>input_sequence_56785
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---------------------------------------------------------CTAT-------ATATAACGCCGA
TGGCTCGGCACCAGTGCTCCCCTGCTTCCACAACCAACCAGTCCGGCGTCAAGTGAGCACTGACTGAGCTACCCATGGAT
CATG------------GC---GGCGGCGGCAGGAGTAGCAGCCGCCTCCGGGACCGGCTGGCCCGGATGTTCCGTCCGGG
CTCGCTGCTCCGCTCGACCTGCAACAACAACACCGCGTCGACCTCCTCTTCCTCCTCGTGCTCGGCCGCGGCGGGCGCGG
CAGCCGACGGGGTGACTGCGTCCAAGCCGCCCCCGAGCTCCGCCTGCTCCTCCAGCCGCGCGCTCTTGCCCGCCGACTCC
GCCATCTCCCGCGACAGGGACTCGTTCCTCACCTCTTCTCGCCGCGACTACGCCACCATCGTCGGCCGCACCGAGTCCTT
CTCCAACGCCCTCGACCGCGTGCACCGCCGTGCCGGCGCCGCGGTGCATTCTCTGCCGCCTCCGGCTCGCTTCTCCATGC
ACGCGTCGCCTCTGATGGAGAGCAAGAAAAAGAGCCCTCTCCACG---GTCATCGGCACCACCGCCACCGCCTCGGTGGC
CGGGTCAAGGGCGACAAGAGCAAGAAGATGTTCTCCAACAACCCCTATGGCTTCAGCACCTCGGACACTGACGGCGACGA
CGTCTTCAGCAGCGACGCTGACGAGCGCAGCCGCAGCGACGCCAAGAAGGGGGACGCGGAGGCCTTCTTCTCCTCCTCCA
GAAGCTTCTCCTTCTCCTCCGACTCCTCCGAGTTCTACAGCAAGAAGAAGAAACCA---AAGAAGAAGTCCCCTGCCGCA
GTGGCGCCCAAGCCGCCGCCGCCGCCGC---CGAGAGCGAGGGCGAGGGGGCAGAGGCGCAAGAATCGCGTGGCGAGCAG
CTGCGACACGTGCGGCGTGAGGGAAGGGTTCCGGCCGGTGGTGTCGGCGGCGGAGGAGCAGGTGCGCAGGGGGTTCGCGG
TGGTGCAGCGGTCGCGGGACCCCTACGCCGACTTCCGGGCGTCGATGGTGGAGATGGTGGTGAGCCGGCAGATGTTCGGC
GCGGCGGAGCTGGAGCGGCTGCTGCGGTCGTACCTCTCGCTCAACGCGCCGCGCCACCACCCCGTCATCCTCCAGGCCTT
CTCCGACATCTGGGTCGTCCTCCACGGCGGCTAGCTAGCGATCTCACTGGCTATCCACTCACTCACTCA----GTTATTA
ATCCAGCCCCAGGACGTTTCCTTAACTACCAGTAGGACTCTGTCATA---------------------------------
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>chr3D_1_TraesCS3D01G159700
TAAAGCATTTTTTTTAGAAAAGGAGGAGGACCCTGGCCTCTGCATCTTAGTATCTCATTAAGGCGTCAAATGGTGTCTTG
TCTGTTGGTTAGCACACACGCGCGTTGGTAGCACCAAGAGGGCCCTGGGTGAACAATATAACCATGAGGCAGGACACCAC
GTGATGCCT-AAATGGAGAAATAATGTTTACATG----------GAGACAATTAAATCAGCAGGAAAATTCCAACTAGAT
GGTCTAATTAAACATAAAATCTTGCTTGATTTACCGGCTAGATTGCAAGGGTGGCACACCTGAGCTCGTGGGTTCGAAAC
TTCGGATCCCTTTTC-CTTTCTTATTTCTCTTTATTATTTCACACGGTATTATTATTACAAATTGCGTTATATCTGTGAT
TTGCATATACACCCATGCTTGGTGTAGCTGATATGCGGGACCCAAACCTGACAGGTTGAACCCATCAGTCTGCATCCGTA
TGTGATACAATTATGTGTAATTAAATAATTAAATAAAATGTGAGGGGATTCTCGCTGTAAAAAAATGCTCCCGGCCACTA
ACATGCGGTCCGCCACCATACTGGCTCGCCACGTGGGTATGGCCTATGACGGGATATGGTAATAGACATTGTATTTGCAC
ACTTGGACAAGTTAAAACATCATTTTCGTGTATTTTACAACTTTAGGCACTAAACTGATCGCACAAGATAAATTAAGA--
-CCGTGATGTATTTAACTCTAGTAAACTCTGTTTCAGAGTCAGTC-ATAACGAAAATCTTGCATGATTTGCTCAGTGCTT
CAGTGTCAGTAAGTGATTCCATAACCGAAAGCTTACATACATGCCAAAACATTCGTCGGCTTTATTATCCTTGCATAAAC
AAGAAAAATGC-ATGCCTTGATTAATAATTCGTCACGTGACCCACTTTGTACGCACGGCTCGTAGTGCACGTAGCGTACT
GGCAGCTCACACTAGCCATTTCAAACCTTCCTTCGCTCCCGGCTCGTTCTCCCACGGCTAT-------ATATAACGCCGA
TGGCTCGGCACCAGTGCTCCCCTGCTTCCACAACCAACCAGTCCGGCGTCAAGTGAGCACTGACTGAGCTACCCATGGAT
CATG------------GC---GGCGGCGGCAGGAGTAGCAGCCGCCTCCGGGACCGGCTGGCCCGGATGTTCCGTCCGGG
CTCGCTGCTCCGCTCGACCTGCAACAACAACACCGCGTCGACCTCCTCTTCCTCCTCGTGCTCGGCCGCGGCGGGCGCGG
CAGCCGACGGGGTGACTGCGTCCAAGCCGCCCCCGAGCTCCGCCTGCTCCTCCAGCCGCGCGCTCTTGCCCGCCGACTCC
GCCATCTCCCGCGACAGGGACTCGTTCCTCACCTCTTCTCGCCGCGACTACGCCACCATCGTCGGCCGCACCGAGTCCTT
CTCCAACGCCCTCGACCGCGTGCACCGCCGTGCCGGCGCCGCGGTGCATTCTCTGCCGCCTCCGGCTCGCTTCTCCATGC
ACGCGTCGCCTCTGATGGAGAGCAAGAAAAAGAGCCCTCTCCACG---GTCATCGGCACCACCGCCACCGCCTCGGTGGC
CGGGTCAAGGGCGACAAGAGCAAGAAGATGTTCTCCAACAACCCCTATGGCTTCAGCACCTCGGACACTGACGGCGACGA
CGTCTTCAGCAGCGACGCTGACGAGCGCAGCCGCAGCGACGCCAAGAAGGGGGACGCGGAGGCCTTCTTCTCCTCCTCCA
GAAGCTTCTCCTTCTCCTCCGACTCCTCCGAGTTCTACAGCAAGAAGAAGAAACCA---AAGAAGAAGTCCCCTGCCGCA
GTGGCGCCCAAGCCGCCGCCGCCGCCGC---CGAGAGCGAGGGCGAGGGGGCAGAGGCGCAAGAATCGCGTGGCGAGCAG
CTGCGACACGTGCGGCGTGAGGGAAGGGTTCCGGCCGGTGGTGTCGGCGGCGGAGGAGCAGGTGCGCAGGGGGTTCGCGG
TGGTGCAGCGGTCGCGGGACCCCTACGCCGACTTCCGGGCGTCGATGGTGGAGATGGTGGTGAGCCGGCAGATGTTCGGC
GCGGCGGAGCTGGAGCGGCTGCTGCGGTCGTACCTCTCGCTCAACGCGCCGCGCCACCACCCCGTCATCCTCCAGGCCTT
CTCCGACATCTGGGTCGTCCTCCACGGCGGCTAGCTAGCGATCTCACTGGCTATCCACTCACTCACTCA----GTTATTA
ATCCAGCCCCAGGACGTTTCCTTAACTACCAGTAGGACTCTGTCATAATTAATCATGCTCTGCGTTCATGATTAGCTCCA
ACGATGTTCATCAGTTTGGTCTT----AGTTTTAATCTTGGCTGTAACTGGCCGTGCGGTTCTGCTGTAATGTACTCCTA
G---TAGTAGTACTACTGTTCTTGGCTCTGACCCAGTGTGCAAAAGCTAGCTTCTGATTTGGAATTGGATTCAGATTTGG
CCAGAGAGCGCCGTGGGTTTTGTTTGCTAGCTAGAGGAGCTGTACGATGTTTGATTTTGGGCGTCAATGATTTGAAAATC
ATGATGACACAGCAGAACTTTGGGTTTGCGCTTCCTCTGCCATGCCACCACTGCACTATTTAATCCTTTGTGTCGGCAAG
TATCGTATTTTGCT---CGGATGCTCGCCATGTCGAATTTA-------------------------------AAGATGAA
CAAATAATCGTTCATCGGTGCCTAGTAGATTATATTTGTGCGATTCATGTGGAAGTACGTATCATGTAGACTT-------
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-----------------------------------------------------------------------AACCTTTTT
GGAAGAATCAAGAATAACATGGTTAAACAATGAATAACATTTCACA---AAT-AAAAAGAAGAACAATGTCTATTCACAT
AAGAAGTATAATTGACACACGAGAGGCTCCCCCGCGAGCGACCGAGGGGGCAACCCTAGCCGCCGGTGCCTCAGGTCCCC
CCGCCCCTCTTCTCCCCTCGCCGCCGCCGATCCGCGCCGCCGGGCAAAGCCCGGTAGGTGCTGGCGGCGGCGGGGCCCCA
TCTCCTCCTCGCGCAAGGGCTCGGCGCGGGCGGGCGTCCTCGGCGGCGGCGTCGCGTTCATCCGGGGCGCGGCGGCACGC
GGGCAGGTCCGACGGAGGTGCTAAGATGCCTCGTCCTGCGTGTGGAGGGACGGTCACGGCGGGGGCTGCGGGATCACCCG
GAGGCAACATGGGCGACTCCGGTGTTGGATCCGCGAGCAGCAGGTAGGGCGGCGTCCCTTGCCTGTGCGGCGGCGGCCAG
ATCCATGGCCGGCATGGTGCTCCTCCCCTCGGCGGAATCTATGTCTGGAG
>chr1D_51
--------------------------------------------------TATCTCATTTAGGCATCAAATGGTGTCTTA
TCTGTTGGTTAGCACAAACACGTGTTGGTAGCACCGAGAGGTCCCTCGGCGAACAATATAACCACGAGGCAGGACACCAC
ATGATGCCTAAAATGGAGAAATAATGTTTAGATCTTTAGAGGGTGAGACAAATAAATGTGTAAGAAAATTCTAACTAAAT
GCTCTAATTAGACATAAAATCTTTCTTAGTTTATCGGCTAGATTGCAAGGGTGGCACACCTAAGCTCCTGGGTTCGACGC
TTCGGATCCTCCTATTCTTTCTTATTTCTATTTATTGTTTCACATGGTATAATTATTATAAATTGTGTTATATCTGTGAT
TTGGACATACCGCCGTGCTTGGTGTAGCTGATATGTGGGACCCATACCTGACAAGTTGGACCTATCAATATGCATCCGTA
TGCGATACAATTATGTGTAAA--------TAAATAAAATGTGAGGGGGTTG--GCTGTAAACAATTGCTTCCGGTCACTG
ACATGCGGGCTGCCACCATACTGGTTCGCCATGCGGGCAGGTCGTATGCCCGGATACAGTAGGAGGCACCGTATTTGCAC
AGCCGGACAAGTTAGAGCACCACTTTCGTGTATTTTACAACTTTAGGCACTAAACTGACCGGACATGATAAGTTAAGGCA
TCCGTGGTGTATTTAACTCT------------------------------------------------------------
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>chr3A_728
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----------------------TAAAATCTGTTTCAGAGTCAGTCCATAACGAAAATCTTGCATGATTTGCTCAGTGCTT
CGGTGTC----AGTGATTCCATAACCGAATGCTTACATACATGCCAAAACATTCGTCGGCTTTATTATCCTTGCATAAAC
AAGAAAAATGC-ATGCCTTGATTAATAATTCGTCACGTGACACACTTTGTACGCACGGCTCGTAGTGCACGTAGTGTACT
GGCAGCTCACGCTAGCCATTTCAAACCTTCCTTCGCTCCCGGCTCCATCTCCCACGGCTATATATAACATATAACACCGA
TGGCTCGGCACCAGTGCTCCCCTGCTTCCACAACCAACCAGTCCGGCGTCAAGTGAGCACCGACTGAGCTACCGATGGAC
CATG------------GCGGTGGCGGCGGCAGGAGTAGCAGCCGCCTCCGGGACCGTCTGGCCCGGATGTTCCGTCCGGG
CTCGCTGCTCCGCTCGACCTGCAACAACAACACCGCGTCGACCTCCTCCTCCTCCTCCTGCTCCGCCGCGGTGGGCGCGG
CAGCCGACGGGGTGACCGCGTCCAAGCCGCCCCCGAGCTCCGTCTGCTCCTCCAGCCGCGCGCTCTTGGCCGCCGACTCC
GCCATCTCCCGCGACAGGGACTCGTTCCTTACCTCTTCTCGCCGCGACTACGCCACCATCGTTGGCCGCACCGAGTCCTT
CTCCAACGCCCTCGACCGCGTGCACCGCCGCGCCGGCGCCGCGGTGCATTCTCTGCCGCCTCCGGCTCGCTTCTCCATGC
ACGCGTCGCCTCTGATGGAGAGCAAGAAAAAGAGCCCTCTCCACGGCAGTCATCGGCACCACCGCCACCGCCTCGGTGGC
CGGGTCAAGGGCGACAAGAGCAAGAAGCTGCTCTCCAACAACCCCTATGGCTTCAGCACCTCGGACACCGACGGCGACGA
CGTCTTCAGCAGCGACGCTGACGAGCACGGCCGCAGCGACGCCAAGAAGGGGGACGCGGAGGCATTCTTCTCCTCCTCCA
GAAGCTTCTCCTTCTCCTCCGACTCCTCCGAGTTCTACAGCAAGAAGAAGAAACCA---AAGAAG---TCCCCTGCCGCA
GTGGCGCCCAAGCCGCCGCCGCCGCCGCCGCCGAGAGCGAGGGCCAGGGGGCAGAGGCGCAAGAATCGCGTGGCGAGCAG
CTGCGACACGTGCGGCGTGAGGGAAGGGTTCCGGCCGGTGGTGTCGGCGGCGGAGGAGCAGGTGCGCAGGGGGTTCGCGG
TGGTGCAGCGGTCGCGGGACCCCTACGCCGACTTCCGGGCGTCGATGGTGGAGATGGTGGTGAGCCGGCAGATGTTCGGC
GCGGTGGAGCTGGAGCGGCTGCTGCGGTCGTACCTCTCGCTCAACGCGCCGCGCCACCACCCCGTCATCCTCCAGGCCTT
CTCCGACATCTGGGTCGTCCTCCACGGCGGCTAGCCAGCGATCTCACTGGCTATCCACTCACTCACTCACTCAGTTATTA
ATCCAGCCCCAGGACGTTTCCTTAACTACCAGTAGGACTCTATCATAAGTAATCATGCTCTGCGTTCATGATTAGCTCCA
ACGATGTTCATCAGTTTGATCTT----AGTTTTAATCTTGGCTGTAACTGGCCGTGCGGTTCTGCTGTAATGTACTCCTA
GTACTAGTAGTACTACTGTTCTTGGCTCTGACCCAGTGTGCAAAAGCTAGCTTCTGATTTGGAATTGGATTCAGATTTGG
CCAGAGGGCGCCGTGGGTTTTGTTTGCTAGCTAGAGGAGCTGTACGATGTTTGATTTTGGGCGTCAATGATTTGAAAATC
ATGATGACACAGCAGAACTTTGGGTTTGCGCTTCCCCTGCCATACCACCACTACACTGTTTTACCCTTTGTGTCGGCAAT
TATTGTATTATGCT---CGGATGCTCGCCATGTCGACTTTA-------------------------------AAGACAAA
CAAATAATCGTTCATCGGTGCCCAGTAGATTATATTTGTGCGATTCATGTGGAAGTACGTATCATGTAGACTT-------
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-----------------------------------------------------------------------AACCTTTTT
CAAAGAATCAAGAATAACATGGTTAAACAATGAGTAACATTTCGCCAATAGAAAAAAACAACAACAATGTCTATTCACAT
AATAAGAAGTATAATT----------------------------------------------------------------
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>chr3B_729
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-----------------------AAAATATGTTTCCGCGTCACTCCATAACGGAAATCTTGCATGATTTGCTCAGTGCTT
CAGTGTC----AGTGATTCCATAACCGAAAGCTTACATACATGCCAAAACATTCGTCGGCTTTATTATCCTTGCATAAAC
AAGAAAAATGTTATGCCTTGATTAATAATTCGTCACGTGACCCACTTTATACGCACGGCTCGTAGTGCACGTAGCGTACT
GGCAGCTCACACTAGCCATTTCAAACCTTCCTTCGCTCCCGGCTCCATCTCCCACGCCTAT-------ATATAACGCCGA
TGGCTCGGCACCAGTGTTCCCCTGCTTCAACAACCAACCAGTCCGGCGTCAAGTGAGCACTGACTGAGCTACCCATGGAT
CATGGTGGCGGAGGTGGC---GGTGGCGGCAGGAGTAGCAGCCGCCTCAGGGACCGGCTCGCCCGGATGTTCCGTCCGGG
CTCGCTGCTCCGCTCGACCTGCAACAACAACACCGCATCGACCTCCTCTTCCTCCTCGTGCTCCGCCGCGGTGGGCGCGG
CAGCCGACGGGGTGACTGCGTCCAAGCCGCCCCCGAGCTCCGCCTGCTCCTCCAGCCGCGCGCTCTTGGCCGCCGACTCC
GCCATCTCCCGCGACAGGGACTCGTTCCTCACCTCTTCTCGCCGCGACTACGCCACTGTCGTCGGCCGCACCGAGTCCTT
CTCCAACGCACTCGACCGCGTGCACCGCCGTGCCGGCGCCGCGGTGCAATCTCTGCCACCTCCGGCTCGCTTCTCTATGC
ACGCGTCGCCTCTGATGGAGAGCAAGAAAAAGAGCCCTCTCCACGGTCATG---GGCACCACCGCCACCGCCTCGGTGGC
CGGGTCAAGGGCGACAGGAGCAAGAAGCTGCTCTCCAACAACCCCTATGGCTTCAGCACCTCGGACACTGACGGCGACGA
CGTTTTCAGCAGCGACGCTGACGAGCGCGACCGCAGCGACGCCAAGAAGGGGGACGCGGAGGCCTTCTTCTCCTCCTCCA
GAAGCTTCTCCTTCTCCTCCGACTCCTCCGAGTTCTACAGCAAGAAGAAGAAACTAAAGAAGAAG---TCACCTGCGGCA
GTGGCGCCGAAGCC------GCCGCCGCCGCCGAGAGCGAGGGCGAGGGGGCAGAGGCGCAAGAATCGCGTGGCGAGCAG
CTGCGACACGTGCGGCGTGAAGGAAGGGTTCCGGCCGGTGGTGTCGGCGGCGGAGGAGCAGGTGCGCAGGGGGTTCGCGG
TGGTGCAGCGGTCGCGGGACCCCTACGCCGACTTCCGGGCGTCGATGGTGGATATGGTCGTGAGCCGGCAGATGTTCGGC
GCGGCGGAGCTGGAGCGGCTGCTGCGGTCGTACCTCTCGCTCAACGCGCCGCGCCACCACCCGGTCATCCTCCAGGCCTT
CTCGGACATCTGGGTCATCCTCCACGGCGGCTAGCTAGCGATCTCACTGGCTATCCACTCACT----CACTCAGTTATTA
ATCCAGCCTCAGGATGTTTCTTTAACTACTAGGA-----CTATCATAAGTAATCATGCTCTGTGTTCATGATTAGCTCCA
ACGATGTTCATCAGTTTGATCTTAATTAGTTTTAATATTGGCTGTAACTGGCCGTGCGGTTCTGCTGTAATGTACTCCTA
G---AAGTAGTACTACTGTTCTTGGCTCTGACCCAGTGTGCAAAAGCTAGCTTCTGATTTGGAATCGGATTCAGATTTGG
CCAGAGAGCGCCGTGGGTTTTGTTTGCTAGCTAGAGGAGCTGTACGATGTTTGATTTTGGGCGTCAATGATTTGAAAATC
ATGATGACACAGCAGAACTTTGGGTTTGCGCTTCCCCTGCCATGCCACCACTGCACTATTTTACCCTTTGTGTCGGCAAG
TATTGTACTATCATACCCGGATGCTCGCCATGTCGATTTTAAAAATGAACAAATAATCTTTTGTTTTAGGGAAAGATGAA
CAAATAATCATTCATCGGTGCCTAGTAGATTAAATTTGTGTGATTCATGTGGAAGTACGTATCATGTAGACTTTGGCCCC
GCTTAGATTGTCGGTTTGCTCCTAAATAACCCCGTATTCAATACAGACCTCCGGCCATCGTTTTCATTCCATACGGAACA
CGGCGGCCGTTAATATACACATGTAGATTAAATCCAGATGTATAAAATTACACCTGTTCCAAGCCGGGTTTAACCTTTTT
GAAAGAATAAAAAATAACATGGTTAAACAATGAATAACATCTTGCAAATAAT-AAAAAGAACAACAATGTGTATTGACAT
AAGAAGTA------------------------------------------------------------------------
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>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------S----S--------------S
----------------S--S--S------------S-----S----S--S--------------S---------------
S-----------------------------S--S-----------------S-----SS-S-S--------S-----S--
-S--------S------------S---SS----S---------------------------S-----S---------SS-
---------SSS-SS--------------S------S-------S-----S-------S------S--------------
---S-S----SS--S--------------------S--------S--------S----S---S----S-S----------
--S-----------------SSSSSSSSS------------------S--SSS--------S--S----S----S----S
--------S-S-------------S------S-S---S-S-S-S----S-S-----SS---SS--S--SS----------
-SSS----------S-S--S--S-----------------------------------S--S---S-----S-----S--
------S-------------SS----S-----------------------------------------------------
-------SSSS---------------------------------------------------------------------
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---------------------------------------------SS---------------------------------
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---------------------------------------------------------------S-------S--------
--------------------------------------------------------------------S-----------
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---------------------------S--S-------------------------------------------------
----------------------------S---------------------------------------------------
-----------------------------------------------------------------SSS------------
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-----------------------------------------S------S-------------------------------
------------------S-------------------------------------------------------------
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-----------------------------------S-------------------------S-S----------------
---S-----S--------------------------S-------------------------------------------
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-S-----------------------------------------S-----------------S------------------
--------SS--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_560
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------------------------------------------------------------AAAAATGCTCCCGGCCACTA
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>reverse_1631
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------------------------------TTCTCCAACAACCCCTATGGC-----------------------------
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>forward_611
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-------------------------------CGTGGGTATGGCCTATGACG-----------------------------
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>reverse_2644
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---CGTATTTTGCTCGGATGCTCG--------------------------------------------------------
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