>input_sequence_75123
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------------------------------------------------------------------------------AT
GACGACACCGTCCCTCCTCTCCTCGCTCGCCACGCTCGGCCTCGGCTACTCCATCGCCATCGCGCTTGGCTTCCTCGTCC
TCCTCGCTTCCGTCCTGCTCGCCTCCTACTTCTGCTTCCGACACGGCGAGGGCGCGGGCGGCCACTTCGCCGGCGCCATC
ACGCCCACGTCCAGCTCCAGCCACCTCTCCATCACCGTGCCGCGCGTGCTGTTCGTCGCCGAGGGGTCCGAGTCCCCCGA
GGCCTACTCCTCGGCAGCCGCGGCCGCCTCGTCGCCAGTCGGGCTCGACCCGGCTGCCATCGCGTCGTATCCCAAGGCCC
CCTTCTCCGGGGCCGCGGGCGGCGACGCCATGTGTTCGATCTGCCTCTCCGAGTACATGGACGGCGAGATGCTACGGCTG
ATGCCCGAGTGCAGGCACAGGTTCCACGTCATGTGCCTCGACGCCTGGCTGCGCAGGAGCGCGTCGTGCCCCGTTTGCAG
GTCGTCCCCAATCCCCACGCCCGTCACCACGCCGCTCGCGACGCCACTCTCGGAGCTCGTCCCGCTCTCGCAATACGCCG
CTGACCGGCGGCGCAGCAGGTGA---------------------------------------------------------
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>chr3D_1_TraesCS3D01G279200
TAGGGGCACGTGCACGTAGACTTTTCAGTTGTCATCGACAAGATTAGGCTGACTCCGGTGTGAGAGCCGCGGCAACGGTG
CGTCGGCAGCTCGTTTTGGCGGCTGCCTGGTTGTTAGATAGTCCATGGACTTCAATGTATTTTTTATTACTTTTGAGGTG
CTTTGTTCGGTCGATGAATCTTTGTGTAAATCTGATCATTTAAAAAAA-------------AAACAATGGATCATGGAAA
AAATAAAGCATTTTACTTAGGTATCAATTTTGCATACAATTTGTCTAATTTACATCTAGATGTACGGATGTCACATTTAA
ACTCTCGCAATAAGGCAGTAACAAGAAACAAAAAAAAAGTTAGGATAAAAAAATAAACCATAAACATAGTGGATATCAGG
TTAGATGTGTGATATAGTTATGTCACATCTAGATGGGTGCAAGACAGACCTTTTGCATATCACCATCACCGGTGGATGGT
GCCTCAACTACAGGATATCTTCCAAGGAATTGACCCCGCTCTGAGTGGCATTGCTCACTAGCATGGCGCTCCG-AGGTCA
AAC-GAGTGACCTCCAACTCCAACATCC-------CATGCCGCAGCAC-TCCAGTACTGAGCACCGGCAGATAGCCCCCC
CTCCTACGCTGCCATGGCACGACGCTCCCGTCCTCTCCCTCCCGAAGTCATGACAGCGGAGCCGAGCAGAGCATCTCCAT
CCGCCGCCATTACTCCTCGGCCCGTGCCACTTCTCCGGCAATAAATGCAGCCGCTGGCGCCGTCCAGCCACCACCACCAG
ATCTAGCGCCCCCTCGCCGCGACGGGACGAGAAGGAAACGAAGAAAAATCACCACGCCACCATCCACATTTACTCCCACC
---------CCACCAGGACTCGACTCTAGCTAG------TCGCTCGATCGACCCACCCCATCCCCACCCCACACGCGCAC
GCCACCGATGCCATTCCTCCACTTCCCCGCTGCAAAATCATCTCGGCCGCCGCCGCCGCCGTTACCGCTACCGTCGCCAT
GACGACACCGTCCCTCCTCTCCTCGCTCGCCACGCTCGGCCTCGGCTACTCCATCGCCATCGCGCTTGGCTTCCTCGTCC
TCCTCGCTTCCGTCCTGCTCGCCTCCTACTTCTGCTTCCGACACGGCGAGGGCGCGGGCGGCCACTTCGCCGGCGCCATC
ACGCCCACGTCCAGCTCCAGCCACCTCTCCATCACCGTGCCGCGCGTGCTGTTCGTCGCCGAGGGGTCCGAGTCCCCCGA
GGCCTACTCCTCGGCAGCCGCGGCCGCCTCGTCGCCAGTCGGGCTCGACCCGGCTGCCATCGCGTCGTATCCCAAGGCCC
CCTTCTCCGGGGCCGCGGGCGGCGACGCCATGTGTTCGATCTGCCTCTCCGAGTACATGGACGGCGAGATGCTACGGCTG
ATGCCCGAGTGCAGGCACAGGTTCCACGTCATGTGCCTCGACGCCTGGCTGCGCAGGAGCGCGTCGTGCCCCGTTTGCAG
GTCGTCCCCAATCCCCACGCCCGTCACCACGCCGCTCGCGACGCCACTCTCGGAGCTCGTCCCGCTCTCGCAATACGCCG
CTGACCGGCGGCGCAGCAGGTGACGGATACTCTACATGGGTGCACCTCGCTGACGCTGCTCTTCATTGTTACTCCTCTTT
TTTTCTTTTTGCGTTG-------AAGGGTTCTGTAAATTTGTCGATTGTTTGATTGGTAAGGACACATGAGGAGTTTTAG
GTGCTAGTACGACTGGTGGTGTGCTTAGGATTTGTAAAGAGTTGCTTGGTTCCCATTACTATTACTTCGAGAAAATTTTG
TAATGTAGAAGTAGATGATGGGTTTCTTGAAAAAAATTTAGATGTTGGAGCAAGGCAT----------------------
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---------------------------------------------------------AGTTGTGAATACAGTGTTGCTGG
TTTGCCTTATCGTGAAATGTGTTATGATTAGTATTGGCTACTGCTACATAAGG---------------------------
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---------TTTACTTTGCATTTCATTTTTCTATTGTGATCATGATGTGGTCGCTTTGATTGTATGAACTAGATATCTTG
AAGATTTGTCTAGTGTTT------TCTGTCTCGTTGCAATGTTTTTATTTTCTTATCTTTTTTTTCAA------------
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--------------------------------------------ACAACTACTTCTAGCATGAAGAAACCCTTGCATGGC
TTCGTCTTCCATGGCCTTACCTCCATGGAGGCGT---GGTAGGCCCATGCCTT------CGGGAGGGCCCCTGTTTTGTT
TTTAGGTGTTCTTTTGTGTTTGTTTAGAGCATCTACACACAGTCAAAAAAGAGCGACCCAACTGGGCCCCCACTTCATCC
CTAAACGTCCGGATCGACGGGTGTACCTCAAACCCATCTCAAATCTAGAGACAATATGAGGGCGACCGGTCACACCCGGA
CGCTCCCGCTCTGACGTGGCGTACAAGAGCAAACCCCACCTGCAGCTTCACATTCATGTTTCTGTGCTGTGCATGCCCTC
TCCGTGAACCCGAGCTAGCCGCGCTGGTGCCGAAGCAGGCTGGCGTCGGGGAGGGAAGCCGTCCGAGCTAGGCGCGCTAG
TGACGGAGCACATCCGCGTCGGTGCCGGAGCTCGCCCGCGCCGCGCCGCGCTAGAGACCGAGCTCCCACAGCTCACCCGC
GTCGTGCCGCGCTGAA
>chr3A_1
TAGGGGCACGTGCTTGAAGATTTTTCAGTTGTCATCGGCAAGATTAGGCCGGCCCTGGTGTGAGAGCCGCGACAGCGGTG
CGTCGGTGGCTCGTTCTGGCGGCTGCCTAGTTGTTCGATAGTCCATGGACTTCAATGTAAATTTTATTACATCTGAGGTG
CTTTGTTTGTTTGATGAATCTTTATATAAATCTGATCATGTTTTAGAAAAAACAAACAAACAAACAATGGATCATGGAAA
AAATAAAGCATTTTACTTAGTATCAATG----------------------------------------------------
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----------------------------------------------------TTGCATATCACCATCACTGATCCATGGT
GCCTCAACGACAGGATATCTTCCAAGGAATTGACCCCGCTCTGAGTGGCATTGCTCACCAGCATGGCGCTCCAAAGGTCA
AACGGAGTGACCTCCAACTCCAACATCCAACATCCCATGCCGCAGCAC-TCCAGCAGTGAGCACAGGCAGATAGC-CCCC
CTCCCACGCTGCCATGCCACGACGCTCCCGTCCTCTCCCTCCCGAAGTCATGACAGCTGAGCCGAGCAGAGCATCTCCAT
CCGCCGCCATTACTCCTCGGCCCGTGCCACTTCTCCGGCAATAAATGCAGCCGCTGGCGCCGTCCACCCACCACCATCAG
ATCTAGCGCCCCCTCGCCGCGACGGGACGAGAAGGAAACGAAGAAAAATCACCACGCCACCATCCACATTTACTCCCTTC
CACCCCACTCCACCAGGACTCGACTCTAGCTAGAGCTAGTCGTTCGATCGACC-----------CACCCCACACGCGCAC
GCCACCGATGCCATTCCTCCACTTTCCCACTGCAAAATCATCTCGGCCGCCGCCGCCGCCGGTACCGCTACCCTCGCCAT
GACGACACCGTCCCTCCTCTCCTCGCTCGCCACGCTCGGCCTCGGCTACTCCATTGCCATCGCGCTTGGCTTCCTCGTCC
TCCTCGCCTCCGTCCTGCTCGCGTCCTACTTCTGCTTCCGACACGGCGAGGGCGCGGGCGGCCACTTCGCCGGCGCCATC
ACGCCCACGTCCAGCTCCAGCCACCCCTCCATCACCGTCCCGCGCGTGCTGTTCGTCGCCGAGGGGTCCGAGTCCCCCGA
GGCCTACTCCTCGGCAGCCGCGGCCGCCTCGTCGCCAGTCGGGCTCGACCTCGCTGCCATCGCGTCGTATCCCAAGGTCC
TCTTCTCCAGGGCCGCGGGCGGCGACGCCATGTGTTCGATCTGCCTGTCCGAGTACATGGACGGCGTGATGCTACGGCTG
ATGCCCGAGTGCAGGCACAGGTTCCACGTCATGTGCCTCGACGCCTGGCTGCGCAGGAGCGCGTCGTGCCCCGTTTGCAG
ATCGTCCCCCATCCCCACGCCAGTCACCACGCCGCTCGCGACGCCACTCTCGGAGCTCGTCCCGCTCTCGCAATACGCCG
CTGACCGGCGGCGCAGCAGGTGACGGATACTCTACATGGGTGCACCTCGC------TGATCTTCATTGTTACTCCTTTTT
TT------TTGCGTTG-------AAGGGTTCTGTAAATTTGTGGATTGTTTGATTGGTAAGGATACATGAGGGGTTTTAG
GTGCTAGTACGACTGATGGAGTGCTTAGGATTTGTAAAGAGTTGCTTGGTTCC-ATTACTATTACTTCGAGAAAATTTTG
TAATGTAGAAGTAG---ATGGGTTTCTCGAAAAAAAAGTAGATGTTGGAGCAAGGCATAGTTGTGAAGAGCAGTGCTATA
CGGACGATAAAACACAGACGATTCACGCACGACAGTGAAATCCAGCCACACATGCAGGTGTACAGGAGAGCAACGGCCGC
TGGATACTTAGTCGTCTTCACATCGTGTACGCTTTTATCGTGTGTAGAGCAGTTTCGAGTTGTGAATACAGTGTTGCTGG
TTTGCCTTATTGAGAAA--TGTTATGATTAGTATTGTCTACTGCTACATAAGG---------------------------
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---------TTTACTTTGCATTTCATTTTTCTATCGTGATCATGATGTGGTCGCTTTAATTGTATGAACTCTATATCTTG
AAGATTTGTCTAGTGTTT------TCTGTCTTGTTGCAATGTTTTTATTTTCA----TTTTTTTTCTA------------
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--------------------------------------------ATAACTACTTCTAGCATGAAGAAACCCTTGCATGGC
TTCGTCTTGCATGGCCTTTACAGGCGCTGTGGATCCCGGTGGATCCCGGTCCTTGCTGGTGGGAGGGCCCCTGTTTTGTT
TTTAGGTGTTTTTTTTGTTCGTTTAG------------------------------------------------------
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>chr3B_440
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----------------------------------------------------TTGCATATCACCATCACCGGCCCATGGT
GCCTCAGCGACAGGATATCTTCCAAGGAATTGACCCCGCTATGAGTGGCATTGCTCACCAGCATGGCGCTCCAAAGGTCA
AAC-GAGTGACCTCCAACTCCAACATCC-------CATGCCGCAGCACTTCCAGCAGTGAGCACAGGCAGATAGC-CCCC
CTCCCACGCTGCCATGCCGCGACGCTCCCGTCCTCTCCCTCCCGAAGTCATGACAGCGGAGCCGAGCAGAGCATCTCCAT
CAGCCGCCATTACTCCTCGGCCCGTGCCACTTCTCCGGCAATAAATGCAGCTGCTGGCGCCGTCCACCCACCACCA-CAG
ATCTAGCACCCCCTCGCCGCGACGGGACGAGAAGGAAACGAAGAAAAATCACCA-GCCACCATCCACATTTACTCCCTTC
CACCCCACCCCACAGGACTACTCT-----------CTAGTCGTTCGATCGACCCACCCCATCCCCACCCCACACGCGCAC
GCCACCGATGCCATTCCTCCACTTCCCCACTGCAAAATCGTATCG------GCCGCCGCCGTTACCGCTACCGTCGCCAT
GACAACACCGTCCCTCCTCTCCTCGCTCGCCACGCTCGGCCTCGGCTACTCCATCGCCATCGCGCTTGGCTTCCTCGTCC
TCCTCGCTTCCGTCCTGCTTGCGTCCTACTTCTGCTTCCGACACGGCGAGAGCGCGGGCGGCCACTTCGCCGGCGCCATC
ACGCCCACGTCCAGCTCCAGCCACCTGTCCATCACCGTGCCGCGCGTGCTGTTCGTCGCCGAGGGGTCCGAGTCCCCCGA
GGCCTACTCCTCGGCAGCCGCGGCCGCCTCGTCGCCAGTCGGGCTCGACCCCGCTGCCATCGCGTCGTATCCCAAGGCCC
CCTTCTCCAGGGCCGCGGGCGGCGACGCCATGTGTTCGATCTGCCTCTCCGAGTACATGGACGGCGAGATGCTACGGCTG
ATGCCCGAGTGCAGGCACAGGTTCCACGTCATGTGCCTCGACGCCTGGCTGCGCAGGAGCGCGTCGTGCCCCGTTTGCAG
ATCGTCCCCAATCCCCACGCCCGTCACCACGCCGCTCGCGACGCCACTCTAGGAGCTCGTCCCGCTCTCGCAATACGCCG
CTGACCGGCGGCGCAGCAGGTGACGGGTAGTCTACATGGGTGCACCTCGC------TGCTCTTCATTGTTACTCCTCTTT
TT------TCTTTTTGCGTTGAAAAGGGTTCTGTAAATTTGTCGATTGTATGATTGGTAAGGACACATAAGGAGTTTTAG
GTGCTAGTACGACTGGTGGTGTGCTTAGGATTTGTAAAGAGTTGCTTGGTTCCCATTACTATTACTTCGAGAAAATTTTG
TAATGTAGAAGTAGATGACGGGTTTCTCGAAAAAAAAGTAGATGTTGGAGCAAGGCATA---------------------
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----------------------------------------------------------GTTGTGAATACAGTGTTGCTGG
TTTGCCTTATTGTGAAA--TGTTAA-ATTAGTATTGCCTACCGCTACATAAGGCCGGTCACAGTAGGGAGGAACTTAGGA
GTAACATCACATACTCCAATACAACTTTGCTTATGTGGCACGTATTTAATAAAAAGAGAGGTGTTTGTGGTAACTAACTA
AGTTACCGGAACATCACACACTCCAACAAACAATGAGTCTATAACCTAATAAATACATCGTTGCATGACACTACATAGAT
GTTCCTACCCACTATGGAGGTAGTAACATAGTCTAGGGAAGTGTGTAAGTTACTAGCTTATGTTCTTGCTCATTGTGACC
AGCCTAAGGTTTACTTTGTATTTCATTTTTCTATTGTGATCATGACGTGGTCGCTTTAATTGTATGAACTCGATATCTTG
AAGATTTGTCTAGTGTTTCGGTTTTCTATCTCGTTGCAACGTTTTTAATTTCTTACTCCTCCATTCCACTAAGCCCGCGC
TTTTCAAGGTCTAACTTTGACCATAAATTTATCCAACGAGACCGACTGCGGTGGAAGAAAAAAATTATATAATTGAAAAC
TTATTTTAAATACAAATTCACTGATATAACTTTTGCTCCCACCGTAGTCGGTCTTGTTGGTTAAATTTATGATCAAAGTT
GAACTATGGGAAGAAAGCACTACATTATGAAACGAAGGGAGTATATAACTACTTCTAGCATGAAGAAACCCTTGCATGAC
TTCGTCTTCTATGGCCTTGCGGTAATGGAGGCAT---GGTGGATCCCAGTCCTTGCCGACGTGAGGGCTCCTGTTTTGTT
TTTAGGTGTTCGTTT-----------------------------------------------------------------
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>SNPs
-------------SS-S---S----------------S-----------S-S-S-S---------------S--S-----
------SS-------S------------S------S-----------------------SS---------S-S-------
-------S-S-S-----------S-S-------------S-SSS-S----------------------------------
--------------------SSSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------------------SS-----
--------S-------------------------------------------------S-------------S-------
------------------------------------------------------S-S-------S----------S----
----S-----------S---------------------------------------------------------------
------------------------------------------------------------------S---------S---
-----------------------------------------------------------------------------SS-
------------------------------------------S-------------------------------------
----------------------------S---------------------------------------------------
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----------------------S---------------------------------------------------------
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---------------------------------------------------S----------------------------
--------S-----------------------------------------------------------------------
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S-------------------------------------------------------------------------------
--------------------------------------------------SSSSSS------------------------
--SSSSSS------------------------------------------------------------------------
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---------------------------S--------SS------------------------------------------
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----------S------SS-----------------S-------------------------------------------
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---------------------------------------------------------S------------S---------
-------------------------------------------------------SS---------S-------------
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---------------------------------------------S----------------------------------
------------------S--SSS--------S-------S-SS--SS-S-S----------------------------
---------------SSS-SSS--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSS
>forward_450
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------------------------------AGATGGGTGCAAGACAGACC------------------------------
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>reverse_3097
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--------------------------------------------------------TGTTTCTGTGCTGTGCATGC----
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