>input_sequence_72853
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---------------------------------------------------------------------ATGGAGTCGTC
GGGCGACACGGCGCCGTTGCACTCGTCACCGACCCCGACGTCGCCGCCGGCAATGGCGACGGGGACGGCGGTGGTGATGA
GCCCGTGCGCGGCGTGCAAGATCCTCCGCCGCCGGTGCGTGGACCGCTGCGTGCTGGCGCCCTACTTCCCGCCCACGGAC
CCCCACAAGTTCGCCACCGCGCACCGCGTCTTCGGCGCCAGCAACATCATCAAGCTCCTGCAGGACCTGCCCGAGGAGCA
GCGCGCGGACGCGGTGAGCAGCATGGTGTACGAGGCGGCGGCGCGCGCGCGGGACCCCGTCTACGGCAGCGCCGGCGCAA
TCTGCCAGCTCCAGAGGCAGGTCGACGGCCTCAAGGCGCAGCTCGCGCGCGCGCAGGCGGAGCTCGCCGCCGCCCGCGCC
CACCACGCGCACCTCGTCGCGCTGCTCTGCGTCGAGGTGGCCACCGCCGCCGCCACGCCTCCGCAGGACGCCTACTGCAC
CGGCGTAGGCGGATCACAGTCCCAGCTCGCCGCACCGCCTGGTGTAGGCTCCGCGCCCACGGACGCGCTCTACACCGTCG
ACGGCAGCGCGGCGGGCGGCGGCGGCATCATGCAGGCCGGGCACGTCGGCTGGGCCGACGAGCCTCTCTGGACATGA---
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>chr1B_1_TraesCS1B01G080600
GTCAAAAATATGAGAACCAACCAGCGGTTGGATGGGTAGGAGGGTGGTGGTACTTGGGCCCACTAGGGATCAAATTCCAG
GTTTGACATTTT--TGTCTCATCAATGCATATTATTTTTTCAGTGGGAAATGACGTTCACCTCGATAGCGAGGCACATGA
ATT--TCAACCTTGAAGCTCCGCAATTCTCATCCGATCTTCACTACACGTGTGAGCGCGTCAGTGTGGTGTGTGGTGTGT
GCATCTATGTTTCTTACCAAAAGAG------------TAAAAAAAAAACTACCTATTCATCTTGTATATGTCCTATGTTT
TTGTAGTCGAATTTACCATCAGCTAGGATT---------TCTTACTTTCTATGTGGTAAATAGGAATCTTAAAATTCTCT
GAAAATATAGAACAAAAATAAAGTGCAAAGTTGTCAAATTTCTCAAATATGGTGCAATGTAATTTTTAGTATGTTTGAGG
TACTTTGTACTTCCGATGAATTTTGTTACTCCTTTTCGCAAAAGAAACACTACCAACTTGTGTTTTT-CCAAAATCTAGT
GCAAACCGTCTACGCATTATTCATAGGTGGTCC-AAATTACAATTATCTACTCCCT-CGTCTCAAAATGGTATTGTGTTT
TCTACACTACAGAGGGAATATTTATTTAGAG---TGCAAAGCT-CAAAAATATTCAATCTAATCCACCAAGAAATAGCAA
ATCACTTTGTCAAGAACTCCTAATACAGACCCTCCTAAGAACCAAAACTACACCTAGCTTC-------------------
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--------------------------------------TACTCTTTCTCAGATTTTTTTTAA-GTTGTGTAATAAAAC--
--TTTTTTTGAAGTGTAGAAAATGTATTTTCCACAC---AAAAAAAAGGGCTTCGTGCAGC----TCGGCCATCAAATGT
ACTTTCCGCAACTACACCTAGCTTCTACTCCTAGCTTTCCCACACG----GACACCCTATATATACACCACACCAACGGC
GACAGAATTTCGCAACCAGCTAGCTCAGCTCAGCTCGAAGTGAATCGAGCTCGCGCGAAC----CGAACATGGAGTCGTC
GGGCGACACGGCGCCGTTGCACTCGTCACCGACCCCGACGTCGCCGCCGGCAATGGCGACGGGGACGGCGGTGGTGATGA
GCCCGTGCGCGGCGTGCAAGATCCTCCGCCGCCGGTGCGTGGACCGCTGCGTGCTGGCGCCCTACTTCCCGCCCACGGAC
CCCCACAAGTTCGCCACCGCGCACCGCGTCTTCGGCGCCAGCAACATCATCAAGCTCCTGCAGGACCTGCCCGAGGAGCA
GCGCGCGGACGCGGTGAGCAGCATGGTGTACGAGGCGGCGGCGCGCGCGCGGGACCCCGTCTACGGCAGCGCCGGCGCAA
TCTGCCAGCTCCAGAGGCAGGTCGACGGCCTCAAGGCGCAGCTCGCGCGCGCGCAGGCGGAGCTCGCCGCCGCCCGCGCC
CACCACGCGCACCTCGTCGCGCTGCTCTGCGTCGAGGTGGCCACCGCCGCCGCCACGCCTCCGCAGGACGCCTACTGCAC
CGGCGTAGGCGGATCACAGTCCCAGCTCGCCGCACCGCCTGGTGTAGGCTCCGCGCCCACGGACGCGCTCTACACCGTCG
ACGGCAGCGCGGCGGGCGGCGGCGGCATCATGCAGGCCGGGCACGTCGGCTGGGCCGACGAGCCTCTCTGGACATGAGCG
CGCGCAAGCTGGCGCGCACTGGATGATGCACCAGTTACTCAGCTGGCCAACTG---CTACTACTACGTACGCATGATTCG
TGTGTGTAATTACTAGTACTACATTTTACTTAACTGGGTTAACCAAAGGGTTGACCTGCTTGATGAATTTGCTTGATGAA
TTTGTTGGAATTTCAAGATGGAGGAAGATCGAGTTTGTTTTGTTTTGTTGCAAAAATAATACTGCTACGTACTAGCACAT
AGAATAAAAAATTCCGTCATGTTGAAGTTCCAACAAGTTATGAGAAGTCCTAATCAAGACAGAAAGTTGTATCCTTGCCT
TATTCTGCAGTTGTGAAGAAGGATGTGGTTGGTTCTCTTGTGTGATGTTAGGTCAAATTGCATTTCTATCATGAACAAAT
GCACGTCATTTTCAAGAAGACCATCTTTAGTTCCTTACATCCCCATGTAAATGTAACAGTGATTGTCCATTTCACTATGA
ATTAGAGAAAATCACTTAACGTGAATGTGAAATTCTTTGTTTTGTCTAATATACATCATGTGGAGTGTTTTTTTTGTGTG
TGATATACTACTTGATATCAGCTTGATTTTAACATATTATCCTGCTAGCACTTAATGAATCGGCATCTCTTTATTTTCTC
CCGAAACAACAAGACAAAGTAGACAATAATTTGCTTTTTTTTTCA-TTCGAACAACATGATGGAAGTTTCTCAAGAAG-T
AGCATTAGTTGATTCAAATTAAAAAAACGCA------AAGTACTATAGATGAAGAACTATGTTATTTCTCTTGACTTCTT
CGTATGCAGAAAATGAGATGAGGAAGCTCGATGCATTTCTCTATGTTCTTTTCCTCAAACCGTCTTCATTATCCTTTTCG
---AAAAAAAAACATCTTCATTATCAATCTGTCTTTGAA---TTTGACCGAGAGAGCCTAACGAGCCAATGGTAATTGTT
AGTGTTAGTGTGAGGATGAGAGAAAGGAAGACATGACTTAAAGCTTACAACATA
>chr2D_1
GTCAAAAATATGAGAATCACCAGCAGTCGATA--GGTAGGAGGGTGGTGGTATCCGAGCCCACTAGGGATCATT---CAG
GTTTGACGTTTTGGTGTCTCATTAATGTAGATTAGTTTTTCAGTGGGAGATGGTGTTCACCTCGATAGTGAGGCACATGA
CATTGTCAACCTTGAAGCGCCGCAACTCCAATCCGACTTCCGAAGACGTTGTGTGATAGTATTTATGTGGTGTGGTGTGC
GCCTATGTTGTAATCGGTGTTTCAACAGAAAAAAAGTTAAAAAAAATACATCCTATTCATCTTGTATCTCTCATA--TTT
TTGTGGTCAAATTTACCATTAGTTAGGATTAAATTATCATCTTACTTGCTACGAGGTAAGTAGGAATCTTAAAATTCTCT
GAAAATATGGACCCAAAATAAGGTGCAAAATTGTCAAGTTTCCCAAATGTAGTGCAACTCGT------------------
--------------------------------------------------------------TTTCC-CAAAAAGCTAGC
GCAAATCGTCTACTCGTTATTAATAGGTTGTCC-AAATTAGAATTATCTC------------------------------
--------------------TTCATTTGAAGATGCGCAAAACAACAAAAATGTTCAATCAACTCT---------------
-----------------------------CCATCCTAATAACAACTACTACACCGAGTGCATCGTTTGTTAGGACGGGGT
CCATTGAGCCTGTTTTAAAAAAAAAAATCAAAAAATTATATGTAAATGTTTCAAAAAAAAAATCTGCAACTATATATACA
TGTTCTTTAACTATATGTAAAGTTTCATCAAATAGATTATTGTCATGCTACACAAAAAACACAAAAATCTGGCCCAAATT
CAACAAGAAAAATCTCATTTTAATCTATGTATTTGTCTTTTTCTTTTGTACATCACATATAAACATATATGTTCATGAAA
TCTCATACGTACATACTACACATATGTGCTTATGTGTATACTCTATCTCAGATTTTTTTTAAAGTTGTGTTCAAAAAAAA
GGTTTTTTTTAAGTGTAGAAAATGTATTTTCCACGAAATAAAATAAACGGCTCCGTGCAGCTCGATCGGCCATCAAACGC
ACTTTCCGCAACTACACCTAGCTTCTACTCCTAGCTTTCCCACACG----GACACCCTATATATACACCGCACCAACGGC
GACAGAATTTCGCAACCAGCTAGCTCAGCTCAGCTCGAAGTGAATCAAGCTCGCGCGAAC----CGAACATGGAGTCGTC
GGGCGACACGGCGCCGTTGCACTCCTCACCGACCCCGACGTCGCCGCCGGCAATGGCGACGGGGACGGCGGTGGTGATGA
GCCCGTGCGCGGCGTGCAAGATCCTCCGCCGCCGGTGCGTGGACCGCTGCGTGCTGGCGCCCTACTTCCCGCCCACGGAC
CCCCACAAGTTCGCCACCGCGCACCGCGTCTTCGGCGCCAGCAACATCATCAAGCTCCTGCAGGACCTGCCCGAGGAGCA
GCGCGCGGACGCGGTGAGCAGCATGGTGTACGAGGCGGCCGCGCGCGCGCGGGACCCCGTCTACGGCAGCGCCGGCGCCA
TCTGCCAGCTCCAGAGGCAGGTCGACGGCCTCAAGGCGCAGCTCGCGCGCGCGCAGGCGGAGCTCGCCGCCGCCCGCGCC
CACCACGCGCACCTCGTCGCGCTGCTCTGCGTCGAGGTGGCCACCGCCGCCGCCGCGCCTCCGCAGGACGCCTACTGTGC
TGCCGGAGGCGGATCGCAGTCCCAGCTCGCCGCACCCCCTGGTGTCGGCTCCACGCCCGCGGACGCGCTCTACGTCGTCG
ACGGCAGCGCGGTGGGCGGCGGCGGCATCATGCAGGCCGGGCACGTCGGCTGGGCCGACGAGCCGCTCTGGACATGAGCG
CGCGCAAGCTGGCGCGCACTGGATGCAT---TCGTCACTCAACTGGCCAACTGCTACTACTACTACGTACGCATGATTCG
TGGGTGTAATTACTAGTACTACATTTTACTTAACTGGGTTAACCAAAGGGTTGACC-------------TGCTTGATGAA
TTTGTTGGAGTTTCAAGATGGAGGAAGATCGAGTTTGTTTTGTTTTGCTGCAAAAATAATACT----------AGCACAT
AGAATAAAAAATTCCGTCATGTTGAAGTTCCAACAAGTTCTGAGAAGTCCTAATCGAGACAGAAAGTTGTATCCTTGCCT
TCTTCTGCAGTTGTGAAGAAGGATGTGGTTGGTTCTCTTGTGTGATGTTAGGTCAAATTGCATTTCTATCATGAACAAAT
GCATGTCATTTTCAAGAAGAGTATCTTTAGTTCCTTACATCCCCTTGTAAATGTAACATATTGTCCTACGAGCACTTAAC
AAATGCATGTCATTTTCAAGAAGACTATCTTTTACTTTACATCCCCATGTCATTTTTATGTGATA---------------
--------TATTTGATATCAGCTTGATTTTAACATATTGTCCTACGAGCACTTAATGAATTGGCATCTCTTTATTTGCTC
CCGAAATAACCAGATAAATTAGACAATAAAAGGATTTTTTTT---GTTCAAACAACATGATGGAAGTTTCTCA-GAAG-T
AGCATTAGTTGATTGAAATAAGAAAACCGTAAATTACAAGTACTATAGATGAAGAAAAATGTTATT-CTTTTGACTTCTT
CCTATGCAGAAAATGAGATGAGGAAGCTCGATGCATTTCTCTATGTTCTTTTCCTCAAACCGTCTTCATTATCCTTTTCA
-AAAAAAAAAAACATCTTCATTATCAATCTGTCTTCGAGTCGTTTGACCGAGAGAGTTGAACGAGCCAATGGTAATTGTT
AGTTTTAGTGTGAGGATGAGAGAAAGGAAGACATGATTTAGGGCTTACGACAT-
>chr1A_328
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-----------------------TAGGATT---------TCTTACTTGCTATGTGGTAAATAGGAATCTTAAAATTCTCT
GAAAATATAGAACAAAATTAAAGTGCAAAGTTGTCAAAATTTTCAAATCTGGTGCAATGTAATTTTTAGTTTGTTTGAGG
TACTTTGTACTTCCGGTGAATTTTGTTACTCCTTTCCGCAAAAGAAACACTACCAACTCGCGTTTTTTCCAAAATCTAGT
GCAAACCGTCTACTCGTTATTAATAGGTGGTCCAAAATTAGAATTATCTACTTCCTCCGTCTCAAAATGGTATTATTTTT
TAC-----ACAAAGGGAATATTTATTTAGAGATGTGCAAAGCT-CAAAGATGTTCAATCTAATCCACCGAGAAATAGCAA
ATTACTTTGTCAAGAACTCTTAATACAGACCCTCCTAAAAACCACAACTACACCTAGCTTC-------------------
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--------------------------------------TATTCTTTCTCAGATTTTTTTTAAAGTTGTGTAAAATAAC--
--TATTTTTGAAGTGTAGAAAATGTATTTTCCACGAAAAAAAATAAAGGGCTCCGTGCAGCTCGATCGGCCATCAAATGC
ACTTTCCGCAACTACACCTAGCTTCTACTCCTAGCTTCCCCACACCGATCGACACCCTATATATACACCGCACCAACGGC
GACAGAATTCCGCAACCAGCTAGCTCAGCTCAGCTCCAAGTGAATCGAGCTCGCGCGAACCGATCGAACATGGAGTCGTC
GGGCGACACGGCGCCGTTGCACTCCTCACCGACCCCGACGTCGCCGCCGGCAATGGCGACGGGGGCGGCGGTGGTGATGA
GCCCGTGCGCGGCGTGCAAGATCCTCCGCCGCCGGTGCGTGGACCGCTGCGTGCTGGCGCCCTACTTCCCACCCACGGAC
CCCCACAAGTTCGCCACCGCGCACCGCGTCTTCGGCGCCAGCAACATCATCAAGCTCCTGCAGGACCTGCCCGAGGAGCA
GCGCGCGGACGCGGTGAGCAGCATGGTGTACGAGGCGGCGGCGCGCGCGCGGGACCCCGTCTACGGCAGCGCCGGCGCCA
TCTGCCAGCTCCAGAGGCAGGTCGACGGCCTCAAGGCGCAGCTCGCGCGCGCGCAGGCGGAGCTCGCGGCCGCCCGCGCC
CACCACGCGCACCTCGTCGCGCTGCTCTGCGTCGAGGTGGCCACCGCCGCCGCCACGCCTCCGCAGGACGCCTACTGCAC
CGGCGGAGGCGGATCACAGACCCAGCTCGCCGCACCGCCTGGTGTAGGCTCCGCGCACGCGGACGCGCTTTATGTCGTCG
ACGGCGGCGCGGCGGGCGGCGGCGGCATCATGCAGGCCGGGCACGTCGGCTGGGCCGACGAGCCGCTCTGGACATAAGCG
CGCGCAAGCTGGCGCGCACTGGATGATGCACTCGTCACTCAACTGGCCAACTG------CTACTACGTACGCATGATTCG
TG--TGTAATTACTAGTGCTACATTTTACTTAACTGGGTTAACCAAAGGGTTGACC-------------TGCTTGATGAA
TTTGTTGGAGTTTCAAGATGGAGGAAGATCGAGTTTGTGTTGTTTTGTTGCAAAAATACTACT----------AGTACAT
AGAATAAAAAATTCCGTCATGTTGAAGTTCCAACAAGTTCTGAGAAGTCCTAATCGAGACGGAAACTTGTATCCTTGCCT
TCTTCTGCAGTTGTGAAGAAGGATGTGGTTGGTTCTCTTGTGTGTTGTTAGGTCAAATTGCATTTCTATCATGAACAAAT
GCATGTCATTTTCAAGAAGAGTATATTTAGTTCTCTACAACTCC------ATGTAATAGTGATTGTCCATTTCACTATGA
ATTAGAGAAATTAACTTAGCGTGAATGGGAAATTCTTTGTTTTGTCTAATATACGTCATGTGGAGTGCTTTTTATCTGGT
GA-------ACTTGATATCAGCTTGATTTTGATACATTGTTCTATGAGCACTTAATGAATCGGCATCCCTTTATTTGCTC
CCAAAATAACCAGACAAATTAGACAATAACATGATTTTTTTTCCCGTTCAAACAACATGATGGAAGTTTCTCAAGAAGCT
AGCATTCATTGATTCAAATTAAAAAA--GTAAATTACAAGTACTATAGATGAAGAACTATGTTATTTCTCTTGACTTCTT
CGTATGCAGAAAATGAGATGAGGAAGCTCGATGCATTTCTCTATGTTCTTTTCCTCAAACCGTCTTCACTATCCTTTTCC
GAAAGAAAAAAACAACTTCATTATCAATCTGTCTTTGAGT---TTGACTGAGAGAGTTGAACGAGCAAATGGTAATTGTT
AGTATTAGTGTGAGGATGAGAGAAAGGAAGACATGACTTAGGGCTTACGACATA
>SNPs
----------------S--S-SSSS-SSSSS-SS------------------SSS-S---------------SSSSS---
-------S--------------S----S-S----S-------------S---SS--------------S-----------
SS----------------S------S--SS------SS-S-SSSSSSSS----S-SSS--SSS-S--SS----------S
--S-S-S-SS-SS-SSSSSSSSS-S---------------------S--SS----------------S-S--S--SS---
----S---S----------S--S------------------------S--------------------------------
------------------------------------------------S---------------------S---------
---------------S-------------------S----------------------S-S-------------------
-------------S-S-----S------------------S-----------S---------------------S-S---
-SSSSSSS---S---------------------------------------S----------------S-----------
--S----------------S------------------S-----S-----------------------------------
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------------------------------------------------------------------------S-------
----------------------------------SS-------S--------S--------------------------S
---------------------------------------------------------------------S----------
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------------------------S-------------------------------------------------------
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-----S----------------------------------------------------S--------------SS-----
----------------------------------------------------------------S---------------
-------------------------------SS--S-----S--------------------------------------
--S-----------------------------------------------------SSSSSSSSSSSSS-----------
---------S-----------------------------------------------------SSSSSSSSSS-------
---------------------------------------S---------------S------------------------
-S------------------------------------------------------------------------------
---S----------------SS----------------------S-----------------------------------
----------S-S-----------------------------------------S------------S-----S-S--SS
SSSSSSSS------------------------------S----S-S------------------------------S---
------S---S-------S----------SS--S--------S-S----S------------------------------
--------------------------S--S--------------------------------------------------
-------------------------------------------------------------------------------S
--------------------------------------S-----------------SSS---------------------
---S------------------------------------SS------S-----
>forward_54
----------------------------------GGTAGGAGGGTGGTGGTACT--------------------------
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>reverse_2042
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-----------------------------------------GCTGGCCAACTGCTACTACT-------------------
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