>input_sequence_68858
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-----------ATGGTGGCTGTGGATGCCTCCACAGGGGTGATGAACGCCCTCCTGTGCAAGCTCTCCAAGCTGCTGGAG
GACGAGTACTCCAGGCTCAAAGGCGTGCGCCGTCAGATAACTTTCCTGAGGGACGAGCTGAGCAGCATGAACGCCGTGCT
GGAGACGCTCGCCGACGCGGAGCAGCTCGACCCTCTCAAGAGGGAATGGCGGGACAAGGTGCGCGAGCTCTCCTACGACA
TAGAGGATTGCATCGACGACTTCGTGGACCGCG---------------GCGAGGAGCTGCGGACAGGCCTCAAGGGGTTC
TTCAGCAAGCTGAGGAAGCTCAAGGCCCGCCGCGAGATCGCCGGCGAGATAGAGCAGCTCAAGATCCGCACCATCGAGGC
GAGCGAGAGGCGCAGGAGGTATGACTTTCTTGAGCCGGCCCAGAGTTCTGGCGCTTCTTCTGCG-TCGACCCTCGGCTGC
CGGCGCTGTACGAGGATGCGGCTAGGCTTGTGGGCATCGATGGCCCCAAGGAGCATATCCTTGGCTGGTTCTGCAAGGAG
AAGGAGCATGATGACCTCAGGGTGTTGCCGATTGTGGGTTCCGGAGGCCTTGGCAAGACCACTCTTGCAAACCAAGTGTA
CTGTCAGTTAAAAGGCCAATTTCAGTGCACAGCTTTTGTGTCGGTGTCTCGGAATCCAAACATGCAGAAGATTTTACGGC
AAATGCTCACGGAGTTTGGGATCAGCGGTGGTGCACTGGATGAGGAACGGCAACTCATCGACAGGATAAGAGACCACCTC
AAAGATAAAAGGTAA-----------------------------------------------------------------
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>chr3A_1_TraesCS3A01G076000
GTAGACGCGTAGCAGCATCCTTCTAAAAAAGGTTCAAATATTAAA-AAAATGTCTACATTATTTTATTAAGAAATTCAGA
ATTTTCTCCATGTTTTTTTAGAACT--AGAATTTTCTCCATGTGGGCATGACTTTCGCATGTGGCCTGAACCGTGCCACG
GGCCGGTGGGCTGGCCCGATACTTCCACA-AAATCCCGGGCCCACTGTCACTCCACCACCATGGAGGCTCCCACCCCGGT
GACGGCGACCTCCTCTCCTCTCCTTGGAGGCTCGGCGGCGGCGACGGCGGCCATCGCCCTCGGGCAACTCACTGGTTTTA
GTCCTGATTTGACCACCCGCCATTCCTTCGTAGCTAACTCACCACCTGCATCCCTTGCCTTGCTTTGTAGGCCGCTGCCC
GGCTCGCAAGGACGACCTAGCCCCCTTCTGAGTTCTGAGCTCCCCTCCTATCGCTGATGCATACGGGGAGGTTACTTCGA
AATCTGCGGAGGAGGTTCAAGCGTCTTCTCCGACTCCGGCCGACCACCGGCCCCTTCTGTTGGTCCCGGTGAGCCTGCCT
GCTTATCTTGTTACATGTACCAGTATGTATTAGCTTCAGAAGAGGTGTCAGCCGTGTGTGCTTTCTGCCGACGCCGTGCT
GATAATAATCGTGAAACCACCACGTTCACATGGCATTGCTCCATAGGATACCCACAAGGTGCTCCATCCCCATGTGGCCA
TCAGTGTCACATCCCATCTCCTCCTGTCAATGCATGACTAGTTGGAAACTTGCAAGGGAAAAGTTTCCCCATTTCCCCAG
ATCCGTTTGAAAATTGAGG-CGGGGCACCTAGAATTCTTGAATGCGTCCAAAGAAAATGACAGCGCCCGGACCGTAATGT
CATATCTTTCCATCTCTTGCTAAATGGGATGCCACCTAGTTGCTCAACTCACACCACATCCTCTCAATTCGGCAGCTAGC
CACGC---------TTGTCCAGCTCGCAGAT-------------------------------------AATCTCGAGAGA
GAGAGGGAGCTATGGTGGCTGTGGATGCCTCCACAGGGGTGATGAACGCCCTCCTGTGCAAGCTCTCCAAGCTGCTGGAG
GACGAGTACTCCAGGCTCAAAGGCGTGCGCCGTCAGATAACTTTCCTGAGGGACGAGCTGAGCAGCATGAACGCCGTGCT
GGAGACGCTCGCCGACGCGGAGCAGCTCGACCCTCTCAAGAGGGAATGGCGGGACAAGGTGCGCGAGCTCTCCTACGACA
TAGAGGATTGCATCGACGACTTCGTGGACCGCG---------------GCGAGGAGCTGCGGACAGGCCTCAAGGGGTTC
TTCAGCAAGCTGAGGAAGCTCAAGGCCCGCCGCGAGATCGCCGGCGAGATAGAGCAGCTCAAGATCCGCACCATCGAGGC
GAGCGAGAGGCGCAGGAGGTATGACTTTCTTGAGCCGGCCCAGAGTTCTGGCGCTTCTTCTGCG-TCGACCCTCGGCTGC
CGGCGCTGTACGAGGATGCGGCTAGGCTTGTGGGCATCGATGGCCCCAAGGAGCATATCCTTGGCTGGTTCTGCAAGGAG
AAGGAGCATGATGACCTCAGGGTGTTGCCGATTGTGGGTTCCGGAGGCCTTGGCAAGACCACTCTTGCAAACCAAGTGTA
CTGTCAGTTAAAAGGCCAATTTCAGTGCACAGCTTTTGTGTCGGTGTCTCGGAATCCAAACATGCAGAAGATTTTACGGC
AAATGCTCACGGAGTTTGGGATCAGCGGTGGTGCACTGGATGAGGAACGGCAACTCATCGACAGGATAAGAGACCACCTC
AAAGATAAAAGGTAAACCCGGTAACCCACTCATATCATGATTTCTTATTAACATTTTTTTTGAGTTGGTCTTTTTAACAT
TTTGGTAATGCACATAGTAATGAATATTCGTACACTTCAAGAAATAAAGATGGTCATATGTCTTCAATTCTGTGCAAAAT
AAGTTTGAAGCATATTTTTAGGGTTGAATGAAAAGTTCAAAGCAATAATAGGCAACTCTCTGTTAAAACATGTAACAGGT
ACTTGGTTGTAATTGATGATGTATGGGACGTCGAAGCATGGAAAGCTATCAGGCTTGCTCTGTTCAACAAATAAGTGCGG
TAGCAGAATCATCACCACAACGCGTAACGTTGCCATCGCATCATATTGCTCAGGCGACAGCAGTTATGTTTATCAAATGG
AGTCCCTTAATTCTTCCGACTCCAGACGGCTATTTTTTAAAAGATCATTTGGTTCAGAAGAACTGTGCTACCCTCACCTG
GAAGAAGTTTCTAGCCAGATATTGGCAAAATGTGGTGGACTTTCATTGGCGATTATTACCTTGTCCAGCTTGTTAGCTGA
CAAGCATGCAAACGATGAATGGAACAGGGTGGAGTGAATAGCAAAAAACTACCACATTACGGGCTATCGTTCCGAAAAAC
TACCGCTTTTTTAAATTTTTCAAAAAACTACCACAAAAGTTGCTGGCTGTTCCAAAAAACCCAAGTGGCCGAACGGTTAA
GTTTTAACTGGGGTTATGACATGTGGGGCCCGCCCGTCAGGGTTTTGTCGGCCACAGTGCTCACGGCACGCGGGTGACGG
CCGTTAGGGCGCACGGGCCGCCCCGACCAGGTCAAAACGGCCGCCCCCTCACTCTGTCTCCCTCGCGCTCACTCACTCTC
ACTCTCCCCCCTCACTCTCACTCCCCCCTCGCTCTGTTTCCCCTGGCCGAGCTCTCCATCGTCGCCGACCACCTCAGTTC
CTCGTCGCCGGCCAGGATGCCTTCTTGGAATGATGGGGATGAGAGCTCCGACGAC
>chr3D_21
--------------------TTCTAAAAAAGGTGCAAATCTTAAAGAAAATGTCTACATTTTTGTATTAAGGAATTCTTT
TTTTTGAGGGTATGTATTAAGGAATTCAGAATTTTCTGCATGTGGGTGTCACTTTCGCAGGTGGCCTGCACCGTGCCACC
GGCTGCTGGGCTGGCCCGATACTTTCACAAAAATCCCGGGACCCCCTGGCACT--CCACCATGGAGGCTCCCACCCCGGT
GACGGCGACCTCCTCC-----CCTTGGAGGCTCGTCGGCGGCCATCGCCCGTGGCAAA----------TCACTGTTTTTA
GTCCTGATTCCAGCACCCACCATTCCTCCCCACCTAACTCCTCACCTGCATCCCCTGCCTTGCTTTGTAGGCCGCGGCCC
GGTTCGCAAGGACGACCTAACCCCCTTCTGAGTTCCCCTCCTCC-------CGCTGATGCATACGGGAAGGTTAATTCGA
AACCTGCGGAGGAGGGTCGAGCGTCTTCTCCGACTCCGGCCGACCACCGGCCCCTTCTGTTGGTCCCGGTGAGCCTGCCC
GCTTATCTTCCACCTGTTAATGTATGTAGAGCTTCCGGGGTGTC------GCCGTGTGTGCTTCCTGTCGACACCGTGCT
GATAATAATCGTGAAACCACCACGTTCACATGGCATTGCTCCATAGGATACCCACAAGGTGCCCCATCGCCATGTGGCCA
TCACTGTCACATCCCATCTCTTCCTGTCAATGCATGGCTAACTGGAACTCTGGAAGGGAAAAGTTTCCCCATTTCCCCAG
ATCCGTTTGAAAACTGAGGCCGGGGCACCTAGAATTCTTGAATGCGTCCAAAGAAAATGACACCACATAC----------
----TCTTTCCATCTCTTGTTAAATGGGATGCCACCTAGTTGCTCAAATCACACCACACACTCTCAATTCCTCAGCAACA
TCCTCCTGCCCTCGTTGTCCAGCTCGCAGATGCCTCAGCTTCTCTGTAGCAGGAGGTCAGGCTGACCAAATCTCGAGCGA
GAGAGAGAGCTATGGTGGTCGTGGATGCCTCCACGGGGGTGATGAACGCCCTGCTGTGCAAGCTCTCCAAGCTGCTGGAG
GACGAGTACTCCAGGCTCAAAGGCGTGCGCCGTCAGATAACTTTCCTCAGGGACGAGCTGAGCAGCATGAACGCCGTACT
GGAAACTCTCGCCGACGCGGAGCAGCTCGACCCTCTCAAGACAGAATGGCGGGACAAGGTGCGCGAGCTCTCCTACGACA
TCGAGGATTGCATCGACGACTTCGCGGACCGCGTCGGCGATGACCGTGGCGAGGAGCTGCGGACAGGCCTCAAGGGGTTC
TTCAGCAAGCTGAGGAATCTCAAGGCCCGCCGCGAGATCGCCGGCGAGATACAGCAGCTCAAGATCCGCACGGTCGAGGC
GAGCGAGCGGCGCAGGAGGTATGATTTTCTTGAGCCGGCGCCGAGATCTGGCGCTTCTTGTGCCATCGACCCTCGGCTGC
CGGCGTTGTACGAGGATGCGGCTAGGCTTGTGGGCATCGATGGCCCCAAGGAGCATATCCTTGGCTGGTTCTGCAAGGAG
AAGGAGCATGATGATCTCAAGGTGTTGCCGATTGTCGGCTCAGGAGGCCTTGGCAAGACCACTCTTGCAAACCAAGTGTA
CTGCCAGTTAAAAGGACAATTTCAGTGCATGGCTCTTGTGTCGGTGTCTCGGAATCCAAACATACAGAAGATTTTACGGC
AAATGCTCACCGAATTTGGGATCAGCGGTGGTGCACTGGATGACGAACGGCAACTCATCGACAGGATAAGAGACCACCTC
AAAGATAAAAGGTAAACCCGGTAACCCGCTCATATCCTGATTTC--------------------------TTTCTAACAT
TTTGGTAATGCAGATAGTAATGAATATTCTTACACTTCAAGAAATAAAGATAGTCATATGTCTTCAATTCTGTGCAAAAT
AAGTTTGAAGCATCTTTTTTTAGGT---TGAAAAGTTCTAAGCAATAATAGACA--------TTAAAACATGTAACAGGT
ACTTGGTTGTAATTGATGATGTATGGGACGTCGAAGCATGGAAAGCTATCAGGCTTGCTCTGTTCAAT-AATAAGTGTGG
TAGCAGAATCATCACCACAACGCGTAACGCTGCCGTCGCGTCATATTGCTCAGGTGACAGCAGTTATGTTTATCAAATGG
AGTCCCTTAATTCTGCTGACTCCAGAAGGCTATTCTTTAAAAGAGCATTTGGTTCCGAAGAAGTGTGCTACCCTCACCTG
GAAGAAGTTTCTAACCAGATATTGGCAAAATGTGGTGGACTTCCATTGGCGATTATAACCTTATCCAGCTTGTTAGCTGA
CAAGCATGCAAAAGATGAATGGAACAGGGTG-------------------------------------------------
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>SNPs
SSSSSSSSSSSSSSSSSSSS-------------S-----S--------------------S--S-------S-----SSS
S----SSSSS-S-S-S--S--S-S-------------S--------SS-S---------S--------S----------S
---S-S------------------S---------------S--S-SSSSSSSSSS-------------------------
---------------SSSSSS-------------S-------S-SS--SSSSSS-SSSSSSSSSSSSS------S-----
---------SS-S-----S--------S-SS-S-------SS------------S--------------------S----
--S----------------S---------------SSSS-SS--SSSSSSS----------------S------S-----
--S------------S--S------------------------------------------------------------S
---------SSSS-SSS--SSSSSSSSSSSSSSSSSSS-SS-SSSSSSSS-------------S---S----S-------
--------------------------------------------------------------S-----S-----------
---S----------------S---------------S---SS-----SSS--S---------------------------
-------------S------------------------------------------------S-S-SSSSSSSSSSSSSS
SSSS---------------S---------------------------S----------SS----------SS----S-SS
SS-S-------------------------------------------------------------------------S--
-----S------------SS--------------S-----------------S---------------------------
-----------------------------------------------S-----------------------------S--
---S--S----------------------------------SS-------------------------------------
-S----------------------S-------------------------------------------------------
-----------------S---------------------------------S-------------------SS-------
-------S----------------S--------------S-S---S-------------S---S----------------
-----S--------------------------------------------------------------------------
--------------S----S---------------S--S--S--------------------------------------
---S-----------S-------------SS---S----------------------------S----------------
----------S--S-----------------------------S------------------------------------
---------------------------S--------S-------SSSSSSSSSSSSSSSSSSSSSSSSSS---S------
------------S----------------S---------------------S----------------------------
-------------S-----SSS-S-SSS----------S------------S--SSSSSSSS------------------
-------------------------------------------------------------------SS--------S--
-----------------------------S----S----S--------------S-------------------------
--------------S-S---------S-------S---------S----------S------S-----------------
-------------S----------------------------S-------------S-----S-----------------
------------S------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_438
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------------------AGCCCCCTTCTGAGTTCTGA------------------------------------------
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>reverse_1526
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-----CTGTACGAGGATGCGGCTAG-------------------------------------------------------
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>forward_869
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-------------------------------------------------AAAGAAAATGACAGCGCCCG-----------
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>reverse_2711
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----------------------------------------------------------------------ACTCACTCTC
ACTCTCCCCC----------------------------------------------------------------------
-------------------------------------------------------
