>input_sequence_55293
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----------------------------ATGCCGCCACATTTTCCCAGCAATCCTGACCACGGGCCACACGTCGTGAGGC
CGTTCCACAGGCACAAATCGATCCACCGGATCCTGGGCGGAGGGAAAGGTACGCCGTTCTTGTTCTGTTTCTAGGCAATT
AC---------TCTGCATTACCATAGTTTTCTCTCCAAGTCGTGGGAGTAGTTACGAACACCGGTGTTGGGCTTTGATTG
CAGCTGCGGACATTCTGCTGTGGAAGAACAGGAAAGTGTCTGCTGGGGTTCTCGCTGGGGCCACGTTGACATGGTTCCTG
TTCGACGTGGTTGAATACAATGCAGTTCCGCTCCTTTGCCAGATCGCCATCTTCGCTATGCTTGCCATCTTCATTGCCTC
AAATGCTGCGCCGCTCTTCGACAGGCATGGCTTCTTTTCTTTCCACAGAGAGGAGATATCCCAGTATTTATTTTTC----
GAGTAATTGCCCCAGTATTTAGCTTTAAAGAATTTCAAAAGGTCGGCTGACCAATTTAAAATCGCAGGGCCCCGCCAAAG
ATACCACAAGTCGTCGTCTCTGAACACGCCTTCAGAGAAATGGCCATGACCATTCACCACAAACTGGAATATGCTGCATC
TCTTCTTTATGATATCGCATGTGGAAAGGATCTGAAGAAATTTCTCATGGTACGAAATTCTCTTATTTGCTATCTTCGTC
AAGAAAAGACAAACCATGTGACAAGTCTTGTTCCAGACCGATATTATGGATTAATACAGAAACACTTAAGAGATCTGAAT
CAACCAGATTAGACATGACACGACACTCAAAACAACGTTTAGCCAATATAATTCACAACGTTATTTTGCTATTGCT---C
AACTTAAACTTGTACTGACATTCAAATTGTTTCTATTGTTATAAGGTGGTAGGATCCCTGCTGTTATTGTCAGTGATTGG
AGGTTCTTGCAGCTTCACAAGCCTACTCTACCTTGGTAAGTAGAACAGAAATAGTAACGTTCAACAAAACCAAATACAGA
AGGTAGAACTAACTAGTAACTACAGAAAGGATGCTAGGAGAACACATAAACTAATGCAGTCTCACAGAAAAATGTAAAAC
TGAAATTTCTAAATAGTATAACAAGTAGTATGTGTTTCTTACTTTCACAGGATTCTTGTGTGCCCACACTTTGCCAGTGT
TGTACCAACATTACGAGACAGAAGTGGACCATCTCGTTGCAAGGGGTGGCCAAGACATCAAGAAGTTCTATGAGAAGGTT
GATTCCAATTTGCTCAACAAAATACCAAGAGGCCCTGTCAAGACGAAATTCAGATAA-----------------------
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>chr3B_1_TraesCS3B01G294700
GCGCACGGCCGCAGCGCCCATGGGTCGCACTCCGAGCGCGCTGCCATGGACGCCCCGCGCACCACCGCACCGGACGCGGC
GAGCATGGCTACGAGGAACAGCACCGCGCAGGGCTTCATGGCTTCT----------TTGCAGTGGACTCTGTCTGGTTTT
GGGAGCACAAGAGAGGGTTGGCATACTATTTGTAGCAAGAGAACAGCTCACCCGGCACCCGCGCCATGCTCTATCTGGAA
CCGTGCTGCTAAAACTTACTAAAAGCTTTTGCATTGCACGGTTGCGTAAACGGTAGAGCACGGGCATTCCCAT-GAGTGC
TTGGGACTCCGGCACTGCTCCGGAGCTCGGGTAGCGCGAAGCACGCTGCTGCTGCTGCGTAGCAAGACATGTCCAAGGTT
TGCTGTGCAGATTACGTTTGCTAATTGAAGTGGGGTGACCGCGGAGCACACCGATAAAAGTGTCTGGTCTATAAACACTC
AACCAAGCGTTGATAAC----ACAGGTGTTGAACAGATTTTCCGACGTTGAGCAATGGCGAAATGGCGATAGTTGTTTCT
GGGGTAAGGAGGCTAAGAAGCAACACGGCTGCCGGCTGGGACGAGCACCGTGAGAAATGCGGAGTAAGAAAGACGGCATC
TTCATCACCGGGTCACAAAAGCTCTC-CACTTGAGTAGGAGACAGCGAGTGCAGTCGCGAGTTCA---------------
---------------------------CATTGATGTTGACAGAATATCAAGATGCAGTTCCGGCAAGCTTCTGGCATAAA
CTACTGGCAAACAGCTAAACTTGCTTCTAGTCTGGGCTCTGACGAAGAAAACATCTGGTTCAAGGAAACCCTTGCCCTGC
ATCCG-TTTATTCCCCTCCCTCAATGGCTCATCCTCCTATAGGCCAAGCTATCCTTTCCTTGTCAACATGGGCTTACCCT
TTAGAGCTCATACTAGCATTTAGGTGCCTATAAAGACGCAATTTATGCAAGATCAGACA---------TAACAAATCAAT
CAGGTGGACATCCCAAACGCGTGAAGCCATGCCGCCACATTTTCCCAGCAATCCTGACCACGGGCCACACGTCGTGAGGC
CGTTCCACAGGCACAAATCGATCCACCGGATCCTGGGCGGAGGGAAAGGTACGCCGTTCTTGTTCTGTTTCTAGGCAATT
AC---------TCTGCATTACCATAGTTTTCTCTCCAAGTCGTGGGAGTAGTTACGAACACCGGTGTTGGGCTTTGATTG
CAGCTGCGGACATTCTGCTGTGGAAGAACAGGAAAGTGTCTGCTGGGGTTCTCGCTGGGGCCACGTTGACATGGTTCCTG
TTCGACGTGGTTGAATACAATGCAGTTCCGCTCCTTTGCCAGATCGCCATCTTCGCTATGCTTGCCATCTTCATTGCCTC
AAATGCTGCGCCGCTCTTCGACAGGCATGGCTTCTTTTCTTTCCACAGAGAGGAGATATCCCAGTATTTATTTTTC----
GAGTAATTGCCCCAGTATTTAGCTTTAAAGAATTTCAAAAGGTCGGCTGACCAATTTAAAATCGCAGGGCCCCGCCAAAG
ATACCACAAGTCGTCGTCTCTGAACACGCCTTCAGAGAAATGGCCATGACCATTCACCACAAACTGGAATATGCTGCATC
TCTTCTTTATGATATCGCATGTGGAAAGGATCTGAAGAAATTTCTCATGGTACGAAATTCTCTTATTTGCTATCTTCGTC
AAGAAAAGACAAACCATGTGACAAGTCTTGTTCCAGACCGATATTATGGATTAATACAGAAACACTTAAGAGATCTGAAT
CAACCAGATTAGACATGACACGACACTCAAAACAACGTTTAGCCAATATAATTCACAACGTTATTTTGCTATTGCT---C
AACTTAAACTTGTACTGACATTCAAATTGTTTCTATTGTTATAAGGTGGTAGGATCCCTGCTGTTATTGTCAGTGATTGG
AGGTTCTTGCAGCTTCACAAGCCTACTCTACCTTGGTAAGTAGAACAGAAATAGTAACGTTCAACAAAACCAAATACAGA
AGGTAGAACTAACTAGTAACTACAGAAAGGATGCTAGGAGAACACATAAACTAATGCAGTCTCACAGAAAAATGTAAAAC
TGAAATTTCTAAATAGTATAACAAGTAGTATGTGTTTCTTACTTTCACAGGATTCTTGTGTGCCCACACTTTGCCAGTGT
TGTACCAACATTACGAGACAGAAGTGGACCATCTCGTTGCAAGGGGTGGCCAAGACATCAAGAAGTTCTATGAGAAGGTT
GATTCCAATTTGCTCAACAAAATACCAAGAGGCCCTGTCAAGACGAAATTCAGATAAAATAAACTCCATGAAGCTGTCAG
GACATAATAATAATTCCTACCAAGATACTGGAGTAGATTTCAAGAAAAATGAACCTGCTATAAGAAAATATGATTGCACA
AACCAAGTCCCAGATAAGCGAAGTTGATGAAACACCAGTTGAGTTCAGACCTGACTGCTAGCATCCAGATGTACGGTACC
TATTAATGTATACAAGCATACTCCATCAGCGAAGCAATCTATGTGAGAATACCTCTGATGCTATAATCTCAAAAACAGTA
TCCACTGTGACACCGATGAGTCTGTACATGTATGACACATG--AAGTGTCCAATAACAGCATACCCAAAAAGACAAACAG
AAAG-ATTACATGGCTTTCAAGAAAAAAA-AACTGGGCTATCATCGCCTTCTGACATCTGTAGTACTAATGGAATGTGTT
TTTGCTTTTACTAATACAAACATAACAGTTATTATTTGCATGGCAAAACTATGAAATCAAACACTGCCATGACTATTTGC
AAAGCTTCGCCCGAGAGACAAACATCTTGAATCTGGTGTAGGATAGGACCAAGTGTTCGAGACGTCAGAGCCCTTGTTTT
TTTCTTAATTCAGTAGATGAAATGTCTATGCGGAACTTCTCCTCTGGTATAGAGATAAACATGTCCTTCAACTCTGTTGG
AATATTTAATTCTTCAAGGACCTTCAAAACAAATAGTGAAGTACGTGAGCAGACAAAGAATTTCAGTGCATGTAAAACAA
AACATCAAGGCCATTTCATACCTTGAATACTCCTTCAATCTCTCGACCACCAACCAGAAATGTTGTGCCAGTGCTTTTAC
ATTCAAGAAGAATCTCCAGCATTCTGTTGTAGTCACCTCCATAATACTTAGGCTGCCATGAGTAAACTTCATTTAGTTTG
AAAAATAAAACACTCAATTGTCGAACATCCATTCTAAGATAGCATTCAATAACTGAATTCGAGAATTATATGACTCAGCC
AAATATATCCTGAATAACAAA
>chr3A_1
GCGCACGGCCGCAGCGCCCATGGGTCGCACTCCGAGCGCGCTGCCATGGACGCCCCGCGCACC---GCGCCCGACGCGGT
GAGCACGGCTACGAGGAACAGCACCGTGCAGGGCTTCATGGCTTCTCAGTGAAGGATTACTCTGTCTGG----TGGTTTT
GGGAGCACAAGAGAGGGTTGGCATACTATTTGTAGCAAGAGAACAGCGCACCCGGCACCCGCGCCATGCTCTATCTGGAA
CAGTGCCGCTAAAACTTCGT-AAAGCTTTTGCATTGCACGGTTGCGTAAACGGTGGAGCACGGGCATTCCAAT-GAGTGC
TTGGGGCTCCGGCACTGCTTCAGAGCTCGGGTCGCGTGAAGCACGCTGCTGCTGCTGCTTAGCGAGACATGTCCAAGGTT
TGCTGTGCAGATTACGTTTGTTAATTGAAGTGGGGTGACCGTGGAGCACACCGATAAAAGTGCCT---------------
--------------------------TGTTGAACAGATTTTCCAACATTGAGCAATGGCGAAATGGCGATAGTTGTTTCT
GGAATAAGGAGGCTGCTGGGACGA------------------GAGCGCCGTCAGAAATGCGGAGTAAGAAAGACGGCATC
TTCATCACCGGGTCACAAAAGCTCTCACACTTGAGTAGGAGACGGCGAGTGCAGAAACGCTGGGGTGCGTCGCAAGTTCA
CATTGATGCGTGTCACGGTCAGAACCCCATTGATGTTCACAGAGCATCAAGGTGCAGTTCCGGCAAGCTTCTGGCATAAA
CTACTGGCAAACAGCTAAACTTGCTTC-AGTCTGGGCTCTGACGAAGAAAACATCTGGTTGAAGGAAACCCTTGCCCTGC
ACCCG-TTTATTCCCCTCCCTCAATTGCTCATCCTCCTACAGGCCAAGCTATCCTTTCCTTGTCAACATAGGCTTACCCT
TTAGAGCTCATACTAGCATTTAGGTGCCTATAAAGACGCAATTTCTGCAACTAAACAGATCAGACATCTAACAAATCAAT
CAGGTGAACATCCCAAACGCGTGAAGTCATGCCGCCACATTTTCCCAGCAATCCTGACCACGGACCGCACGTCACAGGGC
CATTCCACAGGCACAAGTCGATCCACCGGATCCTGGGGGGAGGGAAAGGTGCGCCATTCTTGTTCTGTTTGTAAGCAATT
ACCCTACACTATCTGCATCACCATAGTTTCTCCCCAAGCCGAC----GTAGTTATGGACACCGATGTTGGGCTTTGGTTG
CAGCTGCGGACGTTCTGCTGTGGAAGAACAGGAACGTGTCTGCTGGGGTTCTCGCTGGGGCCACGTTGACATGGTTCCTG
TTCGACGTGGTTGAATACAATGCAGTTCCGCTCCTTTGCCAGATCGCCATCTTCGCAATGCTTGCCATCTTCATTGCGTC
AAATGCTGCGCAGCTCTTCGACAGGCATGGCTTCCTTTCTTTCCACGGAGAGGAGATATCCCAGTGTTTATTTATTTTTT
GAGTAATTGTCCCAGTATTTAGCTTTAAAGAATTTCAAAAGGTCGGCTGACCAATTTCAAATCGCAGGGCCCCGCCAAGG
ATACCACAAGTCGTCGTCTCCGAACACGCCTTCAGAGAAATGGCCTTGACCATTCACCACAAACTGGAATATGCTGCATC
TCTTCTTTATGATATCGCATGTGGAAAGGATCTGAAGAAATTTCTCATGGTACGAAATTCTCTTATTTGCTATCTTAGTC
AAGAAAAGACAAACCATGTGACAAGTCTTGTTCCAGATCGACATTATGGATTAATACAGAAACACTTAAGAGATCTGAAT
CAACCAGATTAGACATGACATGCCACTCAAATCAACGTTTAGCCAATATAGTTCACAACGTTATTTTGCTATTGCTCTTC
AACTTAAACTTGTACTGACATTCAAATTGTTACTATTGTTATAAGGTGGTAGGATCCCTGCTGTTATTGTCAGTGATTGG
AGGTTCTTGCAGCTTCACAAGCCTACTCTACCTTGGTAAGTAGAACAGAAATAGTAACGTTCAAGAAAACCAAATACAGA
AGGTGGAACTAACTAGTAACTACAGAAAGGATGCTAGGAGAACACATAAACTAATGCAGTCTCACAGAAAAATGTAAAAC
TGAAATTTCTAAATAGTATAACAAGTAGTATGTGTTTCTTACTTTCACAGGATTCTTGTGTGCCCACACTTTGCCAGTGT
TGTACCAACATTACGAGACAGAAGTGGACCATCTCGTTGCAAGGGGTGGCCAAGACATCAAGAAGTTCTATGAGAAGGTT
GATTCCAATTTGCTCAACAAAATACCAAGAGGCCCTGTCAAGACGAAGTTCAGATAAAATAAACTCCATGAAGCTGTCAG
GACATAATAATAATTCCAACCAAGATCCTGGAGTAGATTTCAAGAAAAATGAACCTGCTATAAGAAAATATGATTGCACG
AACCAAGTCCCAGATAGGCGAAGTTGATGAAACACCAGTTGAGTTCAGACCTGACTGCTAGCATCCAGATGTACGGTACC
TATTAATGTATACAAGCATACTCCATCAGCGAAGCAATCTATGTGAGAATACCTCTGATGCTATAATCTCAAAAACAGTA
TCCACTGTGACACCGATGAGTCTGTACATGTATGACACATGAAAAGTGTCCAATAACAGCATACCCAAAAAGACAAACAG
AAAG-ATTACATGGCTTTCAAGAAAAAAATAACAGGGCCACCATCGCCTTCTGACATCTGTAGTACTAATGGAATGTGTT
TTTGCCTTTACTAATACAAACATAACAGTTATTATTTGCATGGCAAAACTACGAAATCAAACACTGCCATGACTATTTGC
AAAGCTTCGCCCAAGAGAAAAACATCTTGAATCTGGTGTAGGATAGGACCAAGTGTTCGAGACATCAGAGCCCTTGTTTT
TTTCTTAATTCAGTAGATGAAATGTCTATGCGGAACTTCTCCTCTGGTATAGAGATAAACATGTCCTTCAACTCTGTTGG
AATATTTAATTCTTCAAGGACCTTCAAAACAAATAGTGAAGTACATGAGCAGACAAAGAATTTCAGTGCATGTAAAACAA
AACATCAAGGCCATTTCATACCTTGAATACTCCTTCAATCTCTCGACCACCAACCAGAAATGTTGTGCCAGTGCTTTTAC
ATTCAAGAAGAATCTCCAGCATTCTGTTGTAGTCACCTCCATAATACTTAGGCTGCCATGAGTAAACTTCATTTAGTTTG
AAAAATAAAACACTCAATTGTCGAACATCCATTCTAAGATAGCATTCAATAACTGAATTCGAGAATTATATGATTCAGCC
AAATATATCCTGAATAACAAA
>chr3D_1
GCGCACGGCCGCAGCGCCCACGGGTCGCACTCCGAGCGCGCTGCCATGGATGCCCCGCGCACC---GCGCTGGACGTGGT
GAGCACGGCTACGAGGAACAGCACCGCGCAGGGCTTCATGGCTTCTCAGTCACGGATTGCAGTGGACTCTGTTTGGTTTT
GGGAGCACAAGTGAGGCTTGGTGTACTATTTGTAGCAAGAGAAG-------CCGTCACCCGTGCCATGC--TGTCTGAAA
TTGTGCCGCTAAAATTTT---AAGGCTTTTGAATTACACGGTTGCGTAAACGGTGGAGCATGGGCATTCCCATGGAGTGC
TTGGGACTCCGGCACTGCTTCGGAGCTCGGGTAGCGTGAA----GCTGCTGCTGCCGCCTAGCAA---------------
--------AGATTATGTTTGTTATTAATAATGTGCT---------GCACACCGATAAAAGTGTCTGGTCTGTAAACACTC
AACCTAGTGTCGAGCCTAGTGACCGGTGTTGAACAGATTTTCAAATGTTGAGCAATGGCGA---------AGTAGTTTCT
GCAATATGGAGGCTAAGAGGCAACACCGTCGGAGAGTTCGTGT-------------------------------------
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----------------------------------------------------------------AAGCTTCTGGCATAAA
CTACTGGCAAACAGCTAAACTTGCTTCTAGTCTAGGCTCTGACCAAGAAAACATCTGGTTGAAGGAAACCCTTGCCCTGC
ATCCGTTTTATTCCCCTCCCTCAATTGCTCGTCCTCCTATAGGCCAAGCTATCCTTTCCTTGTCAACATAGGCTTACCCT
TTAGAGCTCATACTAGCATTTAGGTGCCTATAAAGACGCAATTTCGGCAACTAAACAGATCAGACATCTAACAAATCAAT
CAGGTGAACATTCCAAACGCGTGAAGTCATGCCGCCTCATTTCCCCAGCAATCTTGACCACAGACTGCACGC--------
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--------------------------------------------------------------CGCAGGGCCA--------
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------TTCCAAATAGTATAACAAGTAGTGTGTG----------------------------------------------
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--------------------------------------------------------------AGGAAATATGATTGCACG
AACCAAGTCCCAGATAAGCGAAATTGATGAAACACCAGTTGAGTTCAGACCTGACTGCTAGCATCCAGATGTACGATACC
TGTTAATGCATACAAGCATACTCCATAAGCGAAGCAATCTATATGAGAATACCTCTGATGCTATAATCTCAAAAAAAGTA
TCCACTGTGACACCAATGAGTCTGTACATGCATGACACATGAAAAGTGTCCAATAACAGCATACCCAAAAAGGCAAACAG
AAATAATTACATTGCTTTCCAAG--AAAATAACAGGGCTACCATTGCCTTCTGACATCTGTAGTACTAATGGAATGTGTT
TTTTCGTTTACTAATACAAACATAACAGTTATTATTTGCATGGCAAAACTATGAAATCAAACACTGTCATGACTATTTGC
AAAGCTTCGCCCAAGAGACAAACATCTTGAATCTGGTGTAGAATAGGACCAAGTGTTCATGACATCAGAGCCTTTGACTT
TTTCTTAATTCAGTAGATGAAATATCTATGCGGAACTTCTCCTCTGGTATAGAGATAAACATGTCCTTCAACTCTGTTGG
AATATTTAAATCTTCAAGGACCTTCAAAACAAATAGTGAAGTACGTGAGCAGACGAAAAATTTCAGTGCATGTAAAACAA
AACATGAAGGCCATTTCATACCTTGAATACTCCTTCAATCTCTCGACCACCAACCAGAAATGTTGTGCCAGTGCTTTTAC
ATTCAAGAAGAATCTCCAGCATTCTGTTGTAGTCACCTCCATAATACTTAGGCTGCCATGAGTAAACTTCATTTAGTTTG
AAAAATAAACCACTCAATTGTCGAACATCCATTCTAA-ATAGCATTCAATAACTGAATTTGAGAATTATATGACTCAGCA
AAATATATCCTGAATAACAAA
>SNPs
---------------------------------------------------------------SSS--S----------S
-----S------------------------------------------------------------------S-------
-----------------------------------------------S--------------------------------
-S----S----------SS-S---------------------------------S-------------------------
-------------------S----------------S---------------------S---------------------
--------------------S--------------------S----------------------------S---------
----S--S--S--SSSS------S-------------------S------------------------------------
--SS--------------S-------S-SS-SS-SS-SS-SS----S----S----------------------------
-------------------------------------------S----------SSS--SSSSSS---------------
-------------------------------------S-----SS------S----------------------------
------------------------------------------------------------S-------------------
-------------------------S-------------------------------------------S----------
--------------------------------------------S-----SSSS-S-S----------------------
------S-------------------S------------------------------------S--S------SSSS---
-S--------------S--------------------S------------S----S--------------S--S------
------------------S----------SSS-S-S-SSSSSSSSSS-------S-S------S------------S---
-----------S----------------------S---------------------------------------------
--------------------------------------------------------S--------------------S--
-----------S----------------------S-----------S------------------S-------S-S----
---------S-----------------------------------------------S--------------------S-
--------------------S------------------------S----------------------------------
----------------------------------------------------------------------------S---
-------------------------------------S---S--------------------------------------
--------------------S-S--------S------------------S-----------------------------
-------------------------------S------------------------------------------------
----------------------------------------------------------------S---------------
----S---------------------------------------------------------------------------
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-----------------------------------------------S--------------------------------
-----------------S--------S----------------------------------------------------S
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---------------------------------S------S---------------------------------------
-----S--------------------------------------------------------------------------
------------S--------------------------------------------------S----------------
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>forward_592
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------------CTAAGAAGCAACACGGCTGC------------------------------------------------
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>reverse_2480
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-------------------------------------------------------------------------------A
AACCAAGTCCCAGATAAGCGA-----------------------------------------------------------
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