>input_sequence_54379
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---------------------------------------------------------------ATGGGCGAGGCCGACCA
CTACAGGACGCTGGGGCTCCGGCGAGATGCCAGCAAAGCCGAGGTCAAGGCCGCATTCTCCCGCCTCGCCCTCCTCCACC
ACCCCGACCGCCACGCCCAGGCCGACGCCGCCACCC---------------GCCGCTTCCGCCAGGTGTACGACGCCTAC
CACGTCCTCTACGATGACCACCGCCGCGCCGAGTATGACCTCCGCACCTCCTCGGCTTGGAGCGGCTTCGGTCACGGCGG
CGCCAAGTCCCGCTCCTCCTCGGCCTCGGGTGGCTACGGGCATGGCGGGGCCTCCTCTTCGCCTTCGGGTCGCTACGGGT
ACCCACACGGATGCGGCGGCGATTTTCAGGACTGGCCATCTCCGAGGGAAGGCGAAAGTCTGGGCGTTTGGATGAGAGCC
AATTGGCACCCCTTGCTCTGCTGGTAAGCACAAATTTCGCTGCTAAATCGGCGTCAAAGCTTTTGTTTCTTGTGGCATGA
CCACCCGTTCTAATTCCGGCGATATCGTCTAGTATCTGAAATGTGATTTCTCATGATCATAACTCTGCTGCAGCACCATG
AGGATCGCAAAAGTTGTAATAGATGGCTGGAAGCTGTATAATACCTGGGTAAGTAAACAACCCCTCAACCTCTAAATTAG
TCGATGGGTTTTGATTTCCCCTTAGTTAATCAATCAACTCCCTGTTCTCTTCGGCACATTTGGCTAACATGCATGCTTCA
GTCAATTCTTGCTCCCGTGGTATGTCTACTATTAAATGTAGTCTGCTAAATC----AGTACTAACTATTTTGGAATCATT
GGTCTGTGTGAGTATATGCCATATTGCCATGTGGATGGTAGTCAAGCAAATTGACATGCTGATTAGATTGTTAGTGAGTA
AGCTAATTAAATAAAAGAGTTAGTTAGAAACTGCAGAAGGTGTGCTACTCAAGCTGACAAAAGAGGGGTACAGGGGAATT
CGCTCGTTTCCTCATTGCATCCTCTCATTCTTGACTGATTGTTCGCTTTGTGAAATGGGAAGTATTGTGTTAGCAAGTTA
AAACACGCCAGCTCGATGTGCAATTCGGGATTACAAAATGCAGGTATCGATGTGATGTGCTGAAGTTCCCCTGCCCTATG
GATAAATGCAGCACTAAAATTGTATCCTGCCATTGCTGATGTTTTATTTTACTGATTGCTATTTGGATTGATATTCAGAT
TAAATGCAATGCATGAACTTGGTGTCTGCCTGTTTACTTGCAGAAATCATCAAGGGAGTCGTCAATAGAGAAGGAAGCAG
CGGAGTCTGAAGAGAAGATGAAGAATGAGCCCTCAGAAGAGAAAGAGTAG------------------------------
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>chr3D_1_TraesCS3D01G193500
AAATACTATCCGCTACTATATTGCTTCACCATTCCTTTTGGGAGGAAATCCCAACGCAACTCACAAGTAGCAGAAGCCTC
GGTGTAACATGAACAAGAAGCGCCGTAATAGAGGAAGCAGCAGCGACGCTGAGGAGACCGAGGTTAACGCCGACTTCAGC
AACCAGCGTGGCGTAACAAAAGGAAGCCTTTTCAAGGAGGCAAGGATGGACCGACACAGTTCGACAAGATTCGCGGGTCT
GCGGGCGGGGGCGGGGCGGTGTTGGCTGGGAGGGTCCTTGGCGGTCGGGTGGTAGCCGCGGCGATGGCGGACACGGCGGC
AACGACGAATCGGGC-----------AGCGGCAAATACAACAGACTCGCGGGGCTGCGGGCGGT--------GCAGTGGT
GGCTATGCGGGTGGTTGGCGGTCGGGTAGTTGTTGCGGTGACGGAGGACACGGCGGCGATGGAAAAACGGCTGATTCGTT
GCGTGCGGCGGCGGGCGGCGGGCGAAATCCGACGGAACCGGCAGCGGGGGTGCTGGAGGGG-CGGATCTGGCGCGGGGCG
ACGACGGCAGGGTGTGGGCGGGTGGGCGGGCGGCGAGAGGAAGAAGATGGGGTTGGGGAAATTAAGTGAAACGG-CGGTT
GACGGTTGGCGCGCGGTTGACGTTTT-ACATCTCTGTTGATGGAGATGTATGATTGCATCGTGAGATGTTGTATTTTACT
TCCTCCGTAAACTAATATAACAGTATTTTAATTATCTAAACGCTCTTATATTAGTTTATAGAGTATATCTTTAAAAGGTA
AAGACGTATTTTTTTTTCATCTACGTCATGTGTTGAAGAGGGGGTTTGGGGCGTCGAAAATGAAA-GTCTATTGAAGATG
CTCTAAACGTACCCGTTACCCCCACAAAGGAAAATTAATCAAAGTGAAAAATACAACAAGCCGCACCCTGACAGAACCGT
CGTCACAAACCCCCCGTCTCGATCTTGGAGAGAAGGAAAAGCCAGTTCGCTACCGCAGCCGTGATGGGCGAGGCCGACCA
CTACAGGACGCTGGGGCTCCGGCGAGATGCCAGCAAAGCCGAGGTCAAGGCCGCATTCTCCCGCCTCGCCCTCCTCCACC
ACCCCGACCGCCACGCCCAGGCCGACGCCGCCACCC---------------GCCGCTTCCGCCAGGTGTACGACGCCTAC
CACGTCCTCTACGATGACCACCGCCGCGCCGAGTATGACCTCCGCACCTCCTCGGCTTGGAGCGGCTTCGGTCACGGCGG
CGCCAAGTCCCGCTCCTCCTCGGCCTCGGGTGGCTACGGGCATGGCGGGGCCTCCTCTTCGCCTTCGGGTCGCTACGGGT
ACCCACACGGATGCGGCGGCGATTTTCAGGACTGGCCATCTCCGAGGGAAGGCGAAAGTCTGGGCGTTTGGATGAGAGCC
AATTGGCACCCCTTGCTCTGCTGGTAAGCACAAATTTCGCTGCTAAATCGGCGTCAAAGCTTTTGTTTCTTGTGGCATGA
CCACCCGTTCTAATTCCGGCGATATCGTCTAGTATCTGAAATGTGATTTCTCATGATCATAACTCTGCTGCAGCACCATG
AGGATCGCAAAAGTTGTAATAGATGGCTGGAAGCTGTATAATACCTGGGTAAGTAAACAACCCCTCAACCTCTAAATTAG
TCGATGGGTTTTGATTTCCCCTTAGTTAATCAATCAACTCCCTGTTCTCTTCGGCACATTTGGCTAACATGCATGCTTCA
GTCAATTCTTGCTCCCGTGGTATGTCTACTATTAAATGTAGTCTGCTAAATC----AGTACTAACTATTTTGGAATCATT
GGTCTGTGTGAGTATATGCCATATTGCCATGTGGATGGTAGTCAAGCAAATTGACATGCTGATTAGATTGTTAGTGAGTA
AGCTAATTAAATAAAAGAGTTAGTTAGAAACTGCAGAAGGTGTGCTACTCAAGCTGACAAAAGAGGGGTACAGGGGAATT
CGCTCGTTTCCTCATTGCATCCTCTCATTCTTGACTGATTGTTCGCTTTGTGAAATGGGAAGTATTGTGTTAGCAAGTTA
AAACACGCCAGCTCGATGTGCAATTCGGGATTACAAAATGCAGGTATCGATGTGATGTGCTGAAGTTCCCCTGCCCTATG
GATAAATGCAGCACTAAAATTGTATCCTGCCATTGCTGATGTTTTATTTTACTGATTGCTATTTGGATTGATATTCAGAT
TAAATGCAATGCATGAACTTGGTGTCTGCCTGTTTACTTGCAGAAATCATCAAGGGAGTCGTCAATAGAGAAGGAAGCAG
CGGAGTCTGAAGAGAAGATGAAGAATGAGCCCTCAGAAGAGAAAGAGTAGATGAACGGGGTTTCAGTCTGGCCCATGAGA
TGACCCACTGGCTACACATTCCAAGCCTAGTTCCACATTGTTGTGCAAGGTGTGAGGGAGCAACGCGTAAGGTGTAACTC
TTGCCATTCTCTGAAACTTGTGGCACATGGCATTAGAGATACTAGAATCCTTGTAAATTTTGTCTAA----CTAGATTCC
ACTGCGGAACACATGTTTTCCGTCTTGAAAGATTTGGAAATGTAAGCCATCCACCGCCCCTAAGATTGCACTGGGATTTT
GGTTTGTGTTCCAAGCGGTGTAAGATTACTGTCACTAGCTGCAGAAAGCAATGTACTCCCTTCGTCCCATAATATAGGAC
GTTTTTTGACACTAGTGTAGTGTCAAAAAACGTCTTACATTATGAGACGGAGGGAGTAGTATATAAATATATAATTGATG
TGACGCTCTCACTTTAGCCCATTAACACGTACACATAGTGAATAGATATTACATCTTCTAAAGATAAATAGTGGTATGGT
AAGAGAGACAAACAACTGTACTATTAAAGGGCAGTATGCCGTTGTAATGGTTACCACCTTCCCTCGCATCATTTTTCGCG
CGACTAAAAAAATCGGTTTTGCTAAAGCACATCGAAATCCCGTGTCATTGATTTACATGGAGATTCGTGTTTGTATTTCT
TTTACTTTTATCCGGGTATCTGTCATACTGCGGTTTTTTTGGTGTATCTAAAAAAGAGGCCCAGACTAAGATGAAAGAAA
CTGGGGGAGCACTCAGCCTCCTTGGACTCATCAATATGTTGTATATCCTTTAAACGAAGTTCAATCTATCTTCTGATTAT
TAGTGTTTTCAGTTAGGTGATTAGTCCTTCTACGGCCGCCACCGGCGGTGGCGGCTGGGCACATGTTACTTTTCTAGCAA
TCTTGTACCCTTATATCCGGTCGATGTCTGCCCATTACACATGACTCGAACGAAGCTCGCTCGTGGAGTAGATCAATTCG
TGGTTGAAGCACAC
>chr3B_1
AAATACTATCCGCTACTATATTGCTTCACCATTCCTTTTGGGGGAAAATCGCAACGCAGCTCACAAGTAGCAGAAACCTC
GGCGTAACATGAAAAACAAGCATCGTAATAGAGGAAGCAGTAGCGATGCCAAGGAGACCGAGGTTAACACCGGCTTCAGC
AACCAGCCTGGCGCAACAAAAGGAAGCCTTTTCAAGGAGGCAAGGATGGACCAACACAGTTGGACAAGATTCGCGGCGCT
GCGGGCGGGGGCAAGGCGATGGTGGCTGGGAGGGTCCTTGGCGGTCGGGTGGTAGCCACGGCCATGGCGGACACGACAGT
GGCGACGAATCGGGCGGCAGCGATGGAGCGGCAAATATAACAGACTCGCGGGGCTGTGGGCGGGGCGGCGGGGCAGTGGT
GGCTATGCGGGTGGTTGGCG-TCGGGTAGTGGTAGCGGCGACGGA------------------AAAACGACCGATTCGCG
GCGTGCTGCGGCGGGTGGCGGTTGAAACCCGATGGAACCGGCAACGGGGGTGCTGGAGGGGGCGGATCTGGCGCGCGGCG
ACAACGGTGGAGTGCGGGCGGGA--------GGCGGGATGAAG-AGATGGGGTTGGGAAAATTAAGTGAAACGG-TGGTT
GGCGATTGGCGCGCGGTTGACGTTTTTACATCTCTGTCGGTGGAGATGTATGTTTGCATTGTGAGTTG------------
-------------------------------------------------------TTATATTTTACATCTTTGGGAGGTA
GAGATGTAAAGAAAATTCATCTACGTCATGTGTTGAAGAGGGAATTTGGGGCTTCGAAAATGAAATGTCTATTGAAGATG
CTCTAAACGTACCCGTTACCCCCACAAAGGAAAATTAATCAAACTGAAAAA-----------------------------
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>chr3A_84
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---GTAACATGAACAACAAGCGCCGTAATAGAGGAAGTAGCAGCGACGTTGAGGAGATCGAGGTTAACGCTGGCTTCAGC
AACTAGCGCGGCGCAACAAAAGGAAGCCTTTTCAAGAAGGCGAGGGTGGACCAACACAATTGGACAAGATTCACGGTGCT
GCGGGCG------AGGCGGTGGTGGCTCGGATGGTCCTTGGCGGTCGGGTGGTAGCTGCGACGATGGCAGACACGACGGT
GGCGACGAATCGGGCGGCAACAGTGGAGCGGGAAATACAACAGACTCGCGGGGCCA------------CGGGGCGGTGGT
GGCTATGCGGGTGGTTGGCGGTCGGGTAGTGGTTGCGGCGACGGCGGACACGACGGTGACGAAAAACAATGGATTC----
-------GCGGCGGGCGGCTGTCGAAACCCGACGGAACCGGCAGCAGGGGTGCTGGAGGGGGCGGATCTGGCGCGCAGCG
ACAACAGCGGGGTGCGTGCGAGCGGGCGGGTGGCGGGAGGAAGAAGAT-GGGTTAGGGAAATTAAGAGAAACGGGCGGTT
CACGGTTGGTGCATGGTTGACGTTTTTACATCT-TGTCGGCGGAGATGCATGTTAGCATCTGAGATG-------------
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------------------------------------------TTTATTTTA-----------------------------
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>chr3B_896
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--------------------------------------TCAAACTGGAAAATACAACAAGCCGCACCCTGACAGAACCGT
CGTCACAAACCCCCCGTCTCGATCTTGGAGAGAAGGAAAAGCCAGTTGGCTACCGCAGCCGTGATGGGCGAGGCCGACCA
CTACAGGACGCTGGGGCTCCGGTGAGATGCCAGCAAAGCCGAGGTCAAGGCCGCATTCTCCCGCCTCGCCCTCCTCCACC
ACCCCGACCGCCACGCCCAGGCCGACGCCGCCACCCGCGCTGACGCCACCCGCCGCTTCCGCCAGGTGTACGACGCCTAC
CACGTCCTCTACGATGACCACCGCCGCGCCGAGTATGACCTCTGCACCTCCTCGGCTTGGAGCGGCTTCAGTCACGGCGG
CGCCAAGTCCCGCTCCTCCTCGGCCTCGGGTGGCTACGGGCATGGCGGGGCCTCCTCTTCGCCTTCGGGTCGCTACGGGT
ACCCACACGGACGCGGCGGCGATTTTCAGGACTGGCCATCTCCGAGGGAAGGCGAAAGTCTGGGCGTTTGGATGAGAGCC
AATTGGTACCCCTTGCTCTGCTGGTAAGCACAAATTTGGCTGCTAAATCGGCGTCAAAGCTTTTGTTTCTTGTGGCATGA
CCACCCGTTCTAATTCCGGCGATATCGTCTAGTATCTGAAATGTGATTTCTCATGATGACAACTCTGCTGCAGCACCATG
AGGATCGCAAAAGTTGTAATAGATGGCTGGAAGCTGTATAATACCTGGGTAAGTAAACAACCCCTCAACCTCTAAAATAG
TCGATGGGTTTTGATTTCCCCTTAGTTAATCAATCAACTCCCTGTTCTCTTGGACACATTTGGCTAACATGCATGCTTCA
ATCAATTCTTGCTCCCATTATATGTCTACTATTAAATGTAGTCTGCTAAAATCAGTAGTACTAACTATTTTGGAATCATT
GGTCTGTGTGAGTATATGCCATATTGCCATGTGGATGGTAGCCAAGCAAATTGACATGCTGATTAGATTGTTAGTGAGTA
AGCTAATTAAATAAAAGAGTTGGTTAGAAACTGCAGAAGGTGTGCTACTCAAGCTGACAAAAGAGGGGTGCAGGGGAATT
CGCTCGTTTCCTCATTGCATCCCCTCATTCTTGACTAATTGTTCGCTTTGTGAAATGGGAAGCATTGTGTTAGCAAGTTA
AAACACGCCAGCTCGATGTCCAATTCGGAATTACAAAATGCAGGTATCGATGC-----GCTGAAGTTCCCCTGCCCTATG
GATAAATGCAACACTAAAATTGTATCCTACCCTTGCTGATGTTTTATTTTACTGATTGCTATTTGGATTGATATTCAAAT
TAAATGCAATGCATGAACTTGGTGTGTGCCTGTTTACTTGCAGAAATCATCAAGGGAGTCGTCAATAGAGAAGGAAGCAG
CGGAGTCTGAAGAGAAGATGAAGAATGAGCCCTCAGAAGAGAAAGAGTAGATGAACGGGGTTTCAATCTGGCCCATGAGA
TGACCCACTGGCTACCCATTCCAAGCCTAGTTCCACATTATTGTGCAAGGTGTGAGGGAGCAATGCATAAGGTGTAACTC
TTGCCATTCTCTGAAACTTGTGGCACATGGCATTATAGATACTAGAATCCTTGTAAATTTTGTCTAACTAACTAGATTCC
ACCGCGGAACACATGT----------------------AATGTAAGCCATCCACCGCCCCTAAGGTTGCACTGGGATTTT
GGTTTGTGTTCCAAGCGGTGTAAGATTACTGTCACTAGCTGCAGAAAGCAATGTATTCCCTTTGTTCCTAAATAT-----
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>SNPs
------------------------------------------S-S-----S-------S----------------S----
--S-------------S-------------------------------------------------------S-------
-------------S--------------------------------------S--------S--------------SS--
------------SS-------S-----------------------------------------------------S---S
SS------------------------------------------------------S------S----------------
------------------------------S-------S-------------S---S--S-S-------S-S------SS
------S--------------S-----S-----------------------------------------------S----
--S-----S-----S-------S-------S----S--------------------------------------------
-------------------------------------S-S------------S------------S--SSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----SSS--S------SSS-----
S---S---SSSSSSS---------------------------SS--------S---------------------------
-------------------------------------------S------------------------------------
-----------------------------------------------S--------------------------------
----------------------S---------------------------------------------------------
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------------------------------------------S--------------------------S----------
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-----------S--------------------------------------------------------------------
------S------------------------------S------------------------------------------
---------------------------------------------------------S-S--------------------
----------------------------------------------------------------------------S---
---------------------------------------------------S-S--------------------------
S---------------S-SS------------------------------SS----------------------------
-----------------------------------------S--------------------------------------
---------------------S-----------------------------------------------S----------
----------------------S-------------S-------------------------S-----------------
-------------------S--------S-----------------------SSSSSS----------------------
----------S-----------------S--S---------------------------------------------S--
-------------------------S------------------------------------------------------
-----------------------------------------------------------------S--------------
---------------S-----------------------S-----------------------S--S-------------
-----------------------------------S--------------------------------------------
--S-------------SSSSSSSSSSSSSSSSSSSSSS--------------------------S---------------
-------------------------------------------------------S------S--S--SS-----SSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSS
>forward_83
---------------------------------------------------------------CAAGTAGCAGAAGCCTC
GGT-----------------------------------------------------------------------------
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>reverse_1990
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---------------------------------------------------------------------ACAGGGGAATT
CGCTCGTTT-----------------------------------------------------------------------
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>forward_222
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------------------------------------------AGGATGGACCGACACAGTTC------------------
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>reverse_2135
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------------------------------------------------------ATGTGCTGAAGTTCCCCTGC------
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>forward_237
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---------------------------------------------------------AGTTCGACAAGATTCGCGGG---
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>reverse_2136
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-------------------------------------------------------TGTGCTGAAGTTCCCCTGC------
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>forward_1780
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GTCAATTCTTGCTCCCGTGG------------------------------------------------------------
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>reverse_2986
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-------------------------AGCACATCGAAATCCCGTGT-----------------------------------
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