>input_sequence_79244
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--------------------------------------------------------------------ATATAAATACAC
CC----GTATCCATATGTATGCACACACAAGCATCTA-CACACGATCCGATTA-TATCTTGCTTTAAGAGGAAGGTAGCT
GGAGTAGC----CTGCATCTTTCAGCTGCGCCTGGTCAAACATGGCTTCCATGGGGTTCAGCTATGCGCAGATACATGTG
CGGCAGGAGAAGATCCGGCAGAGGATCAACCAACAAGAAGCCGCCAAGAAGACGACCGTG------------AAGAGT--
----ATCGGTGAAGGAGATAAGATCAAGAAGAAAAACTGCGACTCATGGACCGCCGCCGGCAGGGTGCATCCGTGCGCGT
CTTCCACGGCCGCGGCGGCGGCTACGGCTAGGCCGGTGCCAGAGAGGTGAGGCTGGCTGGCTGTGCGTCTTCTCTTCTCT
GTAGGCCACAAGAGGCTTGATTTGAGAGTTTAGTTTGTGTCTCTGATGAGTAGTTTTAGCTTGTCTCAAGATTTCCTCGA
GGAA----------------------------------------------------------------------------
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>chr1B_1_TraesCS1B01G083600
GCTCAATCATCGTTCAGGTTTTTTCTTGATGAAAATCACAATGCTTCCAAGCATGTTCAATAAGAAAAAT-CAATTCTAC
ATTGGACCAAACTCTTACGTATGAAGTAATTTGCCTTTGTAACATGAAATTAACTTTCAGAGTTTTAAGG-----TCAAA
TACGCAAATACACAAGAACATTGAGGTGTATAGTACATATCTATAAAGTTTCAAGATCAAATACGCA-------------
---------------------------------AATAGTACATGTGTTAGAGTGACATTATTTTATTTTGTGTGTGTG--
---------------------------------------------TACATATCTAGGCTCGTTTGTATTTTCTTTCAAGG
AAAAAGTAAT--------------------------------------------------------CGCCCACCGTGGGG
CTCGAACCCACGACCACAAGGTTAAGAGCCTTGCACTCTACCAACTGAGCTAGACGGGCTTTGTGTCACTTGCTTCATTC
ACGGCTATATATGTGATACACCAAACAAAAGCCTTCCTCTGCCTACCTACCGAGCTCAAGGTTTGCTCAATTATCAGCGT
GCAAGCGAGTGATTAGTTTC-TTTTAACCTGGAAATATCCTTCCATTACTTAACCTCGCC-------CAGCAGAATCACC
AAAGCATACATGGAGTCAGGGACTCAGTTGTTCCTTTCCACCAGGATATCATTAGTCGGATGGAATCATCCATTCATGCA
TTATTATACTACTCCATAGACAAATATAGACGC-------GTCAGTGGGAAGTCGCAAAGGCAACATCGAAACTTGTCGC
GTAGAGGCACAAGCGGCGAAAGTTGGGCA-----GCCGGCAGCCCACCAGGAACACAAAACCGTTTGCTTGTGCCCACAG
GTAGTGCTGCTAATAATTCCGCAACCGTTTCCCGCAGCCAGCAGCGCCTGCGACTGCAACCCTGCAAGCAGAAAAGGCAG
CCGCTGTTTGTGATTGCTTCCGAATTCCTCTCCCTCTGGCGACACCTACCGCCTACCACCACCAGAGGAG----------
---ATAAGTCCACACCGGATATCATCAAGAAACTCGGTGCCCCGCCCCCCAATAATTGCAGCCCGCGCATATAAATACAC
CC----GTATCCATATGTATGCACACACAAGCATCTA-CACACGATCCGATTA-TATCTTGCTTTAAGAGGAAGGTAGCT
GGAGTAGC----CTGCATCTTTCAGCTGCGCCTGGTCAAACATGGCTTCCATGGGGTTCAGCTATGCGCAGATACATGTG
CGGCAGGAGAAGATCCGGCAGAGGATCAACCAACAAGAAGCCGCCAAGAAGACGACCGTG------------AAGAGT--
----ATCGGTGAAGGAGATAAGATCAAGAAGAAAAACTGCGACTCATGGACCGCCGCCGGCAGGGTGCATCCGTGCGCGT
CTTCCACGGCCGCGGCGGCGGCTACGGCTAGGCCGGTGCCAGAGAGGTGAGGCTGGCTGGCTGTGCGTCTTCTCTTCTCT
GTAGGCCACAAGAGGCTTGATTTGAGAGTTTAGTTTGTGTCTCTGATGAGTAGTTTTAGCTTGTCTCAAGATTTCCTCGA
GGAAATAAAGATGTGTGCTCATATGTC--------CCACAAGCTTGTGGATATCAT------ACGAACAATCAAATATAT
AGTCCAGCCACACATTTAAAACTGTTTTTCTTTTGACGAAAAAGCAGCAGATTGCTGATTTTCATTGATAAAGTGGTAGA
AGTAAACAGTTACAGGCCACTGAAAGGAAAAGAAAAAGTGAT-----------------------CTAAAATTGTTTCTG
ACAGGCCTGCCTGTCGACTAACAAAGAGACTCACTAGAAGATGCAGGAACAGAGTTTTTTTTTTTTTTACATAGCCACAG
AGCCATGGTATTGG------TTGC------------GACTGGAATCTTAATATTGCCAAGAACCTAGCTACTGACTAAAA
GTGCTTGATCCTGAACTTCCACTCCCCATTCACGGCATCAAACGCCACGAATTCAGCGCCATTCTTCTTGGTCCATTGCG
CCAGAATCTCCGTATACCTGTCAACTTCTGCCCCCTCCGTCAACTGCAACCCGGTCTTCTTATCGACGCACTTCACATTC
AGGAGTGTGATCTCTGCAGGCTTGTTGAGCTCCTGCCCCACAGGAGGTCTCTTGCTCTCATCTGTGTAGACCAGGATCTC
GCGGTCCTTGAACTCCACGATGGAAGCGATGTCGAGCTTCCTCACATCGGTTTCTCCATCAAACTTGATGCTGCCGTAGC
CATGCCTGCCGACCGTTAAGTCCTTCACATGTGAGCAACAACCTGGCTCGTTGCTTTCTCGTGCAGCAAGCTCTGCGATC
GACGGCGAAGTGTAATAGTCTGCCTTATAGAGCCGAGGTAGGACACTCTCACTCACAGAGGCGCCACCAAATGGAGTTAT
CACAGGATCAAATGGATTA---------------GCACCGTTGATATACCCTTTCTGTTCCCCAGCGGATTCTGATGATG
GTGAACAAGATGTCAGTAACTCAATTGCATATATCATATGGCAACACAAATAGGATGAAGT-AGCTTCGGTTCTGAGATA
TCAAATATTTTGACATTTGGGCTCCACAAGTGCTA---------------------------------------------
-------------------------------------
>chr1A_3
--TCAATCATCTTTGAGATATTTTCTTGATGAAAATTGC-ATGCTTCCAAGAATGTTCAAGAAAAAAAATTCAATTCTAC
ATTGGACCAAACTCTTACGTATGAAGTAATTTGCCTTTGTAACATAAAATTAATTTTCGGAGTTCTAAGATCAAATCAAA
TACGCAAATACACAAGAACATTGAGGTGTATAGTACATATCTATAAAGTTTCAAGATCAAATAAGCTTTGGTGTGATCCG
TATAAAAAG-CAAAATCATGGACTTTTATAGTGAATAGTACATGTGTTAGAGTATCATTAATTTATTTTGTGTGTGTACC
TTAACCAAAACATATTTCATAATGAAAATTTATGTAGATGTTATATACATCCCTAGGCTCATTTGTATTTTCTTTCAGAA
AATTTGGAACTTCAAAATATA-TTTTCTGCCTTTTAAAAAATATGGGCTTTGAT--------------------------
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--------GCAATGCTCTTTTTGTAAATCTGTGTATATTTTGTTCATTCAAT----------------------------
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---------------CATCTTTGAGG------------------------------------------------------
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---------------------------------------------------------------------TATTTTCTTGA
TGAAAATTACATGCTTCCAAGCATGTT--------CAAGAAAAAA-----------------------------------
-----------------AAAACAATTCTTCATTGGACCAAAC--------------------------------------
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-----------------------------------------------------------------------TCTTACGTA
TGAAGTAATTTGGCTTTGTAACATAACATTAATTTTCGGGAGTTTTATCCAATATGCAATACACAAGAACATTGAGGTGT
ATAGTACATATCTATGAAGTTTCAAGATCAAATACGC
>chr1D_129
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-------------------------------------------------TTAACTTTCGGGGTTTTAAGATCAAATCAAA
T--------ACACAAGAACATTGAGGTGTATACTACATATCTATAAAGTTTCAAGATCAAATACGCTTTGGTGTGATCCG
TATAAAAAGGCAAAATCATAGACT------------------TGTGTTAGAGTGACATTATTTTATTTTGTGTGTGACCA
AGAATAGAAAAA----TCATAATGAAAATTTATGGAGATGTTGTATACATCCCTAGGTTCATTTGTATCTTCTTTCAGGA
AATTTGGAACTTCAAAAATAAGTTTTCCGCCTTTTAAAAAATAAGGGCTCTGATCAAAAAAATAAGCGCCCACCGTGGGG
CTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTCTACCAACTGAGCTAGACGGGCTTTGTGTCAGTAGCTTCATTC
GCATGTATATATCAGGTATATCAAGCAAAAAGTCTGAGCTA----------------AAGGTTTGCTCAATTATCAGCGT
GCAAGCAAGTAATTAGTTTTTTTTTAAGCTGGAAACGTCCTTCCATTACTTAACCTCGCTCA----TCATCAGAATCACC
AAAGCATACATGGAGTCAGGGACT----TGTTCCTTTCCACCAGGATATCATGAGTTGGATGGAATCATCCATTCATGCA
TTATTATACTACTCCGTAGACAAATATAGACGCC-------TCAGTGGAAAGTCGCAAAGGCAACATCGAAACTTGTCGC
ATGGAGGCACAAACGGCGAAAGGTAGGCG-----GCCGGCAGCCCACCAGGAACACAAAACCGTTTGCTTGTGCCCACAG
GTAGTGCC---AATAATTCCACAACCGT-------------------CTGCGATTGCAAA--------------------
-CGCTGTTTATGATTGCTTCCGAATCC-TCTCC--CTGGTGACACCTACCGCCTACCACCACCAGATGAGG---------
-AGATAAGTCCACACCGGATATCATCAAGAAACTCGGTGCCCCG-CCCCCAATAATTGCAGCCCGAGCATATAAATACAC
CCGGCTGTATCCATATGTATGCACACACAAGCATCTA-CACACGATCTGATTATTATCTTGCTTAGAGAGGAAGGTAGC-
----TAGC----CTGCATCTTTCAGCTGCGCCTGGTCAAACATGGCTTCCATGGGGTTCAGCTATGCGCAGATACATGTG
CGGCAGGAGAAGGTCAGGCAGAGGATCAACCAACAAGAAGCCGCCAACAAGACGGCCGTG------------AAGAACAA
GAACATCGGTGAAGAAGACAAGATCAACAAGAAAAACTGTGATTCGTGGACCACCGCCGGCAGGGTGCATCCGTGCGCAT
CTTCCACGGCAGCGGCGGCGGCTACGGCTAGGCCAGTGCCAGAGAGGTGAGGCTGGCTGGCGATGCGTCTTCTCTTCTC-
----------------------------------------------TGAGTAGTTTTAGCTTGTCTCAAGATTTCCTCAA
GGAAATAAAGATGTGTGCTCATATATGTGTTTTTTCCACAAACTTGGGGATATCAATCAACGCCAAACAATCAAATATGC
--TCCAGCCACA--------------------------------------------------------------------
---------------------------------------GAT-----------------------CTAAAATTGTTTCTG
ACAGGCCTGCCTGTCGACTAACAAAGAGACTCACTAGAAGATGCAGGAACAGAGTA------TTTTTTACATGGCCATAG
AGCCATGGTATTGG------TACTCTCCTATCTTGAGACTGGAATCTTAATATTGCCAAGAACCTAGCTACTGACTAAAA
GTGCTTGATCCTGAACTTCCACTCCCCCTTCACGGCATCAAACGCCACGAATTCAGCGCCATTCTTCTCGGTCCATTGCG
CCAGAATCTCCTTATACCTGTCGACTTCTGCCCCCTCCGTCAACTGCAACCCGGTCTTCTTATCGACGCACTTCACATTC
AGGAGTGTGATCTCTGCAGGCTTGTTGAGCTCCTGCCCCACAGGAGGTCTCTTGCTCTCATCTGTGTAGACCAGGATCTC
GCGGTCCTTGAACTCCACTATGGAAGCGATGTCAAGCTTCCTCACATCGGTTTCTCCATCAAACTTGATGCTGCCGTAGC
CATGCCTGCCGACCGTGAAGTCCTTCACATGTGAGCAACAACCTGGCTCATTGCTTTCTCGTGCAGCAAGCTCTGCGATC
GACGGCAAGGTGTAATAGTCTGCCTTATAGAGCCGAGGTAGCACACTCTCACTCACAGGGGCACCACCAAATGGAGTTAT
CACAGGATCAAATGGATTACTCCTAGCCAGGACAGCACCGTTGATATACCCTTTCTGTTCCCCACCGGATCCTGATGATG
GTGAACAAGATGTCAGTAACTCAAT-GCATATATCGTATGGCAACACACAAAGCATGAAGT-AGCTTCGGTTCTGAGATA
TCAAATATTTTGACATTTGGGTTCCACAAGTGCTA---------------------------------------------
-------------------------------------
>chr1A_302
AAAAAGCA------------------------------------------------------------------------
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-------AAT--------------------------------------------------------CGCCCACCGTGGGG
CTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTCTACCAACTGAGCTAGACGGGCTTTGTGCCACTTGCTTCATTC
GTCTGTATATATCCAAAATAG--AACAAAAGCCCTCCTCCACCTACTCAGCAGAATGATTA-------------------
----------------CCTTTTTTTAAGCTGGAAATATCTTTCCATTCCTTGACCTCGCTCAGCGCTCAGCAGAATCACC
AAAGCATACATGGAGTCAGGGACTC----GTTCCTTTCCATCAGGATATCATTAGCTCGACGGAAT----CATTCATGCA
TTATTATGC-------TAGACACATATAGACGCCTCAGTGGTCAGTGGGAAGTCGCAAAGGCAACATCGAAACTTGTCGC
GCAGAGGCACAAACGGCGAAAGGTGGGCAGCCTTGCCGCCAGCCCACCAGGAACACAAAACCGTATGCTTGTGCCCACAG
GTAGTGCC---AATAATTCCACAACCGTTTCCCGCAGCCAGCAGCGTCTGCGATTGCAACCCTATGA----AAAAGGCAG
GCGCTGTTTGTGATTGCTTCCGAATCA-TCTCCCTCTGGTGACACCTACCGCCTACCACCACCAGAGGAGATACTCCTAA
CAGATAAGTCCACACCGGATATCATCAAGAAACTCGGTGCCCCG-CCCCCAATAATTGCAGCCCTCGCATATAAATACGC
CCGGCCGTATCCATATGTATGCACACACACAGACATCTCACACGATCCAATTA-TATCCTGCTTAAAGAGGAAGGTAGC-
----TAGCTAGGCTGCATCTTTCAGCTGCGCCTGGTCAAACATGGCTTCCATGGGGTTTAGCTATGCGCAGGTACATGTG
CGGCAGGAGAAGGTCCGGCAGAGGATCAGCCAACAAGGAGCCGCCAACAACTCGACCGTGAAGAACAAGAACAAGAGT--
----ATCGGTGAAGAAGACAAGATCAGCAAGAAAAACTGCGACTCATGGGCCGCCGCCGGCAGGGTGCATCCGTGCGCAT
CTTCCACGGCGGCGGCGGCGGCTG------GGCCGGTGCCGGAGAGGTGAGGCTGGCTGGCGATGAGTTTTCTCTTC---
--AGGCCACAAGAGGCTTGATTCGAGAGTTTAGTTTGTGTTTG---TGACTAGTCTTAGCTTCTCTCAATATTTCCTCAA
GGGAATAAAGATGTATGCTAGTATGTTTGCTTGTCTCAATAGTGCCAATATT----TCAACGACCAACAATCAAATATAC
--TTCAGCCACA--------------------------------------------------------------------
---------------------------------------GTTATCTGATAGCTCGAAATCCCCACCTAAAATTGTTTCTG
ACAGGCCTGCCTGTCGACTAACAAAGAGACTCACTAGAAGATGCAGGA-CAGAGTA------TTTTTACATAGCC---AG
AGCCATGGTATCACCCTGTCTTCC------------AACTGGAATCTTACTACTGCGAAGAACCTAGCTACTGACTAAAA
GTGCTTGATCCTGAACTTCCACTCCCCCTTCACGGCATCAAACGCCACGAATTCAGCGCCATTCTTCTCGGTCCATTGCG
CCAGAATCTCCTTATACCTGTCGACTTCTGGACCTTCCGTCAACTGCAACCCGGTCTTCTTATCGACGCATTTCACATTC
AGGAGGGTGATCTCTGCAGGCTTGTTGAGCTCCTGCCCCACAGGAGGTCTCTTGCTCTCATCTGTGTAGACCAGGATCTC
GCGGTCCTTGAACTCTACGATGGAAGCGATGTCGAGCTTCCTCACATCAGTTTCTCCATCAAACTTGATGCTGCCATAGC
CATGCCTGCCGACCGTGAAGTCCTTCACATGTGAGCAACAACCTGGCTCGTTGCTTTCTCGTGCAGCAAGCTCTGCGATA
GACGGCGAGGTGTAATAGTCTGCCTTATAGAGCCGAGGAAGCACACTTTCACTCACAGGGGCACCACCAAATGGAGTTAT
CACAGGATCAAATGGATTACTCCTAGCCAGGACAGCACCGTTGATATACCCTTTCTGTTCCCCAGCGGATCCTGATGATG
GTGAACAAGATGTCAGTAACTCAAT-GCATATATCGTATGGCAACACACAAAGCATGAAGT-AGCTTTGGTTCTGAGATA
TCAAATATTTTGACATTTGGGCTCCACAAGTGCTA---------------------------------------------
-------------------------------------
>chr5D_1922
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--------------------------------CCCTCCGTCAACTGCAACCCGGTCTTCTTATCGACGCACTTCACATTC
AGGAGTGTGATCTCTGCAGGCTTGTTGAGCTCCTGCGCCACAGGTGGTCTCTTGATCTCATCTGTGTAGACAAGGACCTC
ACGGTGCTTGAACTCCACGATGGATGCGATGTCGAGCTTCCTCACATCGGTTTCTCCATCAAACTTGACGCTGCCGTAGC
CATACCTGCCGACCCTGAAGTCCTTCACATCTGAGCAACAATCTGGCTCGTTGCTTTCTCCTGCAGCAAGCTCTGC----
------AAGGTGTAATAGTCTGCCTTATAGAGCCGAGGTAGCGCACACTCACTCACAGGGGCACCACCAAATGGAGTTAT
CACAGGATCAAATGGATTCCTCCTAGCCAGGACTGCACCATTGATATACCCTTTTTGTTCCCCAGCAGAT----------
-----CAAGATGTCAGTAACTCAAT-GCATATATCGCATGGCAACACACACAGCATGAAGTTAGCTTCGGTTCTGAGAT-
TCAAATATTTTGACATTTGGGCTCCACAAGTGCTA---------------------------------------------
-------------------------------------
>SNPs
SS---------S--S--S-S----------------SS-S-----------S--------S--S----------------
---------------------------------------------S------------S----------S----------
------------------------------------------------------------------S-------------
-----------------------------------------------------------------------------S--
--------------------------------------------------SS--------S----------------S-S
--SSS-S-------------------------------------------------------------------------
----------------------------------S---------------------------------------------
S-SSS-------SS----S-S------------S------S-----SS-S-SSSS-S-----------------------
------S---S--------S-------S-------------------------------S--------------------
-------------------------SSS----------------------------S-----------------------
---------------S----------------------------------------------------------------
------------S---------S---------------------------------------------------------
-------SSSS---------S-------------------------S------S---------SSS-SSSS---------
S------------------------S-S-----------S----------------------------------------
--------------------------------------------S-----------------------------------
----------------------------------------------------------------S--------------S
SSSS----------------------------------------------------------------------------
------------S----------------------------------S--------------------------------
--------------S---S--------S--------------------------------------------------S-
----------S--------------------------------------------------SS----------------S
SS--------------------S-----------------S-SSSS----------------------------------
--------------------------S-------------------S--------S--------S--------------S
SS----------SSSSS-----SS--S---S--S---S---SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----------------------------------------
-------------------------------------------------------SSSSSSS----------S----S--
----------------------S---------------------------------------------------------
---------------------------S----------------------------------------S-----------
-----------S----------S---------------------------------------------------------
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----------------S---------------------------------------------------------------
--------S--------------------------------S----------------S---S-----------------
----------------------------------------------------------------------S---------
-------------------------S---------S------------S-S--S--------------------------
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>forward_1080
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--------------------CGAATTCCTCTCCCTCTGGC----------------------------------------
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>reverse_1993
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------------------------------------------------------------------------AGCCACAG
AGCCATGGTATT--------------------------------------------------------------------
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