>input_sequence_78142
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-----------------------------------------------------------------------------ATG
TCGTGCTGCGGAGGCAACTGCGGATGCGGATCCGGCTGCAAGTGCGGCAACGGCTGCGGAGGGTAATTTATCATCTCCAA
TTTCCTCCTGAT-C--CTGCGTTCGATCTC-TCGATCTTTA-GCCTTCTTTCTCAACCTTTTCTTTAAATCTCTCCTCGA
TCCATCTTGTTGTGCC-------GCCTAACGACATGCACGTCCATCGATCTCCTCTTCTCCTTAACAACTACTCCCTATA
AATTAAGAGATGCGCATGAACAAGC-------------------------------------------------------
-----------CTGTTTGTCTGTCGATTTCTTGGAGAGATCTACAGGAG---TCCTTGTTAATCGCGATTGATAATGATT
GTCTTG-------------TGCATGCAGGTGCAAGATGTACCCTGAGATGGACGAGGGGGTGAACACCACCTCCCAGACC
CTCATCATGGGCGTGGCGCCCTCCAAGGGCACCCCGTCGTTCGAGGCCGCCGCCGAGA------------ACGGAGGATG
CAAGTGCGGCCCCAACTGCTCCTGCAACCCGTGCACCTGCAAGTGA----------------------------------
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>chr3D_1_TraesCS3D01G074400
ATCTCCTTTCCCCCGCAAAAAAAGAGTAGTTTGTGGGTTTGCCTCGCCTTCTTCCCCACTTTTTCCTCGTAGGCCCCCCT
TGGGTTCGTGATCAAATAAAACCAATATAAATAGAGTAATTTAGAATAATCTAGATTGAATCAGTACTTAAAAAAACACA
TCCCGCATCAACACGATCAAATCATATCAAATCTCAACCAAATCAAAACTTCTCTTGCCTTCCCTACTTATACTCAAATC
AAATAATATCATATCAAAACCTAGACTAAAT---AAAAAAAATCCTTGCTTTCACCTACTTATAATCAAATCAAATAATA
TATTGCAAAA-ACATACCCCCTCTGCGTGTCAAAAACGCTCCTATATAATGGGACGGAGGGAGTAGATTTATCTTTTTTG
CGAGAAGCAAAAATATAGAATATGATGGATGTAAGGCATACGCCGGAGAAGATTGATGTTGTATGTCCACGCTGCAACGC
ATGGATAATTAATTAGTCTAGTTAAAAGTGAAATTATATGAAAAAAATGGGATGCAGTAATCACTGTCCGCAT----AGA
AAAAGCAAGCAATTTCTCGGGCAAACGTTGTCACGGGTTGA-TCTGGAAAACCACACCACACTCCAGCCCAGCGGGTGAC
GAGCTAGCATGTTCTGGATGCTCCCTAAAAAAAGCATGTTCTGAATGCTTGGGTGATAATTAATCGGGCGTAGGCCACAC
TTGGCAGGCTCGGGTAGAATTATCGAC---------------------------GGCCGGTAACGCATTTTGTCCGCGTC
CGCCGACGGAT---------------------------------------------------------------------
------------GGCACACGCCAGAAATCGACGGGCACCTCAGCAGTGGCGTCCAGCCCATGGCCCCCACGAGCCCCGAG
ACGTGGACGGTGGATAGCCTCTCTACCCCCTCTATAAATCACGGGACTGCGCACCAACCTTCCCTTCCAAAGCAGAGCAA
GTGCAGATCAGATCAGACCAGACCAGAGACACAGAGCAGAGCGGATAAACTCAGAGGGAGATCATCACCAACCGACCATG
TCGTGCTGCGGAGGCAACTGCGGATGCGGATCCGGCTGCAAGTGCGGCAACGGCTGCGGAGGGTAATTTATCATCTCCAA
TTTCCTCCTGAT-C--CTGCGTTCGATCTC-TCGATCTTTA-GCCTTCTTTCTCAACCTTTTCTTTAAATCTCTCCTCGA
TCCATCTTGTTGTGCC-------GCCTAACGACATGCACGTCCATCGATCTCCTCTTCTCCTTAACAACTACTCCCTATA
AATTAAGAGATGCGCATGAACAAGC-------------------------------------------------------
-----------CTGTTTGTCTGTCGATTTCTTGGAGAGATCTACAGGAG---TCCTTGTTAATCGCGATTGATAATGATT
GTCTTG-------------TGCATGCAGGTGCAAGATGTACCCTGAGATGGACGAGGGGGTGAACACCACCTCCCAGACC
CTCATCATGGGCGTGGCGCCCTCCAAGGGCACCCCGTCGTTCGAGGCCGCCGCCGAGA------------ACGGAGGATG
CAAGTGCGGCCCCAACTGCTCCTGCAACCCGTGCACCTGCAAGTGATCCAT-----------CAAATCAAGACAAGGAGA
-----CGCCATGGACGGACCTGATGAAGGAGCACTAGTG---GTTATGCATGGT--------G--------TGTGTTTCG
TTTTTAATTGCCACCGAGAATAAGATGAGATCTATCG----------CATCGTATCGAGCCACTAGTAGTTCATGGCGTA
TGTGTGCCCCTTGTGGCTTGTACCGTGTGCTGTGTAAGGCGTCTTGTG---------TTGTGATGCGCCTTTTCCTA--T
GTTCGAGATCCGTCCTGGTGTGCCTTCCCCGTCTTATCTACATCTACATGTATGTATAAGACAATAATAATTTGGAGTTT
CTGTCTATGTATGTATGTATGTG----------TATGTGTGGTGCCAGCTCTTATTTTTTTTTCTGTTTGTTCTTCTGCA
CAAGTA-------AATGGCGATTCCCTATTGCAAAAATAAAAAAATAAAATG--AATATGGCAACTCAAATCAACTCCCC
CTTTTA----GTTGTACTAGATGCTTATGCGTTCTCTAGTACTAGTAATTAGCATCTAAAAATTCTGCTATAATTAGCCC
CATAATAATGGACTTGATAACGCTCTAATCAATTGTTTGTTTGTTACAATAGAGATGATGGCTAAATGTGTCTTTAGATC
AAATCAACTGGGTTTAAACAAGTTTCTTTCACCGAGGCAGAAGGAATAAAATTTCGCCACACCTACGAACTGAATATAAT
TTTGTTTTTCCTATGATGGTATGTTTATAAAAAATTGTGATACTTTAAAAAAAATACAGATGCAGACGCTCACACACATG
TACATACACTCATCTCTATGGTTAAGCGCACGCGCACCGGTACCCTTATGAGCACCTGCGAGCGAGGTTTGATCGTTGGG
GCTGGGCTATCTGCCCTCTTATCCATCCAACCACAAATTGAATTTCAAGACTTGTGACACTTAATATATGGCATTGGTTT
TTTGGAAGAAAAGAAGAACAGTCTGGATTGTGCCTATCAACAATTTCGACCTGTTCTAGTGAAATACTCATGTTGCTTTG
GCTGG
>chr3A_1
ATCTCCTATCCTCCGCAAAGAAAGAGTAGTTTGTGGGTTTGTCTCACCTTCTTCCCCAGTTTTTCCT-GTAGGCCCCCCT
TGGGTTCGTGATCAAATAAAACCAATATAAATAGAGTAATTTAGAATAATCTAGA-----------------AAAACACA
CCCCGCATCAACTCGGTCAAATCATATCGAATCTCAACTAAATCAAAACTTCTATTGCCTTCCCTACTTATACTCAAATC
AAATAATATCATACCAAAACCCAAACTAAATGAAAAAAAAATTCCTTGCTTTCACCTAATTATAATCAAATCA-----TA
TATTGCAAAACACATACCCTCTCCGCGTGTCAGAAACGCTCCTATATAATGGGACGGAGGGAGTAGATTTATCTTTTTTG
TGAGAACCAAAAATATAGAATA-GATGGATGTAAGGCATATGTCGAAGAAGATTGATGCTGTATGTCCACGCTACAACGC
ACGGATAATTAACTAGTCTAGTTAAAAGTAAAATTATATGAAAAAA-TAGGATGTAGTGATCTCTCTCCATATATACAGA
AAAAGCAAGCAATTTGTCGGGCAAATGTTATCACGGGTTGA-TCCGGAAAA----ACCACACTCCGGTCCAGCGGGTGAG
TAGCTAGCATGATCTGGATGCTTC---------------------------GTTGATAATTAATCGGGCGTAGGCCACAC
TTGGCAGG-----GTGGAACTATCGACGGTGGACGTGTAGCGCGGATGCATGCACGCCGGTAGCGCATTTTGTCCGCGTC
CGCCGTCCATGGCGTGGCGATGGACGGACGGGCGACGGTCACCGTTCGTGGGTGCGTGCGTTGGTTCAATCAG--CAGTG
AGGGGCCAAAACGGCACACGCCAGAATG-GACGGGCACCTCGGCAGTGGCGTCCAGCCCATGGCCCCCACGCGCCCCGAG
ACGTGGACGGTGGATAGCCTCTCTACCCCCTCTATAAATCACGGGACTGCGCACCAACCTTCG-----AAAGCAGAGCAA
GATCAGATCAGAGA----------------ACAGAGCGGAGCGGATAAACTCGAGTTC----GATCATC-ACCAACCATG
TCGTGCTGCGGAGGCAACTGCGGGTGCGGATCCGGCTGCAAGTGCGGCAACGGCTGCGGAGGGTAATTTTTCATCTCCAA
TCTCCTTCTAAAAC--CCGCGTTCGATCTC-CCGATCTTTATGCCTTCTTTCTCAACCTTTTCCTTAAATCTCTCCTCGA
TCCATCTTGTTCCGCTGGCCGCTGCCTAACAGCATGCATGTCCATCGATCTCCTCTTGTCCTTATAACAACAAC----TA
AATTAAGAGATGCGCGTGAACAAATCTGCTGAGGAGGAGGGAAAAAAAAATCAAAAAATCTCCCTCCCTTAGATGAGGCC
ATGCACGATGTCTGTTTGCCTGTCGATTTCTTGGAGAGATCTACAAGAG---TCTCTGTGAATTGTGACTGATAATGATC
GTCTTG-------------TGCATGCAGGTGCAAGATGTACCCTGAGATGGACGAGGGAGTGAACACCGCCTCCCAGACC
CTCATCATGGGCGTTGCCCCCTCCAAGGGCACCCCGTCGTTCGAGGCCGCCGCCGAGA------------ACGGAGGGTG
CAAGTGCGGCCCCAACTGCACCTGCAACCCGTGCACCTGCAAGTGATCCATGAGGCCTCAATCAAATCAGATCAAGGAGA
-----TGGCATGGATGGACCTGATGAAGGAGCG--AGTAGTAGTTATGCATGAATCGCAAGCG--------TGTGTTTCG
TTTTAAATTGCCACCCAGAATAAGACGAGATCTATCG----------TATCGTATCGAGC------TAGTTAATGGATTA
TCCGTGCCCCTTGTGGCTTGTACCGTGTGCTGTGTAAGGCGTCTTGTG---------CTGTGATGCGCCTTTTCCTACCT
GTTCTAGTTCCGTCCTGATGTG----------------------------------------------------------
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>chrUn_548
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-----------------------------------------------------------------------AT----AGA
AAAAGCAAGCAATTTATCGGGCAAACGTTATCACGGGTTGATTCTGGAAAACCACACCACACTCCAGCCCAGCGGGTGAC
GAGCTAGCATGTTCGGGATGCTTC---------------------------GGTGATAATTAATCGGGCGTACGCCACAC
TTGGCAGG-----GTAGAATTGTCGACCGTGGACGTGGAGCACGGATGCATGCAGGCCGGTAGCGCATTTTGTCCGCGTC
CGCCGTCCATGGA-----GATGGACGGGCGGGCGGCCACCGTGCAA-----GTGCGTGCGTTGGTTCAATTCAATCAGCG
AGGGGCCACAGCGGCACACGCCAGAAATCGACGGGCACCTCAGCAGTGGCGTCCAGCCCATGGCCTCCACGAGCCCCGAG
ACGTGGACGGTGGATAGCCCCCCTGCCCGCTCTATAAATCACGGGCGCAC-CAACAACCTTCCCTTCCAAAGCAGAGCAA
GTGCAGATCGGAT-----CAGACCAGAGACACAGAGCAGAGCGGATAAACTCGAGGGCAGTAGATCATC-ACCAACCATG
TCGTGCTGCGGAGGCAACTGCGGGTGCGGATCCGGCTGCAAGTGCGGCAACGGCTGCGGAGGGTAAACCACCAT------
----CTCCTGATTTTTCTGCGTTCGATCTCTCCCATCTTCACGCCTTCTTTCTCAATCTTTTCTTTCGTTTC--CCTCGA
TCCATCTCGTTCCGCTGCCTAAGAGATGAGGCCATGCATGTCCGTAGACCCCCTCTGCTCCTCAAGCACGAGAGAGGGAT
CTGTTTGTTT-----------------------------------------------ATCGCCCCCTTTGAGATGGGGCC
ATCCACGCTGTCTGTTTGTTTATCGATTTCTCAGAGAGATCTACGAGGATGATACTTCTTTCTTGTGATTGATGATGATT
TCTGACTCGGATCGATGTATGCATGCAGGTGCAAGATGTACCCTGAGATGGACGAGGGGGTGACCACCACCTCCCAGACC
CTCATCATGGGCGTCGCCCCCTCCAAGGGCACCCCGTCGTTCGAGGCCGCCGCCGAGACCGGAGCCGACAACGGCGGGTG
CAAGTGCGGCTCCAACTGCACCTGCAACCCGTGCACCTGCAAGTGATCCAT-----------CAAATCAGGACAAGGAGA
TGGCATGGCATGGATGGACCTAATGAAGGAGCACTAGTAGTAGTTATGCATGGT--------GTGTGCGTTTGTGTTCTC
TTTTTAATTGCCGCCGAGAATAAGACGAGATCTATCGTATCGTATCGTATCGTATCGAGC------TAGTTCATG-----
-----GCCCCTTGTGGCTTGTACCGTGTGGTGTGCAAGGCGCGCGTACGTCCTGTGTCTGTGACGCGCCTTTTCCTACTG
TTCTAAGCTCCGTCCCGTGCCTT----CCCGTTTTATCTACATATATGT---------AGACAACAATAATTTGGAGTTT
CTCTCTATGTATGCATGTGTATCTGTATCACTATATGTGTGGCGCCAGCTCTTTGCTA-TTTTCTGTTTGTTCTTCTGTG
CAAGTACAGGTAAAATGGCGATCCCCCATCGCAACACATAAAAAATAAAAATAAAATATGGCGACTCAAATCAACCTCCC
CCCTTTAGTTGTAGTACTAGATGCTCATGCGTTAATTTGCTCTA-TAATTAGCATCTCAAAAA-----------------
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>SNPs
-------S---S-------S---------------------S---S------------S--------S------------
-------------------------------------------------------SSSSSSSSSSSSSSSSS--------
S-----------S--S------------S---------S--------------S--------------------------
-------------S-------S-S-----------------S----------------S--------------SSSSS--
-------------------S---S--------S-----------------------------------------------
S-----S---------------S-----------------S-S--S------------S--------------S------
-S----------S----------------S----------------S-S-----S---S---S--S---SS---------
---------------S-------------S--------------------------------------------------
----------------------S-SSSSSSSSSSSSSSSSSSSSSSSSSSS-----------------------------
--------SSSSS-------------------------------------------------S-----------------
-----S-SSSS---------------------------------------------------------------------
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-------------SSSSS----------------------------------SSS--S--SSS----S-S---S------
-----------------------S--------------------------------------------------------
-S-----------------------------S------------------------------------------------
-----------SS--S---------------S------S--------------------------S---S-SS-SSSS--
---------------S-------SS-------------------------------------------------------
---------------------------------------------S-----------------S-S--------------
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--------------S--S-----------------------------------------------------------S--
-------------------S-------------------------------------------------S----------
-----S-S------S-----------------------S-----------------------------------------
-------------------------S---------------------S------------SSSSSS----------SS--
-SS------------------------------------------------------S----------------------
----S--S---------S----SSSSS-----S----------S--SS-SSSSSSSSS------S---------------
--S----------S----S-S-S-------------------S----------SSS-SS-------------------SS
----------------------S---S--S----S-SSS-----------SS----------S------------SS---
-SS--S------S------------S-------SSS-S-SS---S------------S----SSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSS
>forward_666
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------GCATGTTCTGGATGCTCCCT------------------------------------------------------
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>reverse_2103
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----------------------GTATGTGTGGTGCCAGCTCT--------------------------------------
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