCGCGCCCTCCAGGCCCGCCTCCGCCAGCTCGCCG
CCGCCGAGGAGTCGCAGGGCGCTTCCGCTG---CTACCCCACCTCCTCCCCTGCAGCAGCCCCCGCCGCCGACGACGACT
GGGCCGGGCAAGCCCCCCTCCCCGCCGTGA--------------------------------------------------
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>chr3A_1_TraesCS3A01G374200
TTCTATATAGAGTAGTATTTCATAAAAGAAAATGGATATCTTTTACATGTATTCATATCTACTAGATGTTTGCACAAAAT
ACTTTTTTGGGTGAATTATTAGTACATGAATTGCAAAACATGTTGTCGTAGTCTAAATTTTTGGTATTGCATACGTTAAT
ATTTTCTCTATAAACATATTCAAGTTCCTAGAAAAAAAAAGTCTTAGTCAGACTTAAAAGGTTTGACTTACATTTTAGAA
AAAAT---------------------------------------------------GTAATAAGTAAGAAATGATTTGCC
-ATTTTGTGTTGTATACAGAATGGTTCAAGTATTATCTTTGTAGCCGGCACTTGAGTAGTTGGTTACTTATCATATCTCT
AGAGTTGTTTATTGTATAATTTTTTTGTGCTAAATCCCCAGCGTAATCCAGCGAGATGATAATTTAGCATATGTGGATCA
ACAGTGGTTAGAT----TTTTTTAATTATATAATAGTTATATG---------------------------------GAAG
AATTTAAAGATGATGATATACAACAATTTAAAGGGGCTGAT---TTACATCTAAGCACCATCATCTCAAATTTCAACTAT
TCTGTCATTCAAAACATAGCCTAAGTATTTTTTTGGTGTTGTCAAATGGACACACCGCGCATACTACCGCCACGACATGA
GCCTGATCTACCTCATGCGTTATCGGGTGTGCCTCCATTTTGGGCACATAGCCACATAGCCTAAGTATTGTACATCCCTT
TTTTTGCATTTACAAC-------TGGCTTGGCTATGGACCTGGCTTTTTTCCTTAAAAAGAACTGAACCTATCTTTTTTT
AGACAAACCTGTCTTTT--TTTTCTTAATATATATTCTGAGAATATATCATGGACGCAATATTTTACGCAAGAAGTTTAA
GCCCACGATGTAGCCCAGCCCACGTATATGCAAAGCGAGACAAAAAGACAGGGTCCATTCTAGCCTGGGCCAAATTACCC
GACCAATTCGGCCATTCCCACTTGCCCTAAGAACAAGGCGAAAAAGTAGCGCACCACACCAATGGCGACTCCTGGGGATG
GCGAGGACGCGCCGCCGCCGCCGCCGGTGAGCGCGGCGGGGGCTGGAGGCAGCTTGATCGCGAAGCTGCGGGAGCAATGG
AGGAGCACGAAAGAGCACGCGGAGACGTACCCGTACGTGTGGGGCTCCTACATCCTCGTCTACGGCGGGCTCGGCGCGTA
CATCACCTGGCGATGGTGCAAGCTCCGCCGCACCGAGGACCGCGTCCGCGCCCTCCAGGCCCGCCTCCGCCAGCTCGCCG
CCGCCGAGGAGTCGCAGGGCGCTTCCGCTG---CTACCCCACCTCCTCCCCTGCAGCAGCCCCCGCCGCCGACGACGACT
GGGCCGGGCAAGCCCCCCTCCCCGCCGTGAAGAGTAAGGCCCCTTAGGCAACTTCTTGACATGAAAT-------GTTACA
GAACAATCCCTGCATCGTTCGAGATCGAGGCATTCCTTGCCTCTGTTTACTCTATGATCCTGGACCTAAAGAAACGGTGG
GATCTCGCCCCCCAAAAAGTTGGAAGGTC-AATTCTGTGTCCATACTGGAGATCATTCTGGAGAAGGTTTAAATTGTTGT
GATTCATGTATGCTTACCCT-----------------------------TTTT-TCTAGCCATTCCGCATCGTATTTGTT
GTGTTTCTCGCTGCTTCTCTAAATAGATACAATGTTTCATTGTCGTGGTTCATGTACTCATCGTATAGTTCTTGATAATA
CTAATATTTCATCTCAGTCCTCTGTT------------------GGGTAGTATGGTA--TGCACTGTTGTGAGCATTTGA
TAGAGAAGTCTGAACGAACATGCTGATGTATTATGCACTGTTGGGGTAGTATAGCTGCTGAATTGGATTTGGAAGAGAAC
ATAGCATGGTCCTCTGAAACAGAAGGCTCAACCAGCATGCTAGCAGTGGCCTTAACATTATTGTTATCTTCTGATATCTG
TAGCTTTCATAAAATTGTCTTTTAATCCTAAATGATGGTGGTAGGAATTTTAATGTGCTCATGAAAGAGTTTACTCCAGC
GACATTTTTATTCGGGAAACAGTCCATTATCAAACTTCCCTTACG-TATTTCCGTAGCATTATTCCTCCCCAAATTCCTG
ATCTGTTATAGCGAACTATTTG-ACTTATCTATGCAGTTATCTTGTGTTGGATAGCTGAAACCAATTAATTGCTAGTTTC
CCCCAAAGTCCCTCTTAGCCACTAAAGAGTGGTGTTTTGCTATGCATGCAGTTCTGTCT-AAATCTGAACCTTGGCTGTT
GAGATTTTTGTGAATATTTCGACCGGAAACATCAAAATATTATGTGTTTATGT------CACGATCAACAGTTCCACCAT
GTTTTAGCTCTGTCAGGTTTTATTTTTACCAATGAACTTACTCATCCAAGCTTCATT
>chr3B_1
TTCTATATAAAGTAGT-TTTCATAAAAGAAAATTGATATCTTTTATACATATTCATATCTACTAGATGTTTGCACAAAAT
ACTTTTTTG-GTGAATTATTGGTACATGAATTGCAAAACATGTTGTCGTAGTCTAAGTATTTGGTATTGCATATGTTAGT
ATTCTCTCTATAAACATATTCAAGTTCCTAGAAAAAAAA-GTCTTAGTCAGACTTAAAAGGTTTGACTTACATTTTAGAA
AAGATGTACTCCCTTCGTCCCAAAATAATTGAGACACTTATTTTGGGACGGAGAGAGTAATAAGTAAGAAATGATTTGCT
TATTTTATGTTGTATACA----------AGTATTATCTCTGTAGCAGGCACTTGAGTAGTTGGTTACTTATCATATATCT
GGAGATATTTATCGTATATTTTTTTTGT--TAAATCCCCAGCTTAATCCAGCGAGCTGATAATTTAGCATATGTGGATCA
ACAGTGGTTAGCTTTTATTTTTTAATTATATAATAGTGTAATACTAATATATAGTTATATGAAATAACCCTTTTTAGAAG
AATTTAAAGGTGATGATATACAACAATTCAAAGGGGCTGATTTATTACATCTATGCACCATCATTTCAAATTTCAACTAT
TCCGTCATTCAAAACATAGCCTAAGTATTTTTTCAGTTTT----------------------------------------
-------------------TTATCGGGTGTGCCTCCATTTTGAGCACATAGCCACATAGCCTAAGTATTGTACATCCCCT
TTTTTTTAGCATCTAAGTATTTTTGGCTTGGTTATGGACCTGCCTTTTTCCTTAAAAAA--ACTGAACCTGT-TTTTTTT
AGACAAACCTGTCTTTTTATTTTCTTAATATATTCTGAGA----ATATCATGGACGCAATATTTTCCCTAAGAAGTTTAA
GCCCACGATGTAGCCCAGCCCACGTACATGCAAAGCGAGAC-AAAAGACAGGGTCCATTCTAGCCTGGGCCAAATTA---
-ACCAATTCGGCCATTCCCACTTGCCCTAAGAACAAGGCGAAGAAGTAGCGCAC--CACCAATGGCGACTCCCGGGGATG
GCGAGGACGCGCCGCCGCCGCCGCCGGTGAGCGCGGCGGGGGCTGGAAGCAGCTTGATCGCGAAGCTGCGGGAGCAATGG
AGGAGCACGAAAGAGCACGCGGAGACGTATCCGTACGTGTGGGGCTCCTACATCCTCGTCTACGGCGGGCTCGGCGCGTA
CATCACCTGGCGATGGTGCAAGCTCCGCCGCACCGAGGACCGCGTCCGCGCCCTCCAGGCCCGCCTCCGCCAGCTCGCCG
CCGCCGAGGAGTCGCAGGCCGCTTCCACTCCCCCTACCCCATCTCCTCCCCTGC------------CGCCGCCGCCGACT
GGGCCGGGCAAGCCCGCCTCCGCGCCGTGAAGAGTAAGGCCCCTTAGGCAACTTCTTGACTTGAAATGTTACAAGTTACA
GAACAATCCCTGCATCGTTCGAGATCGAGGCATTCCTTGCCTCTGTTTACTCTGTGATCCTGGACCTAAAGAAATGGTGG
GATCTCGCCCCCCAAAAAGTTGGAAGGTAGAATTCTGTATTCATACTGGAGATCATTCTGGAGAAGGTTTTAATTGTTGT
TATTAATGTATGTTTACCCTTCCCACTAGGGAATTTTGTCACCGTGACCTTTT-TCTAGCCATTCCACATCGTATTTGTT
GCGTTTCTGACTGCTGGTCTAAACAGATACAATGTTTCATTGTTTTAGTTCATGTACTCGTCGTATAGTTCTTGATAATA
CTAATATTTCAACCCTATCGAAACCTGTTGAACTATCACCGTTGCGGTGGTATAGTA--TGCACTGTTGTGAGAATTTGA
TAGAGAAGTCTGAACGACCA---TGCTGTATTATGCATTGTTGGGGTAGTCTAGCTGCTGAATTGGATTTGGAAGAGAAC
ACAGCATGGTCCTCTGAAACAGAAGGCTCAACCAGCATGCTAGCAGTGGCCTTAACATTATTGTTATCTGCTGATTTCTG
TAGCTTTCATAAAATTGTCTTTTGATCCTAAATGATGGTGGTAGGAATTTTAATGTGCTCATCAAAGAGTTCACTCCAAC
GACATTTTTATGCGGGGAA-AGTCCATTATCAAACTTCCCTTACCTTATTTCTGTAGCATTGTTCCTCCCAAAATTCCTG
ATCTGTTATAGCGAACTATTTTTACTTATCTATGCAATTATCTTGTGTTGAATACCTGAAACCAATTAATTGCTAATTTC
ACCCAAAGTCCCT---------------------TTTAGCTATGCATGCGGTTCTGTCTAAAATCTGAACCTTGGCTGTT
GAGGTTTTTGTGAATATTTCGACCGGAAACATCTACATATTTTGTGTATATGT------CA------ATAGTTCTACTAT
GTTTTAGCTCTGTTAGGTTTTATTTTTACCGATGAACTTACTCATCCAAGCTTCATT
>chr3D_798
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----------------T--TTTTCTTAATATATTCTGAGA----ATATCATGGATGCAGTATTTTCCGCAAGAAGTTTCA
GCCCATGATGTAGGCCAGCCCACGTATATGCAAAGCGAGAC-AAAAGACAGGGTCCATTCTAGCCTGGGCCAAATTACCC
GACCAATTCGGCCATTCCCAGTTGCCCTAAGAACAAGGCGAAGAAGTAGCGCAC--CACCAATGGCGACTCCCGGGGATG
GCGAGGACGCGCCGCCGCCGCCGCCGGTGGACGCGGCGGGGGCTGGAGGCAGCTTGATCGCGAAGGTGCGGGAGCAATGG
AGGAGCACGAAAGAGCACGCGGAGACGTACCCGTACGTGTGGGGCTCCTACATCCTCGTCTACGGCGGCCTCGGCGCGTA
CATCACCTGGCGATGGTGCAAGCTCCGCCGCACCGAGGACCGCGTCCGCGCCCTCCAGGCCCGCCTCCGCCAGCTCGCCG
CGGCCGAGGAGTCGCAGGCCGCTTCCACTCCTCCTACCCCATCTCCTCCCCTGC------------CGCCGCCGCCGACT
GGGCCGGGCAAGCCCGCCTCCGCGCCGTGAAGAGTAAGGCCCCTTAGGCAACTTCTTGACTTGAAATGTTACAAGTTACA
GAACAATCCCTGCATCGTTCGAGATCGAGGCATTCCTTGCCTCTGTTTACTCTGTGATCCTGGACCTAAAGAAATGGTGG
GATCTCGCCCCCAAAAAAGTTGGAAGGCAGAATTCTGTGTTCATACTGGAGACCATTCTGGAGAAGGTTTTAATTGTTGT
TATTAATGTATGTTTACCCTTCCCGCTAGGGAATTTTGTCACCGTGACCTTTTTTCTAGCCATTCCACATCGTATTTGTT
GCGTTTCTCACTGCTGGTCTAAACAGATACAATGTTTCATTGGTTTAGTTCATGTACTCGTGGTATAGTTCTTGATAATA
CTAATATTTCAACCCTATGGAAATCTGTTGAACTATCACCGTTGGGGTAGTATGGTATGTGCACTGTTGTGAGAATTTGA
TAGAGAAGTCTGAACGAACA---TGCTGTATTACGCACTGTTGGGGTAGTATAGCTGCTGAATTGGATTTGGAAGAGAAC
ATAGCATGGTCCTCTGAAACAGAAGGCTCAACCAGCATGCTAGCAGTGGCCTTAACATTATTGTTATCTGCTGATATCTG
TAGCTTTCATAAAATTGTCTTTTTATCCTAAATGATGGTGGTAGGAATTTTAATGTGCTCATCAAAGAGTTCACTCCAGC
GACATTTTTATGCGGGAAACAGTCCATTATCAAACATCCCTTACCTTATTTCAGTAGCATTGTTCCTCCCAAAATTCCTG
ATCTGTTATAGTGAACTATTTTTGCTTATCTATGCAATTATCTTGTGTTGAATAGCTGAAACCAATTAATTGCTAGTTTC
CCCCAAAGTCCCTCTTAGCCACTAAAGAGTG----------------------CTGTCTAAAATCTGAACCTTGGCTGTT
GAGATTTTTGTGAATATTTCGACCGGAAACATCAAAGTATTATGTGTATATGTCATGATCA------ACAGTTCCTCCAT
GTTTTAGCTCTGTCAGGTTTTATTTTTACCAATGAACTTACTCATCCAAGCTTCATT
>SNPs
---------S------S----------------S-----------S-SS-------------------------------
---------S----------S-----------------------------------S-S--------------S----S-
---S-----------------------------------S----------------------------------------
--S----------------------------------------------------------------------------S
------S-----------SSSSSSSSSS----------S------S------------------------------S---
S---S-S-----S-----S---------SS------------S------------S------------------------
-----------S-------------------------SSS--S-------------------------------------
---------S------------------S------------------------S----------S---------------
--S------------------------------SS--S--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSS-----------------------S-----------------------------------S-
-----SS-SSSS-S-S---------------S----------S------S-S-S-----SS---------S-S-------
---------------------------------SS-SS--SSSS---------------------S--------------
-----------------------------------------S--------------------------------------
------------------------------------------S-----------SS----------------S-------
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------------------S-------S--S-----------S------------SSSSSSSSSSSS-----S--S-----
---------------S-----S--------------------------------------S-------------------
-----------------------------------------------------S--------------------S-----
----------------------------S-----------S-----------------------------S---------
S---S-------S-----------------------------------------------------S-------------
-S-------S-----SS------S-------------------SS-S------------S--------------------
-----------S-S-SS--SSSSSS------------------------------------------------S------
--------------------SSS--S------------------------------------------------------
---------------------------------------------------------------------S----------
-----------------------S--------------------------------------S--------S--------
-----------S--------------------------------S-------S--------S--------S---------
---------------------S--------------S-------------S-----------------------------
-------------------------------SSS---S-----------S------------------------------
-----------------------------------------------S-------------SSSSSS-------------
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>forward_718
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----------------------------------------------------------GCATACTACCGCCACGACAT--
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>reverse_2358
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-------------------------------------TGCTATGCATGCAGTTCTGTC----------------------
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