>input_sequence_87074
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----------------------ATGGAGAAGGGGAAGGCCCCAGCGGAGGCAGCGGAGTCGGCCGCGGCGTATGCGGCGC
GGCTGGCGCGTGAGTGGAGCACTTGGGCGATGAAGAACACGAAGGTGGTCGCGCACTACGGCTTCATCCCCCTCGTCATC
CTCGTCGGCATGAGCTCCGAACCCAAGCCCAGCCTCGCCCAGCTCCTCTCCCCCGTTTAG--------------------
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>chr3D_1_TraesCS3D01G281200
GGCGGCGCCCCTCCTTTCCTTTCCCTCCTCTCTCTCCTT-CCTCTCCTCTCCTACTCCCACATGGAAGGGGGGAGTC---
GAGTAGG--------AC--TCCTCATGGGGCGCGCCTAGGGTGGCCGGCCCC-T-CCCCTCCTCCACTTCTTTATATACG
GGGAGGGAGGCACCCCTTGGAGACACACCAATTGATCTCTTGGATCTCTTAGCCGTGTGCGGTG--CCCCTCTCCACCAT
AATCCACCTCGATAACATCGTAGCGGTGCTTAGGCGAAGCCCTACGTCGGTAGAA-CATCATCATCGTCACCACGCCGTC
GTGTTGACGGAACTCTCCCTCAAAGCTCGGCTGGATCGGAGTTCGAGGGACGTCATCGAGTTGAACGTGTGCTGAACTCG
GAGGTGCCGTGCGTTCGGTACTT-GATCGGTCGGATCGTGAAGACGTACGACTACATCAACCGCGTTGTGCTAACGCTTC
CATTTTTGGTCTACGAGGGTACGTGGACACA-CTCTCCCCTCTCGTTGCTATGCATCATCATGATCTTGCGTGTGCGTAG
GATTTTTTTTTGAAATTACTACGTTCCCCAACAGGGACGTGGGCCGGCCCCGCACACGGTTAATCGGGTCATGGCCGACA
CGTGACCCGCCTAGGGTGGTGTCTGGGCCGCAAGGCTCGGCACACGTGCCGAGACGACACGCCCCGTTTAGTTTTT---T
TAGTTCTTTTATATATTAGTACAAAACAGCCCAAATAGGCCCCAAAAAATAGCCTAAGTATGCGGGCTGGTGGGCTAAAA
GTGCGAGTGTTGTCGGCCCATTTCCTCGTTGTGCCGTGCC-------------TGGGCACGCGGGCCGGGCCGTGCCGGG
TGCGTTAAGCCCTGGGCCGGGCCATGGGGCCACCAGAT-CCCATCGCATCCTGAACCTCCTCTCCTCTGGTTCTCCT--C
CCATCATCACAACTCACAA----------------------GCTGCAATATCCAAAATTCCTAATCATTCTTCTCTCGGC
GACACGATTGGCAGAGGCGGCCATGGAGAAGGGGAAGGCCCCAGCGGAGGCAGCGGAGTCGGCCGCGGCGTATGCGGCGC
GGCTGGCGCGTGAGTGGAGCACTTGGGCGATGAAGAACACGAAGGTGGTCGCGCACTACGGCTTCATCCCCCTCGTCATC
CTCGTCGGCATGAGCTCCGAACCCAAGCCCAGCCTCGCCCAGCTCCTCTCCCCCGTTTAGCCCCGTCCCCCGGCCCGATC
CGCACGGTTGTGCTCGTATTGAATTGATCAATTTTTGTATTTCTCCCTGAATAATTTCGATTACCCTTTGAATTGCTCTG
ATTTTGGGTCGCCCTGATTGCCACCGAGAGCCTACTACCTAATTTATTTGCATGACTGTATTAAGCTAAGAGCTGTACGA
CGCGTTTGGTTCAGGTCAGGTAATGTTTTCAGATTTGTAATCAGAATACAGTGTATTAGGCTGTGGATTGGCTGATTACG
TGATGCGTTTGGTTCGACGAAGGGTTGGTTTCCCAAACCAGAGCGTTAGAAAAGAAGTGAGGAGAAGGGAGAGGCTCGGC
CGGCATGCCTGCTTGCGACGAAGAAGGGGATGTCCGGCAAGGGGGCTGCGACGAAGAAGGGGAAGTCCGGCAAGGGGGCT
GCTCGCGACGGGGATGGGGAGAGCTCCGCTGCCAGCGTGGCTGCTAGCGACGGAGAAGGGGGAGATCCGGCTAGAGCTGT
TGCTCGCGAGAAGGAGGCCCGGCCGGCGCTGCTGCTTGTGGTGGGGATGGGGGATGTTCGGCCGGCGTCACTGCTCGTGG
CGGGGAGGGGAGGGGAGGGGAGTGGGGGGATCCGGCTCCTCTACCGTGCCCAACGGCACGGTACTCTGCGGTGCCTTCTT
CCTACCCAGGGGTACGCACTGGTATAGGCCAGAATATCCCTAAAAAAAAAGATATGGGCCAGAATCCAACCAGCCTATCA
AATCTGACACGTACATCACACACCGCTCAAAAGAAAAACCTAATGCATCACACCCCTGCATATTAACTAATTAACTATTA
CTTTTTGAAAAAAGTAATTAAGTATTATTATTTTCCCCAAAAATATTATTATCTTAAAAACACCAATTTTGTATCTCAGT
CATATATTATGCGGAGCGAATTTTGTATTTTATATATTTCCTTTTCCTAATTTTTATTACTTATTATTGTTTTATCATTT
GGATCGGTCCTTTTATTTTT
>chr3D_1
GGCGGCGCCCCTCCTTTCCTTCCCCCC----CTCTCCTTCCCTCTCCTCTCCTACTCCCACATGGAAGGGGG-AGTC---
GAGTAGG--------AC--TCCTCATGGGGCACGCCTAGGGTGGTCGG-CCCCTCCCCCTCCTCCACTCCTTTATATACG
GGGAGGGAGGCACCCCTTGGAGACATAACAATTGATCCTTTGGATCTCTTAGCCGTGTGCGGTG--CCC--CTCCACCAT
AATCCACCTCGATAATATCGTAGCGGTGCTTAGGCGAAGCCCTGCGCCGGTAGAA-CATCATCATCGTCACCACGCCGTC
GTGTTGACGGAACTCTCCCTCAAAGCTCGGCTGGATCGGAGTTCGAGGGACGTCATCGAGTTGAACGTGTGCTGAACTCG
GAGGTGCTGTGCGTTCGGTACTT-GATCGGTCGGATCGTGAAGACGTACGACTACATCAACCGCGTTGTGCTAACGCTTC
CGTTTTCGGTCTACGAGGGTACGTGGACACA-CTCTCCCCTCTCGTTGCTATGCATCACCATGATCTTGCGTGTGCGTAG
GAA-ATTTTTTAAAATTACTACGTTCCCCAACA-----------------------------------------------
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>chr3D_1
GGCGGCGCCCCCCTTTCCTTTCCCCCTCTCTCTCTCCTTCCCTCTCCTCTCCTACAACCACTTGGAAGTGGGGAGTCCTA
-----------CTCCCACATCCTCATGGGGCGCGCCTAGGGTGGCCGGCCCCCTCCCCCTCCTCCACTCCTTTATATACA
GGGAGGGAGGCACCCCTTGGAGACACAACAATTGGTCTCTTGGATCTCTTAGCCGTGTGCGGTGCCCCC--CTCCACCAT
AATCCACCTCGATAATATCGTAGCGGCGCTTAGGCGAAGCCCTGCGTCGGTAGAA-CATCATCATCGTCACCACACCGTC
GTGCTGACGGAACTCTCCCTCAAAGCTCGGCTGGATCGGAGTTCGAGGGACGTCATCGAGTTGAACGTGTGCAGAACTCG
GAGGTGACGTGCATTCGGTACTT-GATCGGTCGGATCGTGAAGACATACGACTACATCAACCGCGTTGTGCTAACGCTTC
CGCTTTCGGTCTACGAGGGTACGTGGACACA-CTCTCCCCTCTCGTTGCTATGCATCACCATGATCTTGCATGTGCATAG
GAA-AA-TTTTGAAATTACTACGTTCCCCAACA-----------------------------------------------
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>chr6D_1
GGCGGCGCCCCCCTTTCCTTTCCCCCTCT--CTCTCCTTCCGTCTCCTCTCCTACTCCCACTTGGAAGGGGGCAGTCCTA
-----------CTCAAC--TCCTCATGGGGCGCGCCTAGGGTGGCCGGCCCCCTCCCCCTCCTCCACTCCTTTATATACG
GGGAGGCAGGCACCCCTTGGAGACACAACAATTGATCTCTTGGATCTCTTAGCCGTGTGCGGTGCCCCC--CTCCACCAT
AATCCACCTCGATAATATCATAGTGGTGCTTAGGCGAAGCCCTGTGTCGGTAGCAACATCGTCATCATCACCACGCCGTC
GTGCTGACGGAACTCTCCCTCAAAGCTCGGCTGGATCGAAGTTCGAGGGACGTCATTGAGTTGAACGTGTGCAGAACTCG
GAGGTGCCGTGCGTTCGGTACTT-GATCGGTCGGATCGTGAAGACGTACGACTACATCAACCGCATTGTGCTAACGCTTC
CGCTTTCGGTCTATGAGGGTACGTGGACACA-CTCTCCCCTCTCGTTGCTATGCATCACCGTGATCTTGCGTGTGCGTAG
GATTTTTTTTTGAAATTACTACGTTCCCCAACAG----------------------------------------------
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>chr6D_1
GGCGACG-CCCCCTTTCCTTTCCCCCTCT--CTGTCCTTCCCTCTCCTCTCCTACTCCCACTTGGAAGGGCGGAG-----
GAGTAGG--------AC--TCCTCATGGGGTGCGCCTAGGATGGCCGGCCCCCTCACCCTCCTCCACTCCTTTATATACG
GGGAGGGAGGCACCCCTTGGAGACACAACAATTGATCTCTTGGATCTCTTAGCCGTGTGTGGTGCCCCG--CTCCACCAT
AATCCACCTCGATAATATCGTAGCGGTGCTTAGGCGAAGCCCTGCGTCGGTAGCAACATCATCATCGTCACCACGCCGTC
GTGCTGACAGAACTCTCCCTCAAAGCTCGACTGGATCGGAGTTCGAGGGACGTCATCGAGTTGAACGTGTGCAAAACTCG
GAGGTGCCATGCGTTCGGTACTT-GATCGGTCGGATCATGAAGACGTATGACTACATCAACTGCGTTGTGCTAACGCTTC
CGCTTTCGGTCTACGAGGGTACGTGGACACA-CTCTCCCCTCTCATTGCTATGCATCACCATGATCTTGCGTGTGCGTAG
GAA-TTTTTTTGAAATTACTACGTTCCCCAACAG----------------------------------------------
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>chr5D_1
GGCGGCGCCCCCCTTTCCTTTCCCCCTCT--CTCTCCTTCCCTCTCCTCTCCTACTCCCACTTGGAAGGGGGGAGTCCTA
-----------CT----------CATGGGGCGCGCCTAGGGTGGCCGGCCCCCTCCCCCTCCTCCACTCCTTTATATACG
GGGAGGGAGGCACCCCTTGGAGACACAACAATTGATCTCTTGGATCTCTTAGCCGTGTGCGGTGCCCCC--CTCCACCAT
AATCCACCTCGATAATATCGTAGCGGTGCTTAGGCGAAGCCCTGCGTCGGTAGAA-CATCATCATCGTCACCACGCCGTC
ATGCTAATGGAACTCTCCCTCAAAGCTCGGCTGGATCGGAGTTCGAGGGACGTCATCGAGTTGAACATGTGCAGAACTCG
GAGGTGTCGTGCGTTCTGTACTT-GATCAGTCGGATCGTGAAGACGTACGACTACATCAACCGCGTTGTGCTAACGCTTC
CGCTTTCGGTCTACGAGGGTACGTGGACACA-CTCTCCCCGCTCGTTGCTATGCATCACCATGATCTTGCGTGTGCGTAG
GAA-TTTTTTTGAAATTACTACGTTCCCCAACAG----------------------------------------------
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>chr5D_1
GGCGGCGCCCCCCTTTCCTTTCCCCCTCT--CTCTCCTTCCCTCTCCTCTCCTACTCCCACTTGGAAGGGGGGAGTCCTA
-----------CT----------CATGGGGCGCGCCTAGGGTGGCCGGCCCCCTCCCCCTCCTCCACTCCTTTATATACG
GGGAGGGAGGCACCCCTTGGAAACACAACAATTGATCTCTTGGATCTCTTAGCCGTGTGCGGTGCCCCC--CTCCACCAT
AATCCACCTCGATAATATCGTAGCGGTGCTTAGGCGAAGCCCTGCGTCGGTAGCA-CATCATCATCGTCACCACGCCGTC
ATGCTAATGGAACTCTCCCTCAAAGCTCGGCTGGATCGGAGTTCGAGGGACGTCATCGAGTTGAACGTGTGCAGAACTCG
GAGGTGTCGTGCGTTCGGTACTT-GATCAGTCGGATCATGAAGACGTACGACTACATCAACCGCGTTGTGCTAACGCTTC
CGCTTTCGGTCTACGAGGGTACGTGGACACA-CTCTCCCCGCTCGTTGCTATGCATCACCATGATCTTGCGTGTGCGTAG
GAA-TTTTTTTGAAATTACTACGTTCCCCAACA-----------------------------------------------
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>chr4D_4
---GGCACCCCCCTTTCCTTTCCCCCTCT--CTCTCCTTCCCTCTCCTCTCCTACTCCCACTTGGAAGGGGGGAGT----
-AGTAGGACTCCT----------CATGGGGCGCGCCTAGGGTGGCCGGCCCCCTCCCCCTTCTCCACTCCTTTATATACG
GGGAGGGAGGCACCCCTTGGAGACACAACAATTGATCCCTTGGATCTCTTAGCCGTGTGCGGTGCCCCC--CTCCACCAT
AATCCACCTCGATAATATCGTAGCGGTGCTTAGGCGAAGCCCTACGTTGGTAGAT-CACCATCATCGTCACCACGCCGTC
GTGCTGACGAAACTCTTCCTCAAAGCTCAGCTGGATCGGAGTTCGAGGGACGTCATCGAGTTGAACGTGTGCTGAACTCG
GAGGTGCCGTGCGTTCGGTACAT-GATCAGTCAGATCGTGAAGACGTACGATTACATCAACCACGTTGTGCTAACTCTTT
CTCTTTCGGTCTACGAGGGTACGTGGACACA-CTCTCCCCTCTCGTTTCTATGCATCACCATGATCTTGCGTGTGTGTAG
GAA-TTTTTTTGAAATTACTACGTTCCC----------------------------------------------------
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>chr2D_4
---GGCGCCCCCCTTTTCCTTTCCCCCCT--CTCTCCTTCCCTCTCCTCTCCTATTCCCACATGGAAGGGGGGAGACCGG
GAGTAGGACTCCT----------CATGGGGCGCGCCAAGGGTGGCCGGCCCCCTCCCCCTCCTCCACTCCTTTATATATG
GGGAGGGAGGCACCCCTTGGAGACACAACAATTGATCCCTTGGATCTCTTAGCCGTGTGCGGTGCCCCC--CTCCACCAT
AATCCACCTCGATAATATCGTAGTAGTGCTTAGGCGAAGCCCTGCGTCGGTAGAA-CATCATCATCGTCACCACGCCGTC
GTGCTGACGGAACTCTCCCTCAAAGCTCGGCTGGATCGGAGTTCGAGGGACGCCATCGAGTTGAACGTGTGCTGAACTCG
GAGGTGCCGTACGTTCGGTACTT-GATCGGTCGGGTCGTGAAGACGTACGACTACATCAACCGCGTTGTGCTAACACTTC
CGCTTTCGGTATACGAGGGTACGTGGACAACGCTCTCTCCTCTCGTTGCTATGCATCACCATGATCTTGCGTGTGCGTAG
GTA-AATTTTTGAAATTACTACGTTACCCAACAG----------------------------------------------
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>chrUn_7
------GCCCCCCTTTCCTTTCCCCCTCT--CTCTCCTTCCCTCTCCTCTCCTACTCCCACTTGGAAGGGGGGAGTCCTA
CTCC---ACTCCT----------CATGGGGCGCGCCTAGGGTGGCCGGCCCC-TCCCCCTCCTCCACTCCTTTATATACG
GGGAGGGGGGCACCCCTTGGAGACACAACAATTGATCTCTT-GATCTCTTAGCCGTGTGCGGTGCCCCC--CTCCACCAT
ATTACACCTCGATAATATCGTAGCGGTGCTTAGGCGAAGCCCTGCGTCGGTAGCATCATCATCACCGTCACCACGCCGTC
GTGCTGACGGAACTCTCCCTCAAAGCCCGGCTGGATCGGAGTTCGAGGGACGTCATCGAGCTGAACGTGTGCTGAACTCG
GAGGTGCCGTACGTTCGGTACTCAGATCGGTCGGATCGTGAAGACGTACGACTACATCAACCGCGTTGTGCTAACGCTTC
CGCTTTCGGTCTACGAGGGTACGTGGACACA-CTCTCCCCCCTCGTTGCTATGCATCACCATGATCCTGTGTGTGCGTAG
GAA-TTTTTTTGAAATTACTACGTTCCCCAACA-----------------------------------------------
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>chr3A_573
GGGCAC--------------------------------------------------------------------------
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--------------------------------------GTGGGTCGGCCCCACACATGGTTAATCGGGTCATGGCCGACA
CATGGCCCGCCTAGGGTGGTGTCTGGGCCGCAAGGCTGGGCACACGTGCCGGCACGACACAGCCCGTTTAGTTTTTCCTT
TAGTTCTTTTATATATTAGCACAAAACAGCCTAAATAGG-CCCAAAAAGTAGCCTAAGTAGGCGGGCTGGTGGGCTAAAA
GTGCGACTGTTGTCGGCCCATTTCCTCGTTGTGCCGTGCCTGGGCCCAAACACTGGGCACCCGGGCCGGGCCGTGCCAGG
TGAGTTAAGCCCTGGGCCGGGCCATGTGGCCACCAGATCCCCATCGCATCCTGAACCTCCTCTCCTCTGGTTCTCCT--C
--ATCATCACAACTCACAA----------------------GCTGCAATATCCAAAATTCCAAATCATTCTTCTCTCGGC
GACGCGATTGGCAGAGGCGGCCATGGAGAAGGGGAAGGCCCCAGCGGAGGCAGCGGAGTCGGCGGCGGCGTGTGCGGCGC
GGCTGGCGCGTGAGTGGAGCACTTGGGCGATGAAGAACGCGAAGGTGGTCGCGCACTACGGCTTCATCCCCCTCGTCATC
CTCGTCGGCATGAGGTCCGAGCCCAAGCCCAGCCTCGCGCAGCTCCTCTCCCCCGTGTAGCTATTTTCCGCGGCCCGATC
CGCACGGCTGTGCGCGTATTGAATTGATCAACATTCGTATTTCTCCCC-AATAATTTCGATTACTCTTTGGATTGCTCTG
ATTTGGGGTCTCCTTGATTGCCACCGAGAACCTACCAGCTAGTTTATCTGTATGAT--TATTAAGCTAGGAGCT------
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>chr3B_719
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----------------------AAAACAACCCAAAAAGGCCCAAAAAATTAGCCTAAGTAGGCGGGCTGGTGGGCTAAAA
GTGTGAGTGTTGTCGGCCCATTTCCTCGCTGTGCCA-----GGGCCCGAAGACTGGGAACACAGGCCGGGCCGTGCCAGG
TGCGTTAAGCCCTGGGCCGGGCCATGTGGCCACCAGATCCCCA-----TCCTGAACCTCCTCTCCTCTGGTTCTCCTTCC
--ATCATCACAACTCACAAAGCTGCAATATCCAAAAAAAAAGCTGCAATATCCAAAATTCCAAATCATTCTTCTCTCGGC
GACACGATTGGCAGAGGCGACCATGGAGAAGGGGAAGGCCCCAGCGGAGGCAGCGGAGTCGGCCGCGGCGTGTGCGGCCC
GGCTGGCGCGTGCGTGGAGCACTTGGGCCATGAAGAACGCGAAGGTGGTCGCGCACTACGGCTTCATCCCCCTCGTCATC
CTCGTCGGCATGAGGTCCGAGCCCAAGCCCAGCCTCGCGCAGCTCCTCTCCCCCGTGTAGCTCTATTCCGCGGCCCGATC
CGCACGGCTGTGCGCGTATTGAATTGATCAATATTTGTATTTCTCCCC-AATAATTTCGATTACTCTTTGGATTGCTCTG
ATTTGGGGTCTCCTTGAT--------------------------------------------------------------
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>SNPs
-------------------------S------------------------------------------------------
--------------------------------------------------------------------S-----------
---------------------------S-----------------------------------------SS---------
---------------S----------------------------------------------------------------
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-S----S---------------------------------------------------S---------------------
----------------------------------SSSS-----S-------S----S-----------------------
-S--S--------------------------------S-------------SS-------SS------------------
-------------------S----------------------------S-----------S-------------------
------------------------------------------------------------S----------------S--
--------------------------S-----------------------------------------------------
SS-----------------------------------------------------------S------------------
-----------------------------------------------------------------------S--------
--------------------------------------S-----------------------------------------
--------------S-----S-----------------S-----------------S----S-SS-S--S----------
-------S-----S------------------S--------------SS---------------S-----S---------
----S-----S--S---------------S-----S-S---S-----S--S----SSS----------S-----SSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSS
>forward_962
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--------------------------------------------------------------TCTCCTCTGGTTCTCCTC
CC------------------------------------------------------------------------------
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>reverse_1974
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-----------------------------------------------------ATGGGCCAGAATCCAACCAG-------
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