>input_sequence_49198
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--------------------------------------------------ATGGCCTCGGAGCGTCGAGGACACCGTTCC
ATTTCCTCGTGCATCCTCCTCGTCGCGGTCGTCCTGCTGCTCAGCGCTCCCGGGTCATCTGCTAGTTGCTACAAGCGCAT
CTTCTCCTTCGGCGACTCCATCATCGACACCGGCAACTTCGTGTATTCGACCGGCAGCGCTCCAAACGCGTTGAAGGAGT
TCCCATATGGGATGACCTTCTTCCACCACCCCACAGGCCGCGTCTGTGACGGGCGCGTCCTCCTTGATTTCTACGGTGAG
TGCAGTGCACAGCACATG----GATATAGCTACCTCTTTGTGCTCACAATAGTGTCTGGCTGTGCTGACAACTGTGTCCG
TACGTGTTGCAGCGCAAGCGCTGGGTCTGCCGCTGGTACAGCCAAGCTTGCCCGAGCAGAGATCGGGACAATGCACATTC
GGTGCCAACTTCGCAGTGTTTGCTGCCACGGCGCTTCCCC-GGAGTACTTCAAAAGATGGGGCCTTGGTATTCCCGGGTC
TGCCAACCTGGGCATGCAGATGGGCTGGTTCAAAGAAGTATTACAACGGATAGCACCAGGGCCCGGTAATCAAACTAACC
ACGGGGTTTAGCA------------------TATCAGTTTTAGTTACTAGAGTAGCTACTAGTACATGATAAGTACTGCT
TTATTAATTGGGCTACGTACGATGATGTGCCAGGTGCGAGGAGACTCCTGGGAGAGTCTCTCATCATATTGGGCGAGATC
GGTGGCAACGACTACAACTTCTGGTTACTCAACAATAATAAAACACGTGAAACAGCCTACCAGTTCATCCCAGACGTAGT
CAACCGCATCATCAGTATTGCTCAGGTGCTTACACGCCATCAATTAGCCAGTACAAACAAATCATGCATATATACATCAA
TGCATCGTATTCGTAGGT------GGTTTCATCTGTCATCGTATGCATGCAGGAGCTCATCGACCTCGGCGCGAAGACGA
TCATGATCCCGGGGAACTTCCCCATCGGGTGCGTGCCCAAGTACCTGAACGATCACCAGACGGGTAACCGTGCAGACTAC
GACCAGTTCGGCTGCCTCAGGTGGTACAACGACTTCTCCATGAGGCACAACACGGCGCTGTCCAACGAGGTCAACAGGCT
CAGGGCGCGGCATCCATGGGTGAAGCTCATCTACGCCGACTACTTCGGCGCCGCCATGGAGATCTTCAGGAACCCACACA
GATTTGGTCAGTAACCGACGCCCGATCGCATTCCTTCTCCTAATCTAAGCGGACTACATGTGTATTTGGTTCCATGCGCC
GCGCTCATTGCTCGACCGTTTTGCGTTTGGGAATGCAGGTATCGGTGATCCTCTGGTGGCATGCTGCGGCGGCGGTGGCC
GGTACCACGTCGGGACATGCGACAAGCACTCCACTATTATGGGTTCCCCGGCTAACTGCGCCAATTGGGACGGCATCCAC
ATGACTGAGAAGGCCTACAACGTCATCGCCGATGGGGTGTTGCATGGGCCGTACGCGAACCCGCCGCTGTTGCATTCTTG
CTAG----------------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G235900
CTGCTGGTGAAATTAATATATTTTCTTCCAAAATTGCGCCGAATTTGGGTTCTCTTCTTCTCTATTCTTGTCCAGAATTT
GCATTTCCATTTGATATCAAGTTCATCTTGATTTTATTTTCAACCAAAGTCTATATTTTTGTCGTCCCAAATAAGTTTTG
TTTGAAGTTATTGAGGATCGGTTGTGAAAAATATGCATTTTTTTCAAAAACAAATGTATAACTATCTTCCTTATTTTGTT
TTCGACAATTGTCTTAATAATTGCCCTCATTGCAATTGGATTTTCTTTCAAATATGTTCTAACCTATTATTAGAATCCAT
TCCTGAAACCTACCACATGTTAACATTTATATAACATTGTGTGCGTCTTTCTATCGGATGCACATCTGTTGGCTAGTGGC
ATCCATTTGTAGAAGTGTTGGAATATACATTGTAGCTTCTTAATTTAGAACATTTGTAGGGTTTTTTTTTGTACAAATAT
AACCAATGGGCCAGTTCGGCAGTTTCTAGAGTCAACCAGTGGATATATATGAAGAATATCATTTTCATAGTAATATTATG
TCATTATAATAGATATATGTGCATATTAATGTATATGCCATGGTACAATTAATGTATGTGCCCTCGTTCGATTTGATATC
ATCGG---------------------------------------------------------------------------
---------------ATGTAATAAGATTTTATATTATGGGACGGAGAGAGTATCTTGAATTATTGAACTGTATTATTAAG
ATTAAGGGCTGGCGACGCGAAGAAATTATTCGTCAAACTTTATATATAGAGGATATAAATCTCAAAAAAAAATATAGAGG
ATACAAATCTATCGTTTAGATACATAACAAAAGAAGAGAAACGCAAGAAATGTATCTTCAGGATATCGGTGTACTCACTG
CCATCGTATTTACCCCTGCTAGTAGAATTCGGCCTGAAGATGCTATAAAAAGGAGGTCAAATGAACTACTTCGGATCACA
AACCAGTCACCGTGTCAGCCTGCAAACGTTGTAGCAACAGCAGTGTCTCGATGGCCTCGGAGCGTCGAGGACACCGTTCC
ATTTCCTCGTGCATCCTCCTCGTCGCGGTCGTCCTGCTGCTCAGCGCTCCCGGGTCATCTGCTAGTTGCTACAAGCGCAT
CTTCTCCTTCGGCGACTCCATCATCGACACCGGCAACTTCGTGTATTCGACCGGCAGCGCTCCAAACGCGTTGAAGGAGT
TCCCATATGGGATGACCTTCTTCCACCACCCCACAGGCCGCGTCTGTGACGGGCGCGTCCTCCTTGATTTCTACGGTGAG
TGCAGTGCACAGCACATG----GATATAGCTACCTCTTTGTGCTCACAATAGTGTCTGGCTGTGCTGACAACTGTGTCCG
TACGTGTTGCAGCGCAAGCGCTGGGTCTGCCGCTGGTACAGCCAAGCTTGCCCGAGCAGAGATCGGGACAATGCACATTC
GGTGCCAACTTCGCAGTGTTTGCTGCCACGGCGCTTCCCC-GGAGTACTTCAAAAGATGGGGCCTTGGTATTCCCGGGTC
TGCCAACCTGGGCATGCAGATGGGCTGGTTCAAAGAAGTATTACAACGGATAGCACCAGGGCCCGGTAATCAAACTAACC
ACGGGGTTTAGCA------------------TATCAGTTTTAGTTACTAGAGTAGCTACTAGTACATGATAAGTACTGCT
TTATTAATTGGGCTACGTACGATGATGTGCCAGGTGCGAGGAGACTCCTGGGAGAGTCTCTCATCATATTGGGCGAGATC
GGTGGCAACGACTACAACTTCTGGTTACTCAACAATAATAAAACACGTGAAACAGCCTACCAGTTCATCCCAGACGTAGT
CAACCGCATCATCAGTATTGCTCAGGTGCTTACACGCCATCAATTAGCCAGTACAAACAAATCATGCATATATACATCAA
TGCATCGTATTCGTAGGT------GGTTTCATCTGTCATCGTATGCATGCAGGAGCTCATCGACCTCGGCGCGAAGACGA
TCATGATCCCGGGGAACTTCCCCATCGGGTGCGTGCCCAAGTACCTGAACGATCACCAGACGGGTAACCGTGCAGACTAC
GACCAGTTCGGCTGCCTCAGGTGGTACAACGACTTCTCCATGAGGCACAACACGGCGCTGTCCAACGAGGTCAACAGGCT
CAGGGCGCGGCATCCATGGGTGAAGCTCATCTACGCCGACTACTTCGGCGCCGCCATGGAGATCTTCAGGAACCCACACA
GATTTGGTCAGTAACCGACGCCCGATCGCATTCCTTCTCCTAATCTAAGCGGACTACATGTGTATTTGGTTCCATGCGCC
GCGCTCATTGCTCGACCGTTTTGCGTTTGGGAATGCAGGTATCGGTGATCCTCTGGTGGCATGCTGCGGCGGCGGTGGCC
GGTACCACGTCGGGACATGCGACAAGCACTCCACTATTATGGGTTCCCCGGCTAACTGCGCCAATTGGGACGGCATCCAC
ATGACTGAGAAGGCCTACAACGTCATCGCCGATGGGGTGTTGCATGGGCCGTACGCGAACCCGCCGCTGTTGCATTCTTG
CTAGAGTTGTTGATTGCTCGCTTTGTTCCCATACTTGCATCGGCCTGTGAACTGAATGAAAGAAATAAAATAGTCAACTA
AACAGTATAGTACTTTGTCTTGCTCAATGCAGATTCACCGTAGTACACCCTCCGTCTCATAATATAAAATGTTTTATATC
ATGAGACGAAGGGAGTATTATTTAAGCTAATCGTCATACTCGCCTAAACCCTTGTTTCAAAAAACATACTCGCCTAAACA
CAATACAACTTCGAAGCGCGCACATACACGTATAAATACA----------------------------------------
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---------------------------CCAAACATCAACGTTTTCTTTTTGAAAAGGAGGCCCTCGGTCTCATCAAAGTG
ATGCGCACAGCCATACACCCAGACATTGAGCATGAGACGGGTCTAGCGTTTACATT-GTAAATGACACTCTCTTTTTTTC
GGA--TGAAATGATACTCTTTATTTGTCATGCCAAGACTCTGACAATTTTCACAACTCATCTCAATGTCTCACTCCAAAG
TTTGGGCTATATAATCATTGGTGTCGACGACTAATGCATCTC-GATCTTACGATTTACTAGAGATCGCAGAAGACTATAG
AGGGAATAGTTATGCCCGAAGTGGTCTCATCGGCGATGATGGTGAAACGGTGGCTTTATCCCTGGAGACCTTCTGCCCTA
TTTTTAGGTTGACATGTGCTCGTGATTAGGTAGCTAGCTTCGGGGAGAGACAATATGGTCTATTGCTACCACAGTTACGT
GAACGTAGCACCTATAACAGTCAAGTCCTAGACTTTGCGTGCACATCCTTGTCCTTTCGAGTGTCTACTCAAGCATGACT
AGTGCGGGGGCGCATAGATATTTGTTGGTGGACTTGATCCATGCACGCCCATAGGGATACCCTGCCTATATACACCTGTA
CACGGTGAAAAGCCCATGGTAATATCTGAAATGAAGTTGCAATTTTACTCAAAAGAGATGGAGTTGGGGGAGTAGCATCC
AACATTGTCCTCTGCGAGTCTTTCCCGTCTATCTT
>chr3A_6
-----GGTGAAATTAATATATCTTCTTCCGAAAGTACGCCTAATTTGGGTTCTCTTCTTCTCTATTCTTGTCCAGAATTT
GCATTTCCATTTGATGTCAAGTTCATCTTGATTTTATTTTCAACCAAAGTCTATATTTTTGTCGTCCGAAATAAGTTTTT
TTAGTTC--ATTGAGAATCAATTGTGAAAATATGCA--TTTTTTTAAAAACAAATGTATAACTATTGTCCTTATTTTGTT
TTCTACAATTGTCTTGATAATTGCCCTCATTGCAATTGGATTTTCTTTCAAATATGTTCTAACCTGTTATTAAAATCCAT
TCCTGAAACCTACCACATGTTAACATTTATATAACATTGTGTGCGCCTTTCTATTGGATGCACATCTGTTGGCTAGTGCC
ATCTATTTGTAAAAGTGTTGG-ATATACATTGTAGCTTCTTAATTTAGAACATTTGTAGCGC---TTTTTGTACAGAGAT
AACCAGTGGGCCAGTTCGGCAGTTT-----------------ATATATATGAAGAATATCATTTTCACAGTAATATTATG
TCATTATGATAGATATATGTGCATATTAATGTATATGCCACGATGCAATTAATATATGTGCCCACGTGTGATTTGATATC
ATATACTTCCTCCATCCCATAACATAAGATCTTATTAGATCCAATATACTCACGTATTGAATGTAATAAGATCTTATGAG
ACGGCAGTATATTGAATGTAATAAGATTTTATATTATGGGACAAATGGAGTATCTTGAATTACTGTACTGCATTATTAAG
ATTATGGCCG------GCGAAGAAATTATTCATCAAACGTTATAAATAGAGGATATAAATCTCAAAAAAA--TATAGAGG
ATATAAATCAATCATTTAGATACATAAGAA---AAGAGAAATGCAAGAAATGTATCTTCACGATGTCACCGTACTCACTG
CCATCGTATCTACCACTGCTAGTAGAATTCGGCCTGAAGATGCTATAAAAAGGAGGGCAAATGAACTCCTTCGGATCACA
AACCAGTCACCGTGTCAGCCTGCAAACGTTGTAGCAACAACAGTGTCTCGATGGCCTCGGAGCGTCAAGGACACCGTTCC
ATTTCCTCGTGCATCCTCCTCGTCGCGGCCGTCCTACTGCTCAGCGCTCCCAGGTCATCTGCTAGTTGCTACAAGCGCAT
CTTCGCCTTCGGCGACTCCATCATCGACACCGGCAACTTCGTGTACTCGACCGGCAGCGCTCCAAACGCGCTGAAGGAGT
TCCCATATGGGATGACCTTCTTCCACCACCCCACAGGCCGCGTCTGTGACGGGCGCGTCCTCCTTGATTTCTACGGTGAG
TGCAGTGCACAGCACATGCATGGATCTAGCTACCTCTT-----------TAGTGTCCGGCTGTGCTGACAACTGTGTCCG
TACGTGTTGCAGCGCAAGCGCTGGGTCTGCCGCTGGTACAGCCAAGCTTGCCCGAGCAGAGATGGGGACAATGCACATTC
GGTGCCAACTTCGCGGTGTTTGCTGCCACGGCGCTTCCCCCGGAGTACTTCCAAAGACGGGGCCTTAGTATTCCCGGGTC
TGCCAACTTGGGCATGCAGATGGGCTGGTTCAAAGAAGTGGTGCAACGGATAGCACCAGGGCCCGGTAATGAAATTAACC
ACGCGTCCATGCATGCATGCTAAAACCGTACTATCAGTTTTAGCTAGCTACTGTACTGCT-------------------T
TTATTAATTGGGCTACGTACGATGATCTGCCAGGTGCGAGGAGACTCCTGGGAGAGTCTCTCATCATATTGGGCGAGATC
GGTGGCAACGACTACAACTTCTGGTTACTCAACAATAATAAAACTCGTGAAACAGCCTACCAGTTCATCCCAGATGTTGT
CAACCGCATCATCAGTATTGCCCAGGTGCTTACACGCCATCAATTAGCCTGTACAAACAAATCATGCATTTATACATCCA
TGTATCGTATTCGTAGGTGTAGGTGGTTTCATCTGTCATCGTATGCATGCAGGAGCTCATCGACCTCGGCGCGAAGACGA
TCATGATCCCGGGGAACTTCCCCATCGGGTGCGTGCCCAAGTACCTGAACGACCACCAGACGGGCAACCGTGCAGACTAC
GACCAGTTCGGCTGCCTCAGATGGTACAACGACTTCTCCATGAGGCACAACACGGCGCTGTTCAACGAGGTCAACAGGCT
CAGAGCGCGGCATCCATGGGTGAAGCTCATCTACGCCGACTACTTCGGCGCCGCCATGGAAATCTTCAAGAACCCACACA
GATTTGGTCAGTAACCGACGCCCGATCGCATTTCTTCTCCTAATTAAAGCGGACTACATATGCGTTTGG-TCCATGCGCC
GCGCTCATTGCTCGATCGTTTTGCGTTTGGGCATGCAGGTATCGGTGATCCTCTGGTGGCATGCTGCGGCGGCGGTGGCC
GGTACCACGTCGGGACATGCGACAAGCACTCCGCTATTATGGGTTCCCCGGCTAACTGCGCCAATTGGGACGGCATCCAC
ATGACTGAGAAGGCCTACAACGTCATCGCCGATGGTGTGTTGCATGGGCCATACGCGAACCCGGCGCTGTTGCATTCTTG
CTAGAGTTGTTGATTGCTCGCTTTGTTCCCGTACTTGCATCGGCCTGTTAACTGAATGAAAGAAATAAAATAGTCAACTA
AACAGTATAGTAGTTTGTCTGGCTCAGTGCGGATTCGTCGTAATACTTCATCCGTCTCATAATATAAAACGTTTTATATC
ATGAGACGGAGAGAGCACCATTAAGCTAACT---------------------------------CATACTTGCCTAAACA
TATACAATAACTGATCAGTATTATTAGATTTATTATTAAATATACTTTCACATCATATAAATTTGTTTAAGTAAATATTT
CTACGTTTTTCTATAAACTTTGTCAAACTTCACGAAGTTTGATTTCAGTCAACTCTAATATGCAGAGTAAATAAAAATAG
AAGAAGTATACGTAACTTCTGAAACACCCAAATATCAACGTTTTCTTTTTCAAAAGGAAGCCCTCGGTCTCATCAAAGTG
ATTCACACAGCCATACATCCAAACATTGAGCATTAGACGAGTCTAGCGTTTACATTTGTATATGATACTCTCTCTTTTTT
GCCGGTGAAATGCTACTCTTTATTTGTCATGCTAAGACTCTGGCCATTTTCACAACTCATCTCAATGTCTCACCCAAAAG
TTCCGGCTATATAATCATTGGTGTCAACAACTAATGCATCTTTGATCTTACGATTTACTAGAGATTGTGGAAAACTGCAG
AGGGAATGGTAGTGCCTGAAGTGATCTTATCGGCGATGATGGTGAAACGCTGATTTTATCCTA-GAGACCTTCTGCCCTA
TTTTTAGGTTGACATGTG--------------------------------------------------------------
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>SNPs
SSSSS----------------S-------S---S-S----S---------------------------------------
---------------S---------------------------------------------------S-----------S
--S-SSSSS------S---SS---------SSSSSSSS------S--------------------SS-------------
---S-----------S-------------------------------------------------S------S-------
---------------------------------------------S--------S-----------------------S-
---S-------S---------S-------------------------------------S-SSSS----------S-S--
-----S-------------------SSSSSSSSSSSSSSSSS-------------------------S------------
-------S--------------------------------S-S-S--------S---------S---SS-----------
--SSS---------------------------------------------------------------------------
------------------------------------------SS-SS---------------S--S----S---------
----S--S-SSSSSSS---------------S------S-----S-------------------------SS--------
---S-----S---S-------------S--SSS--------S------------------S---S--SSS----------
---------S----S-----------------------------------------S----------S------------
---------------------------------------S--------------------------S-------------
----------------------------S------S---------------S----------------------------
----S----------------------------------------S------------------------S---------
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-------------------------S------------SSSSSSSSSSS-------S-----------------------
---------------------------------------------------------------S----------------
--------------S------------------------------------S-----S--------S-------------
-------S-------------------------------SS-S---------------------------S---S-----
---S-SSSSS---------------------------------S--SSSSSSSSS--S--SSSSSSSSSSSSSSSSSSS-
--------------------------S-----------------------------------------------------
--------------------------------------------S-----------------------------S--S--
---------------------S---------------------------S-------------------S--------S-
--S-----------------------------------------------------------------------------
----------------------------------------------------S-----------S---------------
--------------------S----------------------------------------S------------------
---S--------------------------------------------------------S-------S-----------
--------------------------------S-----------SS-------------S--SS-----S----------
---------------S---------------S------------------------------------------------
--------------------------------S-----------------------------------------------
-----------------------------------S--------------S------------S----------------
------------------------------S-----------------S-------------------------------
------------S-------S-----S---S-----SS----S---SS-S-------------------S----------
--------S--S---S-SS---S-SSSS-S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------S---------
S-SSSS-SSSSS--SSS-SSSSSS--S-SS---S-S--S-----------------------------------------
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--------------------------------S-----------------S-------S---------------------
--S-S------------S---S-----------S-----S--------------------S----S-------S-----S
-SS---------S-------------------S---------S-S----------------------------S-S----
--SS---------------------S--S------------S-----------------------S-SS---S---SS--
-------S--SS----S------S---S---------------------S--SS-------SSS----------------
------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_399
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-----------------------------------------------------------GCACATCTGTTGGCTAGTGG-
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>reverse_1942
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---------------------TCAGGTGCTTACACGCCATC---------------------------------------
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>forward_1246
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--------------------------ACACCGGCAACTTCGTGTAT----------------------------------
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>reverse_2895
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--------------AGCGCGCACATACACGTATA----------------------------------------------
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