>input_sequence_81685
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-ATGTCGCCCTCCGCCCCGCCCGCGCCCGCCCGCTTCCTCCTCTTCGCCGCGGCCCTCGCGCTGCTCCTCCTCTCCCCAA
CCCTAGCGGCCTCCGACCCCGCCGCCGAGCCCTGCGCGGCGCCCCTCGACGCCCCCGCGCTCGACGGCGGG---------
GGCGGGGGAGAGGTCGCGCTCTGCCCCGTGCGGTGCTTCCGCCCCGACCCCGTCTGCGGCGCCGACGGGGTCACCTACTG
GTGCGGCTGCCCCGAGGCCGCCTGCGCCGGCGCGCGCGTGGCGCGCCGCGGCTACTGCGAGGTCGGCGCCGGCTCCGCAC
CCGTCTCCGGCCAGGCGCTCCTGCTCGTCCACATCGTCTGGCTCTTCGTGCTCGGCGCCGCCGTCCTCCTCGGCTTCCTC
TGA-----------------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G329000
GGGTGGAGGGTATTGCTTAGATGTGGATTTGGAGGCTTGGATTTCGGTGGGTCTTCCCTCAAGGGTGGGCTCAGTGGCTT
TGGTGCCTCGAGTGGCACTGGCGGGTTCCCAA-GCGAAAACTCCGCGATTTGTTGTCGATGGCGGCGACACCTGCGGGTG
TCGCTATCCTCTTGAAGGCATCATTGTAGTTCCCCTTCCCCCGCCAGTGCTTTGAGGGGAAACTCATGTCTGTCCCTTCA
GACTCGGCAACGGTTACGCTTCACCTCGTTACCCTCTT-GGGGCACTGCCATGGAGCTCAGGTGCTCATTGACATTGTCA
TGGCGTGGCGTCGTTTTCTGGCTCCGCAGTGCTCCTGCCTGGCAGCGTAGTCGTGTCGTTATTAGCCCTTTTGCGTGATT
G--TTTAGGTGCGATTTATGTTGTTCAATTTCTCTGTGATCTGCTTTGTAAGCAGGACGAAAGCCTTTTCTATTCTTTCT
CGAACGTTCTGTGTGTGTGTGTTTTGCGAAAGGAAGGTTCTGTGTTTTTTCTAGGTACAACCAAACAAACTCCTGTGCAA
ATTTAATGTTGTGCTTTATGCGGTTTATT----------------AATTCCCTACATTTAATTAG------------ATC
CTTTTTGCATTTGTTCGTCGTCCTTAGAGGCGAAGCATTCGTGCGGTCAAAAACATTAGGAAACGACCGGAACGTGTGGG
AATTCTATTCTCGGACGCAGTAAAGCGGAACAAGACAAGGCAGTGGCTGGCGCCCGGCAGGCGGCCAGCCCCACGTCTGC
ATACGCGTAACGCGTCTGCCTTTGCTCTCTCTCGAAGGAAGGAAATTGAAAAGGTAGTCGCCAACGGCCAGCGCGAGCCA
GCTAAGTCCAACCGAGCGGGCAAGGCACCCAGCCACCCACCCACCCCGCCCAGACGCGTCGCCTCGGCGGCCCCGAAGCT
CCTCGCCACCGGCCCGCCCCCGCCGCGCCCCTTGCCCCCGGCCCGCCCCCCCGCGGCCGGGTG---------GACGCCGC
CATGTCGCCCTCCGCCCCGCCCGCGCCCGCCCGCTTCCTCCTCTTCGCCGCGGCCCTCGCGCTGCTCCTCCTCTCCCCAA
CCCTAGCGGCCTCCGACCCCGCCGCCGAGCCCTGCGCGGCGCCCCTCGACGCCCCCGCGCTCGACGGCGGG---------
GGCGGGGGAGAGGTCGCGCTCTGCCCCGTGCGGTGCTTCCGCCCCGACCCCGTCTGCGGCGCCGACGGGGTCACCTACTG
GTGCGGCTGCCCCGAGGCCGCCTGCGCCGGCGCGCGCGTGGCGCGCCGCGGCTACTGCGAGGTCGGCGCCGGCTCCGCAC
CCGTCTCCGGCCAGGCGCTCCTGCTCGTCCACATCGTCTGGCTCTTCGTGCTCGGCGCCGCCGTCCTCCTCGGCTTCCTC
TGACGCGCGCGCCTC-------CGCCCCCCTTCCTGTAATTGACGTCTCCCCCCTCCCCACAATTGGTAGAACTACTCAT
TTCAAGATTCTTTGTTGGATTTCGGTGCGCTCTTGAGCGCTGAGGGGG-GTGGTGCTGGAACGGAATGTTTCGTTGCGAG
GATTTGGTCCAGGGATGTCACACAATTCTTTCATAGATAATGAGATTGGTTGGCTTGGTGCTTTAGATTTCGGACCTCAG
CTGTCCAGATTGGTCGCCAAATTTAGGTTGAGATCGTGTAAAACAGCTT-GTAAATTTCGGCTAAATACATTTTGCAGTG
ATCTGGTTGTGCTTGTCTATAAATTTCAGCTT-CTTGGTTTTATTATTCTGCTTTGTCTAATTGTCTATAAATTTGAGCT
CTATGGTCGACAGACGAGCTAGCTTCCTAAGGCACATGAGCGATTGACA------TTTCA--------------------
-----TGCAATGGAGCCAACTTGACATTTT-CTCTTTCTTAAGAATATGAAATTTAAAAATAGAAGAGCAGCTATAACTT
GAGCATGGACCTGA-CACGTTCATGC---ATAATGGATGTAATCAGAGGTTGTGAGCATGTTCATGTAGCCATAAGTTGT
TA----TGTCAGTAACATGTATTACTCT----------CTCTCTGATCTATAATAGCAGTTCTCAATGCCTTCCCATTTT
ATGTACTTGAGATAAAGTAGTGTGAGGAGGAGTAAAACAGAGAAATGTGGGTATTTGCATACATGAACT---ACATGTTA
AAAGGAATGTCAGTGCATCCTAGAGGTGTTCTTCAATG-GCTGGTATGCTGGGATTGTCATTGACTCATACGTTGATGCT
TCTGGTGGTGTCGAACGGTGCAGCAA-TAGCCCTGCACCTTATGAAGGACAGCTACCTCCTGTGTTTTGCCAGGAAGGCA
ATATCGAAGCTCTTGTGTTGCTTATTTAGTCTGGTGAGCACTATTCCTTCTGTTTTGTCATTGTTTCCTTG---TAGATA
ACACTGATAAATTCTGTGATATCCTTCATTA
>chr3B_9
--------GGTATCACTTAGATGTGGATTTGGAGGCCTGGACATCGGTGGGTCTTCCATCAAGGGTGGGCTCAGTGGCTT
TGGTGCCTCGAGTGGCACTGGCGGGTTCCCAAAGCGAAAACTCCGCGATTTGTCATCGATGGTGGCGACATCTGCGAGTG
TCGCTATTCTCTTAAAGGCGTCGTTGTGGTTCCCCTTCCCTTGTCAGTGCTCCGAGGTGAAACCCATGTCCGTCCCTTTG
GACTCGGTAACGGTGACGCTTCGCCTCGTTACCCTCCTAGGGGCATCGTCGTGGAGCCCAGGTGCTTATTG------TCA
TGGCGTGCCGTCGCCTTCTGACTCTGTAGCGCTCATGCTCGGCAACGTAGTCGTGTTGTTTTTAGTGCTTTTTTGCGATT
TTTTTTAGGTGTGATATATGTTGTTCAATTTCTCTTTGATCTAATTTGAGGGGTGGGGG--AGCCTTTTCCATTCTTTTT
CGAAGGTTCCGTTTTTGTTTTTCCTAGGTAC---------------------AGGTACAACCAAACAAACTCGGGTGC-A
ATTTAATGTTGTGCTTTATGCGGTTTATT---------------TAATTCCCTACATTTAGTTAG------------ATC
CTTTTTGCATTTGTGCGTCGTCCTTAGAGGCGAAGCATTCGTGCGGTCAAAAACATTAGGAAACGACCGAAACGTGTGGC
AATTCTATTCTCGGACGCAGTAAAGAGGAACAAGACAAGGCAGGGGCTGGCGCCCGGCAGGCGGCCAACCCCACGTCTGT
ATACGCGTCTCGCGTTA-GCTTTGCTCTCTCTGGAAGGAAAGAAATTGAAAAGGTAGTCGCCAACGGCCAACGCGAGCCA
GCTAAGTCCAACCGAGCGAGCGGGCAAGG----CACCCACCCACCCCGCCCAGACGCGTCGCCTCGGCGACCCCCGAAG-
-CTCGCCACCGGCCCGCCCCCACCGCGCCCCTTGCCTCCGGCCCG-CCCCCCGCCGCCGGGTGGACGCCGGCGACGCCGC
CATGTCGCCCTCCGCCCCGCCCGC------CCGCTTCCTCCTCTTCGCCGCGGCCCTCGCGCTGCTCCTCTTCTCCCCAA
CCCTAGCGGCTTCCGACCCCGCCGCCGAGCCCTGCGCGGCGCCCCTCGACGCCGCCGCGCTCGACGGCGGGGCCGGCGGC
GGCGGGGGCGAGGTCGCGCTCTGCCCCGTCCGGTGCTTCCGCCCCGACCCCGTCTGCGGCGCCGACGGCGTCACCTACTG
GTGCGGCTGCCCCGAGGCCGCCTGCGCCGGCGCGCGCGTGGCGCGCCGCGGCTACTGCGAGGTCGGCGCCGGCTCCGCGC
CCGTCTCCGGCCAGGCGCTCCTGCTCGTCCACATCGTCTGGCTCTTCGTGCTCGGCGCCGCCGTCCTCCTCGGCTTCCTC
TGACGCGCGCGCCTC-------CTCCCCCCTTCCTGTAATTGACGTC-TCCCCCTCCCCACAATTGGTACAACTACTCAT
TTCAAGATTCTTTGTTGGATTTCGGTGCGCTCTTGAGCGCTGAGGGGG-GTGGTGCTGGAACGGAATATTTCGTTGCGAG
GATTTGGTCCAGGGATGTCACACAATTCTTTCATAGATGATGAGATTGGTTGGCTTGGTGCTTTAGATTTCGGACCTCAG
CTGTCCAGATTGGTCGCCAAATGTAGGTTGAGATCGTGTAAAACAGCTTTGTAAATTTCGGCTAAAAACATTTTGCAGTG
ATCTGGTTGTGCTTGTCTATAAATTCCAGCTT-CATGGTTTTATTATTCTGCTTTGTCTGATTGTCTATAAATTTGAGCT
TTATGGTCGACAGAAGCGCTAGCTTCCTAAGGCACCTGAACGAATGGGAATGACATTTCAGTGAAATTACTTCCGTCTAG
CA--TTGCAATGGAGCCAACTTGACATTTT-CTCTTTCTTAAGAACATGAAACTC-AAAATAGAAGAGCAGCTATAACTT
GAGCATGGACCTGAACACGTTCACGCATAATAATGGATGTAATCAGAGGTTGTGAGCATGTTCATGTAGCCATAAGTTGT
TGTTGTTGTCAGTAACATGTGTTACTCT----------CTCTCTGATCTATAATAGCAGCTCTCAGTGCCTTCCCATTTT
ATGTACTTGAGATAAAGAAGTGTGAGGAGGAGTAAAACAGAGAAACGTGGGTATTTGCATACATGAACTAAAACATGTTA
AAAAGAATGTCAGTGCATCCTAGAGGTGTTCTTC-AAAAGCTGGTATGCTGGGATTATCGTTGGCTCATACGTTGATGCT
TCTGGTGGTGTTGAACGGTGCAGCAAATAGCTCTGCACATTATGAAGGACAGCTACCTCCTGTGTTTTGCCAGGAAGGCA
ATATCGAACCTCTTGTGTCGCGTATTTAGTCTGGTGAGCACTATTCCTTGTGTTTTGTCATTGTTTCCTTG---TAGATA
ACACTGAGAAATTCTGTGATATGCTTCATTA
>chr3A_509
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--------------------------------GAAGGTTCTGTTTTGTTTT----TACAACCAAACAAGCTCCGGTGCAA
ATTTAATGTTGTGCTTTATGCGGTTTATTAATGTTTTCCTTTATTAATTCCCTACATTTAGTTAGCAGTAGATCCTCATC
CTTTTTGCATTTGTGCGTCCTTG---GAGGCGAAGCATTCGTGCGGTCAAAAACATTAGGAAACGACCGGAACGTGTGGG
AATTCTATTCTCGGACGCAGTAAAGCGGAACAAGACAAGGCAGGGGCTGGCGCCCGGCAGGCGGCCAACCCCACGTCCGC
ATACGCGTAACGCGTCTCGCTTTGCTCTCTCTCGAAGGAAGGAAATTGAAAAGGCAGTCGCCAACGGCCAGCGCGAGCCA
GCTAAGTCCAACCGAGCGGGCAAGGCACAACCCCCCACCCAC-CCCCGCCCAGACGCGTCGCCTCGGCGGCCCCGAAGCT
CCTCGCCACCGGCCCGCCCCCGCCGCGCCCCTTGCCCCCGGCCCGCCCCCCCGCCGCCGGGTGGACGCCGGCGACGCCGC
CATGTCGCCCTCCGCCCCGCCCGCGCCCGCCCGCTTCCTCCTCTTCGCCGCGGCCCTCGCGCTGCTCCTCCTCTCCCCAA
CCCTAGCGGCCTCCGACCCCGCCGCCGAGCCCTGCGCGGCGCCCCTCGACGCCGCACCGCTGGACGGCGGG---------
GGCGGGGGAGAGGTCGCGCTCTGCCCCGTGCGGTGCTTCCGCCCCGACCCCGTCTGCGGCGCCGACGGCGTCACCTACTG
GTGCGGCTGCCCGGAGGCCGCCTGCGCCGGCGCGCGGGTGGCGCGGCGCGGCTACTGCGAGGTCGGCGCCGGCTCCGCGC
CCGTCTCCGGCCAGGCGCTCCTGCTCGTCCACATCGTCTGGCTCTTCGTGCTCGGCGCCGCCGTCCTCCTCGGCTTCCTC
TGACGCGCGCGCGCGCCTCCGTCGCCCCCCTTCCTGTAATTGACGTCCTCCCCATCCCCACAATTGGTACAACTACTCAT
TTCAAGATTCTTTGTTGGATTTCGGTGCGCTCTTGAGAGCCGAGGGGGTGTGGTGCTGGAACGGAATGTTTCGTTGCGAG
G-------------ATGTCACACAATTCTTTCATAGATGATGAGATTGGTTGGCTTGGTGCTTTAGATTTCGGACCTCAG
CTGTCCAGATTGGTTGCCAAATGTAGGTTGAGATCGTGTAAAACAGCTT-GTAAATTTCGGCTAAATACATTTTGCAGTG
ATCTGGTTGTGCTTGTCTATAAATTTCAGCTTTCATGATCTTACTATTGTGGTTTGTGTGGTTGTCTTTATATTTGAGCT
TCATGATTGACAGACGAG--AGCTTTTTAAAGCACTTCAGCAAATTGCT------TTTCATTGAAATTTACTTCCGTTGT
AGGGTTGCAATGGAGCCAACTCGACATTTTTCTCTTTGTTAAGAATATGAAATTT-AAAATGGTAGAGCAGCTATAACTT
GAGCATGGACCTGA-CACCTTCACAC---ATAATGGATGTAATCAGAGGTTGTGA---TGTTCATGTGGCCATAAGTTCT
TA----TGTCAGTAACATGTATTACTCTTTGTCTCTCTCTCTCTGATCTATATTAGGAGCTCTCAATTCCTTTCCATTTT
ATGTACTTGAGATAAAGAAGTGTAAGGAGGAGTAAAACAGAGAAATGTGGGTATTTGCATACATGAACCAAAACATGTTA
AAAGGAATGTCAGTGCATCCTAGAGGTGTTCTTC-ATG-GCTGGTATGCTGGGATTGCCATTGACTCATACGTTGATGCT
TCTGGTCGTGTAGAACGGTGCAGCAAATAGCCCTGCACCTTATGAAGGACAGCTACCTCCTGTGTTTTGCCAGGAAGGCA
ATATCGAACCTCTTGTGTCGCTTATTTAGTCTGGTGAGCACTATTCCTTGTGTTTTGTCATTGTTTTCTTGTACTAGATA
ACACTGAGAAATTCTGTGATATGCTTCATTA
>SNPs
SSSSSSSS-----SS---------------------S----SS--------------S----------------------
-----------------------------------------------------SS-------S-------S-----S---
-------S-----S-----S--S----S------------SS-S-------SS----S-----S------S-------SS
-------S------S-------S-------------S--------SS-S-S------S--------S----SSSSSS---
-------S-----SS-----S---S-S--S----S---SS----S-----------S---S----SS-----SS-S----
S----------S---S-------------------S------SS----SSS-SS--SS-SS---------S-------S-
----S----S--S-S---S-S-SS-SS-S-SS-----------S--S---SS---------------------S------
------------------------------------------------------------S-------------------
--------------S-----------------------------------------------------------------
-------------------------------------------S-----------------------S------------
-----------------SS-------------------------------------------------------------
----------------------------SSSS------------------------------------------------
------------------------------------------------------S-------------------------
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-----------------------------------------------------S--------------------------
--------------------------------------------------------------------S-----------
------------------------------------------------------------------------------S-
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-----------------------------------------------SS--------------------S----------
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--------------------------------------S-----------------------------------------
----------------------S---------------------------------------------------------
----------------------------------S------------------------S--------------------
S----------------------------------S-------S--S---------------------------------
-------------------------------------------------------S------------------------
-----------------------S--------------------------------------------------------
-----------------------------------------------------------S--------------------
-----------------S--------------------------------------------------------------
----------------------------------S---------------------------------------------
-----------S--------------------------------------------------------------------
--------S---------S------------------------------S------------------------------
-------S--------------S--------
>forward_174
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--------------------------------------------------------------------------CGGGTG
TCGCTATCCTCTTG------------------------------------------------------------------
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>reverse_2275
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----------------------------------AATGGCTGGTATGCTGGGAT--------------------------
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