>input_sequence_68040
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---------------------------------------------------------------------ATGGCGCTCAA
CTACATGGGCGCCGCGGCCATCAACGCGGTGGCGGCCCTGCTGTCCATCCCGGTGATCGCGGCCGGCATCTGGCTCTCCA
CGCAGGCCGACAACGCCTGCGTCCAGATCCTCCAGTGGCCACTCGTCGGCCTCGGCGTCGCCGTCCTCGCCGTCGGCCTC
GCGGGCTTCATCGGCGCCTTCTGGCGCCTGCCCTGGCTCCTCCTCGCCTACATGGTCCTCATGCTCCTCCTCGTCGCCGC
GCTCGCCTGCCTCGCCGTCTTCGTCTTCGTCGCCACCACCGGCACCTCCGGCCGCCCCGTGCCCAGCCGCGCCTTTCTAG
AGTACGACCTGGCCGACTACTCCGGCTGGCTGCGCCGCCGCGTCGCCGACGAGCCGGGGAGGTGGGACGAGATCAAGACG
TGCCTGGCCGCCACCGCGCCCGTCTGCTCCGAGCTCAACCAGACGTACGCCGCGCCGCAGGACTTCTTCGCCGCCTGGCT
CTCCCCGATGCAGTCCGGCTGCTGCAAGCCGCCGACGAGGTGCGGCTACACCTTCGTCAGCGCGACCAACTGGATCAGCC
CGATCGACGGCGCCGCCGACCCCGACTGCGCTGCCTGGAGCAACGACCAGGACCGGCTCTGCTACTCCTGCGACTCCTGC
AAGGCCGGCCTACTGCAGAATCTCCGCCGGGAGTGGCGCCGCGCGGACGTCGTCCTCGCCGTCACCGTCGTTGCCCTCCT
TGCAGTCTACGCCATGGGCTGCTACGCGTTCCGCACCGCCAGGACGGACGAGCTCTTCCGCCGCTACCGGCAGGGCTACA
CGTGA---------------------------------------------------------------------------
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>chr4D_1_TraesCS4D01G272000
GAACAATTTTTAAAATTTGTGAACATTTTTTTAAAACAGGAACATTTTTTGAACATTGTCAAAAAATTCAAAA--AGAAA
CATTCAAACATTTTTTTTGTTAAACAAGAACAATTTTTT-AAAATTCCAGAACAATTTTCGAAGATTTCAAAAATGCGAA
CAATTTTTTGAAAAAGAA-----------ATTT--TTTGAATTTGTGAACAATTTTTG--------------------AG
GATTTCAAAAATGCGAT---TTTTTTTAAAAAGGAACA-TTGTTGAATTTATGAACATTTTTTTAAAACATGAACAT--T
TTTTGAAATTTTGATCTTTTTTAAAAACAGGAACA-TTTTTTGAAATTTTCAACAATTTA-GAAAGATGTTTTTTT--AA
AATAAACTTGAAAAATAAAATAAACGAAAAAGCAAAAAAAAGTAGAAAACAGA----------------AAAAAAAAGAA
ACATAAAAGCAGAAAAAGAAGAAAAGAT-AAAACGAAAAACAAAAAAACCCAAGAAGAAACAAGAAATCTGATCAAAAAG
AAAAAA-AGGTCCAGGGAACCTTCTAGAAGGTTCCCGAAACCGGGATACTGTAGCACGGTAATCCATCAGTAGTGGGCCG
GCCCATGTCGCTCGCTCGCTCCTCTTCCCTGTGCGTTCCTTCGACAATTTGCGGCAATAAGCGTCAAATAGGATATTCCG
GAATGAACTGCCAATGAAGCAAAGAATACCCAGCTATGAAGTGCAGCATGCATATATGCTCCATGCACGCGCATACATT-
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-----------------------------------CCATCTAGGAGTACACATGCTATCTGATGCATGGTGTGCGCTGCT
ATCCTTTTTTTGTTTGTTACTTTACCTAAAGTGAG--AAAAGCAGCAGAAAGAAAATTAATTTAAGGCATAGTCGTTGGA
AGGAAGGAAGGAAGGATTTGCTACCACCGGCACCAGCACGTATCGCATCACAGCTTTGGCCGGCAGGCGGTGCAAGAGCT
AAGCCCCATATAGCGAGATCAGAATCAGACGAGAGGCCGGCTAG-------GTCGTCTGCTCCGGCGAAATGGCGCTCAA
CTACATGGGCGCCGCGGCCATCAACGCGGTGGCGGCCCTGCTGTCCATCCCGGTGATCGCGGCCGGCATCTGGCTCTCCA
CGCAGGCCGACAACGCCTGCGTCCAGATCCTCCAGTGGCCACTCGTCGGCCTCGGCGTCGCCGTCCTCGCCGTCGGCCTC
GCGGGCTTCATCGGCGCCTTCTGGCGCCTGCCCTGGCTCCTCCTCGCCTACATGGTCCTCATGCTCCTCCTCGTCGCCGC
GCTCGCCTGCCTCGCCGTCTTCGTCTTCGTCGCCACCACCGGCACCTCCGGCCGCCCCGTGCCCAGCCGCGCCTTTCTAG
AGTACGACCTGGCCGACTACTCCGGCTGGCTGCGCCGCCGCGTCGCCGACGAGCCGGGGAGGTGGGACGAGATCAAGACG
TGCCTGGCCGCCACCGCGCCCGTCTGCTCCGAGCTCAACCAGACGTACGCCGCGCCGCAGGACTTCTTCGCCGCCTGGCT
CTCCCCGATGCAGTCCGGCTGCTGCAAGCCGCCGACGAGGTGCGGCTACACCTTCGTCAGCGCGACCAACTGGATCAGCC
CGATCGACGGCGCCGCCGACCCCGACTGCGCTGCCTGGAGCAACGACCAGGACCGGCTCTGCTACTCCTGCGACTCCTGC
AAGGCCGGCCTACTGCAGAATCTCCGCCGGGAGTGGCGCCGCGCGGACGTCGTCCTCGCCGTCACCGTCGTTGCCCTCCT
TGCAGTCTACGCCATGGGCTGCTACGCGTTCCGCACCGCCAGGACGGACGAGCTCTTCCGCCGCTACCGGCAGGGCTACA
CGTGATTTAATTTATTTCTGGATCCAGCGTGTCACATTTCCTGAAAATTTACATACATTTGTAAGATGCACCCAATGTGT
ATGAGACTATGAGTTTGTCCGGCAGATTTTCAGAAATCATTACCAATCTAAAGCTAAGCCAAAGTGTATCTGTGTCGAAA
ACCGAAAATAGTGTGCTTTTTTTAACACAGTACAATTAAAGTTGCTCACATATACGAGTATGCACTCACGCCCCTGAACG
CACGCGCACCCACACACTACCCCTATGAGCATCTCCGAGAGACTGAGTTGGAATAGCGTCTTGAGATTCTACACCATAGA
CGCCTCGCAGTCAACGATAACGTCTTCTCCAACTGAACAAACATCGCCAAAAGTCTGAAATAAATCCAGAAATAACGCGA
GCACCAATGTCAAATCTAAGACTTGAACCCTGTTGGGCTAGGAATACAACTGTCCTTCTAACCATTCAACCACAGGTTGG
TTCACAAAAAAAAATTACAACATGTTTGACTACTCTGGGGAAAGGGAATGAAAAATAGAAAATTTATAGTGGGGATTTTT
TGCTCAATACAAAAGTTCAAATTGAAGCATCTATAATCGCATCAACTGAGTTTCATTTTACAATAACCACAATTTCCTTA
GCAAATTGTCACCCCGAAGAAGAAAATGTATGAGAGGGCCTCT---AAAACGCCCCAGGTCCTGCCCTACAGAGTCAGAT
GACACAAATCTCGGATACCCCAATGAGGTCGAGACTGTCCAAACTTTATCGGTCAGAACTGTAGCTGGAGGACCAAGTAG
GACAGCAAGACCGAGACAAACATGGAAAAGAAAACGCCGGACTCGGAGAATCAGACCTGTTTCACAGCCTTCCGACATTA
CGAGGAAGCATCTCCGAATCCGGGCAAGGCAGAGAGACCTTATTCCACGCCCGGCGGCACCATCATCTCGCTGCCAGTGA
ATGGAGACATATCCTAAATTTATTTCTAACCCTACCACTATCAGGATA
>chr1A_1
GAACAATTTTTTTAATTTGTGAACAATTTTTTAACGCAGGAATATTTTTTGAACATTGTAAAAAATTTGAAAA--A-AAA
CATTCAAACATTTTTTGTAATACAAGAGA---ATTTTTCTAAAATTCCAGAACAATTTTCGAAGATTTCAAAAATGCGAA
CAATTTTAGAATATTTTAAAAATGCGAACATTT--TTTAAATTTGTGAACAATTTTCAAAAAATGTGAACAATTTTCGTG
GATTTCACAAATGCAAACAAATTTTTTAAAAAGGAACACTTTTTGAATTTATGAAAAGAAATTTAAAACACGGACAT--T
TTTTAAAATTTTGAATTGTTTCCAAAACAGGAACA-TTTTTTGAAATTT-CAACAACTTTCGGAAGATGGTCTTC-AAAA
AATAAACTTGAAAAAGAAAATAAACGAAAAAGCAAAAAAAC--AGAAAACAGGAAAAAAAATAAGAAAGAAGAAAAAGAA
ACAGAAAAGCGGAAGACGAAGAAAAGAAAAAAACAAAAAACAAAAAACAA-------AAAAAGGAAAACTGGCCAAAAAG
AAAAATGCGATTCAGGGA-------AGAAGGTTCCCAAAACCGGGATACAGTAGCACGGTAATCCACCAGTAGTGGGCCG
GCCCATGTCGCTCGCTCGCTAATGTTCCCTGTGCGTTCCTTCGACAATTTGCCGCAATTAGCGTCAAATAGTATATTCCC
GAA-----------------------------------------------------------------------------
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>chr4D_20
-------------------TGAACAATTTTTTAAAACAGGAACATTTTCTGAACATTGTCAAAAATTTGAAAAGAA-AAT
CATTCAATTTTTTTTGTAAAAATAAGAAC---ATTTTTG-AAAATTCCAGAACAATTTTAGAAGATTTCAAAAATGCGAA
TAATATTTTACAAAAGAA-----------ACATACTTTGAATTTGTGAACAATTTTCAAAAATTGTGAACAATTTTTTAA
GATTTAAAAAATGCGAACAATTATTTTAAAAAGGAAAAAAAATTGAATTTATGAAAA-------AAAACACGAACATTGT
TTTTAAAATTTTGAACTTTTTCCAAAACAGGAACAATTTTTTAAAATTT-CAACAATTTTCGAAAGATGCTCTTTAAAAA
AATAAACTTGAAAAATAAAATAAACGGAAAAGAAAAAA-AC--AGAAAACAGAAAAAAAATTAAGAAAGAAGAAAAAGAA
ACAGAACAGCGGAAAAAGAAGAAAATGAAAAAACGAAAAACAAAAAAACCCAAGAAGAAACAGGAAAACCGGTTAAAAAG
AAAAAA-CGGTTCAGGGAACCTTCTAGAAGGTTCCCAAAACCGGAATACTGTAGCACGGTAATCCACCAGTAGTGGGCCG
GCCCATGTCGCTCGCTTGCTCCTGTTCCCTGTGCGTTCCTTGGACAATTTGCCGCAATTAGCGTCAAATAGGATATTCCG
G-------------------------------------------------------------------------------
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>chr4A_656
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-------------------------------------------------------------------------------G
GAATGAACTGCCAATGAAGCAAAGAATACCCAGCTATGAAGTGCAGCGTGCATATATGCTCCATGCACGCGCATACATT-
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-----------------------------------CCATCTAGGAGTACA--AGCTATCTGATGCATGGTG--CGCTGCC
ATCCTCCTTTTTTTTGTTACTTTTACTTAAAGCGAAAAAAAGCAGCAGAAAGAAATTTAATCTAAGCCATAGTCGTT---
-GGAAGGAAGGAAGGACTTGCTACCACCGGCACCGGCACGTATCGCATCACAGCTTTGGCCGGCCGGCGGTGCAAGAGCT
AAGCCCCATATAGCGAGATCAGG------CGAGAGGCCGGCTAGCTAGGTCGTCGTCTGCCCCGGCGAAATGGCGCTCAA
CTACATGGGCGCCGCGGCCATCAACGCGGTGGCGGCCCTGCTGTCCATCCCGGTGATCGCGGCCGGCATCTGGCTCTCCA
CGCAGGCCGACAACGCCTGCGTCCAGATCCTCCAGTGGCCGCTCATCGGCCTCGGCGTCGCCGTCCTCGCCGTCGGCCTC
GCGGGCTTCGTCGGCGCCTTCTGGCGCCTGCCCTGGCTCCTCCTCGCCTACATGGTCCTCATGCTGCTCCTCGTCGCCGC
GCTCGCCTGCCTCGCCGTCTTCGTCTTCGTCGCCACCACCGGCACCTCCGGCCGCCCCGTGCCCAGCCGCGCCTTCCTCG
AGTACGACCTCGCCGACTACTCCGGCTGGCTGCGCCGCCGCGTCGCCGACGAGCCGGGGAGGTGGGACGAGATCAAGACG
TGCCTGGCCGCCACCGCGCCCGTCTGCTCCGAGCTCAACCAGACGTACGCCGCGCCGCAGGACTTCTTCGCCGCCTGGCT
CACCCCGATGCAGTCCGGCTGCTGCAAGCCGCCGACGAGGTGCGGCTACACCTTCGTCAGCGCGACCAACTGGATCAGCC
CGATCGACGGCGCCGCCGACCCCGACTGCGCCGCCTGGAGCAACGACCAGGACCGGCTCTGCTACTCCTGCGACTCATGC
AAGGCCGGGCTGCTGCAGAACCTCCGCCGGGAGTGGCGCCGCGCGGACGTCGTCCTCGCCGTGACCGTCGTCGCCCTCCT
TGCGGTCTACGCCATGGGCTGCTACGCGTTCCGCACCGCCAGGACGGACGAGCTCTTCCGCCGCTACCGGCAGGGCTACA
CGTAATTTAATTTATTTCTGGATCCAGCGTGTCACATTTCCTGAAAATTTACATACATTTGTAAGATGCA-------TGT
ATGAGACTATGAGTTTGTCAACCAGATTTTCAGAATTC------------------------------------------
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>chr4B_656
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-------------------------------------------------------------------------------G
GAATGAACTGCCAATGAAGCAAAGAATACCCAGCTATGAAGTGCAGCATGCATATATGCTCCATGCACGCGCATACATTC
CATTCCATCTAGATGCTCCATGCACGCGCATACATTCCATTCCATCTAGATGCTCCATGCACGCGCATACATTCCATTCC
ATCTAGATGCTCCATGCACGCGCATACATTCCATTCCATCTAGGAGTACA--TGCTATCTGATGCATGGTG--CGCTGAT
ATCCTTCTTTTGTT----ACTTTACTTAAAGTGAA--AAAAGCAGCAGAAAGAAAATTAATTTAAGGCATAGTCGTTGGA
AGGAAGGAAGGAAGGATTTGCTACCACCGGCACCAGCACGTATCGCATCACAGCTTTGGCCGGCCGGCGGTGCAAGAGCT
AAGCCCCATATAGCGAGATCAAG------CGAGAGGCCGGCTAG-------GTCGTCTGCTCCGGCGAAATGGCGCTCAA
CTACATGGGCGCCGCGGCCATCAACGCGGTGGCGGCCCTTCTGTCCATCCCGGTGATCGCGGCCGGCATCTGGCTCTCCA
CGCAGGCCGACAACGCCTGCGTCCAGATCCTCCAGTGGCCGCTCATCGGCCTCGGCGTCGCCGTCCTCGCCATCGGCCTC
GCGGGCTTCATCGGCGCCTTCTGGCGCCTGCCCTGGCTCCTCCTGGCCTACATGGTCCTCATGCTCCTCCTCGTCGCCGC
GCTCGCCTGCCTCGCCGTCTTCATCTTCGTTGCCACCACCGGCTCCAACGTCCGCCCCGTGCCCAGCCGCGCCTTCCTCG
AGTACGACCTTGCCGACTACTCCGGCTGGCTGCGCCGCCGCGTCGCCGACGAGCCAGGGAGGTGGGACGAGATCAGGACG
TGCCTGGCCGCCACCGCGCCCGTCTGCTCCGAGCTCAACCAGACGTACGCCGCGCCGCAGGACTTCTTCGCCGCCTGGCT
CACCCCGATGCAGTCCGGCTGTTGCAAGCCGCCGACGAGGTGCGGCTACACCTTCGTCAGCGCAACCTTCTGGATCAGCC
CGATCGACGGCGCTGCCGACCCCGACTGCGCTGCCTGGAGCAACGACCAGGACAGGCTCTGCTACTCCTGCGACTCCTGC
AAGGCCGGCCTACTGCAGAATCTCCGCAGGGAGTGGCGCCGCGCGGACGTCGTCCTCGCCGTTACCGTCGTTGCCCTCCT
TGCAGTCTACGCCATGGGCTGCTACGCGTTCCGCACCGCCAGGACGGACGAGCTCTTCCGCCGCTACCGGCAGGGCTACA
CGTAATTTAATTTATTTCTGGATCCAGCGTGTCACATTTCCTGAAAATTTACATACATTTGTAAGATGCACCCATTGTGT
ATGAGACTATGAGTTTGTCCGGCAG------AGAAACCGTTACCAATCTAAAGCTAAGCGAAAAGTG---TGTGCCGAAA
ACCGAAAATAAAATTGCTGGCATACCGATATCCTTCT-------------------------------------------
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----------------------------------------------------------TAACCATCCAACCACAAGTTAG
TTCATAAAAA----TTACAACATGTTTGACTACTCTAGGGAAAGGGAATGAAAA-TAGAAAATATATAAGAGGGATTTTT
CGCTCAATACAAAAGTTCAAATTGAAGCA-CTACAATCGCATCAGCTGAGTGTCATTTTATAATAACCACGATTTTCTTA
GGAAATCGTCACCCCGAGGAAGAAAATGTACGAGAGGGCCTCTAAAAAAACGCCCCAGAACCTGCCCTACAGAGTTAGAG
AACACAAATCTCAGATACCCCGATGAGGCCGAGACTATCCAAACTTTGTCGGCCAGAACTCTAGTTGGAGGACATA-TAG
GACAGTAGGGTCGAGACAAACATGCACAAGAAAACGCCGGCCTCGAAGAATCAGACCTGTTTCTCAACCTTCCAACATTA
CGAGGAAGCATCTCCGAATCTGGGCAAGGCAGAGAGACCTTATTCCATGCCCAATGGCACCATCACCTCGCCACCACTGA
ATGGAGACAGATCCTAAATTTATTTCTAACCCTACTACTA--------
>SNPs
-----------SS------------S---------------------------------------S--S-------S---
------------------SS--S-SS---SSS------S-----------------------------------------
---------S----------------------------------------------SS----------------------
----------------S------------------------S-------------S-SSSS---------S---------
----S---------S------SS--------------------------S---------S---------S-S---S----
----------------------------------------SSS----------------------------S--------
---S------S----------------S----------------------------------S----S---S--------
-------S---S------------------------S-----------------------------S-------------
-----------------------S----------------------------S-----S---------------------
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--------------------------------------------------SS-------------------SS-------
------S---------------------------S---------------------------------------------
----------------------------------------------------------------S---------------
----------------------SSSSSSS---------------------------------------------------
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----------------------------------------S---S-----------------------------------
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---------------------------------------------------------------------------S--S-
----------S---------------------------------------------------------------------
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-S------------------------------------------------------------------------------
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--------------------------------------------------------------S-----------------
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---S----------------------------------------------------------------------S-----
--------------------------------------S--------------------S---SSSSSSS----S-----
----------SSS-SSS-SSSS--S-SSSS-S-SSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-------S--------S---S-
----S-----SSSS----------------------S-----------------S--------S----SSS---------
S----------------------------S---S----------S------S--------S---------S----S----
-S----S----------S------------S---------------------------SS---------------S---S
S-----------S--------S------S-------S----------S----S-------S---S--------SS-S---
-----S-S-SS-------------S-S-------------S----S-----------------S--S------S------
--------------------S--------------------------S----SSS----------S-----SS---S---
---------S-------------------------S----SSSSSSSS
>forward_967
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-------------------------------------------------------------------GGTGTGCGCTGCT
ATCCTTT-------------------------------------------------------------------------
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>reverse_2396
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---------------------------------------------------------------------------CGCGA
GCACCAATGTCAAAT-----------------------------------------------------------------
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