>input_sequence_83023
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---------------------------------------------------------------AGCACAACACCATCACC
CACACAAACACACGGCCGAAGCAACCCAAGCGAGTCCTCGTGTTCCCGTGCACACACGCCTAAGCTCGAACCATGTCGTC
GCAGCGGATGGGGCGTCACCAGCGCCGGGCGTCTCAGAGCGTGTTCGCGCTGCCGGAGAACTTCGCGGCCCTCGACGACG
TGCCGGCGTCCGACGAGCACCGGAAGGCGGACGGCGGCGGCGCGACCGAGCAGCAG---------CAGCAGGGGGCGGGG
CGCCACCGGCGGGCCATGTCCATGGCCGTCGCCTCCTCCAGGGACCTCGAGATGATCAAGGAGGACGTCGGCGGCTACAG
CAACTACAAGATTGGCGCCTAG----------------------------------------------------------
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>chr1A_1_TraesCS1A01G287000
AACGTAATCAAATGGCGCAAACTAATCGGAGAGGCAGAGCGTGGCCGCCCATAGAAATTTCCGCTGTTTTATTCCCCGAG
GAACTGCCGGACTCGACAGGATAAGGACTGATCTCTGTT--TCTCTCTCCTGCAAGTGCATCCTGATGCATGCACGAGGC
GCGGCCGCAGAGATCCAAAATCCTTGTTAAAACGTTGTCGCCAGGCGACATGCCTCATGTCCACGGTACAGGGCTGTCAG
TGCGTGCATGCATGCATGCAC------GGATGCGGCCATTGCAGGCGTTCTGCCACCCAATCCGTGCTGCAATATCTCTT
CCTGCGCGATTATTTTTTTCTCAGCCAATTTTTGCAGCAGCAACTGAA--TTTATAGGTGGGCAGCAGGGCAGGGAAGGG
CAGGAGTAGCTAT---TATATTGACATTGCAAAACATTTCTTGATTTTTCGCAAAGACC----CACTTCTTGATCATATG
CTGGGCTATATATCAGTA---CCCCGCAAAAATGATGAACCCTCCGTCCCAAAATAAGTAACTCAATTTTGTAATAACTT
TAATACT-AATACAAAATTAATGTAACATTGACTCACTTATTTTGAGACGAAGGGAGTATGAATTATTTTTCTGGAATAC
TAAAGCATATGTTTTGAAGGTTTGGCTATTACAAGTCAATGTTGTTTTTGGCTATGAG-TTACGCCTATTTCCAATTGTA
CAGTACAATTTTCATTGGATTTTTTCTTCGTTTTGTATGACTCGTGGCAATGGCACATTGGCACCCGCTCCATTCTATGA
TATGAGATGGACACGATAACTAACTCATGTTTGCGATAATTGTTTCTTGCGAACAATGGAAATATCTAGTACTGGTGTAC
TACCAGGTGAAGCCAAAACAGTTGGTTAATGATGTTTTTTCTCCTCCAAGAAAAGGGAAATTAGCTCCTCTCTTTCTCAC
CGGCCGTCCAAACCGAGCATTC-TCCTCTTATATAAAGCCTCCGCCTCCGCTGCTCTCTTCCCAGCACAACACCATCACC
CACACAAACACACGGCCGAAGCAACCCAAGCGAGTCCTCGTGTTCCCGTGCACACACGCCTAAGCTCGAACCATGTCGTC
GCAGCGGATGGGGCGTCACCAGCGCCGGGCGTCTCAGAGCGTGTTCGCGCTGCCGGAGAACTTCGCGGCCCTCGACGACG
TGCCGGCGTCCGACGAGCACCGGAAGGCGGACGGCGGCGGCGCGACCGAGCAGCAG---------CAGCAGGGGGCGGGG
CGCCACCGGCGGGCCATGTCCATGGCCGTCGCCTCCTCCAGGGACCTCGAGATGATCAAGGAGGACGTCGGCGGCTACAG
CAACTACAAGATTGGCGCCTAGATTAGTGCCAC---CGGCGGCGCGCACGGCCGGCGCGGCTCAGAGCACGCACGTGTAC
GGTGTTCGTAATACGTGCGTGCGC--------GCGTGCTCGGTGGCGCTCTCGGCGGAGCTGGGGCCTCGCGCGCGCGGC
TGAGCTTTGCTGCCGCCGGTGCCGGTGCCGGAGGCCGTGGCGCGTGCTGGTTCGT-TGCT-----TGTATGGTCAAGCGG
CCGAGCCTGGTTGAGGTCTT-GCTTGCTTCGATTCCCTTTTCTTTTGCTCAAGACATGCATGTAAGGTGTGATGTTATTT
GCGAGTTTAAAGCTCTTCAAATTACTAATCCTGCGTGTATCTGATGATGATGTTTCACCATTAGCCTTGC----------
-------------------------------------------------------------------------TCCTAAA
ATGTCTTCGTTTGTTTGCTGGCCCGCAGTTGT------------------------------------------------
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--------------TTTTAGTTTCAATCGATCGCTCACAGCCGTTGGATTAGGATCCAACCAACCTAGGGATTGGGT---
---GGTCGGATCAACCCAACCCCTATAGCCTATTTGGTAAACACTCGGGCAAGGAAATGCGAGTTTGCACAAGGGTTGTA
GGAGTAGATTTTTATTCCCATTCCCTTGATTGGCATATGATAGAAGTTGACATGGGTAAAACTACCCCTAAAAGATATCG
GTGTGAATTGGCTTCCTCAATTTTCAGTCCCCTTCCCACTTAAACTCCCATTAATCCCCTACAACTAAACAATGTCTGGT
GAAAATAGAAAACGAACGTCTCCACCTCCGACTTGCCCTGGCCTAAGAGCAAACTCTAGCAAAGCCTCTAAATTCCCTAC
CCGTCAAATCATTTTATGATTCGCCCTAAAACAATTTTACACGCAATTCATCTCTGACACAGAACAAATATCACAAATTT
AAAAACTTAAACGTAAAAGGTCCCT-CTACATAGATCAGTTCAGATAACTTAGATCGACGGAGGGCCGGCGGCGGCTCAC
CGTTTCACGTTGAGGAAGTGCTCACACATGCCGAGTGGTAGAGGGTGTAGGCGAGCTCGTAGTCCGCCTTCG
>chr1D_1
AACGTAACCAAATGGCGCGAACTAATCGGAGAAGCAGAGCGTGGCCTCCCATCGAAATTTCCGCTGTTTTATTCGCCGAG
GAACCGCCGGACTCGAGAGGATAAGGACTGATCTCTCTCTCTCTCTCTCTTGCAAGTGCATCCTGATGCATGCACGAGGC
GCGGCCGCAGAGGTCCAAAATCCTTGTTAAAACGTTGTCGCCTGGCGACATGCCGCATGTCCACGGTACAGGGCTGTCAG
TGCG----TGCATGCATGCAC------GGATGCGGCCATTGCAGGCGTTCTGCCACCCAATCCGTGCTTCAATATCTCTT
CCTGCACGATTATTATTTTCTCAGCCAATTTTTGCAGCAGCAAACTACATTTTATAGGTGGTC-------------AGGA
CAGGAGTAGCCATTCCTATATTGCCATTGCAAAACATTTCTTTTTTTTTTGCAAAACAAATAACATTTCTTGATTATATG
TTGGGTTGTACATCCAAGTACCCCCGCAAAAAAGGTGAACTCCACTTACA------------------------------
-AACAATAAAAACATCATCTACTGGACATATAGATTTG----------------------------TTTGGCTGGAATAC
TAAAGCATATGTTCTGAACGTTTGCC-ATGAGAGGCCAAAAAAA---TTGGCTGTGTG-TTACACCGATTTCCAAGTGTA
CAGCACCATTTTCATGGGATTTTTCTTCG--TTTCTATGACTCCTGGCAATGGCCACCT-------GCTCGATTCTATCA
TATGAGATGGACAAGGTAACTAACTAATGTGTGTGATAATTGTTTCTCGTGAATAATGGAAATATCTA-------TGTAC
TACCAGGTGATGCCAAAACAGTTCGTTAATGATGTTCCTT-TG-TCCAACAAAAGGGAAATTAACTC------TTATCAC
CAGCCGTCCAAACTGAGCATTCGTCCTCCTATATAAAGCCTCCGCCTCCCTTGCTCTCTTCCCACCACAACACCATCACC
CACCCACACACACGGCCAAGGCGACCGAAGCGAGTCCTCGTGTCCCCGTGCACACACACCTAACCTTGAACCATGTCGTC
GCAGCGGATGGGGCGTCACCAGCGCCGGGCGTCGCAGAGCGTGTTCGCGCTGCCGGAGAACTTCGCGGTCCTCGACGACG
TGCCGGCGTCCGACGAGCACCGGAAGGCGGACGG---CGGCGCGACCGAGCAGCAGCAGCAGCAGCAGCAGGGGGCGGGG
CGCCACCGGCGGGCCATGTCCATGGCCGTCGCCTCCTCCAGGGACCTCGAGATGATCAAGGAGGACATCGGCGGCTACAG
CAACTACAAGATCGGCGCCTAGATTAGTAGCGGCGGCGGCGGCGCGCACGGCCGGCACGGCTCAGAGCACACACGTGTAC
GGTGTTCGTAATACGTGCGTGCGTGCGTGCCAGCGTGCTGGGCGGCGGTCTCGGCCGTGTTCGGGCCTCGCGCGCGCGGC
GGAGCTTTGCTGCAGCCGGT---GGTGCCGGAGGCCGTGGCGCGTGCTGGTTCGT-TGTGGTTTGTGTATGGTCAAGCGG
CCGAGCCCGGTCGAGGTCTTTGCTTGCTTCGATTCCCTTTTCTTTTGCTCAAGACATGCATGTAAGGTGTGATGTTATTT
ACGAGTTTAAAGCTCTTCAAAGTTCAAACTACTAATGGTGTATCTGATGATGTTTCACCATTAGCGGCTGTATGCATCTA
TTGATGCAGAGGCCGGGGAGGCGGGGATTTTAACCTCCTTTTTCAAAAAAAAAAATTAGCGTTACTCTGAAAGTCCTAAA
ATGTCTTTCTTTTGTTTGTTTGCCAATAATGCTACACCTACGTGATGGTTTACTAAAGGTTACGTAAATCCATTCCACGC
TAACTAAACTGCCCCCCCTGATTTTTAGGGTGGGCCCGTGTGACGAGGTAAGGCCCAATATAATTTCACCACGTCGGATG
CTACGTAAGGTAGGTAGAAATCCTTACGTAAGTGTAGCATCACACAGCTGTACCCATAACGTGAAAAAAGAAGGGACCGT
TCAGATGCCTATTCTTTTAGTTTCAATCGATCGCTCACAGCCGTTGGATTAGGATCCAACCAACAACCTAGGATTGGATG
ACAGGTAGGATCAACCCAACCCCT--------------------------------------------------------
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------------------------------------------------------------ACAACTAAACAATGCCTTAG
GAAAATATAAAACGAACGTCTCCGCCTCCGACATGCCCTAGCCTAAGAGCAAACTCTAGCAGAGCCTCTAAATTCCCTAT
CCGCAAAATCATTTTATGATTCGCCCTAAAACAATTTTACGC-CAGTTCATCTCCGATGCAGAACAGATACCGTAAATTT
TAAAACTTAAAATTAAAAGGTTCCCGCTACATAGATCAGTTCGGAAAACTTAGATCAACGGAGGACCGGCGGCGGCTCAC
GGCTTCATGTTGAGGAAGTGCTCGGACA--CCGAGTGGTAGAGGGTGTAGGCGAGCTCGTAGTCCGCCTTCG
>chr1B_125
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----------------------------------------------CTCTTGCAAGTGCATCCTGATGCATGCACGAGGC
GCGGCCGCAGAGGTCCAAAACCCTTGTTAAAACGTTGTCGCCTGGCGACATGCCTCATCTCCACAGTACAGAGCTGTCAG
TGCG----TGCATGCATGCACGCACGGGGATGCGGCCATTGCAGGCGTTCTCCCACCCAATCCGTGCCGCAATATCTCTT
CCTGCACGATTATTTTTTTCTCAGCCAATTTTTGCAGCATCAACTATT--TTTATAGAGCCACTG---------------
---------------CTATATTGCCATTGCAAAACATTTCCTGATTTTTCGCAAAAAATTG--CATTTCTTGATTATATG
CTGGGCTGTATATCCAAGTGCCCCCGCAAAAATGGTGAACTGTACTTACG------------------------------
-AACACT-AAAACATCATCTACTGAACATATGAAATTG----------------------------TTTTGCTGGAATAC
TAAAGCATTTGTTTTGAACGTTTGCTTATGAGAGGCCAAAAAAA---TTTGGATGTGCCTTACACCTATTTCCAAGTGTA
CAACACCATTTTCAAGGGATATTTTCTTCGTTTTCTATGACTCCTGGCAATGGCCACCT-------GCTCCATTCTATCA
TATGAGATGGACAAGGTAACTAACTTATGTTTGTGATAATTGTTTCTCGTGAATAATTGAAATATCTA-------TGTAC
TACCAGGTGATGCCAAAACAGTTAGTTAATGATGTTCCTTGTG-TCCAAGAAAGGGGAAATTAACTCTTCTCTTTCTCAC
CGGCCGTCCAAACTGAGCATTC---CTCTTATATAAAGCCTCCGCCTCCCCTGCTATCTTCCCACCACAACACCATCACC
CACACACACACAC--CCAAGGCGACAGAAGCGAGTCCTCGTGTTCCCGTGCACACGCGCCTAAGCTCTAACCATGTCGTC
GCAGCGGATGGGGCGTCACCAGCGTCGGGCGTCGCAGAGCGTGTTCGCGCTGCCGGAGAACTTCGCGGCCCTCGACGACG
TGCCGGCGTCCGACGAGCACCGGAAGGCGGACGG---CGGCGCGACCGAGCAGCAGCAG------CAGCAGGGGGCGGGG
CGCCACCGGCGGGCCATGTCCATGGCCGTCGCCTCCTCCAGGGACCTCGAGATGATCAAGGAGGATATCGGCGGCTACAG
CAACTACAAGATCGGCGCCTAGATTAGCGGCGGTGGCGGCGGCGCGCACGGCCGGCACGGCTCAGAGCACGCACGTGTAC
GGTGTTCGTAGTACGTGCGTGCC----------------GGGCGGCGGTCTCGGCCGTGTTCGGGCCTCGGGCGCGCGGC
TGAGCCT---TGCTGCCGGC---GGTGCCGGAGGCCGTGGCGCGTGCTGGTTTCGCTGTGGTTTGTGTATGATCAAGCGA
CCAGGCCCGGTTGAGGTC-TTGCTTGCTTCGATTCCCTTTTCTTTTGCTCAAGACATGCATGTAAGGTGTGATC--ATTT
GCGAGTTTAAAGCTCTTCAAA-----------------------------------------------------------
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>SNPs
-------S----------S-------------S-------------S-----S---------------------S-----
----S-----------S-------------------S-S----------S------------------------------
------------S-----------------------------S-------------------------------------
----SSSS------------------------------------------------------------------------
-----S---------------------------------------S-S-------------S-S-SSSSSSSSSSS---S
----------S------------S-------------------------------S-SS------S--------S-----
-------S------SSSS----------------S-----S--S-S-S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
S--S------S---SS--SS-SSS-----SS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----S---------
------------------S-----S----S-S-S-S---SSSSSSSS------S--S------S-----------S----
---S--S--------S------------------S--------S----------SSSS-SSSSSSS------------S-
-------------S-S---------S-------S-------------S-S---S--------------SSSSSSS-----
----------S------------S------------SS--S-SS-------------------S---S------------
-------------S-----------------------------------S--------------S---------------
------S----------S-S--S---S-----------------------------------------------------
---------------------------------S----------------------------------------------
----------------------------------SSS-------------------------------------------
------------------------------------------------------------------S-------------
------------S----------------S-SS-----------------------S-----------------------
-----------------------S---------------S--S----S-------S-S-S-S------------------
-------------S------SSS-----------------------------------SS--------------------
-------S------------------------------------------------------------------------
---------------------S-S-S--SSSSSSS--SSSSSSS---------------------SSSSS----------
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-------SS---SS--SS-SSS--SSSSS--S------------------------------------------------
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----------------------------------------------------------------SSSSSSSSSSS-S---
------S-----------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------------S--SSS
-------S---------------S--------S------S---------------------S-----------------S
---SS-----------------------------------S-S--S--------S--SS-------S---S-SS------
S----------SS--------S--S-----------------S--S----------S-------S---------------
S-S----S---------------SS---SS------------------------------------------
>forward_775
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-----------------------------------TATGACTCGTGGCAATGGCA-------------------------
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>reverse_2146
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-----------------------------------------------------------------TAGGGATTGGGTGGT
CGGAT---------------------------------------------------------------------------
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