>input_sequence_64023
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--------------------------------------------------------------------ATGGCAGCAT--
---CTCACCCCTCTCGAAGCAGTGTCTGCTTAGCCCTGGCTGTTGCCATTTGCATCTTGCTCCCAGGCTGCTTCTCCAGT
AAGTATACATCTAATTCATTTCTTGTTTCATTTT--------------------------CTCGGGAAATTTAGATCAAA
CTCCCACTTGATCTGGACCTCCTTTCTTCCGTTGATTGTTGCAGGCAAAGTTACCCTGGAGATTTTCGAGAGGGCATGCC
ACTGCTTCGACGACCACAATGTAAGTCATCTCGAAGCGCAAACATACCGGGGTTACTAAATCTCAGTCGACTGAGATTTA
ACGTAGTCGCAGTTCATGCTATATTCGTGAGACCTTACGTGGAGATCCGTGTAAAATTTCCTTTTAATTTTTTTATTTCT
TCCTTTTTATATGTTGTGTCATTTGACTGGTTAAGTCTTGATCGATTGAGATCTAGCCACACCTTAGACATATGTGTTTG
TGAAAGTGACGACGTACGTACATATATGGTGTTTGAAACTGCCTGTGGGCCGAAAACTTTGAAGGTGTACAACGAGTGCG
CGGAGGAGCTCCGGCTGGGCGTGGAGGGGGCGTTCCACGTGGGGCGGGAGAGCGTGGACGAGTACTGCGGCGGGGCCTGC
CTCGCCGAGACGGAGATGGCGCTGCGCTGCGTGGAGGAGGTCGCCCACGACGGCTTCAGGTTCTCCAACGGCGCCTCGCT
GCTGGCCGTGAAGCAGGCGCTCGGCAGCGGCTGCAGCTACACGCCGGAGAGAGGAACCTTCGACATACGTGAGCGCAGGG
AGTGCGGCGACGAGTACGGGTACGGCTACCACGGCGC---------------------GCTCGGCTACGGCGAGGAAGGC
GGCGACCGGCGGTACGAGTACCCGGGCGGCGCGTTCGGCAACTACTGCTCCGGCGCCACCGGCGGCGGCGCGGTGCAGAC
GCTCCTCCTCGCCTTCCTCCTTGTCTCCGCGTCGGCGCTGCTTCTTGCCGCATGA-------------------------
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>chr1D_1_TraesCS1D01G227600
GCCTTCTCAGAATTACAGGTATTGCAGTAGGCAGAGGAGCTGGGATTTTCTTCCCATGTAAGAAATCCTGTTAGAGGGTC
CT------TGATTATAGCGATCAAGTAAATAAATCGATAAAAAATAGGCAGAGCCGTTTAGTGATTTGATACAATTTTGT
TATTTTGCGAAGATTAAGTTGATCACATGAAAAGCATA---CGTTTTACGAGATGAGCAAGTAGGCTTTTGGATATTGGC
AGTGGTTGGCTACAGAATCGGCAAAAGTTACACAGCACCTAGAGAAGCTGGCGTAACAAGTGAAAAAATGTTATCGTGCA
AGACAGCACTTGGACAAAGA-TTGGTTTGCCCGGCGGGCAGAATTGGCAAAAGTTGGGAGTCCTGCAGAGAGAGGAGGTC
AGATTAGAGTAGCAATATCAAATGCAGACTTGTTACGCATGGACCTGTTGTTTTTCCTCCGGCGCATATCAAAAGCTGAG
ATGAAACTTGA-TGCCGGTGAAGTGCTTTTCTG--------ATAGAAACTGTTGGTGG-TGCACACCTTACGAAAGTGCA
CCTAGAGGAGTCGAAATATTCTCACGAACTCTTGACATATACCAATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
CTCTCTCTCTCTCTCTCTCTCTCTCTTTATAACAAGGATAAGAGAATTTACAGATTCTGTGTTGATGTTATTCCGTGTTA
TGCCACCAGCGCCGCCTAGGTCAGACTTCAAGTGTCAGAATTTCTTTTCAGATCTTCGCAAAAAAAAAATCT-TTGCAGA
AAGTTGGACCGTGAGCATTTCTTGTGGGCAAACTTAGCAAAGAGTGAGCAATTGACCGTCCAT----TGGAGTAATGGTA
GGGCAAGGCAGGGAACGTTCTCTGCTCAGACGGGCAAGAAATTAAACCCGTATATATAGTCAATCAACCG---CCCCGGA
TGAAAACGATCAGATACGACGGCACTGGCGTAAAACACATCTGCTCAACTGTTAGCCCGTGTATTACAATGGCAGCAT--
---CTCACCCCTCTCGAAGCAGTGTCTGCTTAGCCCTGGCTGTTGCCATTTGCATCTTGCTCCCAGGCTGCTTCTCCAGT
AAGTATACATCTAATTCATTTCTTGTTTCATTTT--------------------------CTCGGGAAATTTAGATCAAA
CTCCCACTTGATCTGGACCTCCTTTCTTCCGTTGATTGTTGCAGGCAAAGTTACCCTGGAGATTTTCGAGAGGGCATGCC
ACTGCTTCGACGACCACAATGTAAGTCATCTCGAAGCGCAAACATACCGGGGTTACTAAATCTCAGTCGACTGAGATTTA
ACGTAGTCGCAGTTCATGCTATATTCGTGAGACCTTACGTGGAGATCCGTGTAAAATTTCCTTTTAATTTTTTTATTTCT
TCCTTTTTATATGTTGTGTCATTTGACTGGTTAAGTCTTGATCGATTGAGATCTAGCCACACCTTAGACATATGTGTTTG
TGAAAGTGACGACGTACGTACATATATGGTGTTTGAAACTGCCTGTGGGCCGAAAACTTTGAAGGTGTACAACGAGTGCG
CGGAGGAGCTCCGGCTGGGCGTGGAGGGGGCGTTCCACGTGGGGCGGGAGAGCGTGGACGAGTACTGCGGCGGGGCCTGC
CTCGCCGAGACGGAGATGGCGCTGCGCTGCGTGGAGGAGGTCGCCCACGACGGCTTCAGGTTCTCCAACGGCGCCTCGCT
GCTGGCCGTGAAGCAGGCGCTCGGCAGCGGCTGCAGCTACACGCCGGAGAGAGGAACCTTCGACATACGTGAGCGCAGGG
AGTGCGGCGACGAGTACGGGTACGGCTACCACGGCGC---------------------GCTCGGCTACGGCGAGGAAGGC
GGCGACCGGCGGTACGAGTACCCGGGCGGCGCGTTCGGCAACTACTGCTCCGGCGCCACCGGCGGCGGCGCGGTGCAGAC
GCTCCTCCTCGCCTTCCTCCTTGTCTCCGCGTCGGCGCTGCTTCTTGCCGCATGAGCGATGGTGATCTTACGATGTACT-
--GTATTTGTAATGATTTTGGTTTCAGGTTGAGTTTTATCCCATGA-----TCCGCATATTGTAATTCTCCCTTCTTATT
TTTGCACGATGCACCTGCGCATGGTATTCTCTCACAGGGCAAGGAATAACTAAAAAAAGAGTACTTACTTTGATCT-TAA
AAACAAGGATATCTCCATGACTGAGATTTACCTAGCAAACAAAAATCCTCCAAAAATGTTCATTTGCACCAAGCCCTTTT
CCTGACGAGAGAATTTGACAGGATATA-------------GTTCAATTCACTCAAGAGTAGGAGAAAACAGAATTGGAAT
GCCATCACGTGTAGAACGAAAATGCTAGAGCTACATGTGGAATGCTGAACAGACCCTCGCAAAAAAAAAGAAAAAAAAAG
AGAGAAAAGAATGCTGAACAGACGTGCCGCAAGAATTTGCAGCAAAGTGTGTTTAGACTTTGGAGGCTTCACTAAAAAG-
TACTCCCTCTATATAA-CTTAATATAAGACG---TGTTTTGACACTGTCAATCTGT---GGACTCTAAAAACATCTTATA
AAAAGTTACAGAGGTAGTAGAATTAATATTCAACGTGTACATGCTTGTTACTGAGAAGCAAAAGGAAG-GAAAATCCTCT
AAATATGAAGATAGTTTTCGCATCCTACAGGTACCTTTAAAGCAAATCATACAATCAAAACACCTTTAGGTCCATCTAAT
TGTTTTTAAAAACAAAGATTCATTTTCCTACTGGAGCGCAGAAACATCAACCATATGCGCGGACCAACTCAAACAGGGCT
AATATTGCTTTCTCACTAAAAAAAAGAGGCTAAATATTGCTTACAACCAATTGGACCTCTACACATGAGCACAGCTACGG
CCCTATAGAAATTTCACAAGAAAAAGATGATACAGAGTATTTCCCGTAGAAACCATTTTAGATCATAGAGATGGTGCTAC
CAAATTCTTATAGGTTGTTTTCCCATCCCCCCATTTTCTAGAACAG
>chr1A_1
GCCTTCCCAGAATTACAGGTATTGCAGTAGGCAGAGGAACTGGGATTTTCTTCCCATGTAAGAAACCCTGTTAGAGGGTC
ATTGATTATGATTATAGCGATCAACTAAATAAATCGGTAAAAA-TAGATAGAGCCATTTAGTGATTTAATACATTTTTGT
TATTTTGTGAAGATTAAGTTGGTCACATGAAAAGCATA---CGTTTTACAAGATGAGCAAGTAGGCTTCTGGATATTGGC
AGTGGTTGGCTACAGAATCGGCAAAAGTTACACAGCACATAGAGAAGCTGGCGTAACAAGTGACAAAATCTTATCGTGCA
AGACAGCACTTGGACAAAGA-TTGGTTTGCCCGGCGGGCAGAATTGGCAAAAGTTGGCAGTCCTGCAAAGAGAGGAGGTC
AGGTTAGAGTAGCAAACGCAAACTTGTTCC-----TGCATGCACCTCTTGTTTTTCCTCCGGCGCATATCTAAAGCTGAG
ATGAAACTTTAGTGCCGGTGAAATATTT---TACTAATATAATAGAAACTGTTGGTGGGTGCACACCTTGAGAAAGTGCA
TCTCGAGGAGTACAAATATTTGTAAAAAGAAAA-----------------------------------------------
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------------------------------------AGAATTCCTTTTCAAATCTCCGCCGAAAACAAAAACACTGCAGA
AAGTTGGGCCATGAGCATTTCTTGTGGGCAAACGTAGCAAAGAGTGAGCAATTGACCATCCTTTGGATGGAGTAATGGAA
GGGCAAGGCAG--------------------------GAAATTAACCCCGTATATATAGCCAATCAACCCACACCCCAGA
TGTAAACGATCAGAGACGACGGCACTGGCGTAAAACATATTTGCTCTGCTCAGCACACCTTCCGCGGGCAATGGCAATGC
CTCCTCACCCTTGTCGCGCCAGTGGCTGCTTGGCACTGGCCGTTGCCATCTGCATCCTGTTGCCAGGCTGCTTCTCTAGT
GAGTGTATATCTATCTCTTG------TTTTATTTTCACCATCAAATTTTAAAAAATCAGTCTCGGGAAAACTAGTTCAAC
TTTTCTG----------------TTTTCTCCATG---GTTGCAGGCAAAATTGCCCTGGAGATCTTCGAGAGGGCGTGCC
ACTGCTTCGACGACCACAATGTAAGTCATGTCGAAGCGTAAACATACCGGGGTTGCTAAATCTCAGTCGACTGAGACTTA
ATGAAGTCACAGTCGATGTTATATTCGTGAGATCTTACGTGGAGATCCATAT-----------------------TTTTT
TTCTTTTTATATGTTGTGCCATTTGACTGA-------------GACTGAGATCTGGCCCCACCCTAAACATACATGTTTG
TGAAAGTGACGACA----TACATATATGGTGTTTGAAACTGCCTCTGGGCCGAAAACTTTGAAGGTGTACAACGAGTGCG
CGGAGGAGCTTCGGCTGGGCGTGGAGGGGGCGTTCCACGTGGGGCGGGAGAGCGTGGACGAGTACTGCGGCGGGGCCTGC
CTCGCCGAGACGGAGATGGCGCTGCGCTGCGTGGAGGAGGTCGCCCACGACGGCTTCAGGTTCTCCAACGGCGCCTCGCT
GCTCGCCGTCAAGCAGGCGCTCGGCAGCGGCTGCAGCTACACGCCCGACAGAGGAACCTTCGACATACGCGAGCGCAGGG
AGTGCGGCGACGGGTACGGGTACGGCTACCACGGCTACGGCGAGCAGCAGCAGCAGCAGCTCGGCGACGGCGAGGAGGGC
GGCGACCGGCGGTACGAGTACCCGGGCGGCGCGTTCGGCAACTACTGCTCCGGCACCACCGGCGGCGGCCCGGTGCAGAC
GCTCCTCCTCGCCTTCTTCCTTGTCTCCGCGTCGGCACTGCTTCTTGCCGTATGAGCGATAGTGATCTTAGGAT------
--GTACTTGTAATGCTTTTGGTTTCAGGTTGAGTTATCTCATTATATATACTCCGCATATTGTAATTCTCCCTTCTTATT
TTTGCACGATGCACATGCGCGTGGTATTCTCTCACGGAACAAGGAAGAACTAAAACAAGAGTAC---CTTTGATCT-TAA
AAACAAGGATATCTTTATGACTGAGATTTACCTAACAAACAAAAATCCTCTA----------------------------
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------------------AAAATGCTAGAGCTACATGTGGAATGCTCA--------------------------------
----------------AAGAGACATGCCGCAACAATTTGCAGTAAAGTGTGTTTAGACTTTGGATGCTTCACTAAAAAAA
TACTCCCTCTATATAA-CTTAATATAAGACAGTTTTTTTTTACACTGTCAATCTGTCATGGGCTCTA-------------
-----------AGGTAGTAGAATTAATATTCAACTTTCACATGCTTGTTATTGAGAAGCAAATGGAAGAGAAAATCCTCT
ACATAGGAAGATAGTTTTCGCATCCTACAGCTACCTTTAAAGCAAATCATACAATCCAAACACCGTTATGTCCATCCAAT
TGCTTTTAAAAACAAAGATCCATTTTCCTACTGGAGCGCAAAAATATCCACCATGTGCGTGGACCAACTCAAACAGGGCT
AATAGCTACGGCCCTATAGA----------------------------AATTGGACCTCTACACATGACCACAGCTACGG
CCCTATAGAAATTTCACAAGAAAAAGATGATACAAAGTATTCCCCACAGAAACAATTTTAGATCATAGAGATGGTGCTAC
CAAATTCTTATAGGTTGTTTTTCCATCCCCCCATTCTCTAGAACAG
>chr1B_3
--CTTCCCAGAATTACAGGTATTGCAGTAAGCAGAGGAACTGGGATTTTATTCCCATGTAAGAAATCCTGTTAGAGGGTC
CT------TGATTACAGCGATCAACTAAACAAATCGGTAAAAA-TAGGCAGAGCCATTTAGTGATTTAATACATTTTTGT
TATTTTGCGAAGATTAAGTTGGTCACATGAAAAGCATAGTACGTTTTACGAGATGAGCAAGTAGGCTCTTGGATATTTGC
AGTGGTTGGCTTCAGAATCGGCAAAAGCTACACAGTTCC------AGCTCGCGTAACAAGTGACAAAATGTTATCGTGCA
AGACAGCACTTGGACAAAGATTTGGTTTGCCCGGCGGGCAGAATTGGCAAAAGTTGGGAGGCCTGCAAAGACAGGAGGTC
AGGTTAGAGTAGCAAACGCAAACTTGTTCC-----CGCATGCACCTCTTGTTTTTTCCCCTGTGCATATCTAAAGCTGAG
ATGAAACTTTAGTGCCGGTGAAATGTTTTACTACTAATATAATAGAAACTGTTGGTGG-TGTGCACCTTGAGAAAGTGCA
TCTAGAGGAGTCGAAATATTCGTTAAA--AAAA-----------------------------------------------
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------------------------------------AGAAATTCTTTTCAAATCTTCGCCAAAAACATAAACATTGCAGA
AAGTTAGACCGTGAGCATTTCTTGTGGGCAAACGTAGCAAAGAGTGAACAATTGACCGTCCTTTGGATGGAGTAATGGAA
GGGCAAGGCAG--------------------------GAAATTAACCCCGTATATATAGTCAATCAACACACACCCCGGA
TGTAAACGATCAGAGACGACGGCACCGGCGTAAAACATATCTGCTCTGCTCAGCGCACCTTCCGTGGGCAATGGCAATGT
CTCCTCACCCCTCTCGAACCATTGGCTGCTTGGCCCTGGCCGTTGCCATTTGCGCCCTGCTCCCAGGCTGCTTCTCCAGT
GAGTATATATCCATTTTATTTCTTGTTTCTATTTTCACCGTCAAATTTTGAAAAATCAGTCTCAACTCTC--------AA
GTCCCGCTTGATTTGGAGCTCCTTTTTCTCCATG---GTTGCAGGCAAAGTTGCCCTGGAGATCTTCGAGAGGGCGTGCC
ACTGCTTCGACGACCACAATGTAAGATTGTAAGCCATGATGGATGCAATATATAGTTAGTTCAATTCGATGTGTGGCATG
GTGTTGATAATGTCGTCTGTGGACCGAAA---------------------------------------------------
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----------------------------------------------------AAAACTTGGAAGGTGTACAACGAGTGCG
CGGAGGAGCTTCGGCTGGGCGTGGAGGGGGCGTTCCACGTGGGGCGGGAGAGCGTGGACGAGTACTGCGGCGGGGCCTGC
CTCGCCGAGACGGAGATGGCGCTGCGCTGCGTGGAGGAGGTCGCCCACGACGGCTTCAGGTTCTCCAACGGCGCCTCGCT
GCTGGCCGTGAAGCGGGCGCTCGGCAGCGGCTGCAGCTACACGCCGGATAGAGGAACCTTCGACATACGTGAGCGCAGGG
AGTGCGGCGACGAGTACGGGTACGGCTACCACGGCGC---------------------GCTAGGGTACGGCGAGGAGGGC
GGCGACCGGCGGTACGAGTACCCGGGCGGCGCGTTTGGCAACTACTGCTCCGGCGCCACCGGCGGCAGCGCGGTGCAGAC
GCTCATCCTCGCCTTCTTCCTTGTCTCCACGTCGGCACTGCTTCTTGCCGTATGAGCGATACTGATCTTACGTGTACTAG
TAGTATTTGTAATGATATTGGTTTCAGGTTGAGTTATACCATGATATATACTCCGCATATTGTAATTCTCCCTTCTTATT
TTTGCACGATGCACCGGCGCATGGTATTCTCTCACAAGGCAAGGAAGAGCTAAAACAAGAGTAC---TTTGATCTTATAA
AAACAAGGGTATCTTCATGACTGAGATTTACCTAGCAAACAAAAATCCTCTAAAAATGTTCATTTGCACCAAGCCCTTTT
TCTGACGCGAGAATTTCGCAGTAGACTGCTGAACAAAAATGTTCAATTCACTCAAGAGTAGGAAAAAACAGAATTGGAAT
GCCATCACGTGTGGAACAAAAATGCTAGAACTACATGTGGACTGCTGAATAGACCCTCGCAAAAAACGAAAAA-------
--AGAAAAGAATGCTGAACAGACGTGCCGCAAGAATTTGTAGCAAAGTGCGTTTAGACTTCGGGTGCTTCACTAAAAAG-
TACTCCCTCTATATAAACTTAATATAAGACG---TTTTTTGACACTGTCAATCTGTCATGGACTCTACAAACGTCTTATA
AAAAGTTACAGAGGTAGTAGAATTAATATTCAACATGTACATGCTTGTCACTGAGAAGCAAATGAAAGAGAAAATCCTCT
AAATATGAAGATAGTTTTCGCATCCTACAGGTACCTTTAAAGCAAATCATACAATC------------------------
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>SNPs
------S-------------------------------S-----------------------------------------
------------------------S-----------S------S-----------S-----------S-----S------
---------------------S----------------------------------------------------------
---------------------------------------------------------------S----------------
-------------------------------------------------------------------S------------
--S------------SSS----SSSSSS-SSSSSS------S----S-----------------------S---------
---------S------------S--S---S--S------------------------------------SS---------
S--------------------SS-SS--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------------S--------S-----S---SSS--------
---------------------------------S---------------------------S----------------S-
-----------SSSSSSSSSSSSSSSSSSSSSSSSSS--------S-----------------------S----------
--S-----------S----------------------S--------SS--SSSS--S-S-SSSS-SSSSSSSSSSS----
------------------S-----S------S--------S---------------S-----------------------
S------S-----S---------------SS--------------------------------------SS---S-----
S----S------S----S-------S-SS-SS--SSS---------------S----------S-----------S----
-----------------------------S--------S---------------S---------------------S---
-S------S----SS---S-------------S---------------S-S-SSSSSSSSSSSSSSSSSSSSSSS---S-
-S----------------S----------SSSSSSSSSSSSSS--S--------S---S----S--S-----SS------
-------------SSSSS--------------------------S-----------------------------------
----------S---------------------------------------------------------------------
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------------------------------------------------S-------------------------------
----------------------------------------------------------------------------S---
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----------------S-------------------S-------------S---------S-------------SSSSS-
-----------------------------------S----SSSSS-----------------------------------
----------------------------------------------S--------S--------SSS-------------
--------------S-----------------------------------S-----------------------------
S------S--------SS---S-S-SS------------------------------------S----------------
------------S----S-------------------------------S----------------SS-S---SSSSSSS
SS--------------------------------------------------------------S---------------
-----------------------------------S-------------------------------S----S-------
----------------------------------S---------------------------S-----------------
--------------------------------------------------------S-------S---S-------S---
--S----------------S--------------------S---S---S-----S----S--------------------
----SSSSSSS-S-SS--S-SSSSSSSSSSSSSSSSSSSSSSSSSSSS--------------------S-----------
----------------------------------S------S---SS------S--------------------------
---------------------S-------------S----------
>forward_903
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---CAAGGCAGGGAACGTTCTCT---------------------------------------------------------
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>reverse_2949
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--------------------------------------------------------------------GCACAGCTACGG
CCCTATAG------------------------------------------------------------------------
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