>input_sequence_57406
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-ATGTCCAGGGAGCGGTGGCCGCCGCTCGCCCTGGCCCTGGCGGTGGCGGCGGCGGTGGTGGGCGTCCTGGCGGCTGCGT
CGCCGCGGGCGGAGGCGGAGCTGCAGGTGGGGTTCTACAATGCGACGTGCCCGATCGCGGAGGGGGTGGTGTTCGCGGAG
ATGCACGCCATCCTGCACGAGGACCCCACGCTGGCGCCCTCGCTGCTCCGGATGCACTACCACGACTGCTTCGTCCAGGG
CTGCGACGGCTCCATCCTGCTCAGGTCCCGCCGGGGCACGGCGGAGCGGGACGCCACCCCTAACCGGAGCATGCGCGGCT
ACGACGCCATCGAGCGGATCAAGGCCAGGCTCGAGACGCTCTGCCCGCTCACCGTCTCCTGCGCCGACATCATCGCCATA
GCCGCCAGGGACGCCGTCTACCTGGTGAGTAGCTGCAGAGACCACGACGACAAGTTGATTTAATTGG-GCATCTTTTTCA
CCGGCTCTCGTGCTTACTTTGCAGAGCAAGGGGCCGTGGTACGGCGTGGAGACCGGGCGGCGGGACGGCAACGTGACGGT
GGCCGAGTACGCTGAGAACGACCTGGCGCCGCCGGACTCCAACATCGTCGACGTCAAGACCTTCTTCAGCGTCAAGTCGC
TCACCGCCAAGGACATCGTCGTCCTCTTCGGTACGCACCTCTCCTTTCCTCTCCATGACTCCATCGCTTCACGCGTACGT
GCGTCCGTGGACGACAGCAACAGCCCAACACACGCCGCACTGACAATGGCATCCTTCCTCCCCCTCCAGGGAGCCACAGC
ATCGGGACCTCCCACTGCGAGGCGTTCCGGAAGCGGCTCTACAACTTCACGGGCGCCATGGACCAGGACCCGTCGCTGGA
CGCCGGGTACGCGAGGCAGCTGAGGAAGCTCTGCCCGCGCCGCCACGGCGGCCGGGGCAGGAGGACCAAGGTGCCCATGG
ACCCCGGCAGCGGCTTCACCTTCGACCTCAGCTACTACCGCCACGTGCTGGCCACGGGGGGCCTCTTCCAGTCCGACGGC
AGCCTCCTCCACGACGCCGCCACCAGGGGCTACGTCGAGAGGATGGCCAACGCGTCGTCGCCGGACGAGTACTACCGGGA
CTTCGCGGCGGCCATGGTCAAGATGGGCCGCACCGACGTGCTCCTCGACAGCCTCGGCGAGGTCAGGGCCACCTGCGGCG
TTTTTGTTGACTAG------------------------------------------------------------------
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>chr1A_1_TraesCS1A01G319000
TAAAACCCATGTTGCACAACCTTTTCTAGTGTTCTGAGACAAGACTCTTATTACAAAAACTGTTTAGGACACATCTAAAT
GTGATATAATTATGTCACATCTAACCTGATATTCATTATATTTATGGTCTATTTTATTTTTGTCCCAATTTTTTTTCTGC
GTTATTTATGAGAGCTTAAATATGACATCTTAACAAAAACAACTAGATGTGAATTAGACAAACTGTTGCAAAAATCGCAA
CATCTTCACCGCATATAATTTTCTGCGTATGTTGCAAAAATTGCAACACATCTTCGGCCGCGCCACGCGCTTGGGCAAGT
TATCTTGGCGGTCACCGTTGTTGCCGAGGGACAGAGACATGCGTGGTTAAGCAGGCCACCTGTCCACGCCAGATCGGCCG
GCTGATCCCTATAGGATCGGCCTTGGGCTTGAGCATATTTCCAGCTCTTTCTTTTTTTTGCGGGATTAAGCACATTATGT
AAAAGTGCATGCTCTAACCAATGCAATCAAAAGATCGATTTGATGAAAAAGACTAGACAACACATTATACGTCGACACAT
TCTAACTGACGCCTAGTCTGACTGCGAGTCCCCGAGATACGAGTATACGACCGCTTCCCCCAAAAGACCATCCGTAATAA
ATCGCCAGCGACGCCGATGGCGACAAGACGAGCACGCGCCCGTCCATGGAGCCGAC------------------------
----CCGACGAGAGCATCCGAGCCCGGCCGACGCGCGCCCCCCCT-----CACCCACCAAGCAACCAACCAACCCCTCCA
CTCAAAGCAAAGCCTCGAGGCGGAGTCCGTCCTACTCCATCCATCGCGTCGCGTCACACACCGGCCCGGGACTACAGTCG
GAAAAGCACGGCGCAACCACACTCTTTGACCTTTGCCCCGTGCTCCCACCATCGCCCA-TCCATTCCACTGTGCCGCCGC
TCCGCCCAAGCCCGCCCCCATTTCCACCCTCGATCGTTCTCCGGTCTGC-------TCGTCGACCGCCTCGCGCTTTCTT
CATGTCCAGGGAGCGGTGGCCGCCGCTCGCCCTGGCCCTGGCGGTGGCGGCGGCGGTGGTGGGCGTCCTGGCGGCTGCGT
CGCCGCGGGCGGAGGCGGAGCTGCAGGTGGGGTTCTACAATGCGACGTGCCCGATCGCGGAGGGGGTGGTGTTCGCGGAG
ATGCACGCCATCCTGCACGAGGACCCCACGCTGGCGCCCTCGCTGCTCCGGATGCACTACCACGACTGCTTCGTCCAGGG
CTGCGACGGCTCCATCCTGCTCAGGTCCCGCCGGGGCACGGCGGAGCGGGACGCCACCCCTAACCGGAGCATGCGCGGCT
ACGACGCCATCGAGCGGATCAAGGCCAGGCTCGAGACGCTCTGCCCGCTCACCGTCTCCTGCGCCGACATCATCGCCATA
GCCGCCAGGGACGCCGTCTACCTGGTGAGTAGCTGCAGAGACCACGACGACAAGTTGATTTAATTGG-GCATCTTTTTCA
CCGGCTCTCGTGCTTACTTTGCAGAGCAAGGGGCCGTGGTACGGCGTGGAGACCGGGCGGCGGGACGGCAACGTGACGGT
GGCCGAGTACGCTGAGAACGACCTGGCGCCGCCGGACTCCAACATCGTCGACGTCAAGACCTTCTTCAGCGTCAAGTCGC
TCACCGCCAAGGACATCGTCGTCCTCTTCGGTACGCACCTCTCCTTTCCTCTCCATGACTCCATCGCTTCACGCGTACGT
GCGTCCGTGGACGACAGCAACAGCCCAACACACGCCGCACTGACAATGGCATCCTTCCTCCCCCTCCAGGGAGCCACAGC
ATCGGGACCTCCCACTGCGAGGCGTTCCGGAAGCGGCTCTACAACTTCACGGGCGCCATGGACCAGGACCCGTCGCTGGA
CGCCGGGTACGCGAGGCAGCTGAGGAAGCTCTGCCCGCGCCGCCACGGCGGCCGGGGCAGGAGGACCAAGGTGCCCATGG
ACCCCGGCAGCGGCTTCACCTTCGACCTCAGCTACTACCGCCACGTGCTGGCCACGGGGGGCCTCTTCCAGTCCGACGGC
AGCCTCCTCCACGACGCCGCCACCAGGGGCTACGTCGAGAGGATGGCCAACGCGTCGTCGCCGGACGAGTACTACCGGGA
CTTCGCGGCGGCCATGGTCAAGATGGGCCGCACCGACGTGCTCCTCGACAGCCTCGGCGAGGTCAGGGCCACCTGCGGCG
TTTTTGTTGACTAGCCTTAGGTTCAGGGCTGCACTTGCACATATACACATACACTGGTTGATTTGTACGGGGGTT-----
--TATCGGGTTCTCTGATCTT----TATGCTAATAGTATTATTAACTGAAGATGCAAAAGAGATGCAAGGCAGTTTCATA
CGCTTTTTAGCTGAGGGGGTCATCACCTGTAACTTGTACAAAT----AGTCCACGTACTAATACTTATACTGTAC-----
-------------------TGCATGGAGCTACTTATCTGTTAAGTACATCTGGTCGTTTGACCAACCACATGTTTCTGTT
TGGTCAACCACAATTCGGTCACCAAACCTGGCCAGTTATAACAAAATAATTTAGCTACAGAGCGTGTCAGCTACTTATCA
TGCAAGTCGAACTTGTGTGAGCAAACTTCTCTATCGAGACAACCGAAACTAAATACTGCTCCCTCCGTCCCAAAATGTAA
GACATTTTTTTGCACTACCATCAAAAAAACGTCATACATTTCGGGACAGAGGGAGTACTTTACTATCCAATGACTGGTGA
TGCACTCAAAAAAACAGCACAAATGCACTACAATTTGCAAGCCAAAAT----------------------------CGTT
TTCCTATTCTAAATGTGCAACTTGAACGTTTTCGGCAGAGTTTTCTGTAGCAATGAACAGGTTTTACCCTAGTAAAATAG
GAAAGCTTTGGAAAGAGACA--TCCAGTGTACAGTGCAGTGAAATTGCTCTTTCATTTGTTCAACTTCGATTCCAGAAAT
TACACCTACTGTATAATGAAAAACTGTAAGTGAGAACTGAACACCCTTTGCTTTTTAGAGACTACACATGACAAGAACAA
AGAACACTTGG-CACATTGGTGCATACATTGTTATTTTTTACCCCATATATAGATTCCAGATGCTACTACTGCGCTTACT
GCTCCAATGGACGCCAAAATTTTCAACTTCGAAGCACCTTTCCTAGGCACAGGTAATTCCATCAAACGTTGTACCTGCAC
GGAAATTTGATAATTGAAATGAGCATTATGAAAAATAGATCTGC
>chr1B_556
CATATTCCAG----------------------------------------------------------------------
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-----CTGATGCCTAGTCTGACTGCGAGTCCACGAGATACGACCGT--------TTCCCCCAAAAGACCATCCGCAATAA
ATCGCCAGGGACGCCGATGGCGACAAGACGAGCACGCGCCCGTCCATGGAGCCGACACCGCTGAGCGAATCAGTCGCACC
CGAGCCGACGAGAGCATTCGAGCCCGGCCGACGCGCGTCCCCCCT-----CACCCACCAACCAACCAACCAATCCCTCCA
CTCAAAGCAAAGCCTCGAGGCGGAGTCCGTCCTACTCCATCCATCGCGTC-----ACACG-----CCGGGACAACAGTCC
GAAAAGCATAGCGCAACCACACTCTTTGACCTTTGCCCCGTGATCACACCGCACCCATCTCCCATCCACTGTGCCACCGC
CCCGCCCCTCCCCGTCCCCATTTCCTCGCCCCATCGTTCTCCCGTCTCTGTTCTGTTCGTCGACCGCCTCGTGCTTTCTT
CATGTCCAGGGAGCGGCGGGTGCCGCTCGTCCTGGCCCTGGCGGCGGCGGCGGTGGTGG---GTGCCCTCGCGGTT----
--------GCGGAGGCGGAGCTGCAGGTCGGGTTCTACAATGCGACGTGCCCGATCGCGGAGGGCGTGGTGTTCGCGGAG
ATGCACGCCATCCTGCACGAGGACCCCACGCTCGCGCCCTCCCTGCTCCGGATGCACTACCACGACTGCTTCGTCCAGGG
CTGCGACGGCTCCATCATGCTCAGGTCCAGGCGGGGCACGGCGGAGCGGGACGCCACCCCGAACCGGAGCATGCGCGGCT
ACGACGCCATCGAGAGGATCAAGGCCAAGCTCGAGATGCTCTGCCCGCTCACCGTCTCCTGCGCCGACATCATCGCCATG
GCCGCCAGGGACGCCGTTTACCTGGTGAGTAGCTGAAGAGACCACGACGAGAAGTTGATTTAATTGG-GCATCTTTTTCA
CCAG--CTCGTGCTTACTTTGCAGAGCAAGGGGCCGTGGTACGGCGTGGAGACCGGGCGGCGGGACGGCAATGTGACGGT
GGCCGAGTACGCGGAGAACGACCTGGCGCCGCCGGACTCCAACATCGTCGACGTCAAGACCTTCTTCAGCGTCAAGTCCC
TCACCGCCAAGGACATCGTCGTCCTCTTCGGTACGCGCCTTTCCTTTCCTCC--------CCATCGCTTCACGCGTACGT
GCGTCCGTGGACGACAGCAACAGCCCAGCACACACCGCACTGACAATGGCATCCT----CCACCTCCAGGGAGCCACAGC
ATCGGGACCTCCCACTGCGAGGCGTTCCAGAAGCGACTCTACAACTTCACGGGCGCCATGGACCAGGACCCGTCGCTGGG
CGCCCGGTACGCGAGGCAGCTGAGGAAGCTCTGCCCGCGCCGCCACGGCGGCCGGGGCAGGAGGACCAAGGTGCCCATGG
ACCCCGGCAGCGGCTTCACCTTCGACCTCAGTTACTACCGCCACGTGCTGGCCACGGGGGGGCTCTTCCAGTCCGACGGC
AGCCTGCTCCACGACGCCGCCACCAGGGACTACGTCGAGAGGATGGCCAACGCGTCGTCGCCGGACGAGTACTACCAGGA
CTTCGCGGCGGCCATGGTCAAGATGGGCCGCACCGACGTGCTCCCCGACCACCTCGGTGAGGTCAGGGCGACCTGCGGCG
TTTTTGTTGACTAGCCTTAGCTTCAGGGCTGCACTTGCACATATACACACAA--TGGTTGATTTGTGTGGGGGTT-----
--TATCGGGTTCTCTGATCTTTATTTATGCTAATATTATTATTAACTGAAGATGCAAAAGAGATGCAAGGCAGTTT----
-GCTTTTTAGCTGAGGGGATCATCACCTGTAACTTGTACAAATAGTCAGTCCACGTACTAATACTTATACTGTACATGGT
CGTCGTTCATGACGAGTACTGCGTGGAGCTAATTATCTGT----TACATCGGGTTGTTTGACCAACCACATGTTTCTGTT
TGGTCAACCACAATTCGGTCACCAAATCTGGCCACATATAACAAAATAATTTAGCTACAGATTGCGTCAGCC----ATCA
TGCAAGTTTAACTTGTGAGAGCAAACATCTGTATGGAGACAACCAAAACTAAACACTAAC--------------------
--------------------------------------------------------------CTATCCAATGACCGGTGA
TGCACTAAAAAAATTTGCACCAATGCACTACAATTTGCAAGCCAAAATGACTCCTGATAATAAAATCAAGTCAAATCGTT
TTCCTATTCTAAATTTGCAACTTAAACATTTTCGCCGGAGTTTTTTGTAGCAATGAACAAGCC--ACCCTAGTAAAATAG
GAAAGCTTTGGAAAGAGACAAATCCAGTGTACAATGCAGTGAA-TTGTTCTTTCATTTGTTCAACTTCGATTCCAGAAAT
TACACCTATTGTATAATGAAAAACTGTAAGTGAGAACTGAACACTCTTTGCTTTTTAGAGACTACACATGACAAGAACAA
AGAACACTTTGACACATTGGTGGATACACTGTTATTTTTTACCCCATATATAGATTCCAGATGCTACTACTGCGCTTACT
GCTCCAATGGACGCCAAAATTTTCAACTTCGAAACACCTTTCCTAGGCACAGGTAATTCCATCAAACTTTGTACCTGCAC
GGAAATTTGATAATTGAAGTGAGCATTATGAAAAATAGATCTG-
>chr1D_566
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-----CTGACGCCTAATCTGACTGCGAGTCCACGAGATACGACCGT--------TTCCCCCAAAAGACCATCCGTAATAA
ATCGCCAGCGACGCCGATGGCGACAAGACGAGCACGCGCCCGACCATGGAGCCGACACCGCTGAGCGAATCAGTCGC---
-----------GAGCATTCGAGCCCGGCCGACGCGCGCCCTCCCCTCACCCACCAACCAACCAACCAACCAATCCCTCCA
CTCAAAGCAAAGCCTCGAGGCGGAGTCCGTCCTACTGCATCCATCGCGTC-----ACACACCGGCCCGGGACTACAGCCC
GAAAAGCACGGCGCAAC--CACTCTTTGACCTTTGCCCCGTGATCACACCACA-CCATCTCCCATCCACTGTGCCGCTG-
-----------CCGTCCCCATTTCCACCCTCGATCGCCCTCCGGTCTGC-------TCGTCGACCGCCTCGCGCTTTCTT
CATGTCCAGGGAGCGGCGGTTGCCGCTCGTCCTGGCCCTGGCGGCGGCGG---TGGTGG---GCGTCCTCGCGGTTGCGT
CGCCGCGGGCGGAGGCGGAGCTGCAGGTCGGGTTCTACAATGCGACGTGCCCGATCGCGGAGGGGGTGGTGTTCGCGGAG
ATGCACGCCATCCTGCACGAGGACCCCACGCTGGCGCCCTCGCTGCTCCGGATGCACTACCACGACTGCTTCGTCCAGGG
CTGCGACGGCTCCATCATGCTCAGGTCCCGCCGGGGCACGGCGGAGCGGGACGCCACCCCGAACCGGAGCATGCGGGGCT
ACGACGCCATCGAGCGGATCAAGGCCAGGCTCGAGACGCTCTGCCCGCTCACCGTCTCCTGCGCCGACATCATCGCCATG
GCCGCCAGGGACGCCGTCTACCTGGTGCGTAGCCAAAGAGACCACGACGAGAAGTTGATTTAATTTGAGCATCTTTTTCA
CCGGCTCTCGTGCTTAATTTGCAGAGCAAGGGGCCGTGGTACGGCGTGGAGACCGGGCGGCGGGACGGCAACGTGACGGT
GGCCGAGTACGCGGAGAACGACCTGGCGCCGCCGGACTCCAACATCGTCGACGTCAAGACCTTCTTCAGCGTCAAGTCCC
TCACCGCCAAGGACATCGTCGTCCTCTTCGGTACGCACTTTTCCTTTCCTCTAT--------ATCGCTTCACGCGCACGT
ACGTCCGTGGACGACAGCAACAGCCCAACACACACCGCACTGACAATGGCATCCTTGCTCCACCTCCAGGGAGCCACAGC
ATCGGGACCTCCCACTGCGAGGCGTTCCGGAAGCGGCTCTACAACTTCACGGGCGCCATGGACCAGGACCCGTCGCTGGA
CGCCCGGTACGCGAGGCAGCTGAGGAAGCTCTGCCCGCGCCGCGGCGGCGGCCGGGGCAGGAGGGCCAAGGTGCCCATGG
ACCCCGGCAGCGGCTTCACCTTCGACCTCAGCTACTACCGCCACGTGCTCGCCACGGGGGGCCTCTTCCAGTCCGACGGC
AGCCTCCTCCACGACCCCGCCACCAGGGGCTACGTCGAGAGGATGGCCAACGCGTCGTCGCCCGACGAGTACTACCAGGA
CTTCGCGGCGGCCATGGTCAAGATGGGCCGCACCGACGTGCTCCCCGACAGCCTCGGCGAGGTCAGGGCCACCTGCGGCG
TTTTTGTTGACTAGCCTTAGGTTCAGACATGCACTTGCACATG---ACATACACTGGCTGATTGTATGAGGATTTATGTC
TCTATACGGTTCTCTGATCTC----CAAGCTAA---TATTATTAACTGAAGATGCAAGA-----------CAGTTTCATG
AGCTCTTTAGCTCAGGAGATCATCACTTGTAACTTGTACAAATAA----TCCACGTACTAATATTTATACTGTACAA---
----GATCATGACGAGTCCTGCA-------------CTGT----TACATCTGGTCGTTTGACCAC----------CTGTT
TGGTCAACCACAAATCGGTCACCAAA-CTGGCCAGAAATAACAAAATAATTCAGCCACAGAGTGCGTCAGCC----GTCA
TGCAAGTTGAACTTGTGTGAGCAAACTTCTGTATGGAGACAACCAAAACTAGATACTAC---------------------
------------------------------------------------------------TACTATCCAATGACCGGTGA
TGCACTAAACGAATAGCTT-CAATGCACTACAATTTGCAAGCCAAAATGACTCCTGATAATAAAATCAAGTCAAATCATT
TTCCTATTCTAAATTTGCAACTTAAACGTTTTCGCCAGAGTTTGTT---------------------CCTAGTAAAATAG
GAAAGCTTTGGAAAGAGACACATCCAGTGTACATTGCAGTGAAATTGTTCTTTCATTTGTTCAACTTCGATTCCAGAAAT
TACACCTATTGTATAATGAAAAACTGTAAGTGAGAACTGAACACCCTTTGCTTTTTAGAGACTACACATGACAAGAACAA
AGAACACTT-GACACATTGGTGCATACATTGTTATTTTTTACCCCATATATAGATTCCAGATGCTACTACTGTGCTTACT
GCTCCAATGGATGCCAAAATTTTCAACTTCGAAGCACCTTTCCTAGGCACAGGTAATTCCATCAAACGTTGTACCTGCAC
GGAAATTTCATAACTGAAGTGAGCATTACGAAAAAATATATCTG
>SNPs
S-S-SS---SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSS--------------------------S----------SSS-SSSSSSSS--------------------------
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-----------------S------------------------------------------S-----------S-------
--------------------------------------------------SSSSS------------------------S
------------------------------------------S--S-----SSS--SS----SS----------------
S------SSS----S-----------------------------------------------------------------
----------------S--SS--------S--------------S--------S-----SSS-------S----S-----
----------------------------S---------------------------------------------------
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----------------S-------------------------------------------S-------------------
-------------------------------------------------------------------------------S
-----------------------------------S--------------S-----------------------------
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------------S-----------------------------------------------------------------S-
----------------------------------------S-----------SSSSSSSS--------------------
---------------------------------S----------------------S----S------------------
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----S---------------------------------------------------------------------------
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----------------------------------------------------------------------------S---
--------------------------------------------S-----------------------------------
------------------------------------------------------------------SS------------
-----------------------------------S-------------------------------------------S
S-----------------S-------------------------------------------------------------
-------------------------------S--------SSSS------------------------------------
--------------------------S--------S--------------------------S-S------SSSSS----
-------S----------------------S---S---------S------------S-SSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------------S-----
------S------SSS----S-----------------------------------------------------------
--------------S--------S----------S---------S--------------S-SSSS---------------
---------------------------------S-------------S--------------------------------
--------S-----------------------------------------------------------------------
---------S----------------------------------------------------------------------
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------------------S------------------------S
>forward_793
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-----------------------------------------------------CCACCAAGCAACCAACCAAC-------
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>reverse_2308
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-------------------------------------------------------------------CGGGGGTTTATCG
GGTTCTC-------------------------------------------------------------------------
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