>input_sequence_82941
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---ATGCTCGGGGGGAGAAACAATGGGCCGTCGACGACGTCGAAGGCCCGAGCGGACGGCGCTGGCCTCGCCGGCGCCAG
CACCGTCGTCGCCGACGGCGGGCAGGCGGAGGTCGCAGCCTCGCAGTTCGTCGTGCAGCTAGGTGAACACCGATCACCTC
CTCGATCGATCTAACATGTCTAGCACTGTATAGTATAGGTGCACGAAATCATTGACTGTA--------TACAAAATCCGG
CATGCAGATGAGGCGGCTCGGGAGAGGCTGGAGCGCATGAACCGGAGGCTGAGTCTGCTGGAGCAGCAGATGGAGATGCT
GGAGGCGGAGGTTGGGAGGGCCAGCAGTACCGCCGACGACTAG-------------------------------------
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>chr3D_1_TraesCS3D01G270600
CCGTGGCGCTCGTACCCTGCACCGAGCAAGCTAAGGTTTCTACTGCCTCCCGCCGACGTTCGTTGTTGGTCTACCTCGTA
TCTTGTGGTCTTAGGACCATGACGGTGCGGTGGATCATGGAGTACATATTAGAAATTTACTACTGTACATGCCGGCTATT
AGGTTGACTCTAAATGAATAACATGACAATT---CCTTATAATTAATTGACTATATTATTAACCATACTCTTACTGGCAA
AAAAGAGAAATTCACTC-GGGTTAAACAATGGACGAGCCATGCCCT---GCCCATGCCCCATGCGCATGCAGTGACGCAA
CAGGACTCCCGGCGGGTAG--TAGCACCTGGCAACTCACAGTTCC------------------CAGATCCCCAAATAACG
CCTGTCGAACTGATCGATTCGGCACGATCGACGCCGCACGATTTAACAATTAACCCGGCTGATTCT------AAAAAAAA
AATTAACCCGGCTGATCAATCAGATTGCAGAAACGGAGCTCCAGGCTCGATCGCCGCCGCCGCCTGCCGGTGCGATGGCC
ATTCGCCGACGTGACATGGTTGCCCGTTCCGTGCGACGGTGTAGAGAGAATCAGGCCGGAGATTGATGCGGGTACACACT
ATGTCGCTGAGGGAAATCTTTGATCTTTCCGGCCGGTCAGCTATGAAGGCAGATTCATGTGCACGGTGGCAGTGGCTGGG
TCGGGTCGGGAGACCGAGCGTCCAAGTCGCCGGGTGGGACTCTTGACC------CAGTAGCAGCAGCGGCATATTTGACC
AGGAACGAGGAACCCGGCCCGAGCTCCATGAATCATCGTCGCGGTGACCTCTCCGCCAAGGCAAGGCAGCCCCTCCCCCA
AGTCTCCCCGCGCGAATAAAAGGCCGGCCGGTCGGTCGGCTTCCAGCGGTCAGGCACGTCTCTTCCATTTCCAACCAGTC
ACAACTCGCCACTGCACCAATAAGCCGGCCGGTC----CGTGCGATCCAAGAGTATCAGTATACTGTATACGTCGCTATA
GCCATGCTCGGGGGGAGAAACAATGGGCCGTCGACGACGTCGAAGGCCCGAGCGGACGGCGCTGGCCTCGCCGGCGCCAG
CACCGTCGTCGCCGACGGCGGGCAGGCGGAGGTCGCAGCCTCGCAGTTCGTCGTGCAGCTAGGTGAACACCGATCACCTC
CTCGATCGATCTAACATGTCTAGCACTGTATAGTATAGGTGCACGAAATCATTGACTGTA--------TACAAAATCCGG
CATGCAGATGAGGCGGCTCGGGAGAGGCTGGAGCGCATGAACCGGAGGCTGAGTCTGCTGGAGCAGCAGATGGAGATGCT
GGAGGCGGAGGTTGGGAGGGCCAGCAGTACCGCCGACGACTAGGAGTAG--CGGCGCC---------------------G
GATGCAAGTAGAAGCCTTCCTTTTCTTCTTTTCCCTTCTCAGCTTCTTGCTGATGGAAGAACACGCACGCACGGTGATAG
TATCATGCGCTTGCTT----GTTAGG----CCTTTTCTTGTAGTGATGGAAGAACATGACTATCCAGAAACAAGCACGAC
AGTGGAAACCCAGGCTTCTCCCCGCTCGGGATTCCTGGCCGTCGGATCTTCC-TTTGATGCATTCTGGACCGTAGGATCT
CGCTCGGGAGAGATCTCGGCCG----------TCGGATCACTGCTACAATGAATAGTGATGAATAATAGCCTCCATTCGA
TTTTTCTTACTGACTTTTCTTACTCCGAAATTACTGTCTTACCTTGCTGACGTGTGGGGTCGATCCCTGGTGGGCCGCGC
CGGTCAGCGACTGTGTCTGCGAGCGTGGTATGTGCGTTATTTAGTGTAGAAGTATTCATGCCACCGCCTGTAAAACTAGA
TGGCCGCCAAGGGTATTTTGGACATTTCGCGTACACCTATAAAACCGAAGCAGCAGCGACTGAAAACCTAGCCGCTTCCT
CCCCTTGCGCGGTC------------------------------------------------------------------
---------------------------------------------GCGCCGCCTCCCCTCGTCCAGCCATCTCCCCGACC
TCGCCGCCCCACACAGACCTCCGCTCGCCCAGCCCTCTCCCCGACCTCACCGCCCCACCCACATCGCCGCCACCGACGCC
CCTCAGACCTCGCCACCGCGGACCTCTCTCCTTGTCTTCCTCGCACCACGGCGCCCGCAACCTCCTCCCTCCCGTCAACA
GAAGGGGAGGAAAGAGAAGAGGGAGAGCGAGCGCGTCAGACGGCGGCCATGGCGGCGCTGTCGTCCGACCTCGGCCTCCG
ACTGCTGACCTCTCTCCTCGTTTTCCTTGCACCACGGCGCCCGCAACTTCCTCTCCCTCCCGTAAACTTCTCCAGGATCT
ACAACATCGACGGCTACGGCAGCGCCACGGTGCACCGCCAGCGCCACG-------------------CGCGCAATGGCTG
GGGGCTCCGCCGGCC
>chr3B_25
------------------------AGCAAGCTAGGGTTTCTACTGCCTCCCGCCGA----------TGGTCTACCTCGTC
TCCTGTGGTCTTAGGACATTGCTGGCGCAGTGAGTCATAGAGTACTTATTAAAAATTTACTACCGCACATGCCGGCTATT
AGGTTGCCTCTAGATGACATGGCAACTCCTTAATTCTTATAATCAATTGGCTATATTATTAACCATGCTTTTACTAG---
--AAAAAAAATCCACTC-GGGTTAAACAATGGACGAGAGCCATGCCCAGGCCCATGCCCCATGCGCATGCAGTGACGCAA
CAGGACTCCCGGCGGGTAG--TAGCACCTGGCAACTCACAGTTCC------------------CAGATCCCCAAATAACG
CCTGTCGAACTGATCGATTCGGCACGATCGACGCCGCACGATTTAACAATTAACCCGGCTGATTCTCGAAAAAAAGAAAC
AATTAACCCGGCTTATCAATCAGATTGCAGAAACGGAGCTCCAGGCTCGATCGCCGCCGCCGCCTGCCGGTGCGATGGCC
ATTCGCCGACGTGACATGGTTGCCCGTCCCGTGCGACGGTGTAGAGAGAATCAGGCCGGAGATGGATGCGGGTACACACT
ATGTCGCTGAGGGAAATCTTTGATCTTTCCGGCCGGTCAGCTATGAAGGCAGATTCATGTGCACGGTGGCAGTGGCTGGG
TCGGGTCGGGAGACCGAGCGTCCAAGTCGCCGGGTGGGACTCCTGACC------CAGCAGC---------ATACTTGACC
AGGAACGAGGAACCCGGTCCGAGCTCCATGAATCATCGTCGCGGTGACCTCTCCGCCAAGGCAAGGCAGCCCCTCCCCCA
AGTCTCCCTGCGCGAATAAAAGGCCGGCCG-------------------------------------------ACCAGTC
ACAACTCGCCACTGCACCAATAAGCCGGCCGGTCCGTGCGTGCGATCCAAGAGTATCAGTATACTGTATACGTGGCTATA
GCCATGCTCGGGAGGAGAAACAATGGGCCGCCGACGACGTCCAAGCCCCGACCGGACGGCGCGGGCCTCGCCGGCGCCAG
CACCGTCGTCGCCGACGGCGGGCAGGCGGAGGTGGCCGCGTCGCAGTTCGTCGTGCAGCTAGGTGAACACCACAATTACC
TCC--TCGATCTAACATGTCTAGCACTGTATAGTATAGGTGCACGAAATCATTGATTGTG--------TACAAAACCCGG
CATGCAGATGAGGCGGCTCGGGAGAGGCTGGAGCGCATGAACCGGAGGCTGAGGCTGCTGGAGCAGCAGATGGAGATGCT
GGAGGCGGAGGTTGGGAGGGCCAGCAGTACCGCCGACGACTAGGAGCAG--CGGCGCCGCCCCTGGTCGGAGAGACGATG
GATGCAAGTAGAAGCCTTCCTTTTCTTCTTTTCCCTTCTCAGCTTCTTGCTGATGGAAGGA----CACGCACGGTGATAG
TATCATGCGCTTGTTAAGGCGTTAGGCCT---TTTTCTTGTAGTGATGGAAGAACATGACCAT-----------------
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>chr3A_127
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----------------------------------------------TATTAAAAATTTACTACTGTACATGCCAGCTATT
AGGTTGACTTTAG----ATGACATAACAACT---TCTTATAATCAATTGGCTATATTATTAACCATACTCTTACCGGCAA
AAAAGAAAAATCCACTCGGGGTTAAACAATGGACGA--------CCCATGCCCATGCCCCATGCGCATGCAGTGACGCAA
CAGAACTCCCGGCGGGTAGTATAGCACCTGGCAACTCACATCATCGCCATCCAGTCCAGTCTACAGATCCCCAAATAACG
CCCGTCGAACTGATCGATTCGGCACGATCGACGCCGCACGACTTAACAATTAACCCGGCTG-------------------
--------------ATCAATCAGATTGCAGAAACGGAGCTCCAC-------CGCCGCCGCCGCCTGCCGGTGCGATGGCC
ATTCGCCGACGCGACGTGGTCGCCCGTTCCGTGCGATGGTGTACAGAGAATCAGGTCGC---------------------
---TCGCTGAGGGAAATCTTTGATCTTTCCGGCCGGTCAGCCATGAAGGCAGATTCATGTGCGCGGTGGCAGTGGCTGGG
TCGGGTCGGGAGACCGAGCGTCCAAGTCGCCGGGTGGGACTCTTGACCCGGCAGCAGCAGC---------ATATTTGACC
GGGAACGAGG----------------------------------------------------------------------
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>chr3A_766
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----ACGAGGAACCCGGCCCGAGCTCCATGAATCATCGTCGCGGTGACCTCTCCGCCAAGGCAAGGCGGCCCCTCCCCCA
AGTCTCCCCGCGCGAATAAAAGGCCGGCCGGTCGGTCGGCTTCCAGCAGTCAGGCGCGTCTC------TTCCAACCAGTC
ACAACTCGCCACTGCACCAATAAGCCGGCCGGTC----CGTGCGATCCAAGAGTATCAG---ACTGTATACG------TA
GCCATGCTCGGGAGGAGAAACAATGGGTCGCCGACGACGTCGAAGGCCCGAGCAGACGGCGCGGGCCTCGCCGGCGCCAG
CACCGTCGTCGCCGACGGCGGGCAGGCGGAGGTGGCCGCGTCGCAGTTCGTCGTGCAGCTAGGTGAACACCAATCGCCTC
CTCGATCGATCTAACATGTCTAGCACTGTATAGTATAGGTGCACGAAATCGTTGACTGTATACGAAATTACGAAATCCGG
TATGCAGATGAGGCGGCCCGGGAGAGGCTGGAGCGCATGAACCGGAGGCTGAGGCTGCTGGAGCAGCAGATGGAGATGCT
GGAGGCGGAGGTCGGGAGGGCCAGCAGCACCGCCGACGACTAGGAGTATACCGGCGCCGCCCCTCGTCGGAGAGACCATA
GCTAGAAGTAGAAGCCTTCCTTTCCTTCTTTTCCCTTCTCAGCTTCTCGCTGATGGAAGAACACGCACGCACGGTGATAG
TATCATGCGC--GCTT----GTTAGGCCTTCCTTTTCTTGTGGTGATGAAAGAACATGGCT-------------------
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>chr2D_1494
ATGAGC--------------------------------------------------------------------------
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-------------------------------------------------------------ATCCAGAAACAAGCACGAC
AGTGGACACCCAGGCTTCTCCCCGCTCGGGATTCCTGGCCGTCGGATCTTCC-TTTGATGCATTCTGGACCGTAGGATCT
CGCTCGGGAGAGATCTCGGCCGTCGGATCAAGCCGGATCACTGCTACAATGAATAGTGATGAATAGTAGCCTCCATTCGA
TTTTTCTTACTGACTTTTCTTACTCCGGGTTTACTGTCTTACCTCGCTGACGTGTGGGGTCGACCCCTGGTGGGCCGCAC
CGGTCAGCGACTGTGTCTGCGAGCGTGGTCTGTGTGTTATTTAGTGTAGAAGTATTCATGCCACCGCCTGTAAAACTGGA
TGGCCGCCGAG-----------------------------------------------------------------TCCT
CCCTTTGCGCGGTC------------------------------------------------------------------
---------------------------------------------GCGCCGCCTCCCCTCGTCCAGCCCTCTCCCCGACC
TCGCCGCCCCACACACACCTCCGCTCGCCCAGCCCTCTCCCTGACCTCGCCGCCCCACCCACATCGCCACCACCGACGCC
CCTCAGACCTCGCCAGCGCGGACCTCTCTCCTTGTCTTCCTCGTACCACGGCGCCCGCAACCTCCTCCCTCCCGTCAACA
GAAGGGGAGGAAAGAGAAGAGGAAGAGCGAGCGCGTCAGACGGCGGCCATGGCGGCGCCGTCGTCTGACCTCGGCCTCCA
ACTGCTGACCTCTGTCCTCGTTTTCCTCGCACCACGGCGCCCGCAACTTCCTCTCCCTCCCGTAAACTTCTCCGGGATCT
ACAACATCGACGGCTACGG-------------------CAGCGCCACG-------------------CGCGCAATGGCTG
GGGGCTCCGCCGG--
>chr2D_1498
CTACC---------------------------------------------------------------------------
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-----------------------------------------------------------------AGAAACAAGCATAGC
ATGAGCCACCCAGTCTCCTCACCGCTCGGCGCTCCTGGCCGTTGGATCGGTGTTTTGATGCATTCTTGGCCGTCCGATCA
CGCCCTCAGATGATATCGGCCGTCGGATCAAGAGGCGACACTGCTACA----------ATGAATAGTAGCTTCCATTCGA
TTTTTCTTACTGCCTTTTCTTACTCCAGAATTACTTTGTTGCCTCGCTGACGTGT-GGGTCCATCCCTGGTGGGCCACGC
TGGTCAGCCGCTGTGCCTGCGAGCGTGGTATGTATGTTACTTAGTGTAGAAGTATTCGTGCCACCGCCTGTAAAACTGGA
TGTCCGCCGAGGGTATGTTGGACATTTCGCGTACCCCTATAAAAACGAAGCACTAGCGACTGAAAACCTAGCCGCTTCCT
CCCCTTGCGCGGTCGCGCCCCCTTCTCCCGTCCCCCCGCATCCGAGCCGCACTTACCCTAGAGGCGCTCGATGCGGTGCT
CCCTCGTCGCTCCTCCGGTCGCTAGGCGACGTGGGGGCTGCAGGCGCGCCGCCTCCCCTCGTCCAGCCCTCCCCCCGACC
TCGCCGCCCCACACACACCTTCGCTCGCCTAGCCCTCTCCCCGACCTCGCCGCCCCACCCACATCATCGCCACCGACGCC
TCTCAAACCTCGCCACAGCGGACCTCTCTCCTCGTCTTCCTCGCACCACGGCGCCCGCAACCTCCTCCCTCCCGTCAACA
GAAGGGAAGGAAAGAGAAGAGAGAGGATGAGCGCACCAAACGGCGGCCATGGCG--------------------------
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>chr5D_1500
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-------------------------------------------------------------ATCCAGAAACAAGCACGAC
AGTGGAAACCTAGGCTTCTCCCCGCTTGGGATTCTTGGCCGTCGGATCTTCC-TTCGATGCATTCTGGACCGTAGGATCT
CGCTCAGGAGAGATCTCGGCCGTCGGATCAAGCCGGATCACTGCTACAATGAATAGTGATGAATAGTAGCCTCCATTCGA
TTTTTCTTACTGACTTTTCTTACTACAGAATTACTGTCTTACCTCGCTGACGTGTGGGGTCGATCCCTGGTGGGCCACGC
CGGTCAGCGACTGTGTCTGTGAGCGCGGTCTGTGCGTTATTTAGTGTAGAAGTATTCATGCCACCGTCTGTAAAACTGGA
TGGCCGCCAAGGGTATTTTGGACATTTTGCGTACACCTATAAAACCGAAGCAGCAGCGACTGAAAACCTAGCCGCTTCCT
CCCCTTGCGCGGTC------------------------------------------------------------------
---------------------------------------------GCGCCACCTCCCCTCGTCCAGCCCTCTCCCCGACC
TCGCCGCCCCA----------------------------------------------CCCACATCGCCGCCACCGACGCC
CCTCAGACCTCGCCACCGTGGACCTCTCTCCCTGTCTTCCTCGCACCATGACGCCCGCAACCTCCTCCCTCCCGTCAACA
GAAGGGAAGGAAAGAGAAGAGGGAGAGCGAGCGCGTCAGACGGC---CATGGCAGCGCCGTCGTCCGACCTCGGCCTCCG
ACTGCTGACCTCTCTCCTCGTTTTCCTCGCACCACGGCGCCCGCAACTTCGTCTCCCTCCCATAAACTTCTCCAGGATCT
ACAACATCGATGGCTACGG-------------------CAGCGCCACGATGCACCGCCAGCGCCACGCGCGCGGTGGCTG
GGGGCTCTGCCGGCC
>chr5D_1500
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-------------------------------------------------------------ATCCAGAAACAAGCACGAC
AATGGACACCCAGGCTTCTCCCCGCTCGGGATTCCTGGCCGTCAGATCTTCC-TTTGATGCATTCTGGACCGTAGGATCT
CGCTCGGGAGAGATCTCGGCCGTCGGATCAAGCCGGATCACTGCTACAATGAATAGTGATGAATAGTAGCATCCATTCGA
TTTTTCTTACTGACTTTTCTTACTCCGAAATTACTGTCTTACCTCGCTGACGTGTGGGGTCGATCCCTGGTGGGCCACGC
CGGTCAGCGACTGTGTCTGCGAGCGTGGTCTGTGTGCTATTTAGTGTAGAAGTATTCATGCCACCGCCTGTAAAACTGGA
TGGCCGCCGAGGGTATTTTGGACATTTCGCGTACCACTATAAAACCGAAGCAGCGGCGACTGAAAACCTAGCCGCTTCCT
CCCCTTGCGCGGTC------------------------------------------------------------------
---------------------------------------------GCGCCGCCTCCCCTCGTCCAGCCCTCTCCCCGACC
TCGCCGCCCCA----------------------------------------------CCCACATCGCTGCCACCGACGCC
CCTCAGACCTCGCCAGCGCGGACCTCTCTCCTTGTCTTCCTCGCACCACGGCGCCCGCAACCTCCTCCCTCCCGTCAACA
GAAGGGGAGGAAAGAGAAGAGGGAGAGCGAGCGCGTCAGACGGCGGCCATGGCGGCGCCGTCGTCCGACCTCGGCCCCCG
ACAGCTGACCTATGTCCTCGTTTTCCTCGCACCACGGCGCCCGCAACTTCCTCTCCCTCCCGTAAACTTCTCCGGGATCT
ACAACATCGACGGCTACGGTAGTGCCACG---------------------------------------------------
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>chr2B_1526
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-------ACCCAGCCTCCTCACCGCTCGGGATTCCTGACCGTCGGATTTGTCTTCTGATTCGTTCTGAACTGTATGATCT
CGCTTGGGAGAGATCTCGTCCGTTGGATCAAGTCGGATCACTGCTACAATGAATAGT----------AGTTTCCATCCGT
TTTTCCTTACTGGTTTTGTTTACTCCGGAATTATTGTCTTACCTTGCTGACGTGTGGGGTCGATCCCTGGTGGGCAGTGC
CGGTTAGCGACTGTGTCTGCGAGCGTGGTCTGTGTGTTATTTAGTGTAGAAGTATTCATGCCACCGCCTGTAAAACTGGA
TGGCCGTCGAGGGTATTTTGGACATTTTGCGTACCCCTATAAAACCGAAGCAGCAGCTACTAAAACCCTAGCCGGTTCCT
CCCCTTGCACGGTC------------------------------------------------------------------
---------------------------------------------GTGCTGCCTCCCCTCGTCCAGCCCTCTCCCCGACC
TCGCCGCCCCACACATACCTCCGCTTGCCCAGCCCTCTCCTCGACCTCGTCGTCCCACCCACATCGCCGCCACCGACGCC
CCTTAGACCTCTCCATCGCGGACCTCTCTCCTTGTCTTCCTCGCACCACGGCGCCCGCAACCTCCTCCCTTCCATCAATA
GAAGGGAAGGAAAGAGAAGAGGGAGGGCGAGCGCGTCAGACGGCGGCCATGGCGGCGCCGTCGTCCAACCTCGGCCTCAG
AGTGCTGACCTCTCTCCTCGTCTTCCTCGCACCATGGCGCCCGCAACTTCCTCTCCCTACTGTAAAC-------------
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>SNPs
-S-S-SSSSSSSSSSSSSSSSSSS---------S----------------------SSSSSSSSSS-------------S
--S--------------SS--SS--S--S---SS----S------S-----S----------------------------
------------S------S----S---------S--------S-----S------------------------------
------S----S-------------------------SSSSSSS-S----------------------------------
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---------------------------------------------------------------------------S---S
-------------S------------------------------------------------------------------
---------------------------------------------------------------S----------------
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---------------------------------------------------------S---SSSSSSSSS----------
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-----------------------------------------------S-------S------SSSSSS------------
-------------------------------------------------------------------------S------
------------S-----------------S-------------------------------S-----------------
---------------------------------S--S--S-------------------------------S---S----
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-----------------------------------------------------------------S--------------
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-----------------------------------------------------------------------------S--
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--------------------------------------------------------------------S-----------
---------------S--------------------------------S-------------------------------
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----------------------------------------------------------S---------------------
---------------------------S----------------------------------------------------
-------------------S--S------SSSSSSSSS------------------------------------------
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>forward_948
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------------------------------------------------GTCAGGCACGTCTCTTCCAT------------
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>reverse_1918
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-----------------------------------------------------------------------------AGA
TGGCCGCCAAGGGTATT---------------------------------------------------------------
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