>input_sequence_54113
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-------------------------------------------------------------ATGGAAGAAGGGTTTGTGT
TTCGGGGGTGCGAGCTGCCGCCGGGGTTCCGGTTCCAGCCCACGGACCAGGAGATCATCGTCTGCTACCTCAAGAGGAAG
GTCGCCTCCGCCGCCTCCGCCGTCACCTCCATCATCGCCGACGTCGACATCTACAAGTTCGACCCGTGGGAACTGCCCGG
TAAGCATGCACGCATGCATACGTACTGCATACGTAGCCACGCCATGCAACCAATGCAAAGTTTTGTTTCTATCTCTTTGA
CTC--TCGTCCATGCACGAGCTTCCAAGAAAAA--AATACCGTTAGCTGCCGACCGGCTATCTACAC----CCATTTTTA
ATGTATATATCATCGTGA-GGAACAAGA--------GACAAGGATTATAATGCTGATTGAATATACTGGTAAATGGATGG
AAGTTTGACATT-----TTTGTGCGTGCGTGCAGACAAGGCGCAGTTCGGGGAGGGGGAGTGGTTCTTCTTCAGCCCGAG
GGACCGCAAGTACCCCAACGGCGCGCGGCCCAACCGCACGGCGGGCTCGGGGTACTGGAAGGCCACCGGCACCGACAAGC
CGATCCTGGCCGCCGGCGGCGCGCGCTGCCTCGGGGTCAAGAAGGCGCTAGTCTTCTACCAGGGCCGCTCCCCGCGGGGC
ACCAAGACTGAGTGGGTCATGCACGAGTACCGCCTCCTCCACGCCGACGCCGGCGCCGCCACCCGCCACAAGCCCCACGA
CTCCATGAGGGTACGTACTATTTCCGTAAAAAAAAATACAAGAGCGTTTATATATCACTAAAGTTAGCAAGGGAGTACCA
AACAAACACGCGTGTATTGATGAATCTACGGTACGGACACA------------GTTGCCGGTCAACTGAATTTCATACTT
ACATATATACGTTGGGTGCAGCTGGACGACTGGGTCCTGTGCCGCGTCCGCAAGAAGGGCGTCGCCGTCGCGCCGGACAT
GGATGGCAACCCCGGAGCGCCGAGCCACGCGGAGGTTCAGGCAATTGATAGTACCACCGCAGCGGCACACGGCGCCTTCG
GCGACGACTGGACCGACGGCCAGCTCCTGCAGTACCTGATGAGCGGCGGATCCGGACAGGTCGACGGTGCCGGCACCATC
AGCGGGGCGGCGGGTCACGTCCATGACGGTGCGCGCCGCGAGAGTGCGCCGGAGGTACAACTGGCGTCGGTGCTGGAGAA
CATCAAGAGGGACCTCTCCTTCCATGCCATGGACGACGTGTATTTCCTCCAGTCCAGCAAGCGGGCCAACTGCATGGGAG
GAGGCGCGGGCCACCACACCGACGGCGACCAGCTGTCGCCGCCGAAGTCCCTGTCCATGTTCGAGGACGATTAG------
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>chr3D_1_TraesCS3D01G170000
ATTCATCAGGAGCTCTTGCGATGGGTGCTAGTAGGAGGGAGAGGAGTCCAACATCTAATTGAGGAGTAGTGTGTATGTGT
TGGAGTGGTGTGTTTGATGTGCCAACCGTTTGTGGATGGCCGTCTATTGTAATTCTTGTATATAACCTCTGCCTTCTATA
AATCAATGGTACGCAATTTGTGTACTCTAAAAAAATATCTAGAAGGGTTGAACTCGTCTTGTGCCATAAGATAAATTATT
TGAAATACTCAATGCACACACTTATTTCGTAAAAGCATTGTCTTCAATCACCAAAACCACTAAGAAAGTAATATGCCCTA
ACACCTTCAAATGTGGACTTTTACTTCTCTAACCAGTTTCAAGTTATCAGCTAGAGATGCTCTTAAGTCAAAAAAACAAA
GATTCGGCAGTAATTA--TTTCTGTCTTATGTACGTACAGTAG-TACGAAAGCTGACGAAGAAC----CGTACGTACGTT
TGCTGTAGCGAAGTGACAGTATTATTTAAGCCTGAGTAAAACTGTAGTTCCACATCAATCACCAGCTGGCTATGGAGCAG
C----ATGCACGCATAAACACAAAATCTGCCTTCGCACTGACATGTGAACGCTGAAAAGGGCGTAAATCATGAAGAGGTT
TGGCCCATTTGGTAGTATTAATATGCGGCTGTCAAGCTCACGCGATGTCACGTTACGCGTAATCATCGGGTAGCTTGACG
TGCCATCGGACGTCAGGGAGGCTAATCCAGCCGTGTGTCCACGATCGATCGGTCTGCGCCACGCGCGTCGCCGTCCAGGA
CTCGAGAGCCATCGCCATGCACGTCGCTCTCGCATAATCTCATTGCTTGGGTACCCTGACGACATGGGCACGTACGGTTA
CTTAGCCTAAGTAACTTACGCGTGTGCATG------TATATATAGGCCATCCGCCAGCCGACTTCTTGGAGCGTTCCCAA
ATCAGGCCATCTCTTCTTCGTCGGCTCCGGCTCCGAGCTAGTGCG----GATCGATCGGTGATGGAAGAAGGGTTTGTGT
TTCGGGGGTGCGAGCTGCCGCCGGGGTTCCGGTTCCAGCCCACGGACCAGGAGATCATCGTCTGCTACCTCAAGAGGAAG
GTCGCCTCCGCCGCCTCCGCCGTCACCTCCATCATCGCCGACGTCGACATCTACAAGTTCGACCCGTGGGAACTGCCCGG
TAAGCATGCACGCATGCATACGTACTGCATACGTAGCCACGCCATGCAACCAATGCAAAGTTTTGTTTCTATCTCTTTGA
CTC--TCGTCCATGCACGAGCTTCCAAGAAAAA--AATACCGTTAGCTGCCGACCGGCTATCTACAC----CCATTTTTA
ATGTATATATCATCGTGA-GGAACAAGA--------GACAAGGATTATAATGCTGATTGAATATACTGGTAAATGGATGG
AAGTTTGACATT-----TTTGTGCGTGCGTGCAGACAAGGCGCAGTTCGGGGAGGGGGAGTGGTTCTTCTTCAGCCCGAG
GGACCGCAAGTACCCCAACGGCGCGCGGCCCAACCGCACGGCGGGCTCGGGGTACTGGAAGGCCACCGGCACCGACAAGC
CGATCCTGGCCGCCGGCGGCGCGCGCTGCCTCGGGGTCAAGAAGGCGCTAGTCTTCTACCAGGGCCGCTCCCCGCGGGGC
ACCAAGACTGAGTGGGTCATGCACGAGTACCGCCTCCTCCACGCCGACGCCGGCGCCGCCACCCGCCACAAGCCCCACGA
CTCCATGAGGGTACGTACTATTTCCGTAAAAAAAAATACAAGAGCGTTTATATATCACTAAAGTTAGCAAGGGAGTACCA
AACAAACACGCGTGTATTGATGAATCTACGGTACGGACACA------------GTTGCCGGTCAACTGAATTTCATACTT
ACATATATACGTTGGGTGCAGCTGGACGACTGGGTCCTGTGCCGCGTCCGCAAGAAGGGCGTCGCCGTCGCGCCGGACAT
GGATGGCAACCCCGGAGCGCCGAGCCACGCGGAGGTTCAGGCAATTGATAGTACCACCGCAGCGGCACACGGCGCCTTCG
GCGACGACTGGACCGACGGCCAGCTCCTGCAGTACCTGATGAGCGGCGGATCCGGACAGGTCGACGGTGCCGGCACCATC
AGCGGGGCGGCGGGTCACGTCCATGACGGTGCGCGCCGCGAGAGTGCGCCGGAGGTACAACTGGCGTCGGTGCTGGAGAA
CATCAAGAGGGACCTCTCCTTCCATGCCATGGACGACGTGTATTTCCTCCAGTCCAGCAAGCGGGCCAACTGCATGGGAG
GAGGCGCGGGCCACCACACCGACGGCGACCAGCTGTCGCCGCCGAAGTCCCTGTCCATGTTCGAGGACGATTAGTTAGGT
GTTGCCTTGCGCACGAGGGATATGCATGCACA----CGTAATCTACAGTCGACAGTGTGCGTGCTTAATTC---------
GGTAGCCACGATTGGGAGTGTTTCTACTCTTGCGGATATCAACTGTGATCGATTTTATTTCCTCCACACTTGCAGAACAA
CTTAATTTATTCTCTATCAGTGCAGCCTTGCTGTGAACCAAAATAACGACGGGCATGTGTGCGTCACCTCTAACAAATAC
TGCTCACAACTCATAACTCAGGTGGCTATCCGTGCTATGGCACGTGGCATCACTTTGAACTCCTAATCATCATCAAGGTT
CTTCCCGCGTCACTTTGAGCTCCTAATAAGGTTCTTCCCGCAAAACAAATACTTATAACGGAGTATGAAATTTTTGTCAA
GGCGTCAGTCACGTACTTATAGGGGTTGAAAATAGATGTGCAAGATTGATACTTCCCTATTTTTTTATACACTTAACTCA
TGGGCGGCAAGTTTCTTTAACCAGCTTTTCCAAAACTAACCTTAATCAGACGGTTCAGATTTAAACTTCCCTATTTGAAG
TGTATCCACACGCCCTCGATGACACTAGAAGCACCAATGAGACGGGGGGCGCTAGGTGGAGAGAACCTTATTCCATCTTC
AGAGAGCCGCCGCCGCTTCGTCTCTCTGAGCAGGACACAAACCCTAAAAAAACTCGGAAAAACATCCAAAAACGAAGCCC
TCCCGCCAGCAAAGGCCGAGATCCACCACGCCTTCATGGCCCTAAAGCCACATGAGACGAGGCAGACCGGGGCCGGCACC
GGCGGGAGGCAAGAGGAACCCTAACGGCGTCTGGGTACGAGCGCCTCCTGAGAGTGGATCTCTTATTTTATTCCTCTATG
ACTGTTCATATATAAGTATATGATTGGATCATTTTCTTTTTGTGTTCTTGGTAAACATGTAGGAGTATACAATTTTTTTG
TTAGAGCAATGCTAAAGAAAATTATGAATGATTTGGGGATCTTTTTA
>chr3B_193
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--------------------------------AAATATCCAGAGGGGTTCAAATCGTCTTGTGCCATAAGATAAATTATC
TGAAATAGTCAATGCACACGATTAGTCCGCAAAAGCATTGTCTTCAATCACCAAAACCACCAAGGAAGAAATATGCCCTA
ATACCTTCAAATGCGAATTTTTACTTCTCTAACTAGTTTCAAGGTATCAGCTAGAGATGCTCCTAAGTCAAAAAATAAAA
AATTCCGCAGTAATTA--TTTCTGTCTTATGTACGTACAGTAGGTACGAAAGCTGACGAAGAAC----CGTACGTAGGTT
TGCTGTAGCGAAGTGACAGTATTGTTTAAGCCTGAGTAAAACTGTAGTTCCACATCAGTCACCAGCTGGCTATCGAGCAG
CATCGATGCGTGCATAAACACAAAATCTGCCTTCGCACTGACATGTGAACGCTGAAAAGGGCGTAAATCATGAAGAGGTT
TGGCCCATTTGGGAGTATTAATACGCGGCTGTCAAGCTCACGCGATGTCACGTTACGCGTAATCATCCGGTAGCTTGACG
TGCCATCGGACGTCAGGGAGGCTAATCCAGCCGTGCGTCCACGATCGATCGGTCTGCGCCACGCGCGTCGCCGTCCAGGA
CTCGAGAGCCATCGCCATGCACGTCGCTCTCGCATAATCTCATTGCTTGGCTACCCTGACGACATGGGCACGTACGGTTA
CTTAGCCTAAGTAACTTACGCGTGTGCATG------TATATATAGGCCATCCGCCAGCCGACTTCTTGGAGCGTTCCCAA
ATCAGGCCATCTCTTCTTCGTCGGCTCCGACTCCGAGCTAGTGCC-------------GTGATGGAAGAAGGTTTTGTGT
TCCGGGGGTGCGAGCTGCCGCCGGGGTTCCGGTTCCAGCCGACGGACCAGGAGATCATCGTCTGCTACCTCAAGAGGAAG
GTCGCCTCCGCCGCCTCCGCCGTCACCTCCATCATCGCCGACGTCGACATCTACAAGTTCGACCCGTGGGAACTGCCCGG
TAAGAATGCATGCATGCATACGTACGGCATACGTAGCCACGCCATGCAACCAGTGCAAAGTTTTGTTTCTATCTCTTTGA
CTCTTTCGTCCATGCACGAGCTTCCAAGAAAAATAAATACCGTTAGCTGCCGACCAGCTATCGACAC----CCATTTTTA
ATGTACATATCATCGTTC-GGAACAAGACTGCAAGAGAGAAGTATTGTAATGC----TGAATATACTGAGAAGTGGACGG
AAGTTTGACAATTTTAATTTGTGCGTGCATGCAGACAAGGCGCAGTTCGGGGAGGGGGAGTGGTTCTTCTTCAGCCCGAG
GGACCGCAAGTACCCCAACGGCGCGCGGCCCAACCGCACGGCGGGCTCGGGGTACTGGAAGGCCACCGGCACCGACAAGC
CGATCCTGGCTGCCGGCGGCGCGCGCTGCCTCGGGGTCAAGAAGGCGCTCGTCTTCTACCAGGGCCGCTCCCCGCGGGGC
ACCAAGACTGAGTGGGTCATGCACGAGTACCGCCTCCTCCACGCCGACGCCGGCGCCGCCACCCGTCACAAGCCCCACGA
CTCCATGAGGGTGCGTACCA-----------------------------------------------------------A
ACC--ATACGCGTAACTCGATGAATCTACGCACACACAGCT-----------GGTTGTCGGTCAACTTAATTACATACTC
TATTTCTTATGTTGGGTACAGCTGGACGACTGGGTCCTGTGCCGCGTCCGCAAGAAGGGCGTCGCCGTCGCGCCGGACAT
GGATGGCAACCCCGGAGCGCCGAGCCACGCGGAGGTTCAGGCAATTGATAGTACCACCGCAGCCGCGCACGGCGCCTTCG
GCGACGACTGGACCGACGGCCAGCTCCTGCAGTACCTGATGAGCGGCGGATCCGGACAGGTCGACGGTGCCGGCGCCATC
AGCGTGGCGGCGGGCCACGTCCATGACGGTGCGCGACGCGAGAGTGCGCCGGAGGTACATCTGGCGTCAGTGCTGGAGAA
CATCAAGAGGGACCTCTCGTTCCATGCCATGGACGACGTGTATTTCCTCCAGCCCAGCAAGCGGGCCAACTGCATGGGAG
GAGGTGCGGGCCACCACACCGACGGCGACCAGCTGTCGCCGCCGACGTCCTTGTCCATGTTCGAGGACGATTAGTTAGGT
GTTGCCTTGCGCACGAGGTATATGCATGC--A----CGTAATCTTCAGTCGACCAGTGTGAGTAGAGTCACGAGTACTCG
GGTAGCCACGACTGG------------------GGATATAAACTGTCATCGATTTTATTTCCTCCACACTTGAGGAACAA
ATTAAT---TTCTCAATCAGTGCAGC-TTCATGTGAAC------------------------------------------
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>chr3A_319
TAACC---------------------------------------------------------------------------
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----CTTCAAAAGTGAACTTTTACTTCTCTAATCAGTTTCAAGGGATCAGCTAGAGATGCTCTTAAGTCAAAAGAAAAAA
---TCCACAGTAATTATTTTTCTGTCTTATGCACGTACAGTAGGTACGAAAGCTGACGAAGAACCGTACGTACGTACGTT
TGCTGTAGCGAAGTGACAGCATTCTTTAAGCCTGAGTAAAACTGTAGTTCCACATCAGTCAGCAGCTGGCTATCGAGCAG
CATCGATGCACGCATAAACACAAAATCTGCCTTCGCACTGACATGTGAACGCTGAAAAGGGCGTAAATCTTGAAGAGGTT
TGGCCCATTCGGGAGTATCAATATGCGGCTGTCAAGCTCACGCGATGTCACGTTACGCGTAATCACCCGGAAGCTTGACG
TGCCATCCGACGTCAGGGAGGCTAATCCAGCCGTGTGTCCACGATCGATCGGTCTGCGCCACGCGCGTCGCCGTCCAGGA
CTCGAGAGCCATCGCCATGCACGTCGCTCTCGCACAATCTCATTGCTTGGCTACCCTGACGACACAGGCACGTACGGTTA
CTTAGCCTAAGTAACTTACGCGTGTGCATGTATATATATATATAGGCCATCCGCCAGCCGACTTCTTGGAGCGTTCCCAA
ATCAGGCCGTTTCTTCTTCGTCGGCTACA----CGAGCTAGCGCGGATCGATCGATCGGTGATGGAAGAAGGTTTTGTGT
TCCGGGGGTGCGAGCTGCCGCCGGGGTTCCGGTTCCAGCCCACGGACCAGGAGATCATCGTGTGCTACCTCAAGAGGAAG
GTCGCCTCCGCCGCCTCCGCCGTCACCTCCATCATCGCCGACGTCGACATCTACAAGTTCGACCCGTGGGAACTGCCCGG
TGA----GCATGCATGCATACGTACTGCATACGTAGCCACGCCATGCAGCCAATGCAAAGTTTTGTTTCTATCTCTTTGA
CTC--TCGTCCATGCACGAGCTTCCAAGAAAAA--AATACCGTTAGCTGCCGACCAGCTATCTACACGTACCCATTTTTT
ATGTATCATCATCGATCCTGGAACAAGA--------GAGGATTATAGTAACACTGAATGAATATACTGATGAATGGATGG
AAGTTTGACAATTTTGGGTTG-GCGTGCATGCAGACAAGGCGCAGTTCGGCGAGGGGGAGTGGTTCTTCTTCAGCCCGCG
GGACCGCAAGTACCCCAACGGCGCGCGGCCCAACCGCACGGCGGGATCGGGGTACTGGAAGGCCACCGGCACCGACAAGC
CGATCCTGGCTGCCGGCGGCGCGCGCTGCCTCGGGGTCAAGAAGGCGCTCGTCTTCTATCAGGGGCGCTCCCCGCGGGGC
ACCAAGACTGAGTGGGTCATGCACGAGTACCGCCTTCTCCACGCCGACGGCGGCGCCGCCACCCGCCACAAGCCCCACGA
CTCCATGAGGGTACGTACCA-----------------------------------------------------------A
ACCCCACACGCGTGCGTCGATGAATCTAGTATTATATACGTACGTACACACAGGTTGTCGGTCAACTTAATTACATTACC
-------TATGTTGGGTGCAGCTGGACGACTGGGTCCTGTGCCGCGTCCGCAAGAAGGGCGTCGCCGTCGCGCCGGACAT
GGATGGTAACCCCGGAGCGCCGAGGCACACGGAGGTTCAGGCAATTGATAGTACCACCGGAGCCGCACACGGCGCCTTCG
GCGACGACTGGACCGACGGCCAGCTCCTTCAGTACCTGATGAGCGGCGGATCCGGACAGGTCGACGGTGCCGGCACCATC
AGCGGGGCAGCGGGCCACGTCCATGACGGTGCGCGCCGCGAGAGTGCGCCGGAGGTGCAACTGGCGTCGGTGCTGGAGAA
CATCAAGAGGGACCTCTCCTTCCATGCCATGGACGACGTGTATTTCCTCCAGCCCAGCAAGCGGGCCAACTGCATGGGAG
GAGGCGCGGGCCACCACACCGACGACGACCAGCTGTCGCCGCCGACGTCCTTGTCCATGTTCGAGGACGATTAGTTAGGT
GTTGCCTTGCGCACGAGGTATATGCATGCACATGCACGTAATCAACATTCGACAGTGTGCGTACTTAATTC---------
GGTAGCCACGATTGGGAGTGTTTCTACTCTTGCGGATATCAACTGTGATCGATTTTATTTCCTCCACACTTGCAGAACAA
CTTCATTTATTCTCTATCACTGCACT-TTGCTGTGAA-------------------------------------------
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>SNPs
SSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-------S---S-----S--S--------------------------S
-------S-----------SS---S-S--S------------------------------S---S---S-----------
-S-------------S---------------------------S--------------------------------S---
S----S--------------------------------------------------------------------------
-----------------------S---------------------------------S---------------S------
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------------S------------------------------------------------------S------------
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--------------------------------------------------S-----------------------------
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-----------------------------S------------------------------------------S-------
-S------------------------------------------------------------------------------
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----S-----S---------------------------------------------------------------------
-------------------------------------------------------S------------------------
----------------SS--------------------S---S---S---------S-----------S-----------
----------S-----------------S---------------------------------------------------
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----------S--------------------------------------S------------------------------
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------------------S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-
-S-SS---------SS-S------------S-SSSSSSS-S----------------S---------S----S------S
SSS-SSS--S----------------------------------------------------------------------
---------------------------------------------------------------S----------------
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--------------S-----------------------------------------------------------------
----------------------------------------------------S---------------------------
---------------------------------------------S----S-----------------------------
------------------S-------------------------------------------S-----------------
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--------------------------S-----------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_52
--------------------------------AGGAGGGAGAGGAGTCCAAC----------------------------
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>reverse_1926
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-----TATACGTTGGGTGCAGCTGG-------------------------------------------------------
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>forward_653
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-------------------------------------------------------------------------AGAGGTT
TGGCCCATTTGGT-------------------------------------------------------------------
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>reverse_2661
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--------------------GGTGGCTATCCGTGCTATGG----------------------------------------
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