>input_sequence_68098
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----------------------------CAGCGCTCTCACTCTCCCCTCGCA-----------GCAGAGCTTGCTCGCAA
GAAGCAGAGCAAGTGGCCGGCGGCGA-CATGAAGCGGACCAGGGCGCAGAACCCCAAGGCCCAGGACCCGGAGCCGCAGG
ACCCCGCG------GCCGCCGGGAGCAACCCCACCCCGAAGCCGCAGCGCCGCGCGAAGCAGCCCCGGCAGCCCAAGGCG
GCGACGGCGGGTGGCAAGAAGACCGCCGCGGCTCGCGAGGCCGCTGCGGTGACCGCGACGGCAGCCGCTGCTG------C
CTCCGTCGCCGCAGCGTCCCCCGCAGCGGAGACGGCGCCGGTCGTCCCCGACGTCTGCGTCGGCGCGGGAGGAGGAGG--
----GGATGTGGCGTGCGGCCTGCCGGCGGAGTGGGACGAGATGG---------ACGGGTCGCCGTGGTGGACGTTCGGG
GTGGAGGAGGAGAAGCTGCTGGGGTGGTTCCCGTTCGTGGAGGAGGACTTCCTGTCCGTCGGCAGCGGCGTCGGCCCCGC
CGCCGCCGAGCC------CTTCGACGACGACATCTGGCGGATCCACCAGATCTACGAGATCCCCAGCTACGCCGCCAAGT
GAAG--AAGCGACGGACGCAAAAT-------GCGGGCGGCATTCCA----------------CCACTTGGAGAG---AGA
AACTACTACTAATCTATGAGGTTACCATCTCATAGATTTGTGCTACCAGCAGCAGTAGTGCTTTTGCGGTACAGGAACAG
GGGAACGGACTAATCTATGAGGTTACCATCTACTACTAATCCCAGTTTAGGCGAGTGAGCGAAGCTAGTTTTAACGCCTT
GTTATGCAAGC-----AAAGAACAAAGAAAAATTTCGACG----------------------------------------
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>chr3D_1_TraesCS3D01G038400
GACAGTGTGGCGTCGTCGTCGACCGATCACGCCCGGT----CCTGACGCGAC--------GCCATAAAAATACAGGC---
--CACCGCCCACTTGTTGCAGCAGCCAAGTTGAGCGAGCCCCACGTCTCGCAATCCATCGGTCAGTTGCTGTATTCTCGG
AC-TGCCGACATACGGGCAGCGTCATGTCGGCCCCTTAAAGTGAAGTGGTAGGAGTACTAGCCCCTCGTCGATCGCTTTA
ATGCCGAGATACGACCGGTGGT---ACGTGCCGCAACCACT-CCACCGGCTCAGTACACGTACGTACGAACAAGTA----
CTGTATTATCGAGTTAGATATT------TTAATTACGAGATGAT----GA------------TAGAAAACCGGTGGAACT
TGTGCACTTGCAGCTTCTAGCAGCAT---GCATGCATTGTTGGACGTTACATACACGAGCGAATCTCTGAACTACGCTTC
ACGGTGTCGGCATGCGGTC------TGCACATGCACGCCGCCCTCGGCGCTCACCTTCCCG---------------GCCT
CCACGTGAGCCGCGACGGGATCAGCGCGACGCG------------------------------------CATGTCGTGCA
ACACGGAG-----------------GCGATCTCCGTCTGTGC------------------------GTACGTGCAACAAT
TAGT-----------------ACACAAGCAAAAGGGTGAATTTGTCACGAAACGC-------ACGGACCGCGATTTACCA
TTGCCATCGCTGCGTCGCCTTGTCGACCGGACCGGAAGGCCAGGAAGAACAGCGACGTGG--------------------
----CCAGGCCCAGTTGCGTTGCATGCACATCCACAAGAGTAGCCGTCACGGGGTCAGGTC---GACGGA----CCCGGT
GCAG----CGTACGCACGCAGCCAGCGCTGAAGGCGGCTGGCGGCAGCCGCATGTGTTTCGGCGGCGACGGCGTGCAAGC
TGCGACCAGGCT---------CAGCCCACCGCTGAACCGAACCGGTGCCGATCAAGTGG----CTCGCCGCACCGCCAAA
AAGGCGACCCGGACCCGACCCCCACCCCGCCCTA-CGAGTACAAAAGGGCCGCAAAGCCCAAGCACCATCGTATCACCCT
AG------CCCCCACCCCCACACTCCCCCAGCGCTCTCACTCTCCCCTCGCA-----------GCAGAGCTTGCTCGCAA
GAAGCAGAGCAAGTGGCCGGCGGCGA-CATGAAGCGGACCAGGGCGCAGAACCCCAAGGCCCAGGACCCGGAGCCGCAGG
ACCCCGCG------GCCGCCGGGAGCAACCCCACCCCGAAGCCGCAGCGCCGCGCGAAGCAGCCCCGGCAGCCCAAGGCG
GCGACGGCGGGTGGCAAGAAGACCGCCGCGGCTCGCGAGGCCGCTGCGGTGACCGCGACGGCAGCCGCTGCTG------C
CTCCGTCGCCGCAGCGTCCCCCGCAGCGGAGACGGCGCCGGTCGTCCCCGACGTCTGCGTCGGCGCGGGAGGAGGAGG--
----GGATGTGGCGTGCGGCCTGCCGGCGGAGTGGGACGAGATGG---------ACGGGTCGCCGTGGTGGACGTTCGGG
GTGGAGGAGGAGAAGCTGCTGGGGTGGTTCCCGTTCGTGGAGGAGGACTTCCTGTCCGTCGGCAGCGGCGTCGGCCCCGC
CGCCGCCGAGCC------CTTCGACGACGACATCTGGCGGATCCACCAGATCTACGAGATCCCCAGCTACGCCGCCAAGT
GAAG--AAGCGACGGACGCAAAAT-------GCGGGCGGCATTCCA----------------CCACTTGGAGAG---AGA
AACTACTACTAATCTATGAGGTTACCATCTCATAGATTTGTGCTACCAGCAGCAGTAGTGCTTTTGCGGTACAGGAACAG
GGGAACGGACTAATCTATGAGGTTACCATCTACTACTAATCCCAGTTTAGGCGAGTGAGCGAAGCTAGTTTTAACGCCTT
GTTATGCAAGC-----AAAGAACAAAGAAAAATTTCGACGGCGATGCAGTTTCACGTGCCCTCTTCTTGTGCCCTGCGTC
TTGATTTTTCGGCT--------------------CATTCTCATGTGCGTTCTTCAAGCAATGCGGCTCGTCGCCAGAGTT
GTTGCTGGGGTTAACTAGGGC-----------------------------------TCCTGAGGGTGGCAAACTGTACTG
TA-----CAGTTGGTTTCATCGTTTCAATGGAGCGGGACGAAATTTGGGCGGGCTAGCGCGC------------------
--------CGGGTTTTCGCGCGCAAACGATGCTAGAACGGCGCGGAAAAGAAAGGAAGAGCAACTCCTGAATTTCTGGAG
CCGGAGGTGGAGTACTGGAGTGCGTTCCCATGTCGGCAACTGTCACAGTCGCGTCGTTTCTGTAACTCTGTTTTC-GTGA
ACCACGGTGCGTTCCCGTGTCAGCAAAATGTGGCTGAATCGCCTTGCTTTTCTCTGTTAACATGAACCAGAAGTTTTCTA
CTAAAAAATTG---------------------------------------------------------------------
-----------------------------------------------------TATAAAGCCCTTTAA-TTTGTACAATG
GATTCATGTCTTTCATCACATGTCAAAGAGCAAAACATTAGCCCGGACATAATGCAAAAGAAAATC-CAATAAACCAAGC
GACATCTCTTTCCTACAACAAGTGTCTATCTCACTACCAGTGAT------------------------------TTTTCT
ATCCTACGAACCAAAGATGATGAAAAACTTGGTGATGGAGAAAACATTTTTAGGGTAGGGGAGAGATGGTTTTTGGGCAT
CCGGCTCTTGCTGCTTTAACACATGATGTAAAAGTGGTGCCAAAAAATATAAAACTCAAGCATGATTCATTCCATACATC
TAAATTTCAAACTCAAATACAAAACATTTACCATTAAACATCAAAACGACATTACAATAGATAATTAAACATTTTACTAT
GATACGTCATCAAACTACCACTCCTCATTTTTTGCAGTAGACCATCACGGGGAAGACGTCTTTGCGTGCGCACGGTACCC
ATCAAATTCGTCTTCGTGATCACCCCTCCGCCGGATCGTACGAAGGCCTAACATCTAAAGCTGAAGGCCCCAACCAAGCC
A
>chr3B_1
GACAAAGTGGCGTCGCCGTCGACCGATCACGCCCGGCCGGCCCTGACGCGACGCCATGGAGCCATAAAAATACAGGCCCG
GCCACCGCCCACTTGTTGCAGCAGCCAAGTTGAGCGAGCCCCGTCCGTCCGTCC----------------GTATTCTCGG
ACTTGCCGACATACGGGCAGCGCCATGTCGGCCCCTTAGCCCCTCAT--------------------GTCGATCGCTTTA
ATGCCGAGATACGACTGGTGGT---ACCGCTAC--TCCACCACCACCGGTGCAGTACACGTA-GTACGAACGAGTA----
GTATATCATCGAGTTAGATACGTACGTGTTAATTATGAGACATGACACGA------------TAGAAAACCGGTGGGATT
TGGGCACTTGCAGGTTCTAGTAGCAT---GCATTTACATGAA-----------------CGAATCTCTTAATTATGCTCC
ACGGTGTCGGCATGCGGCC------TGCACATGCACGCCGCCCTCGGCGCTCACCTTCCCGAGT-----CCCCGGCGTTT
TCACGTGAGC----------------------ACGCCGGCGGCCGCGTCATGGGCGGCTGCCACGCGCACATGTCGTGCA
ACACGGGCACGGCTACGTGGCCGACGCGATCTCCCTCAGGCCTCAGCCCAACCACTCGTGTGTGGAGTACGTACAATACA
ATGATCGTACACGTATACTG---ACAAGCAGAAGGGTGAAGTTTCTTGGGGGAAAACGTAGTACGGATGGTGATTCACCA
TTGCCATCACTGCGTCGCCATGTCGACCGGGAGGGT-----AAGAAGAACAGCGACGTGG--------------------
----CCACCAGGTCCA--GTTGCATGCACATCCACACGGGTCGCCGTCACGGGTCGGGTCGACGGACGGA----CCCGGT
GCGACGGACGCACGCACGCGGCCAGCGCGGAAGGCGGCTGCATGTGTCGCTG-------CGGCGGCGGCGGCGTGCAAGC
TGCGACCGTG----------CCAGCCCACCGCTGAACGGAACCGGTGTTGATCAAGTGGCTGGCTCGCCGCACCGCCAAA
AAGGCGACCCGGACCCGAGCCCCGACCCCGCCCAGCGAGTACAAAAGGGCCGCAAAGCCCAAGCAGCATCGTATCAGCCC
CAGCCCCACCCCCACCCCCACACTCCC-CAGCGCTCTCACTCTCCGCTCGCCGTCTTCCTCCCGCAGAGCGCGCTCGCAA
GAGGCAGAGCACGA-----GCGGCGG-CATGAAGCGGACCAGGGCGCAGAACCCCAAGGCCCAGGACACGGAGCCGCAGG
ACCCCGCGGCCGCAGCCGCCGGGAGCAACCCCAACCCGAAGCCGCAGCGCCGGGCCAAGCAGCCGAGGCAGCCCAAGGCG
GGGGCAACGGGGGGCAAGAAGACGGCCGCGGCTCGCGAGGCCGCCGCGATGGCCGCGACGGCTGCCGCTGCCGCTTCT--
-TCCATCGCCGTAGCCTCCCCTGCTGCGGATATGGCGCCGGTCGTCCCCGACGTCTGCGTCGCCGGCGTCGGAGGAGGG-
--GGGGAGGTGGCGTGCGGCCTGCCGGCGGAGTGGGACGAGATGG---------ACGGGTCGCCGTGGTGGACGTTCGGG
GTGGAGGAGGAGAAGCTGCTGGGGTGGTTCCCGTTCGTGGAGGAGGACTTCCTGTCCGTCGGCGGCGGCGCCGGCCCCGC
CGCCGCCGAGCC------CTTCGACGACGACATCTGGCGGATCCACCAGATCTACGAGATCCCCAGCTACGCCGCCAAGT
GAAG--AAGCGACGGGCGCAAAAT-------GCGGGCGGGCGGCATTCGGCGTGGACGCCTTCCACCACTTCCGAGAAGA
AACTAGATAGGAGCCGCTACCACT-----------------------------AGTAGTGCTTTTGCGGTACAGGAAC-G
GGGAACGGACTAATCGAGGAGGTTACCATCCACTACTAATGTCAATTTAGGCGAGTGAGCGAAGCTAG-TTTAACGCCTT
GTTATGCAAGC-----AAAGAACAAAGAAAA-TTGCGACGGCGATGCAATCTCTCGTTGC--CTTCTTGTGCCCGGCGCC
TTGATTTCTCGGC-------------------------------------------------------------------
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>chr3A_45
------------------------------------------------CGAC--------GCGATAAAAATACAGGC---
GCCACCGCCCACTTGTTGCAGCAGCCAAGTTGAGCGAGCCCCACGTCTCTCAGTCCGTCGGCCAGTTGCTGTATTCTCGG
ACTTGCCGACATACGGGCAGCCTCATGTCGGCCCCTTAAAGTAAAGTACTAATAGC-----CCCCTCGTCGATCGCTTTA
ATGCCGAGATACGACCGGTGGTGGTACCGCTGC--ACCACG-CCACCGGCTCAGTACACGTACACGTACGTACTACGAAC
CAGTGTTATCGAGCTACATTTA------ATTATGATGAGATGAGACGATGATATGATAGTAGTAGAAATCCGGTGGAATT
TGGGCGCTTGCAGGTTCTAGTAATGAGTAGCATGCATTGTTGGACGCCG-------------ATCTCTTAATTATGCTTC
ACGGTGTCGGCATGCGGTCTGCACATGCACATGCACGCCGCCCTCGGCGATCACCTTCCCGAGCCGAGCCCCCGGCGCCT
CCACGTGAGCCGCGACGGGATCGGCGCGACGCACGCCGGCG-------------------------GCACATGTCGTGCA
ACACGGGC-----------------GCGATCTCCGTCTATGC------------------------GTACGTGCAATAAC
----TCGTACTAGCATACTAGACACAAGCAAAAGGGTGAATTTGTCACGGAATGC-------ACGGATCGCGATTTACCA
TTGCCATCGATGCGTCGCCTTGTCGACCGGACCGGAAGGCCAAGAAGAACAGCGACGTGGCCGGCCGCGCCGCGCGGGTC
GCCACCAGGCCCAGTTGCGTTGCATGCACATCCACCCGAGTCGCCGTCACGGGGCCGGGTC---GACGGATGGACCCGGT
GCGG----CGTACGCACGCGGCCAGCGCTGAAGGCGGCTGTGTA--------------------GCGGCGGCGTGCACGC
TGCGACCAGGCCAGCAATGCCCAGCACACCGCTGAACCGAACCGGTGTCGACCAAGTGGC----TCGCCGCACCGCCAAA
AGGGCGACCCGGACCCGAACCCCGCCCCGCCGCTGCGAGTACAAAAGGGCCGCAAAGCCCAAGCACCATCGTATCA----
---CCCCAGCCCCACCCCCACACTCCCCCGGCGCTCTCACTCTCCCCTCGCCGCCTCCCCTGCACCAGAGCTAGCAGAGG
AGGGCTCTCCGGACTCTAGCCGGGCGCCATGAAGCGGACCAGGGCGCAGAACCCCAAGGCCCAGGACCCGGAGCCGCAGG
ACCCCGCC------GCCGCCGGGAGCAACCCCAACCCGAAGCCGCAGCGCCGCGCGAAGCAGCCCCGGCAGCCCAAGGCG
GCGGCGACGGCGGGCAAGAAGACGGCCGCGGCGCGCGATGCCGCCGCGGTGGCCGCGACCGCTGCCGCTGCTGCTGCCAC
CTCCGTCGCCGCAGCGTCCCCTGCTGCGGAGATGGCGCCCGTCGTCCCCGACGTGTGCGTCGCCGCCGGCGGAGGAGGAG
GTGGGGAGGTGGCGTGCGGCCTGCCGGCTGAGTGGGACGAGATGGACGGCGCGAACGGGTCGCCGTGGTGGACGTTCGGG
GTGGAGGAGGAGAAGCTGCTGGGGTGGTTCCCGTTCGTGGAGGAGGACTTCCTGTC---CGTCGGCGGCGTCGGCCCCGC
CGCCGCCGAGCCCTCGGTCTTCGACGACGACATCTGGCGGATCCACCAGATCTACGAGATCCCCAGCTACGCCGCCAAGT
GAAGCGAAGCGACGGACGTCGCAAAATGCGGGCGGGCGGGCGGCATTCGGCGTGGAGGCCTTCCGCTTCGAGAG---AGA
AATTAGATAGGAGCTGCTACCACT-----------------------------ACTAGTGCTTTTGCGGTACAGGAAC-G
GGGAACGGACTAATCGAGGAGG----------CCACTAATGTCACCTTAGGCGAGCGAGCTAGTTAACCAGA-------T
GTTATGCAAGCAAGCAAAAGAAGAAGAAAAA-TTGCGACGGCGATGCGATTTCACGTGCCCTCTTCTTGTGCCCTGCGTC
TTGATTTTAGCCGTGTTGTTGCGCGATTAGCTTCCATTCTCATGTGCGTTCTCCG-GTAACGTGGCTCGTCACCGGAGTA
GTTCTTGGTATTAGGACTTGCATTCCATCACAGCAACGCACAAACGAGGGCTCCTGTCCTGTGGGTGGCAAACTGCACAG
TGCAGTGCAGTTGGTTCCATCGTTTCAATGGAGCGGGACGACAAGCCTGCCTCTGCCTGTTGCCTCCAGAAAGAGACCAA
AATTTGGGCGGGTTTGCGCGCGCAAACGGAGCAAGAACGGCGCGGA---GAAAGGAAGCGGCGCTCCTGAATTTCTGGAG
GTGGAGG--------TGGAGTGCGTTCCCATGTCAGCAAATGCCAGAATCGCGTCGTTTCTGTAACTCTGTTTTCCGTGA
ACCACGGCGCGTTCCCATGTCAGCAAA-TGTGGCTGAATCGCGTTGCTTGTCTCCGTTTCCGTGGAACAGCTGTTGCACT
TCGTAAGAGTATGTAATGTACGTTCAGTTGCAGCACGCGCAAGGTTGAAATATAAAACCGCAGAATGCTACTTTCAAGCC
CTAATGTGGTTTTGTACGATTTTTATAGGACATGATTTCTAATTTTTTTTCTATATAAAGCCCTTTGATTTTGTATAGTG
GATTCATGTCTTCCATCACATATCAAAGAGCAAAATATTAGGCCGGACCTAATGATGAAAAAGAAAACAATAAACCAAGC
AACATCTGTTTCCTACAAGAAGTGATGCACATGTCTATCTCATCACCGATAACTTTTTTCTATTTTCCAATGGATTTTCT
ATCCTATGAACCTAAGATGATGAAAAACTTGGTGACGAC-AAAACATTTTTAGGGTAGAGGAGAGATGGTTTTGGGGCAT
CCGGCTCTTGCTGCTTTAACACATGATGTGAAAGTGGTGCTAATTTTTTTTAAACTGAAGCATGATTCATTCCATGCATC
TAAATTTCAAA---------------------------------------------------------------------
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>SNPs
----SS---------S--------------------S-------------------------------------------
-------------------------------------------------S--S---S----S------------------
------------------------------------------S----SS--SS--SSSSSS-------------------
---------------------------SSSSSSSS-----S---------------------------------------
---------------------S-------------S-------S----------------------------------S-
--S----------S------S-------------------------SSSSSSSSSSSSS---------S--S--S-----
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----------------------S---------S-----------------------------------------------
------SS--------------------------------------------------------------------S--S
SS-S---------------------------------------------S--S--------------S------------
------------------------------------------S-------------------------------------
------------------------------------S----S------------S-S-----------------------
--S----------------S--------------------SSS-SSS-SSSSSSSSSSS--------S------------
-----------S-----------------------------------S--------------------------------
------------------S----S--------S-------------------------------------------S--S
SS-------------------------------------------------S------------------S---------
--S--------S-SSSSS-------S------------------------------------------------------
---------------------------------S----------------------------------------------
---S--S----S-----------S--------------------S------S----------S-----------------
---------------------S--S-------S-----------------------------S---S--S----------
-------S------------------------------------------------------------------------
---------------------------------------------------------------S----------------
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---------------------------------------SSSS-SS----------------------S-----------
-----SSSSSS-S--SSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-------------------------S-
---------------S-S------------S---------SS--S-----------------------S-----------
-------------------------------S--S-------------S-------------------------------
----------------------------------------------------S-SS-S--S-S--------S--S----S
---SS---SS---SSSSSS------------------------------------------S-------------S--S-
-S--------------S------------------------S-SSSSS--SSSSSSSS-SSS------------------
---------------S------------SS--S-------------SSS---------S-SSS-----------------
SS-----SSSSSSSS-------------------S----S--S--S-S--------------------------------
-------S--------S----------S--------------S------S----S---SS-S--S-S---SS---SSSSS
SSSS--S-S-S---------------------------------------------------------------------
------------------------------------------------------------------S--------S-S--
------------S--------S-------------S-----S------S-----SSS--S--S-SS--------------
S------S----------S-----SSSSS-SSSSSSSSSSSSSS------------------------------------
------S-----S----------------------S-SSS------------------S--------------S------
-----------------------------S----------S--SSSS-S-S-----S------------------S----
-----------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
S
>forward_917
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-----------------CGTTGCATGCACATCCACAA-------------------------------------------
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>reverse_3245
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--------------------------------------------TCACGGGGAAGACGTCTTTG----------------
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