>input_sequence_84358
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-------------------------------------------------------------------ATGGCGTCAATCC
CCAGAGCGTCGTCCCTTGTCGCCATGGCCATCGTCGTCGTGCTCGCCTCCGTGGCCAGCGCCCAGGGCCCCGCCCCGGCA
CCCACCGCCAGCGATGGTTAGTGTTTTCTTCCTCTCCTTGTCCTCCCCTCGTGCGTGCGTGTGATGCTTATTAGT---GA
TTTGCTTGGTTTTGTGGATCAATGTTGGCAGGAACGAGCGTGGACCAAGGGATCGCGTACGTGCTCATGTTCGTGGCGCT
CGCCCTCACCTACCTCATCCACCCGCTGGACGCCGCCTCCGCCTACAGGCTCCTCTGA----------------------
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>chr3A_1_TraesCS3A01G238200
ACACCTTTGCTAAAGACCGTTTGGGAGGTATGAGC-ACTCCAAAATGTAAGTCCTTCGCTTGGTTGATCATCCACAATAG
ATTTTGGACGGCTGATAGGCTCCACCATAGGGGGTGGCAAATTACAGTTTGTG-CCCCCTTCGCAACCAAGTTCAAGAAA
CATCGCCCCACCTTCTTTTCCAATGTTGCAACACGATTTTGTTTGAAACGCGGTCAAGGTGCAGATTGGGCTTGGTGAAA
TCATGACTAATGAATGGTCGACTATGGTCGCGTTGGAAGATTGGTGGACCAATATTGC-CCTCAAAAAATCTTCAAATCG
GAAAGCAATGACCTCCCTCATGATGCTTATAGCCTAGGATGTTTGGAAAGAGCTTAACGCTAGGGTCTTCCTGAACACAT
CTACCCCAACTACGACCATTGTTGACAAAATCCTTGAGGCGGCGAGGTTGTGGGTGATTTACAGGCGCTAGGGGGC--TT
GGGTACGGTGTTGTTTTACCTTGCGGGTAATGGTTTTATTTTTGCTACTTT-----------GTCGCTGTTGTCTGGACC
CTCTTCCCCTTTTTTTTCAACTGGACCCCTCTTCTCCTTGATCAATGAAATGGAAAAACTTTTGCCTCGTTTCATCAAAG
GAAAATAATATAAAGTATAGCGACCGTCTATCCAATCCAGGTAGAGATGGGAGGATCTGTGAGTCCCAC-----------
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--------------------------------------------------TTTTTAGGGTAGAGGATCTGATAGTACTGA
TTACAGGTCAAAAC------------------------GTTACTATGCCTGAATCTATCCAAGCCAACGAGGAGCAAGGC
TGGCCACTCCCATTTATGCACGAGCTCCCCTATTTCTGATCAAGGCTATATAAATCCGGGTCTCGCCGAAATTCATGCGA
GCACAACAGAAACGCCAGCCTCTTCTCTTGTGCCTGCCTCCCCTTCCTCTCCT------GATCTCCAGAGCGAGAGGGAG
GGGGATCTAGATTCTAGATAGAAGCTCCAAACCCGGCCGTTTCGGTTATCCAGAGAGACCAGAGGACATGGCGTCAATCC
CCAGAGCGTCGTCCCTTGTCGCCATGGCCATCGTCGTCGTGCTCGCCTCCGTGGCCAGCGCCCAGGGCCCCGCCCCGGCA
CCCACCGCCAGCGATGGTTAGTGTTTTCTTCCTCTCCTTGTCCTCCCCTCGTGCGTGCGTGTGATGCTTATTAGT---GA
TTTGCTTGGTTTTGTGGATCAATGTTGGCAGGAACGAGCGTGGACCAAGGGATCGCGTACGTGCTCATGTTCGTGGCGCT
CGCCCTCACCTACCTCATCCACCCGCTGGACGCCGCCTCCGCCTACAGGCTCCTCTGAACCGAGCTCCCCCTCTTCT---
GTAACTCGACGCCGCCGTGTGTGTAATCAGTTCATCCAGCTTAATCGTTCGTTCCGGAAACCAGGATTGTAGTCCATGTA
GTTTC----TTCTTTCTAGCTTCTCAGTTGGAGATTTGCGAGTGAGGAAAATGATGCCGATTCCTTTACTTCTAGTTCTA
GAGATGTAATGCAGTTATTCTCTGTCCGGAAATATGTTATTCTCTGTCCGGAAATATCCCCGCAGAAGATAAA-AGGGTG
TGTCTAGATGTGCCCTAGTTATTGCACATCTAAATGAGTGAATCAAGCATAAAGAGAAAAAAAAAAGAAAAAGAAAATAT
CCACACGAATCTCGATGTAAGATCAATGACATAGGACTTAGATGTGCAATACTTATGGCATATTTAGATGTGCTTTAGCA
AAACTGAAGATAAAAACACACACACTAGTGCATGCATAGATGCATGCTTGGCATGGTTATTTTGTCCCCTTTCGACCGCT
GCGTCTTCTCATGCATTCGTCGACGGCGGCGGCGGCTGCTGTTCGGTGCTCCAAGGAGGGAACTTGTCATCCTTGTCCAC
ACGCCCAGCGCCCTCGCCGGCAGCGTTACCGTCCCCGCCGGTAGGCCGCGACGATGGTGCCTGTCTTGCCCGATGCGGCG
CTGATGGCGTGGTATGTAGACAACACACGCGTCGGGAATAGCTCGGCCGGCAGAACGAAGGTGGTGTTGTTGGGCCCCTA
GTTTACGAAGAAGAACGTGAGCGCCTCCAGGATTGCGGAGAGGATGCGCTAGTGGTTCTTGAGGCGAAAATATATTTTAG
AGCATATGCACCCAGGCCCTCTCTATCCAGCCATCCATTTTTTGCTTTAAGATCCGTGCAAGTACATTTCTCTTTTTTGT
TTCTCCCACATAAAACATATCTAGAAGTTCAAACCTATGCGGCGTGACAAAGCTTTCTGAGTAGAATCTAGGATAAATCG
TACAGATTTTTTTGTCAAACATAAAT
>chr3D_1
ACACCTTTGCTAAAGACCGTTTGGGAGGTGTGGGCTACTCCAAAATGTAAGTTCTTCGCTTGGTTGATCATCCACAATAG
ATTTTGGACGGCCGATAGGCTTCACCATATGGGGTGGCAAATTACAGTTTGCG-CCCCCTTCGCAACCAAGTTCAGGAAA
CATCGCCCCACCTTCTTTTTCAATGTCGCAACACAATTCTGTTTCAAACACGGTCAAGGTGCGAATTGGCCTTGGTGAAA
TCATGACTAATGAATGGTCGAGTATGGTCGCGTTGAAAGATTGGTGGACCAATATTGC-CCTCAAAAGATCTTCAAATCG
GAAAGCAATGACCTCCCTCATGATGCTTATAGCCTAGAATGTTTGGAAAGTGCTTAACGCTAGGGTCTTCCGGAACACAT
CTACCCCAACTACGATCATTGTTGATAAAATCCTTGAGGCGGCGAGGTTGTGGGTGATTTG-AGGTGCTAGGGAGC--TT
GG-----GTGTTGTTTTACTTCGCGGGTAGTGGTTTTA-----------TT-----------GTCGCTGTTGTCTGGACC
CTCTTCCTCTTGTTTTTAACTGGA--CCCTCTTCTCCTTGATCAATGAAATGGAAAAACTTTTGCCTCGTTTCGTCAAAA
AAAAAAAATG-------CAGCGACCGTCTATCCACTCCAGGTGGAGATGGGAGGATCTG---------------------
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-----------------------------------------TGAGTCCTATTTTTAGGGTAGAGGATCTGATAGTACTGA
TTACAGGTCAAAACGATAGGCAGTGAGAGAGAGAGAGAGTTACTATGCCTGAATCTATCTAAGCGAACGAGGAGCAAGGC
TGGCCACTCCCATTTATGCACGAGCTCGCCTATTTCTGATCAAGGGTATATAAATCCGGGTCTCGCCGAAATTCATGCGA
GCACAACAGAAACGCCAGCCTCTTCTCTTGC----GCCTCCCCTTCCTCTCCTCGTCCTGATCTCCAGAGCGAGAGGGAG
GGAGACCTAGATTCTAGATAGAAACTCCAAGCCCGGCCGTTTCGGTTATCCAGAG--ACCAGAGGACATGGCGTCAATCT
CCAGAGCGTCGTCCCTTGTCGCCATGGCCATCGTCGTCGTGCTCGCCTCCGTGGCCAACGCCCAGGGCCCTGCCCCGGCA
CCCACCGCCAGCGATGGTTAGTATTTTCTTCCTCTCCTTGTCCTCTCATCGTGCGTGTGTGTGATGCTTATTAGTAGTGA
TTTGCTTGGTTTTGTGGATCGATGTTGGCAGGAACGAGCGTGGACCAAGGGATCGCGTACGTGCTCATGTTCGTGGCGCT
CGCCCTCACCTACCTCATCCACCCGCTGGACGCCGCCTCCGCCTACAGGCTCCTCTGAACTGGGCTCCCCCTCTTCTGTA
GTAACTCGACGCCGCCGTGTGTGTAATCAGTTCATCCAGTTTAATCGTTCGTTCCGAAAACCAGGATTGTAGTCTATGTA
GTTTGTTCTTTCTTTCTAGCTTTTCAGTTGGAGATTTGCGAGTGAGGAAAATGATGCCGATTCCTTTACTTCTAGTTCTA
GAGATGTAATGCAGTTATTCTCTGTCCGGAAAT---------------------TATCCCCGCAGAAGATTAACAA----
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-----------------ACACACACTAGTGCATGCATAGATGCATGCTTGGTATGGTTATTTTGTCCCCTTTCGATCGCT
GCGTCCTCTCATGCATTCGTCGACGGTGGTGGCTGTTA---TTCGGTGCTCCAGGGAGGGAACTTGCCATCCTTGTGCAC
ATGCCCAGCGC---------------------------------------------------------------------
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>chr3B_3
--ACCTTTGCTAAAGACCGTTTGGGAGGTGTGGGCTACTCCAAAATGTAAGTCCTTCGCTTGGTTGATCATCCACAATAG
ATTTTGGACAGTTGATAGGCTCAACCATAAGGGGTGGCAAATTACAGTTTGTGCCCCCCTTCGCAACCAAGTTCAAGAAA
CATCGCCCCACCTTCTTT-CCAATGTCTCAACACGATTTTGTTTGAAATGTGGTCAAGGCGCGGATTGGCCTTGGTGAAC
-CATAACTAATGAATAGTCGACTATGGTCACGTTGGAAGATTGGTGGACCAATATTGCTCCTCAAAAGATCTTCAAATCG
GAAAGCAATGACCTCCCTCATGATGCTTATAGCCTAGGATGTTTGGAAAGAGCTTAACGCTAGAGTCTTCCGGAACACAT
CAACCCCAACTACGATCAGTGTTGACGAAATCTTTGAGGCGGCAAGGCTGTGGGTGATTTG-CGGGTGCTAGGGGGTTTT
GG-----GTGTTGTTTTACCTCGCGGGTAGTGGTTTTA-----------TTTTCGCTACTTTGTCGCTGTTGTCCGGACC
ATCTTTCCCTTTTTTTCAACCGGT--CCCTCTTCTCCTTGATCAA--------------------CTCGTTTCATCAAAA
GAAAATAATATAAAATACAGCGACCGTCTATCCGATCCAGGTGGCGATGGGAGGATCTGTGAGTCCCATTTACCGAAAAA
GGGTTTCCCCCCGCTTTGTATTCCAAAGCAACCAACACCGATACATGATCGCTGGGGCGAACAGCACAACAAGCCCAAAA
GAAAAAGAAGAAGAAGCAAATGCCAACAACGGCAGCTCGACAGAGCACGGATGACCCGCCGCCGCTACGCCCACCAAAGA
CAAACCACTACAACCTGAGGCTCCGGACCACCACGTACAAAACAGCACCTCCAAGAAGGAAAGCGACGCCGACGACGCTG
TTGCCCGGACATGTCCTAGGGTTTCCCTGGCACGCGGAGGGAGGTGGGGGATGGATATCACCGACACCCTCCAGGGAGGA
ATGATGGCACCCGCAGGTGTCACCGCATCGGGGCCGAAGACCGCTAAGGATTTCTCCCGTACTCCAATCCCCACCGCCCA
ACGGACCGGAACCGACCAGCCAGACCGCCGCCCACCACCATGCGTCATCGCGGTTGTGCCGTCACCCACGCCGCCTCACT
GCGGACACCAACACGAGGCCAAGAGGACCGGAGAGAAGCGCCCCGCGGAGGGAGAAGCAGCACCGAAACCGAACGGGAGG
GAACCACCTCCACCGCCGTCGTGCGGGAGCCAGAGCCTCCGGCACCGTCGCGGTAGCCGTCCGGACGCAGCAGCAGGGCA
TGCCAGGCCACCCCTGGCCCGCCCAGGCCCGAAACGGGCCCGCTAAGCCCCGCCGCCACGCTGCAGCAAGCCGGCGATGG
CGTCGCCAACACCCTGCCGCGCATCGCCTCTCCCCCGCCTCCCGGAAGCCACGAAGCAGACCCACACCGCCGCCGGCCCG
CCCAGGCCCAGATGGGACCCGAAGGGCCCAGATCTGGGCCGAGCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTCGCCCCGTCCC
GCGCCGGCGGACACCCGAAAGGGGAAAAGCCAGGGGGCCGCCGCCACCAGCGTCGCCCAGGCCAGGCCCGCAGCGGGCGC
CGACGACGGCGGCAGAGAGGAAGAGGGAGGGAGAGGCGCGCGGGGGGAAGGCTGGGCACGGCCGGCCGCCCGCGGGGGCG
GCTCGGTCGCGAGAGGAGAAACTAGGATTCTTCCTCTTTCCTGAGTCCCATTTTTAGGGTAGAGGATCTGATAGTACTGA
TTACAGGTCAAAACGATAGGCAGTGAGAGG------GAGTTACTATGCCTGAATCTATCTAGGCGAACGAGGAGCAAGGC
TGGCCACTCCCATTTATGCACGAGCTCGCCTATTTCTGATCAAGGCTACATAAATCCGGGTCTCGCCGAAATTCATGCGA
GCACAACAGAAACGCCAGCCTCTTCTCTTGTGCCTGCCTCCCCTTCCTCTCCT------GATCTCCAGAGCGAGAGGGAG
GGGGATCTAGAT---AGATAGAAGCTCCAAGCCCGGCCGTTTCGGTTATCCAGAG--ACCAGAGGACATGGCGTCAATCT
CCAGAGCATCGTCCCTTGTTGCCATGGCCATCGTCGTCGTGCTCGCCTCCGTGGCCAGCGCCCAGGGCCCTGCCCCGGCA
CCCACCGCCAGTGATGGTTAGTATTTTCTTCCTCTCCTTGTCCTCTCCTCGTGCGTGTGTGTGATGCTTCTTAGT---GA
TTTGCTTGTTTTTGTGGATCGATGTTGGCAGGAACGAGCGTGGACCAAGGGATCGCGTACGTGCTCATGTTCGTGGCGCT
GGCCCTCACCTACCTCATCCACCCGCTGGACGCCGCCTCCGCCTACAGGCTCCTCTGAACTGAGCTCCCCCTCTTCTGTA
---ACTCGACGCCGCCGTGTGTGTAATCAGTTCATCCAGTTTAATCGTTCGTTAAGAAAACCAGGATTGTAGTCTAGGTA
GTTTC----TTCTTTCTAGCTTCCCAGTTGGAGATTTGCGAGTGAGGAAAATGATGCCGATTCCTTTACTTCTAGCTCTA
GAGATGTAATGCATTTATTCTCTGTCCGGAAAT----------------------ATCCCCGCAGAAGATAAA-AA----
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-----------------ACACACACTAGTGCATGCGTAGATGCATGCTTGGCATGGTTATTTTGTCCCCTTTCGATCGCT
GCGTCTTCTCATGCATTCGTCGACGGTGGTGGCTGCTA---TTCGGTGCTCCAAGGAGGGAACTTGCCATCCTTGTCCAC
ATGCCCAG------------------------------------------------------------------------
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>SNPs
-----------------------------S--S-----------------------------------------------
-----------------------------S--------------------------------------------------
--------------------------S-----------------------------------S------S----------
-------------------------------------------------------------------S------------
-----------------------------------------------------------------------S--------
---------------S--------------------------------------------SS---S--------------
--SSSSS--------------S-------S--------SSSSSSSSSSS-------------------------------
-----------------S-S-S-SSS-----------------------------------------------------S
--------------S--S------------------------S-------------------------S-----------
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-----------------------------------------------------------S----S---------------
---------------------------S----------------------------------------------------
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------------------------------S------------------------SS----------------------S
----------------------------------------------------------------------S---------
----------------------S----------------------S-----------S----------------------
--------------------S-----------------------------------------------------------
------------------------------------------------------------S-------------------
---------------------------------------S----------------S-----------------S-----
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---------------------------------SSSSSSSSSSSSSSSSSSSSS---------------------SSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSS----------------------------------------------------------S----
--------------------------S--S---S---SSSS-------------------------S-------------
-S---------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_709
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-------------------------------------------------GGAGGATCTGTGAGTCCCAC-----------
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>reverse_3485
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--------------------------------------------TGCGCTAGTGGTTCTTGAGG----------------
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