>input_sequence_74891
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-----------------------------------------------------------------------ATGATGAAG
ATGACGCACGACGACTACGTCCACCTCTGCCTCATGGCGCTCGCCTCCGTGGCCACCGGCGGCGACCAAGCACAGGCAGC
GGAGGGGCAATGGCTGCATACCGTGACTGCGGCGGCGCCAGCAGCCTGCGAGCTTCGGTTCCGGTGCTCCGTATGCGGCA
AGGCGTTCCCGTCCCACCAGGCGCTCGGCGGGCACAAGGCCAGCCACAGGAAACGGGCGGCGCTCGTGCTGCCGCTACAA
AGCGTGTCGCCGGCGGAGGAGGCGGTGGCATCGTCGACGTCGTCTGGCGTCGGCGGGCACAGGTGCTCCGTGTGCCACCG
GAGCTTCGCGACGGGGCAGGCGCTCGGCGGACACAAGCGGTGCCATTACTGGGACGGGCTGTCGGTGTCGCTGACGGCGT
CGGCGTCG------GGTTCCGGGTCGTCCGCGAGGGATTTCGACCTCAACCTGACGCCGGTGCCGGAGAAGGCCGCCGCC
GGCATGCGAAGGTGGGGAGAGGAGGAGGAGGTGCAGAGCCCCTTGCCGTTCAAGAAGCGGCGGCTGTCAAGTCCTTCCTT
GGAGCTTAATTTAATACTCCTTGATTAA----------------------------------------------------
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>chr2D_1_TraesCS2D01G088100
ATACACATTATTGATCTGCAAGAGATAATTTTGACTCGAATGCACATTACCGATCTGCAAGAAGAGATGATTTTGACGCG
AATTGAATAATCACAGTGAATCAATCACAATGGAAGACAAATGTATGTAGAGGGTGTTTATGCACACAT-GAAAGTCCTT
ACTGGTCAAAGATTATTTATTTGTTTGTACATGACCAGTAATTAGTTATAACGGTACCAATCATCACAGTGAGCATTCCT
CCTCTTTTTTTTTGT-AAATATTGATTCTCGAGACAGAAGGACAACAAATTCTCTTGTTTTTGTTGTTGATTGATGCCTA
CACACTTTTGCTTTTACTTTCAAAAATCCTGGTCAATCCAATCTAAATCAAGGAGGAAAACAAGAAAGACATTTT-AGCT
CTCAAATTGACGGTTCGTTTGGTTGGGGACAACACAGACTT----CTATTTTTTTATAGAACTGCCCATCTGAACTTCTC
TTCATTCAAAGCGGAACAAGTCCAACATATCCGTGGCGACAATCAGAAATTCATCATGGATACTACTCTACA--------
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-TCATAGGTGCATGAATCAACAGCTAAAGCAAAGGCATTTTTCTTTTTAGCACATTGGAGCGCCGCAACATTGGCCTTCC
TCCGCCCGTAAATGAGTTTGAAACCCTGAAATTCAACGGTTCATGAATTGAATTGCACAGTAGATTCCATCCACTCGTGA
ATGAAGAT----AATAAAATACTGATATCC----TTTCACGCACGCGCGCGCGCACGTTTGGAAAACTGGAAACCACTCC
TCATGCATGCACGTACCCTTCCGCCCGCCCTCGTGCTCCTTTGAACCAACCAAACTCCTCTATCATCACCTTCTTAGATC
CTTCGAATATACACATATATAACTCACAATTGCACGCACCCAGGAGCATATATATAACACGCAGAGCCCGATCAGGACTC
AGTAAACCAGATTCCTAATCCACTACATCAAGCAGCTCGCGTTAGCCACAGCTCTCGCACGCCA-------ATGATGAAG
ATGACGCACGACGACTACGTCCACCTCTGCCTCATGGCGCTCGCCTCCGTGGCCACCGGCGGCGACCAAGCACAGGCAGC
GGAGGGGCAATGGCTGCATACCGTGACTGCGGCGGCGCCAGCAGCCTGCGAGCTTCGGTTCCGGTGCTCCGTATGCGGCA
AGGCGTTCCCGTCCCACCAGGCGCTCGGCGGGCACAAGGCCAGCCACAGGAAACGGGCGGCGCTCGTGCTGCCGCTACAA
AGCGTGTCGCCGGCGGAGGAGGCGGTGGCATCGTCGACGTCGTCTGGCGTCGGCGGGCACAGGTGCTCCGTGTGCCACCG
GAGCTTCGCGACGGGGCAGGCGCTCGGCGGACACAAGCGGTGCCATTACTGGGACGGGCTGTCGGTGTCGCTGACGGCGT
CGGCGTCG------GGTTCCGGGTCGTCCGCGAGGGATTTCGACCTCAACCTGACGCCGGTGCCGGAGAAGGCCGCCGCC
GGCATGCGAAGGTGGGGAGAGGAGGAGGAGGTGCAGAGCCCCTTGCCGTTCAAGAAGCGGCGGCTGTCAAGTCCTTCCTT
GGAGCTTAATTTAATACTCCTTGATTAA----GTGTGCTAGAGCTGTCGGTCCCACCGTTCATTC-TTGTTTATTTCCAC
TTTTGTTTTTGAGCCTATTGTTTATTTCCACTTGAGAGCTCCGTTTGTGATTACCCCTTGATTTGTACCGCATCTCCTGA
TTCATTTGTGACTTTTGGTCAACTGCTAACACATTTGATGCAATAAATTTGGCACAGG----ATGGTTGTTCAATAGATG
ATGGTTGGTCAATCTATTTGACTTTATG----------------------------------------------------
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----------------------------------------------------------TATCCCAGTGATTCTTTCTGAC
TTTATGTAAGTTTGAGAAATGAAATGTGATCCTTAATCAGAAAGCTTATTACCA-----ACGAGGAGTTTCCTTCAACTC
TAGTATCTTTGACGATCAAAGAAGCACAATAAAAGTGAAGATTCAACTCTAGCTAAGGTTAATTTCAAAAAACTTATGAC
GAAATCAAGTGAGCTTGTCT-----CTCTTATGTTCTGCTCATGAAGGATTTCCCTGAACATTATGTCCAATGGATTAAG
CATAATGTCCAGGGTGGTGATGTAACAATCATGGTTAATGGTCAATTAAAGCCCTATTTTTAAACACAGAAAGGATTGAG
GTAGGGGGACGCCTTCTCACCTAATAGGTAAAACATAGGTGTAGACGTCTGTTACAGAAGCTAATTCATAGACCAAATGA
TAGTGGTTTAATTAGTGGTGTAAGTGCCATGGCTGTAGGGCTTAGCAAGTTAGCATGCTCCAATATGTTCATAACA--GT
CTTTTGAATGGAAACGGATTCAATTCATAAAGTGCAAACAGTTTAAAAGATATCCGCTATTTATTAGAGAATTTTCCTGG
TCTAAAGATCATTTTTAATAAAAGTGAATGTGATGCTTTGGAGAAGTTAGATCTGATTTAGACGCTTATA--GAGACAAT
TTAACATGGTTGCTAGAGTTCTTTCTATGAACCTTGGCATTCCCTCATTATGCTAAATTAAGAAATGGTGATTGGAATAA
AGTAGAAGGTACAGTACGAACT-GGCAAGGCAAAATGATGTC
>chr2B_4
---CACATTATTGATCTGCAAGAGATAATTTTGACTTGAATGCACATTACCAATCTGCAAGAAGAGATGATTTTGAGGCG
AATTGAATAATCACAGTGAATCAATCACAATGGAAGACAAATGTATGT--AAAGTGTTTATGCACACACGGAAAGTCCTT
ATTGGTCAAAGATTATTTATTTGTTCGTACATGACCAGTAATTAGTTATAACGGTACCCATCATTACAGTGAGCATTCCT
CCTCTCTTTTTTTTGCAAATATTGATTCCCGAGACAGAAGGACAACAAATTCACTTGTTTTTGTTGTTGATCGATGCCTA
CACACTTTTGTTTTTATTTTCAAAAATCCTGGTCAATCCAATCTAAATCAACGAGGAAAACAAAAGACAT-TTTT-AGCT
CTCAAATCGACGGTTCGTTTGGTTGGGGACAACACAGACTT----TTTTTTGTTTTGAGAATTGCCCATCTGAACTCGGA
AT---------------AAGTCCAACCTATCCGCGGCCACAATCAGAAATTCATCATGGGTATTACG-TACA--------
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-TCATAGGTGCATGAATCAACAGCTAAAGCA--GGCATTTTTATTTTTAGCACATTGGAGAGCCGTCACATTGGCCTTCC
TCCGCCCGTAAATGAGTTTGAAACCCTGAAATTCAACGGTTCATCTATTGAATTTTAT----GATTCCAGCCACTCATGA
GGACAATAAATGAATAAAATACTCATGATATACATTTCACGCACGCGCGCACGTG----TGGAAAACTGGAAGCCACTCC
TCATGCATGCACGTACCCTTCCGCCCGCCCTCGTGCTCCTTTGAACCAACCAAACTCCTG-----TCACCTTCTTAGATC
CTTCAG--ATACACATATAAAACGCACACTTGCACGCACCCAGGAGCATATATAAG-CACCCAGAACTCGATCAGGAC--
-GTAAACCAGATTCCTAATCCACTACATCAAGCAA----CGTTAGCCTCAACTTTCACGCACGCCATGGCCATGATGAAG
ATGACGCACGACGACTACGTCCACCTGTGCCTCATGGCGCTCGCCTCCGTGGCGACCGGCGGCGACCAAGCACAGGCAGC
GAAGGGGCAGTGGCTGCAGACCGTGACTGCGGCGGCGCCAGCAGCCAGCGAGCTCAGGTTCCGGTGCTCCGTCTGCGGCA
AGGCGTTCCCGTCTCACCAGGCGCTCGGCGGGCACAAGGCCAGCCACCGGAAACGGGCGGCGCTCGTGCTGCCGCTACAA
AGCGTTTCGCCGGCGGAGGAGACGGTGGCATCGTCGACGTCGTCTGGCGTCGGCGGGCACAGGTGCTCCGTGTGCCACCG
GAGCTTCGCGACGGGGCAGGCGCTCGGCGGGCACAAGAGGTGCCATTACTGGGACGGGCTGTCGGTCTCGCTGACGGCGT
CCGCGTCGCGTTCCGGCTCCGGGTCGTCCGTGAGGGATTTCGACCTCAACCTGACGCCGGTGCCGGAGAAGGCCGCCGGA
GGCATGCGAAGGTGGGGAGAGGAGGAGGAGGTGCAGAGCCCCTTGCCGCTCAAGAAGCGGCGGCTGTCAAGTCCTTCCTT
GGAGCTTAATTTAATACTCCTTGATTGATTACTTGTGCTAGACTTGTCAGTCCCACCGTTCGTTCATTGTTTATTTCCAC
TTTTGTTTTTGAGCCTATTGTTTATTTCCACTTGAGAGCTCCGTTTGCGATTACCTCTTGATTTGTACAGTATCTGCTGA
TTCACTTGTGACTTTTGGTCAACTGCTAACACATTTGATGCAATAAATTTGGCATAGGATGCATGGTTGTTCAATAGGCA
AAACAGTGGCATCAA-----------------------------------------------------------------
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------------------------TTTATCGGAAATAGTATAAGTGAGAGTATATAC----CCCAGTGATTCTTTCTGAC
TTTATGTAAGTTTGAGCAATGAAGTGTGATCCTTAATCAGAATGCTTATTACCAG-----CGAGGAGTTTCCTTCAACTC
TAGTATCTTTGACGATCAAAGAAGCACAATAAAAGTAAAGATTCAACTCTAGTTAAGTTTAATTTCAAAAAACTTATGAC
AAAATCAAGTGAG-----CT-----CTCTTATGTTCTGCTCATGAAAGATTTCCCTGAACATTATGTCCAATGGATTAAG
CATAATGTTCTGGGTGGTAATGTAACAATCATGGTCAATGGTCAATTAAGGCCCTATTTTAAAACACAGAAAGGATTGAG
GTAGGGGGACGCCTTCTCACCTAATAGGTAAAACATAGTTGTAGAAGTCTGTTACAGAATCTAGTTCAGAGACCTAATGA
TAGTGGTTTAATTAGTGGTGTAAGTGCCATGGATGTAGGGC--------TTAGCATGCTCCGATATGTTCATAACACAAT
CTTTTGAATGGAAGCGGATTCAATTCAGAAAGTGCAAACAATTTAAAAGATATCCTCTATTTATTAGAGAATTTGCCTGG
TCTAAAGATAATTTTTAATAAAAGTGAATGTGATGCTTTGGAGAAGTTAGATCTGATTTAGACGCTTATA--GAGACAAT
TTAACAGGGTTGCTAGAGTTCTTCCTATGAACATTGGCATTCCCTCATTATTCTAAATTAAGAAATGGTGATGA-AATAA
AGTAGAAGGTACAGTAGGAACTTGGCAAGGC-----------
>chr2A_4
---CACATTATTGTTCTGCAAGAGATCATTTTGACTCGAATGCACACTACCGATCTGCAAGAAGAGATGATTTTGACGCG
AATGGAATAATCACAGCGAATCAATCACAATGGAAGACAAATGTATGTAGAAAGTGATTATGCACACACGGAAAGTCCTT
ACTGGTCAAAGATTATTTATTTGTTCGTACATGACCAGTAATTAGTTATAACGGTACCAATCATCACAGTGAGCATTCCT
CCTCTTTTTC---TGCAAATATTGATTCTCGAGACAGAAGGACAACAAATTCACTTGTTTTTGTTGTTGATTGATGCCTA
CAAACTTTTGCTTTTATTTTC-AAAATCCTGGTCAATCCAATCTAAATCAAGGAGGAAAACAAGAAAGACATTTTTAGCT
CTCAAATTGACGGTTCGTTTGGTTGGGGACAACACAGACTTCTTCTTTTTTTTTAACAGAACTGCCCATCTGAACTTCTC
TTTATTCA-AGAGGAACACGTCCAACCTATCCGCGGCGACAATCAGAAATTCATCATGGATACTACTCCCTCCGTCCCAA
AATATAAGAACGTTTTTTACATTAGCATAGTATCAAAAATGTTCTTATATTTTAGGACAGAGGTAGTACATCATACTCCC
TCCGTTCCAAAATAGATGACTCAACTTTGTACTAAGTTTAGTATAACGTTGGGTCATCTATTTTGGAACGGAGGGAGTAG
GTCATAGGTGCATGAATCAACAGCTAAAGCAAAGGCATTTTTATTTTCAGCACATTGGAGAGCCGCAACATTGGCCTTCC
TCCGCCCGTAAATGAGTTTGAAACCCTGAAATTCAACGGTTCATGAATTGAATTGCACAGTAGATTCCATCCACTCGTGA
ATGAAGAT----AATAAAATACTGATATCC----TTTCACGCACGCGCGCGCGCACGTGCGGAGAACTGGAAACCACTCC
TCATGCATGCACGTACCCTTCCGCCCGCCCTCGTGCTCCTTTGAACCAACCAAACTCCTCTATCATCACCTTCTTAGATC
CTTCGAATATG--CATATAGAACGCACACTTGCACGCACCCAGGAGCATATATATAACACGCAGAGCTCCATCAGGACTC
AGTAAACCAGATTCCTAATCCACTACATCAATCAGCTAGCGTTAGCCTCAGCTTGCACGCACGCCACGGCCATGATGAAG
ATGACGCACGACGACTACGTCCACCTCTGCCTCATGGCGCTCGCCTCCGTGGCGACCGGCGGCGGCCAAGCGGAAGCAGC
GAAGGGGCAATGGTTACAGACTCTACCGGCGACAACAGCAGCGGCCTGCGAGCTCCGGTTCCGGTGCTCCGTCTGCGGCA
AGGCGTTCCCGTCCCACCAGGCGCTCGGCGGGCACAAGGCCAGCCACAGGAAACGGGCGGCGCTCGTGCTGCCGCTACAA
AGCGTGTCGCCGGCGGAGGAGACGGTGGCATCGTCGACGTCATCTGGCGTCGGCGGGCACAGGTGCTCCGTGTGCCACCG
GAGCTTTGCGACGGGGCAGGCGCTCGGCGGGCACAAGCGGTGCCACTACTGGGACGGGCTGTCGGTGTCGCTGACGGCGT
CGGCGTCG------GGTTCCGGGTCATCCGCGAGGGATTTCGACCTCAACCTGACGCCGGTGACGGAGAAGGCCGCCGCC
GGCATGCGAAGGTGGGGAGAGGAGGAAGAGGTGCAGAGCCCCTTGCCGTTCAAGAAGCGGCGGCTGTCAAGTCCTTCCTT
GGAGCTTAATTTAATACTCCTTGATTAA----TTGTGCTATACCTGTCAGTCCCACCGTTCATTC-TTGTTTATTTCCAC
TTTTGCTTTTGAGCCTATTGTTTATTTCCACTTGAGAGCTCC-----------------------------------TGA
TTCATTTGTGACTTTTGGTCAACTGCTAACACATTTGATGCAATAAATTTGGCATAGG----ATGGTTGTTCAATAGACA
AAACAGTGGCATGTGATGAGAGAGGATTTTCTACCATGCACGGGACCTTCCGTGCATGCATCCATCGCATTATTTATTAT
TGTGTGGGACCTTTTCTATAGTGTTTTTTCTCACCCAACATAGTACATTCACATGCTATTATGTACTGACTAAGTTTCAT
TCAAATAAAGAGATGCCTAATGCATGTCGAAATAAAAGTTTGATTTACATTTTTTTCCATAATTGTGTTTTTTCTGACAA
GGTCTTTAAAACAAGACCAATATTTAATATATTTTCAGAAATTATTTTTTTGACAACTAAATCACAATGCTTCAAACTTT
TTCCATACAAATTTATTAATTCCATGTGAAAAAATAATAATGCTTCATTGTGTTTTGCAAAAAAAAAATCTAATTGTTTT
ACTATGGCTCCCCATGTTCCGTTGCATTTCATAATGTTACATTGTGTGCTCGTGTGTATCAAACTGATTCTTAGTAATCT
AAAAGTTAGTAAATATTAATAGATTTTATTGCAAAAAAACTTTGAACTTATCTAGAGTTTTAAAAAATATAGCATATTTA
TGTGTACTTTTATAGTGCTTCACCATGTTTCAGAATTTTAATTTTAAAATTTATTGAAATATATTCAAAAGTGGTCTCGT
TTGAAAGGTCTCGTCGTCAAAAACACAAATATGAAAACGGATCATAAATTGTTCTTTTGGTTCAAAAGATAAAATAGATT
TAAACTTGTGAATAAAATGAAAAAGCATGGGTGGAACAGAGTGCTTGCATGTGGTGAGAGAAAGATCGAACAAACTGCGA
GCAGTATAAATGCATTGTGTCGGATCTCCAAGCAAAAATCAACGGCGCATGCATGCACGGTACCTCCCGTGCATGGGAGA
TTAGCTTTTCTCGGCATGTGATCCTTTATCGGAAATAGCATAAATGAGAGTATATATATATCCCAGTGATTCTTTCTGAC
TTTATGTAAGTTTGAGCAATGAAATGTGATCCTTAATCAGACAGCTTATTACCAATGCAACGAGGAGTTTCCTTCAACTC
TAGTATCTTTGACGATCAGAGAAGCACTATTAAAGTAAAGATTCAACTCTAGTTAAGGTTAATTTCAAAAAACTTATGAC
GAAATCAAGTAAG-----CTTATCTCTCTTATGTTCTGCTCATGAAAGATTTCCCTGAACATTATGTCCAATGGATTAAG
CATAATGTCCAGGGTGGTAATGTAACAATCATGGTCAATGGTCAATCAAGGCCCTATTTTAAAACACAGACATGATTGAG
GTAGGGGGACGCCTTCTCACCTAATAGGTAAAACATAGTTGTAGACGTCTGTTACAGAAGCTAGTTCATAGACCAAATGA
TAGTGGTTTAATTAGTGGTGTAAGTGCCATGGATGTAGGGC--------TTAGCATGCTCCAATATGTTCATAACACAGT
CTTTTGAATGGAAGCGGATTCAATTCATAAAGTGCAAACAATTTAAAAGATATCCTCTATTTATTAGAGAATTTGCCTTC
TCTAAAGATTAATTTTAATAAAAGTGAATGTGATGCTTTGGAGAAGTTGGATCTGATTTAGACGTTTATATAGACACAAT
TTAACATGTTTGTTAGAGTTCTTCCTGTGAACCTTGGCATTCCCTCATTAAGCTAAATTAAGAAATGATGATTGGAATAA
AGTAGAAGGTTCGGCAGGAACTTGGCAAGGCAAAATGATGTC
>SNPs
SSS-----------------------------------------------------------------------------
---------------------------------------------------SS---------------S-----------
-------------------------S------------------------------------------------------
-------------SS-------------------------------------S---------------------------
----------------S---------------------------------------------------------------
---------------------------------------------S-S--------S-----------------------
--S-----S--S--------------S------S----------------------------------------------
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------------------------------------------S-----------------S-------------------
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----------------------------------------------------------S---------------------
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-------------------S---S----S--------------------------------------S------------
-------------------------------------S---------S-----S--S-S-S-SS----------------
-----------------------------------------------------S--------------------------
-S----------------S-----------------------------------S-----------------S-------
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---------------------S----------------------------------------------------------
------------------------------S-------------------------------------------------
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--------------------------------S---------S-----S-------------------------------
-----------------------------------------------S-------S------------S-S----S----
------------------------------------------------------S-----------------------SS
-SSSSSS-S--SSSS--SS--SSSS--S----------------------------------------------------
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----------------S---------------------------------------------------------------
------------------------------------S---------------S---------------------------
-------------SSSSS----------------------------S---------------------------------
------------------S----------------S-------------S----------S-------------------
--------------------------------------S------------------------S----------------
--------------------------------S--------SSSSSSSS-------------------------------
-------------S--------------------------S--------------S------------------S-----
---------S----------------------------------------------------------------------
-----------------------S--------------------------------------------------------
----------------S-------------------------
>forward_1158
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------------------TCCACTACATCAAGCAGCTC------------------------------------------
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>reverse_3697
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----------------CGAACTGGCAAGGCAAAATGA-----
