>input_sequence_80291
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-------------------------------------------------------------------------------A
TGCCCGCCTCCATGCCCAAGCTGCTCTTCCTCCTC---CTCCTCCTCCTCGCCGCGGCCGCCCACTCTTCACCGGTAAGC
CTTCCTCTTCCTCTTGTC-------CCGCCCAATTCCGCGAATCTTGGCCCTGACATTGCCT-GTCTGCTCTACGCGCGC
GCAGGAGGTGCCGGATGCGGCGGGAGCGGGGTCCGAGCAGGCGGCGGTGCGCATGGTGCCGATGGCCCCGGCTGGGGGGT
------CGGGGTTCAGCGGGGTGGTGCTGAACGAGACGCGGCGGCGGCTGGGGAGCTTCCAGCTCTGCGCGCCCTGCACC
TGCTGCGGCGGGCCCAGGGGCGTCTGCGTCCTCTCCCCGTGCTGCTACGCCATCAACTGCAACATCCCCAACCGCCCCTT
CGGATTCTGCTCCTTCACGCCCAGGTCATGCGACTGCCTCCACTGCAACGTCTGA-------------------------
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>chr3B_1_TraesCS3B01G458700
AAGTTTTGTGAGGCAACCGGCCGTCCCCCCAACGACCCAG-GTTAAATGCGGGGGGCGATGATGATGATAAGGCGCCGAA
CCTGGTCCAACCACTTTTCTTGTTGCGGGGGTGTCGCATAAATGCCTGCCCCAAATTGTGGTGGCAACCGAATTGCCCTC
CATCTCACGATCGTCGGTCTCATCCACCTTCTCTTTTGTAAGTAGTAGCAGTGGAATCGCCTCCATCTCACGATCGTCGG
TCTCATCCACCTTCGCTTTTGTAAGTAGTAGCAGTGGAATCGTCCTAACCATACGGCACTTCCTCTCAAAGCTGCCGCAC
AAATTTCATTCTTCTTCTTGACCCTTGTGATAATGATCTACTAGACAGTACTACAATTTT-CCAAACAGAAGAAGCCTGA
TTTTTATTTCCTGACTGATGATCCGGTGCCCGTCCGTCCGCCCGTCCAGGTTTAACAACAGTGTCAATTTGTCCTAGGCT
CTTGCAAGATCGATCTCCCTGTAACAAACAGGATTGAAAACAGAATCATCATCTGCCGACGACGCGAGCACCGCCAGCCA
TCCCAGTGACCC----ATCAGCCTCGTCCACATCGAGATCCTATTCCTAGGCAGGCGGATCAGGAGCAATTATCATAGGC
ACTC----------GAAGATCTCGAGTGA----GTATGAACGCGCCGAAGTCGACGGAGGGCGCGTGATTTCAACACGGG
CCGGCACCGGCACATCATGTGCGTATTATTTACTACTG------------------------------------------
--------------------------------------------------------------------------------
--------------------------CCACTCGTGTTTTC---------TACCAGCGTCCACTCGGTGCGGCGCCCACCC
GGCGGGCGAC-GGGGTGACGACGGGCGTGACGGCAGCCACCGAGTGTAC-----TACCGTAGCCTCTGCCTTTCTACGAG
-----ACGAGATCTCGCCA------TCCATCCCAAGT----CGTCCGTCGTCGGCTACTGCCACTTCCCCCGAAGAGGAC
CTCACTCCCCACCCCAGCCCAGCCCTCCCCGCCCGCTGCACAGTCCAAATCCCCGCTCCGGC-CGGCGACCGACCGAGGA
TGCCCGCCTCCATGCCCAAGCTGCTCTTCCTCCTC---CTCCTCCTCCTCGCCGCGGCCGCCCACTCTTCACCGGTAAGC
CTTCCTCTTCCTCTTGTC-------CCGCCCAATTCCGCGAATCTTGGCCCTGACATTGCCT-GTCTGCTCTACGCGCGC
GCAGGAGGTGCCGGATGCGGCGGGAGCGGGGTCCGAGCAGGCGGCGGTGCGCATGGTGCCGATGGCCCCGGCTGGGGGGT
------CGGGGTTCAGCGGGGTGGTGCTGAACGAGACGCGGCGGCGGCTGGGGAGCTTCCAGCTCTGCGCGCCCTGCACC
TGCTGCGGCGGGCCCAGGGGCGTCTGCGTCCTCTCCCCGTGCTGCTACGCCATCAACTGCAACATCCCCAACCGCCCCTT
CGGATTCTGCTCCTTCACGCCCAGGTCATGCGACTGCCTCCACTGCAACGTCTGAGCTCTGCTGCCGAGTGTGATGA---
---------AT---GAGGGTAATGTTGAGAGCGATAGTAAGTA-------TTTTAGAGTGATGAGGGTGGGGGAAAAAAC
GACATGATAGCATGAGAGTTCCCCCAACCCGAATGCTTGCCGATTTGTTATT-GTTTTAGCCCTATAGCCATTTTGCTAC
CGAATTGTTATTAAGTATATGGTGTAGCTGCTACCTCTCGATGGA----ATTGGTTGGTTATTAGCAAAGAGTTGGTGAA
TTGGAGA---------------------------CATTGCTCTGTTTCCTCTCATGGTTGCGTGATTCGTCGCGTGCTTT
CTCTTGATATATAGATTAGTTAATAGCGCGGAGATTCAGTACCTTCCCTTTAAATGCTCGGTAC-----CTCTTGTGTCT
CTATCTATTTCCAATGATTCAGTAAAACTGAACTGCACAGGGCATTTAGAAGGCTGTGTTCTTCTTCTTCTTCATAGTCG
AACCATTTATACATGCCTGCAGATATTCTTATTA-----ATTAGTGTGCGTTGTGTTGGATCGATCCACTCTATGCAACT
CCTCTT-AGCACCTTCTGAAGATCTATTGCTTCACAATTTTGTTACGCAAAGTGTCATGGGTTCAGTACTATGTACATCT
GTCACCGTAGCCTTGATTTATTTTGTGGCAATTTTAGAACTGTAGAAGTTGACCTTTTTTTTGT-----------GTAGT
TTAACACATTGTCTGCTCCTTTACTGACCTTTAAGGAAGCCTAGTTGGGCTCCAGCTTTTGTGAATTCAGTAGGCAGCAT
CCTATATTTAGGCTAAAAAAAGCCTTGCAGTTGTTTTAATAGAACTTGAAGTTTTCATGA---CAAACACTGGTTGTTTA
TTATCAGACATTCATTCTACTGCACACAGTTTAGTTATTATCTACTCCCTCTGTCCCAAAATATAAGACACTTTTTGATG
CTATCACAGTCTCAAAAAACGTCTTACATTTCGGGACGGAGGGAGTAAAGAACACGCTATTTCACTAACTTATAGTTTCA
CCTTTTAGATTTGT
>chr3D_1
AAGTTTTGTGAGGCAACCGGCCGTCCCCCCAACGACCCAG-GTTTAATGTGGGGGGTGATGATGATGATAAGGCGCCGAA
CCTGGTCCAACCACTTTTCTTGTTGCGGGGGTGTCGCATAAATGCCTGCCCCAAATTGTGGTGGCAACCGAATTGCCCTC
GATCTCACGATCGTCG-TCTCATCCACCTTCTCTCTCTTTGG---TAACAGT----------------------------
---------------------------------GTGGAATCGTCCCAACCATAGGGCACTTCCTCTCAAAGCCGCCGCAC
AAATTTTATTCTCCTTCTTGACACTTGTGATGATGAT---CTAGATAGTAC---AGTACCACCTAATCGAAGAAGCTTGA
TTTTCAATTCCTGACTGACGATCCGGTGTCCGTCTCTCCGTCCGTCCAGGTTTAACAACAGTGTCAATTTGTCCTGGCCT
CTTGCAA----GACCTCCCTGTAACAAACAGGATCGAAAACAGAATCATCATCTGCCGACGACGCGAGCACCGCC----A
TCCCAGTGACCC----GTCAGCCTCGTCCACATCGAGATCCTAGGCAA---------GATCAGCAGCAATTATCATGGGC
ATAGGCATGGGAAGGAAGATCTCGAGTGCGCGGGTATGAACGCGCCAAAGTCGATGGGGGGCGCGCGATTTCAACACGGG
------CCGGCACATCATGTGCGTATTATTTACTG---------------------------------------------
--------------------------------------------------------------------------------
--------------------------CCACTCCTGTATCCTGGTTTCTATACTAGCGTCCACCCGGTGCGGTGCCCACCC
GACGGCCGAGGGGGGTGACGACGGGCGTGACGGCAGCCAGCCGGTGAGCGAGCGTACCGTAGCCTCTGCCTTTCTACGAG
-----ACGAGATCTCGCCCTCCGGTTCCATCCCAAGTCGTCCGTCCGTCGTCGGCTACTGCCACTTCCCCCGAAAAGGAC
CTCACTCCCCAGCCCAGCCCACCCCTCCCCGCCCGCTGCACAGTCCAAATCCCCGCTCCGGCCCGGCGACCGACCGAGGA
TGCCCGCCTCCATGCCCAAGCTGCTCTTCCTCCTGCTGCTCCTCCTCCTCGCCGCGGCCGCCCACTCTTCACCGGTAAGC
GCCTACACCTCCTGTCCTGCTTGCGCCGCCCAATTCCGCGAATCTTGGCCCTGACATTGCCTTGCCTGCTCTCGGCGCGC
GCAGGTCGTCCCGGATGCGGCGGGCGAGGGGTCCGACCAGGCGGCGGTGCGCATGGTGCCGATGGCCCCGGCTGGGGGGT
------CGGGGTTCAGCGGGGTGGTGCTGAACGAGACGCGGCGGCGGCTGGGGAGCTTCCAGCTCTGCGCGCCCTGCACC
TGCTGCGGCGGGCCCAGGGGCGCCTGCGTCCTCTCCCCGTGCTGCTACGCTATCAACTGCAACATCCCCAACCGCCCATT
CGGATTCTGCTCCTTCACGCCCAGGTCTTGCGACTGCCTCCACTGCAACGTCTGAGCTCTGCTTCTGCTCTGCCCTGCTC
TCGAGGGTGAT---GAGGGCAATGTTGAGGGCGATAGTAAGTA-------TTTTAGAGTGTGGGT-----GGGGAAAAAG
GACATGACAGCATGAGAGTTCCCCCAACCCGAATGCTTGCCGATTTGTTATT-GTTTTAGCCCTATAGCCATTTTGCTAC
CGAATTGTTATTAAGTATATGGTGTAGCTGCTACCTCTTGATGGATGGAATTGGTTGGTTAGCA--AAAGAGTGGTTGAT
TTGGAGACTGGTTACTTCTGGGGTTGCCTTGTGGCATTGCTCTGTTTCCTCTCATGGATGCGTGATTCGTCGCGTGCTTT
CTCTTGATAGATAGATTAGTTAATAGTGCGGAGTTTCAGTACCTTTCCTTCGAATGCT-GGTATCTATTCTCTTGTGTCT
CCATCTCATTCCACTGATTCAGTAAAACTGAACTGCACAGAACATTTAGAAGGCTGTGTTCTTC---------ATAGTCG
AAGCATTTATACATGCCTGCAGATGTTATTATTTGTTAGTGTGCGTT--GTTGTGTTGGATCGATCCACTCTATTCAACT
CCTCTTTAGCACCTTCTGAAGATTTATTGCTTCACAATTTTGTTACGCAAAGTGTCATGGGTTCAGTACTATGTACATCT
GTCACCGTAGCCTTGATTTATTTTGTGGCAATTTCACAACTCTAGAAGTTGACCTGTTC-----------TTTTGGTAGT
TTAACACATTGACTGCTCCTTTACCAACCTTTAAGGAAGCCTAGTTGGGCTCCAGCTTTTGTGAATTCAGTAGGCAGCAT
CCTTTATTTAGGCTAAAAAAGG-CTTGCAGTGGTTTTAATGGAACGTGAAGTTTTCATTA---CACTGTTTTA-----TA
TTGTCAAACATTCATTCTACTACACACAATTCATTTATATCTA-------------------------------------
--------------------------------------------------------------------------------
--------------
>chr3A_1
AAGTTTTGTGAGGCAACCGGGCGTCCTCCCAACGACCCCGAGTTTAATGTGGGGGCCGATGATGATGATAAGGCGCCGAA
CATGGTCCAACCACTTTTCTTGTTGCGGGGGTGTCGCATAAATGCCTGCCCCAAATTGTGGTGGCAACCGAATTGCCCTC
CATCTCACGATCGTCG-CCTCATCCACCTTCTCTCTCTTTGGTAGTAACAGT----------------------------
---------------------------------GCGGAATCGTCCTAACCATAGGGCGCTTCCTCCCAAAGCTGCCGCAC
AAATTTTATCATTCTTCTTGACACCTGTGATGATGAT---CTAGACAGTACTACAGTACCACCAAACGGAAGAGGCTTGA
TTTTTAATTACTGATTGATGATCCGGTG--------TCCGTCCGTCCAGGTTTGACAACAGTGTCAGTTTGTCCTAGGCT
CCTGCAA----GATCTCCCTGTAACAAACAGGATTGGAAACAGAATCATGATCTGCCGACGACGCGAGCACCGCC----A
TCCCAATGACCCATCCATCAGCCTCGTCCACATCGAGATCCTAGTCCTAGGCAGGCGGATCAGGAGCAATTATCATAGGC
ATGGGCATAGGCT----GATCTCGAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNCCACTCCTGTTT-------------------TCTACCAGCGGCGGCGCCCACCC
GGCGGGCGA-GGGGGTGACGACGGGCGTGACGGCAGCCAGCCGGTGAGCGAGCGTACCGTAGCCTCTGCCTTTCTACGAG
CGAAGACGAGATCTCGCCCTCCGGTTCCATCCCAAGTCGTCCGTCCGTCGTCGGCTACTGCCACTCCCCCCGAAAAGGAC
CTCACTCCCCACCCCAGC-----CCTCCCCGCCCGCTGCACAGTCCAAATCCCCGCTCCGGCCGC-CGACCGACCGAGGA
TGCCCGCCTCCATGCCCAAGCTGCTCTTCCTCCTG---CTCCTCCTCCTCGCCTCGGCCGCCCACTCCTCGCCGGTAAGC
CTTCCTCTTCCTCTTCTC-------CCGCCCAATTCCGCGAATCTTGGCCCTCACATTGCCT-GCCCCCTCTACGCGCGC
GCAGGTCGTCCCGGCTGCGTCCGACCAGGCG---GAGCAGTCGGCGGTGCGCATGGTGCCGATGGCCCCGGCGGGCGGGG
ACGGGGCGGGGTTCAGCGGGGTGGTGCTGAACGAGACGCGGCGGCGGCTGGGGAGCTTCCAGCTCTGCGCGCCCTGCACC
TGCTGCGGCGGGCCCAGGGGCGTCTGCGTCCTCTCCCCGTGCTGCTACGCCATCAACTGCAACATCCCCAACCGCCCCTT
CGGGTTCTGCTCCTTCACGCCCAGGTCCTGCGACTGCCTCCACTGCAACGTCTGAGCTCTGCTTCTGCTCTGCTCTGCTC
TCGAGTGTCACGAGGAGGGCAATGTTGAGGGCGATAGTAAGTACTACGTATTTTAGAGTGGTGAGGGTGGGGGAAAAAAG
GACATGACAGCAT--GAGTTCCCCCAGCCCGAATGCTTGCCGATTTGTTATTTGTTTTAGCCCTATAGCCATTTTGCTAC
CGAATTGTTATTAAGTATATGGTGTAGCTGCTACCTCTCGATGGATGGAATTGGTTGGTTATTAGCAAAGAGTGGGTGAT
TTGGAGA---------------------------CATTGCTCTGTTTCCTCTCATGGATGCGTGATTCGTCGCGTGCTTT
CTACT----GATAGATTAGTTAATAGTGCGGAGATTCGGTACCTTTCCTTTGAATGCT-GGTAT-----CTCTTGTGCCT
CCATCTCTTTCCACTGATTCAGTAAAACTGAACTGCACAGGACATTTAGAAGGCTGTGTTCTTC---------ATAGTTG
AACCATTTAGACATGCCTGCAGATATTATTATTTACAGTATTAGTGTGCGTTGTGTTGGATCGATCCACTCTATGCAACT
CCTC-TTAGCACCTTCTGAAGATTTATTGCTTCACAATTTTGTTACGCAAAGTGTCATGGGTTCAGTACTATGTACATCT
GTCACCGTAGCCTTGATTTATTTTGTGGCAATTTTAGAACTGTAGAAGTTGACCTGTTTTTTTTCTTTCTTTTTGGTAGT
TTAACACATTGTCTGCTCCTTTACTAACCTTTAAGGAAGCCTAGTTGGGCTCCAGCTTTTGTGAATTCAGTAGGCAGCAT
CCTTTATTTAGGCTAAAAAAAGCCTTGCAGTCGTTTTAATGGAACATAAAGTTTTTTTTATCACAAACACTGGTTTTC-A
TTATCAAGCATTCATTCTACTACACACAAGTCAGTTAT------------------------------------------
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>SNPs
--------------------------------------------S----S------------------------------
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----------------S-----------------S-SS-SS------S----SSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------------------S--------------------------
------S---------------S--------S-----SSS---------------S-SSS-------S--------S---
------S---------------------S-----SS----S---------------------------------------
-------SSSS----------------------------------------------------------------SSSS-
-------------------------------------------S------------------------------------
-SSS------------------------S-----------------S-------S--S-------S--------------
SSSSSS----------------------------SSSS------------------------------------------
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--------------------------------S-----S-------------S---------S-----------------
---------S-----------------------------S-SS---SS--------------------------------
------------------S-------------------------------------------------------S-----
---------------------S----------------------------------------------------------
----------------------------------S---------------------------------------------
---------------S------------------------------------------------S---------------
-----SS--S--------------S-S-----------------------------------------------------
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---------------------------S-----------------------------------S-S-SSSSSSSSSS---
-------------------S---------S------------------------------S------------------S
-------S------------------------------------------------------------------------
-------------------------------------------------------------------------S-----S
---------------------------------------------------------S----------------------
---------S----------------S------------------S-----S------S----S----------------
-S----S------S---------------------------S----------------------SSSSSSSSS-------
---------------------------S-----S----------------------------------------------
-----------------------S--------------------------------------------------------
-------------------------------------------------------S------S-----------------
-------------------------S------------------------------------------------------
---S---------------------------S--------S----S------------S----------------S-S--
------S--------------S------S--S------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSS
>forward_251
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-----------------------------------------------------------------------GATCGTCGG
TCTCATCCACC---------------------------------------------------------------------
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>reverse_1664
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---------------------------------------------------------------GCCGAGTGTGATGAATG
AGG-----------------------------------------------------------------------------
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