>input_sequence_80545
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-------------ATGGCAGTCTTCACGAACAATATGGCTGTTGCCGTATGGTTGGGGGCTCTCATGCTCATGGCAACCC
TTCCCGCCTTAGAAGGAAAACCAGCCTTCAGTAAGTACGCTATCTC------AT--------------------------
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---------------------------GTAGTTAGC--ATCGACC-TTTTTCATAAGAT---GTATATATCTTGCGATGT
TGAGCACAATGAATATTGGTA-TTTTTTTTT--ACAGATAGTTATTC---AATATGAAT---TAACTGACTGGAGTAACA
AGTGA--TGTATTGGTTTTGTTTCATGTGTT-TGCTGTTGGATGTTTCGAGGTCCACCAGAACTGCTTCCCAGATGACTC
TCAGAAGAGATGCGAGGATGATCTTGGAAAAGATATGTTAAGTGAATGCCAGTGGGATCATGGCGTACTACAACCGTATC
CCGGGCTTCAGTGTTGTTGTTTTCGAAAGGACGGTACCTGA---------------------------------------
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>chr1B_1_TraesCS1B01G416300
TTGGGTATGCCACAGGAAATAACCGATCATACGAGGAGCCACAGATGCAGGCGGACCTACGTGGTCCTGTTTTCCTGCCG
AGGAAGTGCGCCGCGAGCAGCCGCTCCCAGCCAAACTTCCGTCCGATCCAGCCCAGCGTGGAGCACCGCCGCCGCCGCAG
CAACATCAGCCTTCACAGCTTCCGGCCGCCACCTGCACATCGCCAAATGTCGCTCATAGCACCACGGGAGCGGAACCCTG
CCGCCGCCGTCGGCCGTGCGGGCAAGCCCGGCG----GCGGCGAGGGAAGGGCGCAGGAGGAGAGTGCCTGAAGAAATGG
ATCGTGCCACCCCCGAGTCGCCCACGCAGACGACGCGGGGGATAGGTTACGCCGTGATAGCAAAACGATGGATACCAAGG
TCCTTGAGAATTTCTTTATGAGACGACCTAACTGCTACATCATCAACAACGCATGCAGCTTTGTACAAACTACACTACAG
ATTCTGCCTAAAATTAGTAATTATGTTACTCTCTAAATTCAGAATTAGTAATTAGTTTACCTTCATTTGTAATCAAGAAA
AATATCATTAGTAATCTTCTGTCAGCTCCTACTTATCCATGACATATTGTTCCTGTTTATAGGGTAATCACTTTGACTCA
TAA-TTTTTTTATTTGTTAACATTTGGTACGTCTACGGTGATATAAAACTTCCGCAGCAATTCACACACACATTTCTATA
AGAGCTGAGTCTTTGTAAATTGTCATCAGGAAGTAGTTGTTTTCCTAAGTGACAAAAGTAATTTTGAGAAACTCCCACTT
TCTGGTGCATGATGCATGAGATAAGCCCTATACTACT-------------------------------------------
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-----------------------------------------------------------------AATGTAAGCAC-AAA
AATTAATGCATTAAATCATGAGATAAGTCCTGTTATAATTTTC-GCACAATTAATGCATTAAATACTTC--------TCC
ATGATCTCCACCAATCTGCCT---CTCTATAAATGCAATGAATGAAAGAGCATTGCAACTTC--ATCAGGCTTTC-TTTT
TGGGTC----CTCATGGCAGTCTTCACGAACAATATGGCTGTTGCCGTATGGTTGGGGGCTCTCATGCTCATGGCAACCC
TTCCCGCCTTAGAAGGAAAACCAGCCTTCAGTAAGTACGCTATCTC------AT--------------------------
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---------------------------GTAGTTAGC--ATCGACC-TTTTTCATAAGAT---GTATATATCTTGCGATGT
TGAGCACAATGAATATTGGTA-TTTTTTTTT--ACAGATAGTTATTC---AATATGAAT---TAACTGACTGGAGTAACA
AGTGA--TGTATTGGTTTTGTTTCATGTGTT-TGCTGTTGGATGTTTCGAGGTCCACCAGAACTGCTTCCCAGATGACTC
TCAGAAGAGATGCGAGGATGATCTTGGAAAAGATATGTTAAGTGAATGCCAGTGGGATCATGGCGTACTACAACCGTATC
CCGGGCTTCAGTGTTGTTGTTTTCGAAAGGACGGTACCTGAAAATGATAAACAGAGTGTTTAGTTGATGATGGGCAGATG
ATA----GAACACATCCATATATATATATATATATATGATTGTCTGTTCGATCCACCTGTTGTACTGTAGATCTAATAAA
TGAATGTCTTTCACGACAATCATATTAA----CAAAGGCATTAGCTGCATCAGAAAGTATATC---TTACAATTATTGAG
GGAAATAATAATATTATTGCTTTTTGTGGCGCACTGTGTACTATATATCGAGGGAGGGTCAGTTCTTGCATTGAGAGATC
AATCCACCTATCTTCACATTGTTTTCATTATAGCATGTGTCGAGCCGC--------------------------------
AAGCAGAGATCCCAAATGAAAACCATGGTTTTGTGTAAGCTTCATTATAGCATGTATCAAGTCGCAAGCGGACATTCCAA
ATCAAAACCTTGG-------------------------------------------------------------------
------------------------TTTTGATTAAGCTCTAGACCGCACCCCTACANNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTC--------------------
--------------------------------------------TGAGATTGCTCATACAATTTTGGTACTTACCAGTCG
AGGTCGCTTCTGGGGCTGCACTTCCACGGACAGATGAGATCTGAGGCGCAAATTTTGGAAGCTGGTCCTGAACAAACCGT
ATG------GTTTTTCCTCCACCTCGGCCAGCAAATCATACAGCTTCTCTTTCTTCTTCTGCACCCTTCTCTTCACCTCC
TCGTGTGGCCCTCCGTAAGGATACTTGCCCTTAGGGCCAGTTCTT
>chr1D_1
TTGGGTATGCCACTGGAAACAACCGATCATACGAGGAGCCACAGATGCAAGCGGACCTACGTGGTCCTGTTTTCCTGCTG
AGGAAGTGCGCCGCGAGCAGCCGCTCCCAGTCAAACTTCCGCCGGATCCAGCCCCGCGTGGAGCACCGTCGCCGCCGCAG
CAACATCAGCCTTCATAGCTTCCGGCCGCCACCTGCACCTCGCCAAATGTCGCTCATAGCACCACGGGAGCG-AACCCCG
CCGCCGCGGTCGGCCACGCGGGCGGCGCTGACCGGCAGCGGCGAGGGAAGGGCGCAGGAGGAGAGTGCCTGAAGAAATGG
AT-----------CGAGTCGCCCACGCGGACGACGCGGGGGATAGGTTACGCCGTGATAGCAAAACGATGG--ACCAAGG
TCCTTGAGAATTTCCTTATGAGACGACCTAACTGCTACATCATCAACAACGCATGCAGCTTCGTACAAACTACACTACAG
ATTCTACCTAAAATTAGTAATTATGTTACTCCCTAAATTCAGAATTAGTAATTAGTTTACCTTCATTTGTAATCAAGAAA
AATGTCATTAGTAATCTTCTGTCAGCTTCTACTTATCCATGACATATTGTTCCTGTTTATAGGGTAATCACTTTGATCCA
TAATTTTTTTTATTTGTTAACCTTTGGTACGTCTACGGTGATACAAAAGTTCTGCAGCAACGCGCACAC----------A
AGAGCTGAGTCTTTGTAAATTGTCATCAGGAATTAGTTGTTTTCATAAGTGACAAAAGTAATTTTGAGAAACTCCCACTT
TCTGGTGCATGATGCATGAGATAAGCCCTATACTACT-------------------------------------------
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-----------------------------------------------------------------AATTTAAGCAC-AAA
AATTAATGCATTAAATCATGAGATAAGTCCTGTTATAATTTTT-GCACAATTAATGCATTAAATACTTC--------TCC
ATGATCTCCACCAATCTGCCT---CTATATAAATGCAACGAATGAAAGAGCATTGCAACTTC--ATCAGGCTTTC-TTTT
TGGGTC----CTCATGGCAGTCTTCAGGAACAATGTGGCTGTTGCCGTATGGTTGGGGGCTCTCATGCTCATGGCAACCC
TTTCTGCCTCAGAAGGAAACCCAGCCTTTAGTACGTACGCTATCTC------ATACTCCCTCCGTTCCATATTACTCGTC
GCTGATTTAGTACAAAGTTTTATCAGCGACGAGTAATATGGTTTACTAAATCAGCGACGAGTAATATGGTTTACTAAATC
AGCGACGAGTAATACGGAACGGAGAGAGTAGTTAGC--ATCGACCATTTTTCATAAGAT---GTATATATCTTGCGATGT
TTCACACGATGGATATTGGTA-TTTTT--GT--ACAGATAGTTATTC---AATATGAAT---TAACTGACTGGAGTAACA
AGTGATGTGTATTGGTTTTGTTTCATGTGTT-TGCAGTTGGATGTTTTGAGGTCCACCAGAACTGCTTCCCTGATGACTG
TCAGAAGAGATGCGAGGACGATCTTGGAAAAGATACGTTAAGTGAATGCGAGCGGGATCATGGCGTACTACAACCGTATC
CCGGGCTTCAGTGTTGTTGTTATCGAAAGGACGGTACCCGAAAATGATAAACAGGGTGTTTAGTTGATGATGGGCAGATG
ATA----GAACACATCCAT------------ATATATGATTGTCTGTTCGATCCACCTGTTGTAGTGTAGATCTAATAAA
TGAATGTCTTTCACGACAATCATATTAA----CAAAGGCATTAGCT----------------------------------
----------------------------------------------------------------CTTGCATTGAGAGATA
ATTGTAAGATATATTTTTGACGCTCGTGGACGCAGATCGTCTCAAAGACCTAGGGATCACGGCCGTTTGCGCTCTCATAG
AGGCCCATGTGCCAATTAACATCCATAGATATATTTATAGTACTTGCAATATACTTGAAGTTATTTTGTGTGCTTCTAAT
ATACTTCTATACATTTTTCTATATCCGCTGATAATTTGTCAATATCCACTTCGTCGTTCGTTGTGGTCTTACTCTCTTGT
TTAGTCCTCATGGTCATCATCTTCTTTGGTTTCAGATCCCAGCCAGAAAAGGAGAACTAGGTATGCAAAAGTGAGGTACA
CAGAGACAAAATATTCACTTCGTCCAAATCGTCGGTAGCTAAACCTGAATGCATGCAAATCGACCAGTAGTATGCATGTG
CATGAGATGAATGAAATCACCATGGACGCAGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAGATTGCTCATACAATTTTGGTACTTACCAGTCG
AGGTCGCTTCTGGGGCTGCACTTCCACGGACAGATAAGATCTGAGGCGCAAATTTTGGAAGCTGGTCCTGAACAAACCGG
AGTATACTTGTTTTTCCTCCACCTCGGCCAGCAGATCATACAACTCCTCTTTCTTCTTCTGCACCCTCCTCTTCAGCTCC
TCGTGTGGCCCTCCG------------------------------
>chr1B_610
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-----------------------------------------------------TGTTTATAGGGTAATCACTTTGATCCA
TAATTTTTTT-ATTTGTTAACCTTTGGTACGTCTATGGTGATACAAAACTTCCGCAGCAATGCGCACACACATTTCTATA
AGAGCTGAGTCTTTGTAAATTGTCATCAGGAAGTAGTTGTTTTCATAAGTGACAAAAGTAATTTTGAGAAACTCCGGCTT
TCTGGTGCATGATGCATGAGATAAGCCCTATACTACTAAGAGGGTGCTTGGATCCAAGGAACTTATTTTAGTCTGACTAA
AAATAGTCTCTTTAAGAGGCTAAAGTTTCAAGCACCTCTGACTAAAGAGGGGCTAAAACTGGTCTTGAGACTAATTTTTT
TAGTCAGAGGTACCCCTACTAAAATGTTGATTAGTCCTCTCTCTCCTCATTTAACTCCTCTCCTTTAACAACGGACGAGT
TCGGGATTGGAGGGTTTGGAGGATAATAAATGCTCATTAACTTAATTTTAGTCTATTTAGTATTTGGATCCAAGCATGGG
TGAGGCTAGCGAGTTTTAGTCCCAATACTTTTAGTCATGAGACGAAAGCTATCCAAGCACCCTCTAATTTAAGCACAAAA
AATTAATGCATTAAATCATGAGATAAGACCTGTTGTAATTTTC-GCACAATAAATGCATTAAATACTTC--------TCC
ATGATCTCCACCAGTCTGCCT---CTCTATAAATGCAATGAATGAAAGAGCATTGCAACTTC--ATCAGGCTTTC-TTTT
-GGGTC----CTCATGGCAGTCTTCACGAACAATATGGCTGTTGCCGTATGGTTGGGGGCTCTCATGCTCATGGCAACCC
TTCCCGCCTCAGAAGGAAACCCAGCCTTCAGTACGTACGCTATCTC------A---------------------------
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----------------------------TAGTTAGC--ATCGACCATTTTTCATAAGAT---GTATATATCTTGCGATGT
TGAGCACGATGGATATTGGTA-TTTTG--GT--ACAGATAGTTATTC---AATATGAAT---TAACTGACTGGAGTAACA
AGTGA--TGTATTGGTTTTGTTTCATGTGTT-TGCAGTTGGATGTTTCGAGGTGCACCAGAACTGCTTCCCAGATGACTG
TCAGAAGAGATGCGAGGACGATCTTGGAAAAGATACGTTAAGTGAATGCCAGCGGGATCATGGCGTACTACAACCGTATC
CTGGGCTTCAGTGTTGTTGTTTTCGAAAGGACGGTATCCGAAATTGATAAACAGGGTGTTTAGGTGATGATGGGCAGATG
ATA----GAACACATCCAT------------ATATATGATTGTCTGTTCGATCCACCTGTTGTACTGTAGATCTAATAAA
TGAATGTCTTTCATGACAATCATATTAATTAACAAAGGCATTAGCTGCGTCAAAAAGTATATC---TTACAATTATTGAG
GGAAATTATAACATTATTGTTTTTTGTGGCGCACTGTGTA----------------------------------------
-------CTATCTTCACATTGTTTTCATTATAGCATATATCGAGCCGC--------------------------------
AAGCAGAGATCCCAAATGAAAACCATGGTTTTGTGTAAGCTTCATTATAGCACGTATCAAGCCGCAAGCGGAGATTCCAA
ATCAAAATCTTGG-------------------------------------------------------------------
------------------------TTTTGTTTAAGATCTAGACCCACCGCTACAACC-----------------------
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--------------AATCACCATGGACGCAGTCGCAGTACAATNNNNNNNNNNAAGGC----------------------
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--------------------------------------------------------TTTC--------------------
--------------------------------------------TGAGATTGCTCATGCAATTTTGGTACTTACCAGTCG
AGGTCGCTTTTGTGGCTGCACTTCCACGGACAGATGAGATCTGAGGTTCAAATTTTGGAAGCTCGTCCTGAACA------
----------TTTTTCCTCCACCTCGGCCAGCAGATCATACAACTCCTCTTTCTTCTTCTACACCCTCCCCTTCAGCTCC
TTGTGTGGCCCTCCGTAAGGATGCTTGCCCTTA------------
>chr1B_805
TGATG---------------------------------------------------------------------------
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---------------ACGAGATAAGCCCTATTATAAT-------------------------------------------
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-----------------------------------------------------------------TTCAGTAGCAC-AAT
TTG---TGCCTTAAATCACGAGATAGGTACTATTCTAGTTTTG-GCACTATT-ATGCATTAAGTATTTGATGATCTGTCT
GCGACCTCCACCGATCTGCCT---CTATATAAACGCAACGAATGGGTGAGCATGGCAACATCTGATCAGGCTTTCTTTTT
-GTGTGCTCAGTCATGGCAGCCCTCACGAACAATGGGGCTGTTGCCGTATGGTTGGGGGCTCTCATGCTCATGGCTACCC
TTCTCGCCTCACAAGGAAAACCAGCCTTCAGTAAGTACGCCTTCCC------TTAAC-----------------------
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----------------------------TACCTAGC--ATCCATCATTTTTCACAAGATGCACTACTCATCTGGCGATGT
TGAGCACGATGGGTTTTGATA-TTTTT--GTGTACACATTATTATCTACTAGCATGAAGTAGTAACAAACTGGAGTAACA
AATGT--TGTATTGGTTTTGTGTCACGTGTT-TGCAGTTGGATGTTTCGAGGCCAAGCAGAACTGCTTCCCGGATGAATG
TCAGAAGAAATGCGAGGACAATGTTGGAAAAGATACGTTAGGTGACTGCCATCGGGAGCGTGAGAGT---AAACCGTATC
CTGGGCTTGAGTGCTGTTGCTTCCGAAATGACACTCCACC-AAATGATAAACATGGTGTTTAGTTGACGACGGACAGATG
ATA----GAACGCATCCAT------------ATATAGGATTGTTCGTTCGATCCACTTGT-----TGTAGATCTAATAAG
CGAATGTATTTCACGAAAATCA----AATTAACAAAGGCATTAGCGGCACCAAAAAGT----------------------
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>chr1D_853
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------TGCCTTAAATCACGAGATAGGTACTATTCTAAATTTCCGCACTATT-ATGCATTAAATATTTGATGATCTGTCT
GTGACCTCCACCGATCTGCCT---CTATATAAACGCAACGAATGGGTGAGCATGGCAACATCTGATCAGGCTTTCTTTTT
-GGGTC----GTCATGGCAGTCTTCACGAACAATGGGGCTGTTGCCGTATGGTTGGGGGCTCTCATGCTCATGGCTACCC
TTCTCGCCTCACAAGGAAAACCAACCTACAGTAAGTACGCCTTCCC------TTAAC-----------------------
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----------------------------TACTTAGC--ATCCATCATTTTTCACAAGATGCACTACACATCTGGCGATGT
TGAGCACGATGGATTTTGATA-TTTTT--GT--ACACATTATTATCC---AGCATGAACTAGTAACAAACTGGAGTAACA
AATGT--TGTATTGGTTTTGTGTCACGTGTT-TGCAGTTGGATGTTTCGAGGCCAAGCAGAACTGCTTCCCGGATGAATG
TCAGAAGAAATGCGAGGACAATGTTGGAAAAGATACGTTAGGTGACTGCCATCGGGAGCGTGAGAGT---AAACCGTATC
CTGGGCTTGAGTGTTGTTGCTTCCGAAAGGACACTCCACC-AAATGATAAACATGGTGCTTAGTTGATGACGGGCAGATG
ATATATAGAACGCATCCA------------------------TCCGTTCGATCCACCTGT-----TGTAGATCTAATAAA
TGAATGTCTTTCACGGACC-CA----TATTAACATAGTCATTAGCTGCGTCAAAAAATATACTATGTTACAATTATTCAG
AGAAATAATAATATTATTGCTTTT-GTGCCGCACTGCGTATTAGTATATT---GAGGGTCAGTTCTTGCATTGAGAGATT
AATTCACCTACCTTCACATTATTTTCATTGTAGCACGTATCGAGCCGCT-------------------------------
-AGCAAAGATCCCAAATCCAAACCATGGTTTCGTTTAAGCT---------------------------------------
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>chr1A_914
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--------------------------------------------------------------------C--------TCC
GTGATCTCCACCGATCTGCCTTCCCTATATAAACCCAACGAATGGGTGAGCATGGCAACATCTCATCAGGCTTTGTTCTT
-GGGTCATCAACCATGGCAGTCTTCAGGAACAATGGGGCTGTTGCCGTATGGTTGGGGGCTCTCATGCTCATGGCTACCC
TTCTCGCCTCGCAAGGAAAACCAGCCTTCAGTACGTACACTTTCCTTCTCTTA---------------------------
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----------------------------TAGTTAGCAAATCGATCATTTTTCACAAAAT---CTATATATCTTGCGATGT
TGAGCACGGTGGATCATATTGGTATTC--TT--ATACAAAGTTATCC---AATATGAAT---TGACTGACTGGAGTACCA
ATTGA--TGTATTTGGTTTTGTTGTGTTTGCATGCAGTTGGATGTTACGAGGTCCACCAGAACTGCTTCCCAGATGACTG
TGCGAAGAAATGCAAGGACAATCATGGAGAAGATACATTAAGTCAATGCCAGCGGGATCATGGCGAACTAAAACCGTATC
CCGGACTTGAGTGTTGTTGTTTTC--------------------------------------------------------
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>SNPs
-------------S-----S-----------------------------S----------------------------S-
------------------------------S----------S-S----------S-------------S-----------
---------------S----------------------S---------------------------------S-----S-
-------S-------SS------SSSS-S-S-S-----------------------------------------------
--SSSSSSSSSSS--------------S-------------------------------------------SS-------
--------------S----------------------------------------------S------------------
-----S-------------------------S------------------------------------------------
---S-----------------------S------------------------------------------------SS--
---------------------S---------------------S-----------------S-S----------------
--------------------------------------------S-----------------------------------
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--------------------------------------------------------------------S-----------
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---------S----------------------------------------------------------------------
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-------S---S---------------SS---------------------------------------------------
-----------------------------------S-------------------------------------------S
------------------S----------------S----------------S---------------------------
--------------------------------------S---------------S-------------------------
-------------------SSSSSSSSSSSS-------------------------------------------------
----------------------------------------------------S---------------------------
----------------------------------------S--SSSSSSSSSS--------------------------S
---S----------------------------------------------------------------------------
----------------------------------------------------S---------------------------
-------S------------------------------------------------------------------------
-----------------------------S-----S--------SS--S-SS-S-SSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------------------------------------------
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-------------------------------------------------------------------------------S
-SS------------------------------S--------S--S---------------------S-------S----
----------------------S----------SSSSSSSSSSSS
>forward_176
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----------------------------------------------------------------------------GCAG
CAACATCAGCCTTCAC----------------------------------------------------------------
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>reverse_2210
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-------------------------------------------------GAGGGAGGGTCAGTTCTTGC-----------
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