>input_sequence_86538
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------------------------------------------------------------ATGGCGTTCGTGCCGATCTG
CGTGCAGTGCGGGACGAGGAGCAACCCGTGCCGGTGTAAGGTGGTTGGCCCGACGCTGGGATTCGTGGCGCTCGTCGTGG
CCGGAGTGGTGGAGTGGCCGCTGGGCGCCGCCGTGTACCTTTTCCGCCACCGCAAGGGTCGCCGCATCATGGGTCACCCG
ACCACGGTCGTGTACCCTCGCGTCACCGGCGCAATCCCCATCTAA-----------------------------------
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>chr3D_1_TraesCS3D01G221300
TCTAAGCTATGCACATATATCTTACTAGTAAAATTATTTTACCATGTAATGTATACATATAGAATGACGTTTTGGATCTG
GGTCTTCATGGAGGCCGATTTTTTTT-AAAAAAATTGTACGAGTAAACAAGGATGTGAGGTGTATGTGTGTAAAATTTCA
GAATAAAATACAATGAAGTGGCGTCTTATA-AAAAAGACAAATTCATGGCCTGAGAGGATGAATAGAATCATGTGTTAAA
AAGCCTC---TTTTTTGGACAACCCTTACCTTAACGTATTTCATCCTGAAAATTTACACACTTGTGTATAATGCCTTCAT
GTATGTCAGTATTTTTTTAGAATTTTTTGAAATATAAAAATGTGAATTTTCGTGAATTTTGCATTTTGCATTTAGAGGCC
TCCATGAAGCTCGGCCCCCAAAAGCAATTTCAATTTTAAATGTCAATTATTAATACTTTTACTGATGGTCTGACGGCATG
TGCACTATACGTGTTTCTCCATACGAAGATGGATCGGGTTTCACTATCATCTAGTATTATCATCAGATAACGGCATGCGC
ACTAGTGTCAATTCACAAACTGGAGCTAATTTTTT-TTCACAAACTGGTGCTGAGGAGATCATGTTATTATACATAAAAC
ATAGTCTGATGTGCAATTACGTGCCCCC---CTGCTTGTGCATCTTCCGTTTTGTTGAGAAAGTTCG-GAGAACTCTAAG
AACAACTGAACAGACGTGAGCGGAGTCCCGTGCAACGTGGAAGTGATCCAGCAAGCGGAGTCATCACTAACTTTTTGCAA
CCATGCTGCTAGTGCCACGCGTGCCGGCAGTCGCACCACCCGTCCCCAACGCAACGACGTTATATATATGCCCGAGATGC
GAGAGACCGACCACATCACAACGATTAGCAAGC--------GGACCATCAATTAATTTCTAGCGCATCTATCCATCCACT
AAACTTTGACA--AAGCATTCTATCTGACAGCACTAGCAGAGGCTGGTTCGGCAACAACAATGGCGTTCGTGCCGATCTG
CGTGCAGTGCGGGACGAGGAGCAACCCGTGCCGGTGTAAGGTGGTTGGCCCGACGCTGGGATTCGTGGCGCTCGTCGTGG
CCGGAGTGGTGGAGTGGCCGCTGGGCGCCGCCGTGTACCTTTTCCGCCACCGCAAGGGTCGCCGCATCATGGGTCACCCG
ACCACGGTCGTGTACCCTCGCGTCACCGGCGCAATCCCCATCTAATCGACCGCAGCATCTGCCTCTTCGGTGGTGATCTG
TCACGAGGTACCGCCGTTGGCTTGTCAAGCTGTGTCATGTAATCTGGGAGATTCGTCTCTCCGACTCTCAGCGTGTGTTT
AATAAAGCGAGGTTTTTGTTGTCGTGGTATTTGCAAGGCTTCGCCGTGGCTGTACTTAATATTTGTTCGTCGATGTT---
--GAGTAGCTGTTTTGGTCACCCCGAGTGCTCTCTCCTCCC-----------TGACTCCTCTTTACGGAAAATGCTCTTT
ATGTAGTGCCCCCTCCGATCTTCTCTTCTTTGAAAAATGTTCCTTATGTAATGTTTCCTCCTATCCAAAATAAAATAGGT
GTCGTGGTTTTAGTTTAT--------------------------------------------------------------
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------------------------------------------------------------------------TATAAACT
AAATTCATGAATCCTCTCAGATCCGAAGCAAGTGTCGTGAAGTATTATTCAAACTAGCCATCGTCGTCAGTTCGTCACCA
CCTCGGCGATGTCGAGGAAAAAACGCCTGCATAAGGCGATAGATAGGTCTCCACTCCTCTAGCCGCCATC-AAGGCCGGA
CTGGGAAGAGAAGGAGGACTGAGGCGGCGGTATGTAGGGAAGTTATATGGCATCGTCTCTGTCTCGGGAAGCAGTCTACC
GGGAGAAATAGTATCTCATATGGGGGATACATTTCCTACCAATTCTTATTCGACATCTCATATAAATAATACATTTCATA
CCAATTCCTATTCGACGTCTTTAGCGTCATTTAGAGCATCTAGAGCCGGACATAGTAAATATGACCTCTTAAATGCCCGT
GGACACACTTGGTCAGTGATCAACGCCCGTGGACACGGTCAGCGATTCGGCGTGTCCGTTTTGAGTCCCCTTATTTGTCC
GAGTCCTTATTTGTTCGTCCGTGTAGCCATACTTTTTATTTTTCTTCTCATATTTCCATCACTGAAGAGAGAAAAAAAAG
AAAAAAAAGAAAAAAAGAAAAGGTGGTCAGTGGAGGGGCCCGCGCGCGAGCCCTCGTATCCTCGGGGCTGCTGCGT
>chr3A_1
TCTAAGCTATGCACATATATCTTACTAGTAAAATTATTTTACTATGTAATGTATACATATAGAATGGCGTTTTGGATCTT
GGAAAATTCA---------------AAAAAAAAAGTGTACAAGTAAACAAGGATATAAGGTGTATGCGTGTAAACTTTCA
GAATAAAATACAATGCAGTGGCGACCTGTACAAAAAACAAATTTATGAT-CTGAGAGAATGAATAGTATCACGTGTTAAA
AAGCCTCGATTTTTTTGCACAACCCTTATCTCAACATATTTCATCCTGAAAATTTACACACTTGTGTATTATGCCCTCAT
GTATGTCAGTATTTTCTTTAGAATTTTTTAAATGTAAAAGTATGAATTTTCATGAATTTTGCATTTTGCATTTAGATGCC
TCCATGAAGCTCGGCCTTCAAAAGCAATTTCAGTTTCAAATGTCAATTATTAGTGCTTTTTCTGATGGTTTGACGGCATG
TGCACTATACGTTTTTTTCCATACGAGGACGTATCGGGTTTCACCATCATCTATCATCA------GATAACGGCATGTGC
GCTAGTGTCAATTCACAAACTGGAGCTATTTTTTTTTTCACAAACTGGTGCTGAGGAGAGCATGTTATTATACATAGAAC
ATAGTCTGATGTGCAATTACGTGTCCCG---TTGCTTGTGCATCTTTCG-TTTGTTGAGAAAGTTCCAGAGAACTCTAAG
AACAACTGAACACACGTGAGCGGAGTCCCGTGCAACGTGGAAGTGATCCAGCAAGCGGAGTCATCACCAACTTTTTGCAA
CCATGCTGCGAGCGCCACGCGTGCCGGCAGTCGCGCCAACCGTCCTCAACGCAACGACGTTATATATATGCCCGAGATGC
GAGAGACCGACCACATCACAACGATTAGCAAGC--------GGACCATCAATT----TCTAGCGCATCTATCCATCCATC
AAACTGCGACG-CAAACATTCTATCTGACAGCACTAGCAGAGGCTGGTTCAGCGACAACAATGGCGTTCGTGCCGATCTG
CGTGCAGTGCGGGACGAGGAGCAACCCGTGCCGGTGCAAGGTGGTCGGCCCGACGCTGGGATTCGTGGCGCTCGTCGTGG
CCGGAGTGGTGGAGTGGCCGCTGGGTGCTGCCGTGTACCTTTTCCGCCACCGCAAGGGCCGCCGCATCATGGGTCACCCG
GCCAGGGTCGTGTACCCTCGCGTCACCGGCGCAATCCCCATCTAATCGACCGCAGCATCTTCGTCTTCGGTGGTGATCTG
TCACGAGGTACCGCCGTTGGCTTGTCAAGCTGTGTCATGTAATCTGGGAGATTCGTCTCCCCGACTTTCAGCGTTTGTTT
AATAAAGCGAGGTTTTTGTTGTTGTAGTATTTGCAAGGCTTCGCCGTGGTTGTACCAAATATTTGTTCGTCGATGTAAAG
TAGAGTAGCCTTTTTGGTTACCCCGAGTGCTGTGTAATAGCATCGATCAACTTGACTCCTCTTTTCGGAAAATGCTCTTT
ATGTAGTGCTCCCTCCGATCTTCTCTTTTTCGAAAAATGCTCCTTATGTAATGTTTCCTCCTATACCAAATAAAATAAAT
GTCATGGTTTTTTTATTAATCAACTTAAAATGTCTGATACAATCATTCATTACAAACTTTGTCACCCATGACGAAATAGA
ATGAAAAAGAAAATTATCATATCTATTATCAAAACTAAACTTTGCAACCTGGTGGCCTCTAAATTTGCCCTCATGTTGAT
CTTTGAAATATGTAAATTCACCAGCATCTTTGAGACATTTACCACCGCCTTCTTTAAATCAACAAGGGAGGACCTGTCCA
TACAATCTCTTCCAAGAACAGAGGCAGCAAAGGAGCGATCAGTTTCCTCC------------------------------
-------------------------------------------------AAAATGATGGGCATGTCTAGTGTTGTACTAA
TATACAGG-CCGATAGGAACGCTCTAAATTCCGCTTCCTCGACGCTATAGCAAACTCTAATACAATCTCAGAAAGAAAGA
ATAATTTGTCCACAATGGTTTCTTACAAACTCTAATACAATCCTAGAAAGAAAGAATAATTTGTCCACAATGGTTTCTCA
CAACCACCCACTCTTATGTTGATATTAATATTGTAGACCTTTAATATTGTACTCCCTTCTTTTTGGTTTATAGGGCTTAT
CTCAAGCTCAATTTGGTTGTTCATCATCACATATTCAGACTTCAAAGTGCATTAAATCATTGCATGCAAGTATGAAGAGA
AAACTAATCAATGCATGCACTGCGTGCATGCATTGCATTGCAATTAATGCATTCGTAAACATAATTTTTTTAGGAAAATA
AAAGCATTAATTAGATGCTTTTGTAAACTATAAAAAATATTCCATCACTCATCATTTATCTTGATTGGTGAGATTTTTAA
ATTGAGCCTTATAAATTAGAAAGGAGGGGTAGACCTCTGAGATGGGGGGCTGCCAATGAATAATCTTTCTCTCAATATTA
GTGCTTTGCTGAGATTCAATATTAGCGCTATATTAATATTGTAGACCTCTGAGATGGGGGGCTGCTAACGAATAACTTTC
CTCTCAATATTAGTGCTTTGCTGAGATTCAATATTAGTGCTTTGCTGAGACGGGGGGCTGCCAATGAATAACCTTCCTCT
TAATATTAATGCTTTGCTGAAATTTCAGCTCCACTTGCTTATCTTTACTG-----------TCTTCCCTTGCAATTTAGC
ATGATAAGACGAGAAAGATGTCCAATAATTTTCTACGAAGCTCACTGAGGCTGAGATGGATTATGTTCCCTTACTAAAGA
TCAAATCATTTCTTAGATATCAAACTCTCAAGAACATGAAAATAATTTAATAATTTGCTCATGCACAAGCGAATTTAATT
GATCCAATAAAATAAGAAATCATTCCGGTCCAGAATATTTGAAAATCTCCTCAAATGGTAAATTCCACACTTCTTTCGAC
GCCATACGAAACGCACGTTAGCCTTGGGACAACTCACCAATGCGTGAAAAATACATTCATTTTCAGTATCACAGATTGAG
CACGTACCTAGAATAGATTGATGATGTTTGACCCTATTGACTTGAACCGTCAAACTATTAGAAGCAGCCCTCCACGTAAA
AAATTTAACTTTTTGGAAAACATTAGCATTCCAAATTATATTTCAGAGCCTCCTATTCCCATTCATGGCACCACTAAAAT
TGCCTAAATCGATCTTTGGAACCTTATGATCCAAAGCCAGACTATACACACTCTTCACCGACATTAAACCACTTTTCTCG
TAGTGCTAAGCAATAAA-TCTCCCTCGCCCATTCTAAGAGTGCGCAACTTTAGGATCTCCTCTACATCATGGATAAGAAA
AAGATGTCTGGTCAGGTTTTCATCCAATCTCCTAGTCCCACTCAAAAATAAGTGTCATGGTTGTAGTTTAAATATAAACT
AAATTCATGAATCCTCTCCGATCTGAAGTAAGTGTCATGAGGTATTATTAAAACTAGCCATCA--------TGGTCACCA
CCTCGGTAATGTTGAGGAAAAAACACCTGCA-AAAGAGACAGATAGGTCTCCACTCCTCTAGCCGCCATC-AAGGCCAGA
CTGGGAAGAGAAGGGGGACTGAGGCGGCATTATGTAGGGAAGT--TATGGAATCA--TCTGTCTCCGGAAGCATTCTACC
GTGAAAAATAAAATCTCATATGAGGGCTACATTTCCTACCAATTCCTATTCGACATCTCATATGAGTGATAG--TTCATG
CCAATTCCTATTCGACGTCTTTAACGTCATTCAGCGCATCTACAGCCGAAAAAAGCAAATATGACCTCTTAAATATCCAC
GGACACGTCCGGTCAGTGATCA----------------------------------------------------------
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>chr3B_1
TCTAAGATATGCACATATT--TTACTAGTAAAATTATTTTACTATGTAATGTATACATATAGAATGACATTTTGGATCTC
GGCCTTCATAGAGGCCAAATTTTTGAAAAAAACATTATACAAGTAAACAAGGATGTGAGGTGTATGTGTCTGGAATTTCA
GAATAAAATACAATGAAGCGGCAACCTGTATAAAAAGACAAATTCATGG--------------TAGTATCATGCATTTAA
AAGCCTCTTTTTT--TGCACAACCCTCATCTCAACGTATTTAATCCTGAAAATTTACACACTTATGTATTATGCCATCAT
GTATGCCGGTATTTTTTCAGAATTTTTTAAAATGTAAAAATATGAACTTTAATGAATTTTGCATTTTGCGTTTAGAGGCT
TTCATGAAGCTCGGCCTCCAAAAGCAATTTCAGTTTCAAATGTCAACTATTAATACTTTTTCTGATGGTCTGACGGCATG
TGCACTACACGTTTTTTCCTGTACCAAGATGGATCGGGTTTCACTATCATCTATTATCATCAGAGATG-ACGGCATGCGC
ACTAGTGTCAATTCACAAACTGGAGCTAAATTTTCTTTCACAAACTAGTGCTGAGGAGATCGTGTTATTATACATAAAAT
ATA-TCTGACGCGCAATTACGTGTCCCATCATTGCTTGTGCATCTTCCG-TTTGTTGAGAAAGTTCCAGAGAACTCTAAG
AACAATTGAACACACGTGAGCAGAGTCCCGTGCAACGTGGAAGTGATCCAGCAAGCGGAGTCACCGCTAACTTTTTGCAA
CCATGCTGCTAGCGCCACGCGTGCCGGCAGTCGCACCACCCGTTCCCAACGCAACGACGTTATATATATGCCCGAGATGC
GAGAGACCGACCACATCACAACGATTAGCAAGCGGAGTAGCGGACCATCAATT----TCTAGCGCATCGATCCATCCATC
AAACTTCGAACACAAGCATTCTATCTGACAGCTCTAGCGGAGGCTGGTTCAGTAACAACAATGGCGTTCGTGCCGATCTG
CGTGCAGTGCGGGACAAGAAGCAACCCGTGCCGGTGCAAGGTGGTCGGCCCGACGCTGGGATTCGTGGCGCTCGTCGTGG
CCGGGGTGGTGGAGTGGCCGCTGGGCGCCGCCGTGTACCTTTTCCGCCACCGCAAGGGCCGCCGCATCATGGGTCACCCG
GCCAGGGTCGTGTACCCTCGCGTCACCGGCGCAATCCCCATCTAATCGACCGCAGCATCTTCCTCTTCGGTGGTGATCTG
TCACGAGGTACCGCCGTTGGCTTGTCAAGCTGTGTCATGTAATCTGGGAGGTTCGTCTCTCCGACTCTCAGCGTGTGTTT
AATAAAGCGGGGTTTTTGTTGTCGCAGTATTTGCAAGGCTTCGCCGTGGCTGTACCTACTATTTGTTCGTCGATGTGAAG
TAGAGTAGCTGTTTTGGTCACCCCGAGTGCTGTGTAATAGTATCGATCAACTTGACTCCTCTTTTCGGAAAATGCTCTTT
ATGTAATGCTCCCTCCGATCTTCTCTTTTCTGAAAAATGCTTCTTATGTAATGTCTTTTTTTAGAAAAAAAACTCCATCA
TG-----------TATTAATCAACTTAAAATGTCCG-TACAATCATTTATTACAAACTCCGCCACACAGGGCGGAACAGA
ATGAAAAAGAAAATCATCAGATCTATTATCAAAACTAAACTTATCTCGGGA---GCCACCAAATTTGCCCT---GTTGAT
CTTTGAAATATGCAAATTCAACAGCATCTTTGAGATATTTACAACATCCTCCTTTAAATCAACAAGGGATGACATGTTCA
TACAATTTCTTCCAAGCACAAAGGGCACAACGGAGCAATCAATTTTTAAAATAACAGATACGTCTAGTGTCATTTCAATA
TACAGGCCCGGCAGGGACGCTCTAAGTTTCGCTTCCTGACACTATTTTTAAAATGACGAATACGTCTAGTGTCATTCCAA
TATACAGGCCCGACAGAAACGCTCTAAGTTTCGCTTTCT-GACACTATAGCAACCTCTTATATAATCGG-----------
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------------------------------TATTAATCTTGTAGACCTATGAGGT-------------------------
----------------------------------------------------GGGGGCTGCCAATGAATAACCTTCCTCT
CAATATTAATGGTCGGCTGAAATTCCACCTCTGCTTAGCTTTACTTTACCTTTATTGCACATCTTCACATGCAATTTAGC
ATGACAAGATGAGAAAGATGCTCAATAAAGTTTTACGAAGCTCATTAAGTCTAAGATGGATTCCGTTTCCTTACCAAAGA
TCAAACCATTTCTCAGATGCTAAACTCTTCGGAACATGAAAATAGTTTGCTCGTGCAGA----------CGAATTTAATT
GATCCAATAAAATAAGAAC-CATTCCGGTC---AATAGTTGAAAATCTCTTCATGCGGTAAATTCCACACTTCCTTCAGT
GCCATATGAAATGCACG--AGCCTTGGGATAACTCACCAACGTGTGGAAAGTACATTCATTTCCAGTACCATAGATTGAG
CATGTACCTAGAATAGTTTGATGATGTTTGACCCTGTTGACTTGAACCGCCAGACTATTAAAAGCAGCTCTTCAGTCAAA
AATTCTAATTTTTCAAGGAACATTAGCATTTCAAATATATTGCAGAGA-CTTCTATCCCCATTTATGACATCATTAGAAT
TGCCTAAATTGAT-------------TGATCCAGAGCCAGTCTATATGCATTCTTCATAAAAAATAAACCATTATTTTCA
TAGTGTCAAGCAATAAAATCTCCCTCACTCATTCTAAGAGTGTGTAACTTTAGGATCTTCACTGCATCATGGATAAGAAA
TAGATGTTTTTT---------ATCCTATCCCCTAGTCTCAGTCAAAAATAAGTGTCATGGTTTTAGTTTAAATATAAATT
AAATTCATGAATCCTCTCCGATCCGAAGTAGATGTCGTGAAGTATTATTCAAACTAGTCATCA--------TCGTCACCA
CCTCGGCGATGTCGAGGAAAAAACACTTGCA-AAAGAGACAAATAGGTCTCCATTCCTCTAGCCGCCGTCAAAGGTAAGA
TTGGGAAGAGAAAGGGGACAGAGGCGACGGTATGCAGGGAAGT--TATGGCATCATCTCTGTCTCGGGAAGCATTCTATC
AGGCGAAATAGAATCTCATATGAGGGATACATTTCCTACCAATTCCTATCCAACATCTCATATGAGTGATACATTTCATA
CCAATTCCTATTCGACATCTTTAGCA-----TAGAGCATCTATTGCCGGACATAGCAAATATGACATTTTAAACGTTCGC
GGACGTGCCCGGTCAGTGATCA----------------------------------------------------------
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>SNPs
------------------------------------------S------------------------------------S
--S------S------S-S-----SS--------------S---------------------------------------
-----------------------S-S-S---------------------S-------S--------S-------------
-----------------S----------S--S-------------------------------------S-----S----
----------------------------S----S-------S---------S----------------------------
----------------S---------------S---S-----------------------S-------------------
------------S---S------------------------------------S---S----SSS---------------
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-----------------------S---S---S-----------------S----------------S-------------
------------S-------------------------------------------------------------------
------------S-------------------------------------------------------------------
-----------------------------------------------------SSSS---------------------SS
------S---S---------------------------------------S-----------------------------
------------------------------------S--------S----------------------------------
----------------------------------------------------------S---------------------
S---S-------------------------------------------------------S-------------------
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-------------------------S-----------------------------S--------------------S---
-------------------------------S-S-SS-SS------------------------S---------------
---------S-----------------S-----------S------------------------S------------SS-
---S-------SS-S-SS--------------------------------------------------------------
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------------------S---------S---------------------------------SSSSSSSSS---------
------------------------S------S--S-S--S-------------------------------------S--
--------------S----------------------------SS---------S------------------S------
-----------S----------S----------------------S-----------------S-S-S------------
------------------------------------------S------------S-------------------S---S
------S-SS------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_493
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-------------------------------------------------------------------------CGGCATG
TGCACTATACGTG-------------------------------------------------------------------
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>reverse_4010
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---------TTTGTTCGTCCGTGTAGCCA---------------------------------------------------
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