>input_sequence_81916
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ATGGTTGACTCCGGCGTGGCCATAGCTCTCGGCGTGGTCGGGTTCCTCGTGGTGGTGCTCGCGATCGCCTGGGCGGTGCG
CTGCGCCGTCGCCCGGCGCCGCGCCGAGGAGGCGAAGGAGGCCGTCGGCGTCGGCGTCGGCGCGGGGCTGCTGGACAAGG
AGGCCGTCGTCGTCGACGTAGAGACCAAGCGCGAGGA---GCCGCTCTGCGCGATATGCAAGGGGCCGCTGGCGGCGGGC
GGGGGGAGGTGCCGGCGGCTGCGCGCGTGCGGCCACGTCTACCACGCCGAGTGCGTCGACCTGTGGCTCCAGCGGAAGCC
GATCTGCCCGCTGTGCCGGGCCGGCGTCGTACTGTCGCGGACGGACATCGTCGACGCCATCGTGTGA-------------
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>chr3D_1_TraesCS3D01G339500
AACCTTCAAAACCTAAAACTTCAAAATTTGTGTGCCCCGTG--CGAAATCCAACGAGTTTGCGAAACGCGAGGCAATCAG
CCGGCGGGGACGACTGGGCTCATGCGTGTCCCTACGAGTTTCCGTGGAGCT--GGTCATGCCATAGTGCTATATTGTGAG
GGCAGCACCCTACTTGTGTACACATAGAAAAATAATAGATTGGGGTTCAGTGTCATTCAAAAGTCTATACTTTTGAACAT
G-AACGCTACTTATATCTACTGATAAATAAAGATCTCTTTAGCGACTCGTTTTATTGTGCTTAACCCATGCATACTCTTT
GATCTAGAGACTAGAAAATGAATTCCACGACCAAACAGCTCCGCATATACGTGCTTAAACAGCCCAAAGGGGCAAAAGCC
CAACGTGATTATACTTTCTTTTCCAGGGACCAACGTGCTTATACTTTGCGGAACTAAAGCTTCTGTAAACAATTCAGTAT
TT-GGGGGCAAAGCATTGCCATCTTTGCATGGTCT-ACGTGTAAATCCAGCCAGCGCTCGTGATTAACAACGCAAAATCT
CAGAATTAATTATATGGCTAATTATCGCACGACTGCACGTGATGCCCCCTCCCTCTGCGCCACCGTCAACACGCAGGCAA
CGTACGTGAACTACGTAGCACGATCGAT------------CTTCTATTTTGGGTCGTGTCACTGAACGGATTCCTCTTGC
GGTCAGCGCCGATTGCGCTGGATTCGCTGCGGTAGTTTGTTTGGGTAAGATCAGATCACACGTAC---AGTACTTATCCG
ATGCTGGGTTCCTTTCCTCGAGCGCGGATCTGTTTCCTCTGCGGAACAAACGTA---TCAGAGGATATGGAAACGA---A
CTACAACAACAAACTTCTTGGACCTGGACTGCACCCAGTACGACTACTGCTCACGCTCATATGCGGAGATCTGGTACGTA
CTACTAGGTAGGTACGTGCCGTCACAACTCACAACA-----------ACACGCGGCGAC-TTGATCCCACGGACGCACCG
ATGGTTGACTCCGGCGTGGCCATAGCTCTCGGCGTGGTCGGGTTCCTCGTGGTGGTGCTCGCGATCGCCTGGGCGGTGCG
CTGCGCCGTCGCCCGGCGCCGCGCCGAGGAGGCGAAGGAGGCCGTCGGCGTCGGCGTCGGCGCGGGGCTGCTGGACAAGG
AGGCCGTCGTCGTCGACGTAGAGACCAAGCGCGAGGA---GCCGCTCTGCGCGATATGCAAGGGGCCGCTGGCGGCGGGC
GGGGGGAGGTGCCGGCGGCTGCGCGCGTGCGGCCACGTCTACCACGCCGAGTGCGTCGACCTGTGGCTCCAGCGGAAGCC
GATCTGCCCGCTGTGCCGGGCCGGCGTCGTACTGTCGCGGACGGACATCGTCGACGCCATCGTGTGAGCCGTCTGCGCAG
GTCCTCGGCGCGGCGCGGCGCGGTGCACGGGTACGTGCGTGCGGTCTGCGCCGCCGTACGTCCTTCTGCAGTCCGCGTAC
ACGGCCGTGTCCTCATCC------------GCG------------TGCGTGCGTTGGGGAATTTTGCTCCTGACAAAGGA
AGACATAC----TAGTAGTTTTGTGTATTCGGAGGGAGGAAGATACTGTATTTGTTTCGTTGGTTCGCTTGCTTGTACTC
AAGGATACGTACGAGCACTTTTTACTT--------TTTAGTGCTTTCTGACAAGCATTATCTTACGGAAACACTAAAAAT
CTGACATCAGATTTTTAGACATGCCAAATCTAGCATTTTTCATGACAATTTATATTGGTGTGATGATGACCAATTTACTC
CCTCCGTTCCAAAATAGATAACTCAACTTTGTACTAACTTTATACTAAAGTCGAATATTCAATTATGAGCCCCGCCTCGT
CTGCACCCGGTCAAGAAATAATTCATAAAAAATAAATAAAAATCA-----------------------------------
--------------------------------------------------------------------------------
--------------------------AAAAAATCCAAATTTTTTGTGCATGGTAGATAATTTGGTGTGTGAGGTGCGCAC
CTCACA--------------------------------AAACAAACAAAAATCCAGCCCATAAAACAAAAAA-GTGGCCC
ATTTTGAAAATACATATTTGTCTTTTCTTTGAACACCACGTGTGAAGTAAA-----------------------------
----ATGTGTGTGCGTGTTTACAG-----AAAAAACAATTC-TTTTGCG---CTGTAGAAAATGGTTTGTTTGAAACGGC
CACCATGGTGCTCGTGCACAACTAGCAATTTTTGCAAATAGTTGTGCTATTTGGCATAGCTCGCTAGTAGTTATAGCTAA
AGCTATTATTTTG-------------------------------------------------------------------
---------------------------------------------TAAGTGTGTATGGACCAATAATAGCTTGTAATCAT
TTGGACCTACAAATTTAATCCAAACGGCCAGTTTTTTTTGCGAGAAAACTTCCGATCTATTCATCAACTGTTAAGGTAGT
ACAAAGAACACTAGAAGTAAAATTTACATTCAGATCCGTAGACCACCTAGCGACGACTACAAACACTGGAG
>chr3B_5
----TTCAAAACCTAAAACTTCAAACTTTGTGTGCCCCGTG--TGAAATCCAACGAGTTTGCGAAACGCGAGGCAATCAG
CCGGCGGGCACGATTGGGCTGATGGGTGTCCCTACGAGTTTCCGTGGAGCC--GGTCATGCCATAGTGCTATATTGTGAG
GGCAGCACCCTACTCGTGTACACATAGAAAAATAATAGATTAGGGTTCAGTGTCATTC-AAAGTCTATACTTTCGAACAC
GAAACGCTACTTATATCTACTGATAAATAAAGATCTCTTTAGCGACTCGTTTTGTTGTGCTTAACCCATGCATACTCTTG
ATGTG-GAGACTAGAAAATGAATTCCACGACCAAACAGCTACGCATATACGTGCTTAAACAGCCCAAAGCGGCAAAAGCC
CAACGTGATTATACTTTCTTTTCCAGGGACCAACGTGCTTATACTTTGCAGAACTAAAGCTTCTGTAAAGAATTCAGTAT
TTGGGGGGTAAAGCATTGCCATCTTTGCATGGTCTTACGTGTAAATCCAACAAGCGCTCGTGATTAACAACTCAAAATCT
CATAATTAATTATATGGCTAATTAGCACACGACTGCACGTGATGCCCCCTCCCTCTGCGCCACCGTCAACAGGCAGGCAA
CGTACGTGAACGACGTAGCACGATAGATTTATTATTACTGCTTCTATTGTGGGTCGTGTCACTGAATGGATTCCTCTTGC
GGTCAGCGCCGATTGCGCTGGATTCCCCGTGGTAGTTTGTTTGGGTAAGATCAGATCACACGTAC---AGTACTTATCCG
ATTCTGGGGTCCTTTCCTGGGGCGCGGATCTGTTTCCTCTGCGGAACAAACGTAGTGTCAGAGGATATGGAAACGA---A
CTACAACAACAAACTTCTTGGACTTGGACTGCACCCAGT---ACTACTGCTCACGCTCATATGCGGAGATCTGGTACGTA
CT---AGGTAGGTACGTGCCGTCACAACGACACACGCTAGAGACTCCACACGCGTCGACTTTGATCCCACGGACGTACCG
ATGGTTGACTCCGGCGTGGCGATAGCTCTCGGCGTGGTCGGGTTCCTCGTGGTGGTGCTCGCGATCGCCTGGGCAGTGCG
CTGCGCCGTCGCCCGGCGCCACGCCGAGGAGGCGAAGGAGGC------CGTCGGCGTCGGCGCGGGGCTGCTGGACAAGG
AGGCCGTCGTCGTCGACGTCGAGACCAAGCGCGAGGA---GCCGCTCTGCGCGATATGCAAGGGGCCGCTGGCGGTGGGC
GGGGGCAGGTGCCGGCGGCTGCGCGCGTGCGGCCACGTCTACCACGCCGAGTGCGTCGACCTGTGGCTCCAGCGGAAGCC
GATCTGCCCGCTGTGCCGGGCCAGCGTCGTGCTGTCGCGGACGGACATCGTCGACGCGATCGTGTGAGCCGTCTGTGCAG
GTCATCGATGCGGCGCGGCGCGGTGCACGGGTACGTGCGTGCGGTTTGCGCCGC----CGTCCCTCTGCAGTCCGCACAC
GCGGCCGTGTCCTCATCCTCGTGCGTCCGTGCG------------TGCGTGCGTTGGGGAATTTTGCTCCTGACATAGGA
AGACATAC----TCGTAGTTTTGTGTATTCGGAGGGAGGAAGATACTGTATTTGTTTCGTTGGTTCGTTGGCTTGTACTC
AAGGATACGTGCAAGCTCTTTTTGACAACGATTTCTTTAGTGGTTTTTGACAAGCATTATCTTACGGAAACACTAAAAAT
CTGACATCAGATTTTTAGACATGACAAATCGA--ATTTTTCATGACAATTTATATTGGTGTGATGATGACCAATTTAGGC
TGCAAGCACGGTAATTTTCTGTC---------------------------------------------------------
--------------------------AAAAAATAAATTAAGGCGGATTTGCTATGCTCATCATCTAAACTTGACATCCTC
GAAGAACAAATATTTAAATTGCTAGC-------------TAGGTTTTGGGGCACCATGCTACCCTTTATTTTGAAAAAA-
TAAGAAAACATATTTGAAAGTTTCAGAAAAAATCCAAAACAATTATGTGAAAACTTTGATGTGCTCACTACAGATCCATG
AAATTTTGTTTAGAAAAAATGTAGTTTGTAATTTGTGCAAAAGG---AAAACCCAGCCCAAAAAGAAAAAAAGGTGGTCC
ATTTTGAAAATACATATTTGTCTTTTCTTTGAACACCATGTGTGAAAGTAAAATGTTGTGAAATTTTGCACATACATAGT
ATACATGTGCGTGCATGTTTTTTACAAACAAAAAAAAATTC-ATTTTTTTTACTGTAGAAAATGGTTTCTTTGAAACGGC
CACCATGGTGCTTGTGCACAACTAGCAATTTTTGCAAATAGGTGTGCTATTTGGCATAGCTCGCTAGTAGTTATAGCTAA
AGCTATTATTTTGTACTCCCTCCGTCCGGAAATACTTGTCATCAAAATAAATAAAAGACGTATTTTAGTTCTAGATACAC
CCCTTTTTATCCATTTTGATAACAAGTATTTTCGAACGGAGGGAGTAAGTGTGTATGGGGCAATAATAGCTTGTAATCAT
TTGGACCTACAAATTTAATCCAAACGGACAGTT-----------------------------------------------
-----------------------------------------------------------------------
>chr3A_10
---------AACCTAAAACTTCAAACTTTTTGTGTGCCCCATACGAAATCCAACGAGATTGCGGATCGTGAGGCAATCGG
CCATTTG------CTGGGCAGGTGCGTGTCCCCATAAGTTTCCAATGGAGTGGGGTCATGCCCTAGTGGTATATTGTAAG
GGCAGCGTCCTACTCGTGGACACATAGTAAAAGGATAAATTGGAGTTCAGTGGCATTC-AAAGTGTACACTTTTGAACAT
GAAACCCTACTTATATCTTCCGATAAATAAAGATCTCTTTAGCGACTCATTTTCTTGTGCTTCACCCATGCATACCC-TT
GATCTAGAGACTAGAAAATGAATTCCACGACCAAACAGCTCCGCATATACGTGCTTAAACAGCCCAAAGTGGCAAAAGCC
CAACGTGATTATACTTTCTTTCCCA--GACCAACGTGCTTATACTTTGCAGAACTAAAGCTTCCGTAAATAATTCAGTAT
TT-GGGGGCAAAGCATTGCCATCTTTGCATGGCC-TACGTGTAAATCCAACCAGCGCTCGTGATTAACAACTCAAAATCT
CATAATTAATTATACGGCTAATTAGCGCACGACTGCACGTGATGCCCCCTCCCTCTGCACCACCGTCAACACGCAGGCAA
CGTACGTGAACGACGTAGCACGATCGAT------------CTTCTGTTTTGGGTCGTGTCACTGAACGGATTCCTCTTGC
GGTCAGCGCCGATTGCGGTGGATTCCCCGCGGTAGTTTGTTTGGCTAAGATCAGATCACACGTACAGTAGTACTTATCCG
ATTCTGGGGTCCTTTCCTCTGGCGCGGATCTGTTTCCTCTGCGGAACAAACGTA---TCAGAGGATGTGGAAACGAACTA
CAACAACAACAAACTTCTTGGGCTTGGACTGCACCCAGTACGACTACTGCTCACGCTCATATGCGGAGATCTGGCACG--
-TACTAGGTAGGCACGTGCCGTCACAACTCACAACA-----------ACACGCGGCGAC-TTGATCCCACGGGCGCACCG
ATGGTTGACTCCGGCGTGGCGATAGCTCTCGGCGTGGTCGGGCTCCTCGTGGCGGTGCTCGCGATCGCCTGGGCGGTGCG
GTGCGCCGTCGCCCGGCGGCGCACCGAGGAGGCGAAGCAGGC------CGTCGCCGTCGGCGCGGGGCTGCTGGACAAGG
AGGCCGTCGTCGTCGACGTCGAGGCCAAGTGCGAGGAGCCGCCGCTCTGCGCGATATGCAAGGGGCCGCTGGCGGCGGGC
GGGGGGAGGTGCCGGCGGCTGCGCGCGTGCGGCCACGTCTACCACGCCGAGTGCGTCGACCTGTGGCTCCAGCGGAAGCC
GATCTGCCCGCTGTGCCGGGCCGGCGTCGTGCTCTCGCGGACGGACATCGTTGACGCCATCGTGTGAGCCGTCTGTGCAG
GTCGTCGGTGCGGCGCGGCGCGGTGCACGGGCACGTGCGTGCGCTCTGCGCCGCCGTACGTCCTTCTGCAGTCCGCACAC
GCGGCCGTGTCCTCATCC------------GCGACCGTGCGTGCCTGCGTGCGTTGGGGAATTTTGCTCCTGACATAGGA
AGACAATACTGGTAGTAGTTTTGTGTATTCGGAGGGAGGAAGATACTGTATTTGTTTCGTTGGTTCGCTCGCTTGTACTC
AAGGATACGTGCAAGCACTTTTTGACAAGGATTTCTTTAGTGGTTTTTGACAAGCGTTATCTTACAGAAACACTAAAAAT
CT-----------------------------AGCATTTTTCATAGCAATTTATATCGGTGTGATGATGACCAATTTAGGT
TGCAAGCACCACAATTTTCTGTAAG-------------------------------------------------------
--------------------------AAAAAATGAATTGAGGCGGATTTGCCATGCTCATCATCTAAACTCGTCATCCTC
GAAGAACAAAGATTTAAATTGCTAGCTATATATGTGCTATAGGTTTTTGGGCACCATGCTACCCTTTATTTGGAAAAAAA
TAAGAATACATATTTGAAAGTTTCAGAAAAAATCGAAAACAGTTATGTGAAAACTTGTATGTATTCACTACAGATCCATG
AAA-TTTGTTTCAAAAAAATGTAATTTGTAAGTTGTACAAAAAAACAAAAATCTGGCCCAAAAACAAAAAAAAGTGGCCT
ATTTTGAAAATACATATTTGTCTTCTCTTTGAACAAAC-GTGTGAAAGTAAAATGTTGTGAAATTTTGCACATAAGTAGT
ATACATGTGTGTGCGTGTTTACAG-----GAAAAAACAATTATTTTGCG---CTTTAGAAAATGGTTTCTTTGAAACGGC
CACCGTGGTGCTCGTGCACAATTAGCAATTTTTGCAAATAGTTGTGCTATTTGGCATAGCTCGCTAGTAGTTATAACTAA
AGCTATTATTTTG-------------------------------------------------------------------
---------------------------------------------TAAGTGTGTATGGACCAATAATAGCTTGTAATCAT
TTGGACCTACAAATTTAATCCAAACGGCCAGTT-----------------------------------------------
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>SNPs
SSSS---------------------S------------------------------------------------------
--------S-----------S-----------------------------------------------------------
--------------S-------------------------------------------S---------------------
-----------------------------------------------------S--------------------------
---------------------------------------------------------------------S----------
-------------------------------------------------S-------------------S----------
-------------------------------------------------S---------------------S--------
--S---------------------S-------------------------------------------------------
-----------S--------------------------------------------------------------------
-------------------------S-S----------------------------------------------------
--S-----S-----------S-----------------------------------------------------------
-----------------------S--------------------------------------------------------
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--------------------S-----------------------------------------------------------
------------------------------------------SSSSSS--------------------------------
-------------------S------------------------------------------------------------
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------------------------------S--------------------------------------------S----
---S----S-------------------------------------------------------------------SS--
S--------------------------------------------------------------------------S----
---------------------------------------------------------------------S----------
----------S-S----------SSSS---------------S---S---------------------------------
-----------------------S------S----------------------------------------------SS-
SSSSS-SS---S---SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSS-----------S--SSSSS-----------------------------------
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--------------------------------------SSSS--S--SSSSSSSSS-S--S--S-SSS-SSS-SS-SSSS
SSSSSS-----------------------------------S------------------S---SS--------------
--------------------------------------S-------SSS-------------------------------
-----------------------------------S--------------------------------S-----------
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---------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_552
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----------------------------------------------------AGCGCTCGTGATTAACAACG--------
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>reverse_1899
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----------------------------------------------------------TCAATTATGAGCCCCGCCTC--
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