>input_sequence_77619
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-------------------------------------------------------------------------ATGACCA
TGAAGTTGTTGGTGGACACCAAGGCCCAACGCGTGGTCTACGCGGAGGCCGGCAAGGACGTCGTCGACTTCCTCTTCTCC
CTCCTCACCTTGCCGCTCGGCACGGTCGCCGGCCTCCTCAACCCGGGCTCCATGTTTGGCAGCGTCGGCAACCTCCACTC
CAGCGTCGGCAACCTCCACTCCAGCGTCACCAACCTCGACGACGCTTACATGTGCCGCGACGATGCCAAGGCCGCCCTGC
GCACACCGGCCGGTCGCAAGCTTCTCCAACCGGCGCCGGCGGAGTCCGGTGACGGCGGCGTGGCGTCTCGCGCTGCTGCA
TCTGGATTTGTGCAGGGGGTCGTCACGTGCACGGTGAGGGACGGTCTCAAGGTCACGCCCGTGTCAGCCATCTCCGGGAT
CACGCTCCTCAAATCCTTGGGCATCAAGGACATCGCCTCGCTCCAGGAGAAGACGGTGCAGCTTGCCCACGCCGAGGTGA
CAAATGACTTGCTAATTCGTCAAAAAATTTAA------------------------------------------------
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>chr3D_1_TraesCS3D01G089700
ATCGGTTCGGACCTAAGAGGCACAGTCGGTGCCAATATATT--TTTTGTCAAAATCAATCCC---GCGGTGATCCGGTGG
CCCGCTTCTGAGAGCGAGGGCCGAACACAAGACCCACACTTCATCCAAAAAGTCACTTTGGTGGACGGGTGCATTGAAGT
CCTATATTTTGAATAGTGTGACATTGATATTTTTGAAGTTTCAAATTTTTAAAAAATAATTCCACATGTTCATATGGATG
TATGTTACACATGTGCAAGTTTTGATGGTGAGGTAAGTAACCATGTGAGTTACACACAAATGACAAAAACCGTGACTTTG
AAAAGATGAACAGTGCATGTATTATTCACTACTCCCTTTGTAAACTAATATAAGAGCGTTTAGATCACATAGTGATCTAA
ACGCTCTTATATTAGTTTACAGAGGGAGTACTATTTAGAAATGACCATTTT-------TTTTATAGCTCACATATTTACT
TATTTCATCACCATACTTCACACATGTGTAATA-----------------ATGATCATGCAGAATTCTTT-CGGGATTTT
TTGAAATTTTAACTGTGATTTTTAAACTATTTAAAATAAAGTCCTCCAATGCACCCATGTTCCAAAAATCCACTCTCCCA
-TCCATCTCTCTAGCTTCTCTTCCATCTCTTTTACGCAGTTAATGCAGCTGTGGTCTATTGGTCTTTCCAATATTTCATC
TTTCCCAAGTTCCACAGGATGATCATGCATATGCATGGGCATCGAGCATTGCGCTAATAAACTCACCACACGCGTGCTGG
GGTAAATCAATTCCCCAAAAAATCATCGCAGAAGATTCCCCATGAATTCTGCTTCTCTTCGCATGTATACTGTACTTATA
TATACACCCAAT--AAGAGAAGAACTACACCGTCCAAAAAGTGCATCCAGAAAACAGTCGCTACTCAGATGGCCAACGCA
AAGAGAAAGGGAGCCGGCTCTCGCAAGAAGAAAGCAAAGAAGGGAGCCACTGCCAAATGCCAATGGCACTCTAATGACCA
TGAAGTTGTTGGTGGACACCAAGGCCCAACGCGTGGTCTACGCGGAGGCCGGCAAGGACGTCGTCGACTTCCTCTTCTCC
CTCCTCACCTTGCCGCTCGGCACGGTCGCCGGCCTCCTCAACCCGGGCTCCATGTTTGGCAGCGTCGGCAACCTCCACTC
CAGCGTCGGCAACCTCCACTCCAGCGTCACCAACCTCGACGACGCTTACATGTGCCGCGACGATGCCAAGGCCGCCCTGC
GCACACCGGCCGGTCGCAAGCTTCTCCAACCGGCGCCGGCGGAGTCCGGTGACGGCGGCGTGGCGTCTCGCGCTGCTGCA
TCTGGATTTGTGCAGGGGGTCGTCACGTGCACGGTGAGGGACGGTCTCAAGGTCACGCCCGTGTCAGCCATCTCCGGGAT
CACGCTCCTCAAATCCTTGGGCATCAAGGACATCGCCTCGCTCCAGGAGAAGACGGTGCAGCTTGCCCACGCCGAGGTGA
CAAATGACTTGCTAATTCGTCAAAAAATTTAAGCGAAATTGGATTCATAGC-------TCATGCTTGATAATGTGGTTGT
GTAGGGCTTGGGGATACTGCGGGCGTCGCTGCGATCCAAGACGGTGCTCACCGACGTCTTCCTCGG---GAAGAAGAAGC
GGAAGGCTGCGAAGGCGTCCCGCCATGAAGCGGTCTCTCGAGTTGCCAGGAGGCGCCGTGCTTGGGCTGGTTCGTGGCGC
CCATGGTACGTGAGCGCCGGGCCATGCTCGACTTGTGGCTCTCGTCGTGCCAGCTGCACGGCCCGCCAACTTGCTGCTGG
CCAGCGCAAACAAGGCTGCGTTTAGAATTGATTGATCCACTAGCTTGTCGTGGTCATATTGA-CTCGTTGTTGTGAGGAT
TCTTGCGGAGTTGTCGTGTTGCCGCGTGAAGTTTGTATTCCTATTAAAATTCATGTTAGCTTCGGATGAAGAAATGATAT
ATCACTTCACTCATTTGGAGATCCTTATCTCACGTGCTAGAGCATGTCTAGCAGATCCTTATCTCACGGTATGTAAAAGA
T---TATAAGGAAAAACTAAAACCTGTTTTACGGTACCCTCCGTGATGTGTTGGAACAGATACTGCAAAAATTTACCGCA
-------------CCCGTGGTCTTCTTCTTCTTCCTCTCACGCGCGA------CTGTCTGAATCCCGAGCGGAACAGATC
ATCATCAACCATTGCACACATGGTGTAGATTGAAGGCTAGAATGAATCAGGAAGACTGGAGCGTGACCCCTAGCGAGTCG
CCGTACTTGGAGTCGACGGCCC-GGGCAGGTCAGGATGGGAAGCAGCTTGGGCCGCCGCACACCACACAGTCCGTTGCTG
CACACGATGAACCAGGCACTGCTGCACACCGCGCAGGCTGCCTCGCACACGTGGCGAAGCATCTGGCAGAGCCGCAACTG
CTTGTGCACCGCGACCACCTCTTCAGCGATGCCAACATACCTCCCGTCCACGAACAGCCGTGGCAGCAGCGGCATGTCGT
CGTCCCTCCCAAGGAGCAGCGCAGGG
>chr3B_1
ATCGGTTCAGACCTCAGAGGCACAATCGGTGCCA--ATATT--TTTTTTCAAAATCAATCCCAAGGCGGTGATCTGGTGG
CCTACTTCTGATAGCGAGGGCCGAACGCAAGACCCACGCTCCATCCGAAGAGTCACTTTGGTGGATGGGTGCATTGAAGC
CCTATATTTTGAATAGTGTGACATGGA-ATTTTTTAAGTTTCAAAAATTCCAAAAATAATTTCACATGTTCATATGGATG
TATGTTACACATGTGCAAATTTTGATGATGAGATAAGTAACCGTGTGAGTTACAAACAAATTGC-AAAACCCTGATTTTG
GAAAGCTGAACAGTGCTTGTTTT--TCAC---------------------------------------------------
-------------------------------TATTTAGAAATGGCCATTTTGGCATTCTTGTATAGCTCACATGTTTACT
TATTTCATCACCAAACTTT--ACATGTGTGTAATATCGA------TCCATATGATCATGTAGAATTCTTTTCGGGGTTTT
TTGAAATTTTAAATGTGATTTTAAAACTATTTAAAATAAAGCCCTTCAATGCACACATGTTCCAAAAATCCACTCTCACG
CTCCATCTCTCTAGCTTCTCTTCCATCTTTTTTACGCAGTTAATGCAGCTGTGGTCTTTTGGTCTTTCCAATATTTCATC
TTTCCCAAGTTCCATCATCAG--CATGCATATGCATGGGCATCGAGCATTGCGCTAATAAACTCACCAC--GCGTGCTAG
GGTAAATCAAGTCGCC-AAAAATCGTCGCAGAAGATTCCCCATGAATTCT---TCTCTTCGAATGTACTGTATATATATA
TACACACCCAAT--AAGAGAAGAACTACACCGTCCAAAAAGTGCATCCAAAAAACAGTCGCTACTCAGATGGCCAACGCA
AAGAGAAAGGGAGCCGGCTCTCGCAAGAAGAAAGGAAACAAGGGAGCCAC-------TGCCAATGGCACGGTAATGACCA
TGAAGCTGCTGGTGGACACCAAGGCCCAACGCGTGGTCTACGCGGAGGCCGGCAAGGATGCCGTCGACTTCCTCTTCTCC
CTCCTGACCTTGCCGCTCGGCACGGTCGCCGGCCTCCTCAATCCAGGCTCCATGGTCGGCAGCGTCGGCAACCTCCACGC
CAGCGTCAAGC-------------CGTCAACAACCTCAACGACTCTTACATGTGCCGCGACGATGCCAAGGCCGCCCTGC
GCACGCCGGCTAGTCGCAAGCTCCTCCAACTGGCGCCGGCGGAGACCGGTGATGGCGGCGTGGCGTCTCGCGCTGCCGCA
TCTGGGTTTGTGCAGGGGGTCGTCACGTACACGGTCAGAGACGATCTCAAGGTCGCGCCCGTGTCAGCCATCTCCGGGAT
CACGCTCCTCAAATCCCTCGGCATCAAGGACATCGCCTCGCTCCAGGAGAAGACCGTGCAGCTTGGCCACGCCGAGGTGA
CAAATGGCTTGTTAATTCGTCAAAACTTTTAACCGAAATTGGATTCGTAGC-------TCA-----GATAATGTGATTGT
GTAGGGCTTGGGAATACTGAGGGCGTCGCTGCCATCCAAGACGGTGCTCACCGACGTCTTCCTCGGGAAGAAGAAGAAGC
GGAAGGCTGCAGAGGCGTTCCGCCATGAAGCGGTCTCTCGAGTCGTCAGGAGGCGCCGTGCTTGGGCTGGTTCGTGGCGC
CCGTGGTACGTGAGCGCCAGGTCATGCTCGGCTTGTGGCTCTCGTCATGCCAGCTGCACGGCCCGCGAACCTGCTGGTAG
CCAGCGCAAACAGGGCTGCGTATAGAATTGA----TCCAGTAGCTTCTGGTC-----ATTGA-CTCATTGTTGTGAGGAT
CCTTGCGGAGTTGTGGTGTTGCCGAGTGAAGTTTGTATTTCTATTAAAATT-----------------------------
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>chr3A_1
ATCGGTTCAGACTTCAGAGGCACATTCGGCGCGA--ATATTGTTTTTTTCAAAATCAATCCCAACGCGGTGATCCGGTGG
CCTGCTTCTGAGAGCG-------AACGCAAGACCCACGCTCCATCTAAAATGTCACTTTGGTGAACGGGTGCATGGAACA
CCTATATTTTGAATAGTGTGACAACAGTATTTTTGAAGTTTCAAAACTTCCAAAAATAATTCCACATGTTCATATGGATG
TATGTTACACATGTGCAAATTTTGATGATGAGATAAGTAACCATGTGAGTTACACATAAATGAC-AAAACCGTTATTTTG
GAAAGATGAGTAGTGCATGTATTATTCAC---------------------------------------------------
-------------------------------AATTTAGAAATGGCCATTTTGTCATTTTTGTATAGCTCACATGTTTACT
TGTTTCATCACCAAACTTT--ACACGTGTAATAGCGATCCATAATTCCATATGATCTTGTAGAATTCTTTTCGGGATTTT
TTGAAGTTTTCAGTGTGATTTTTAAGCTATTTAAAATAAAGTCCTCCAATGCACCCATGTTCCAAAAATCCACTCTCACC
CTCCATCTCTCTAGCTTCTCTTCCATCTTTTTTACGCAGTTAATGCAGCTGTGGTCTTTTGGTCTTTCCAATATTTCATC
TTTCCCAAGTTCCACACGATGATCATGCGTATGCATGGGCATCGAGCATTGCGCTAATAAACTCACCAC--GCGTGCTGG
GGTAAATCAATTCCCC-AAAAATCGCCGCAGAAGATTGCCCATGAATTCTGCTTCTCTTCGCATGTGCTGTACTTATATA
TATATATACACCCAAAGAGAATAACTACACCGTCCAAAAAGTGCATCCAGACCCTAAAAAAAAAAAGTGCATCCAGAAAA
C-------------------------------------------------------------------------------
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-----------------------------------------------AGAAGACCGTGCAGCTTGGCCACGCAGAGGTAA
CAAATGACTTGTTAATT-GTCAAAACTTTTAGCCGAAATTGGATTCGTAGACCGTAGTTCA-----GATAATGCGGTTGT
GTAGTGCTTGGGAATACTGAGGGCGTGGCTGCGATCCAAGACGGTGCTCACCGCCGTCTTCCTCGGGAAGAAGAAGAAGC
GGAAGGCTGCGGAGGCGTCCCGCCATGAAGCGGTCTCTCGAGTCGTCAGGAGGCGCCGTGCTTGGGCTGGCTCGTGGCGC
CCGTGGTACTTGAGCGCCGGGCCATGCTCGGCTTGTGGCACTCGTCGTGCCAGCTGCACGGCCCGCGAACCTGCTGCTGG
CCAGTGCAAACA---------------------------GTAGCTTCTAGTC-----ATTGACCTCATTGTTGTGAGGAT
TCTTGCGGAGTTGTGGTGTTACCTCGTGAAGTTTGTATTCCTATTAAAATTCATGTTAGCTTCGGATGAAGAAATGACAT
GTCACTTCATTCATCGTTACTCGT---------GTGCTAGAGCATGTCTAGCAAATCCTTATATCACGGTACGGGAAATC
ACTATATAAGGAAAAACTAAAACCTGTTTTTCTGTACCGTCCGGGGTGCGGCCGAACAGATCCTGCAAAAATTTACCGCA
AAATCAAATATTTCCCGTGGTCTCCTTTTTTTTCCTCTCACGCGCGTGCGCGTCTGTCTAAATCCCAAGCGGAACAGATC
ATCATCAACCATTGCATACATGGTGTAGAT------------TGAATCAGGAAGACTGGAGCGTGACCCTGAGCGAGTCG
CCGTACTTGGGGTCGACGGCCCCGGGCAGGTCAGGATGGGAGGCAGCTTGGGCCGCCGCACACCACACATTCCGTTGCCG
CACACAATGAACCAGGCGCTGCCGCACACAACGCAGGCTGCCTCGCGCGCGTTGTGAAGCATCGGCCAGAACCGCGACTT
CTTGTGCAGCACCACCACCTCTTCAGCGATGCCGACGTACCTCCCGTCCACGAACAGCCGCGGCAGCAGCGGCATCTCGC
CGTCCGT-CCAAGGAGCAGC------
>SNPs
--------S-----S---------S---------SS-----------S--------------------------------
--S-----------------------S----------S--S--------------------------------------S
------------------------S--------------------SS--SS-----------------------------
------------------S--------S----S-------------------------------S----------S----
S----------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------S----------------S------------S------
-------------S----SSS--------------------------------------S--------------------
------------S----------------------------------------------------------------S-S
----------------------------S----------------------------S----------------------
----------------S----------------------------------------------------SS---------
----------------S-------S------------------------------------------SSS-S--SS----
--------------------------------------------------------------------------------
----------------------------------S---S-----------SSSSSSS------------SS---------
-----S--S-------------------------------------------------S-S-------------------
-----S-----------------------------------S--S---------S-S---------------------S-
-------SSSSSSSSSSSSSSSSS-----S-------S-----S------------------------------------
----S-----SS----------S-------S-------------S-------S-----------------------S---
-----S----------------------S------S--S----S----------S-------------------------
----------------S-S-----------------------------------S----------S--------------
-----------S-------------SS-----S-------------S--------------SSSSS--------------
------------S------S------------------------------------------------------------
-----------S-------------------------------S-S----------------------------------
--S---------------------------S-----------------------------------S---S---------
------------S--------S---------SSSS----S------S-S--SSSSSS---------S-------------
--------------S--------------------------------------------------------------S--
S--------S----SSSS-SSSSSSSSSSSSSS--------------------S--------S--------S-SS---SS
S-----------------------------S-S-----S----S-S--S-SSS--------S------------------
-----------------------S---S--S---------------S------------S------S-------------
----------------S-------------SSSSSSSSSSSS---------------------------SS---------
----------S------------------------------S---------------------------S--------S-
-----S-----------S----S------SS---------------S-S---S-S--------S-S----S----S---S
--------S-S-S--------------------S--S-----------------------S--------------S---S
-----S-S------------SSSSSS
>forward_1012
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--------------------------------AGCAAAGAAGGGAGCCACTG----------------------------
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>reverse_2220
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-----------------------------------------------------------GAATCCCGAGCGGAACAGAT-
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