>input_sequence_57543
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---------------------------------------------------------------ATGGCATTGGACGTGCT
CCTCAGGCTGCTGATCCTCGCGGCCGTCGCGAGCGCCATGCCGGTGCCGGGCCCCACGGACCCCGCCGCCGCCGGGCTCG
CCATCGGGTTCTACAACAAGACGTGCCCGAAAGCGGAGGAGCTGGTGCTGGAGGAGATGCGGGACATCGTCCACGAGGAC
CGGACCCTCGGCCCGGCGCTGCTGCGGCTTCTCTTCCACGACTGCTTCGTCAGGGTGCGTGCTGCGCTGCTTCTTTGCCG
TGCCGTGCCGCGTCGCGTGCACGGGTCGTCTGAATGTGTTTCGCTTAACTTGAACTGGATGCGTGGTCTGCAGGGGTGCG
ACGGGTCGATCATGCTGAAATCGAGGAGCAAGAAGGGGGAGAGGGACGCCATGCCGATGAGCTACAGCCTCCGCGGCTTC
GATGAGGTCGAGAGGATCAAGGCGAAGCTGGAGGACGAGTGCCCGCTCACCGTGTCCTGCGCAGACATCATCATCATGGC
CGCGCGGGACGCCGTGTACCTGGTAATTTAAGCAGATCAATAATCCCCCCTTTCATGTC-CTCCATGGATTTTCTCAGGC
TTTCATTTTAGCTGACCACCAGACTGCCTCCTTGTTTCTTCCAGAGCAACGGGCCACGGTTCCCGGTGGAGACCGGGCGC
CGGGACGGCAAGGTGTCCCTGTGCATCGACGCCGAGAACGACCTGGCGCCGCCGCACGCCAACATCGTGGACCTGAAAAC
CTACTTCAGCGTGAAGAACCTGTCGTGGAAGGACCTGGTGGTGCTGTCGGGGAGCCACACGATCGGGAGGGCGCAGTGCG
CGGCGTTCGCGCCGGACCGGCTCTACAACAACAGCGGCCTAGGGGTGCAGGACCCGACGCTGGACAAGGCGTACGCCCCG
GAGCTGCGGGAGAGGTGCGAGCCAGGGAACAAGGAAGACGAAACGCTCGTCGACATGGACCCCAAGAGCCCCTACGAGTT
CGACCTCAGCTACTACCGGGACGTGCTCAGCAACAAGACCCTGTTCGTCTCCGACCAGGCGCTGCTCGACGACAGGTGGA
CGAGGGACTACGTGGCGAGGATGGCGGCCGCCGAGTCGACGGAGGAGTACTTCGAGGACTACGCCGCCGCCATGATCAAC
ATGGGCAGGATGGAGGTGCTCACCGGCGGCAACGGGGAGATCAGGAAATTCTGCAGCGCGTACGTTGACTAA--------
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>chr3A_1_TraesCS3A01G325100
TATTGTTGTTCTACTTTGTAAGGTCCTCGAGAATAATCAATAAAATAGCCGCATACATTTCTCAGATGCAGAGGTCGGGG
GTCATCCTTCTTTTTTTTAAAAAAAAAAGAAGTATGGCCGTCTGTTTCTACTATTGGGTTCCGTTAAACACAGCACTGTG
CTTTGACCTTGACAAGTTCTAGTTTGCGTAAACAGCGATAACCGGCAGGTGGAGTAGCTTACCACGAAGAAGCGTATGCC
TCCGCAGCCTGTCCTCCGCCCGTGCTACACGCCAACTGCCCCTGGTCAGCACAGCCACCAGAGACCAGTTAAAATGCATG
CGCCTGAATATTTGTTTGTTCATTTGGTCAGCTCACTTCCCATTAGATGCTTTTATGCCTCTACAAATGCATCGATCGGT
TCGTCAATCTTGCCTTCATATATGCACTGCCATGTTCAACTATTCATCGATGTGCAGAAAAGCTATCTCGTAGTCGGCCG
AGTATGGCGTGTGAACAGCGTGCGTTGACAAGCGCAAAAGCCCGCATCCACGACCGCCATCCAGTCCAGACGCGGAACCA
ATCTGCTCGGCGCACTCGCGCC------TCCAGTCCAGTCTCATGCGCCGCGTGAAATGGGGGGAATTTTTGTTTCCTTC
TGCT-CGCCTTTGCGCGTAGCCTCCAACACCCCATTCCCGTTCCC----------AGCTGTGCTAGCCAGCCATTGTCCG
CCTCAGTTTTTAACTAACTTGCGAATTCCGAGCTTCTCGACAGCGATCGCCAACCCACCCGTGCCTCTCCAACTCTTTCT
TTATTCTCGCCATTCCGGCTCCGGGGTTTTCATGCTCGGGCGGTCGACGCCGGCCAGCAAATTTAATCTCCTTCTCTTGA
TCTCTTCCCCTTCCGTGAGTTCCCGGCTGACCCGA------GTTAAGTTTCAACGCCTCCTGAGCAGCTGCTTCCCCCCG
TCACGACCAAGCAACCTCGCTCGTCGACGACTCGATTCGGCTCTGTTCCTCCGGTCCGGCCGGATGGCATTGGACGTGCT
CCTCAGGCTGCTGATCCTCGCGGCCGTCGCGAGCGCCATGCCGGTGCCGGGCCCCACGGACCCCGCCGCCGCCGGGCTCG
CCATCGGGTTCTACAACAAGACGTGCCCGAAAGCGGAGGAGCTGGTGCTGGAGGAGATGCGGGACATCGTCCACGAGGAC
CGGACCCTCGGCCCGGCGCTGCTGCGGCTTCTCTTCCACGACTGCTTCGTCAGGGTGCGTGCTGCGCTGCTTCTTTGCCG
TGCCGTGCCGCGTCGCGTGCACGGGTCGTCTGAATGTGTTTCGCTTAACTTGAACTGGATGCGTGGTCTGCAGGGGTGCG
ACGGGTCGATCATGCTGAAATCGAGGAGCAAGAAGGGGGAGAGGGACGCCATGCCGATGAGCTACAGCCTCCGCGGCTTC
GATGAGGTCGAGAGGATCAAGGCGAAGCTGGAGGACGAGTGCCCGCTCACCGTGTCCTGCGCAGACATCATCATCATGGC
CGCGCGGGACGCCGTGTACCTGGTAATTTAAGCAGATCAATAATCCCCCCTTTCATGTC-CTCCATGGATTTTCTCAGGC
TTTCATTTTAGCTGACCACCAGACTGCCTCCTTGTTTCTTCCAGAGCAACGGGCCACGGTTCCCGGTGGAGACCGGGCGC
CGGGACGGCAAGGTGTCCCTGTGCATCGACGCCGAGAACGACCTGGCGCCGCCGCACGCCAACATCGTGGACCTGAAAAC
CTACTTCAGCGTGAAGAACCTGTCGTGGAAGGACCTGGTGGTGCTGTCGGGGAGCCACACGATCGGGAGGGCGCAGTGCG
CGGCGTTCGCGCCGGACCGGCTCTACAACAACAGCGGCCTAGGGGTGCAGGACCCGACGCTGGACAAGGCGTACGCCCCG
GAGCTGCGGGAGAGGTGCGAGCCAGGGAACAAGGAAGACGAAACGCTCGTCGACATGGACCCCAAGAGCCCCTACGAGTT
CGACCTCAGCTACTACCGGGACGTGCTCAGCAACAAGACCCTGTTCGTCTCCGACCAGGCGCTGCTCGACGACAGGTGGA
CGAGGGACTACGTGGCGAGGATGGCGGCCGCCGAGTCGACGGAGGAGTACTTCGAGGACTACGCCGCCGCCATGATCAAC
ATGGGCAGGATGGAGGTGCTCACCGGCGGCAACGGGGAGATCAGGAAATTCTGCAGCGCGTACGTTGACTAATGGAGCCG
GCGGTTGGTCGATGTGAGTTGGTGCGCGTGCCTCCATCGATCGTCATGTGGACGGGGTCACGACGGCCGGTGTGCCCGCC
AGCCGCAAGGCACTTGCATTATTCTAGGGGTGGTTAGAGAATTGACACCGTCACACCGCCACGCGGCGAATCTTCCGGTG
TATGTA---AAAAAAAGTCGTCTCTTTGTTCTTGACCGAGTGCCCATTGAGATTTGGCGAGCTGTAATTATAATTTTTCT
CCTTAATTAACTAGTTACTTGCAGAAAGTATGAATACATTGCTAAGAGTATTTCTAGCAGAGCCCTCGATAGCTTAATTT
AAGGGGGAAATTATCTTTTGAGGGATTTAAGTGCTACTCCTATCTAAGTTCAAAAAAAAAGTGCTACTTCTATCTAACAG
ATCCCTCAAATGTTTAGTTTCTTAAAATCATGGATTTTGATTCCTCAAAGCTCAACCTCCTAGCCTATTTTTATGAAGAA
TGTCATACGAAAACCAATATTCAATAAAAACTTCGTGAAAACCACATTTTAAAGTTTCGAAAAAAATCTAAAGAAAATGC
GGGATGTTAAGGGTATGTACAATGGTGGCATATAGATACATATGTCCCATGACAAAAAGTAATTTGAGGCACTTATATTA
ATTTTTTCTCTCCAATGCAAGCTATCACTAGTGGGCCTCATTAAGAAATAGAAAATAAAGACTCTAGTACACATGCATCT
CTATTTTTCACTCCAACCTTTTCAGCTTTTGTTATCGGACCACACTTTTTCTCTTCAAGCAACCGCCTCGTAGAGAGGAT
CCCGCTTCCTTATCCGAACCTACTTTACATCATATCCGATCCCATGGCATGCGAGGTATCATCTTGAGGCTATGCATTGT
ACATGCCCTAAGAGGGTGATGTTTTATGGCCACATAAAATTTCAAGTTGAAACACATTAGGGCATGTACAATGGTGGCAT
ATGGATACATATGCCCCATGACAAAAAGTAATTTG
>chr3B_110
--------------------------------------------------------------------------------
-----------------------------AAGTATGGCCGTCTGATTCTACGATTGGGTTCTGTTAAACACATCACTGTT
CTTTGACCTTGACAAGTTCTAGTTTGCGTAAACGGCGATAACAGGCAGGTGGAGTAGCTTACCACGAAGAAGCGTATGCC
TGCACAGCCTGTCATCCGCCCGTGCTACACGCCAACTA-CCCTGGTCAGCACGGCCACCAGAGACCAGTTAAAATGTAGG
CGCCTGGATATTTGTTTGTTCATTTGGTCAGCTCATTTTCCATTAGATGCTCGCATGCCTCTACAAATGCATCGATCGGT
TCGCCAATCTTGCCTTCATATATTCACTGCCATGTTCAACTGTTCATGGATGTGCAGAAAAGCTATATCGTAGTCGGCCG
A----GGCGTGTGAACAGCGTGCGTTGACAAGTGCAAAAGCCCGCATCCACGACCGCC-----GTCCAGACGCGGAACCA
ATCTGCTCGGCGCACTCGCGCCCCCTGGTCCAGTCCAGTCTCATGTGCCGCGTGAAATGGGGGGAGGTTTTGTTCCCTTC
TGCT-CGCCTTTGCGCGTAGCCTCCACCACCCCATTCCCATTCCCGTTCCCAGCTA-----GCTAGCCAGCCATTGTCCG
CCTCAGTTTTTAACTAACTTGCGAATTCCGAGCTTCTCGACAGCGATCGGCAACCCACCCGTGCCTCTCCAACTCTTTCT
TTATTCTCGCCATTCCGG------GGTTTTCATGCGCGGGCGGTCGACGCCGGCCAGCAAATTTAATCTTCTTCCC----
---CTTCCCCTTACGTGAGTTCCCGGCTGACCCGA------GAT-TGTTTCAACGCTTCCTGAG-AGCTGCCTCCCCTCG
TCACGACCAAGCAACCTACTTGCGGCTCTTC---------------TCCTCCCGTCCGGCCGGATGGCATTGGACGTGCT
CGTCAGGCTGCTGATCCTCGCGGCCGTCGCGAGCGCCATGCCGGTGCCGGGCGCCGCGGATCCCGCCGGCGCCGGGCTCG
CCATCGGGTTCTACGACAAGAGGTGCCCGAAAGCGGAGGAGCTGGTGCTCGAGGAGATGCGGGACATCGTCCACGAGGAC
AGGACCCTCGGCCCGGCGCTGCTGCGGCTTCTCTTCCACGACTGCTTCGTCAGGGTGCGCATTGCGCTGCTTTCTT----
TGCCGTGCCGCGTCGCGTGCACGGGCCGTCTGAATGTGTTTTGCTTAACCTGAACTGGATGCGTGATCTGCAGGGGTGTG
ACGGGTCGATCATGCTGAAATCGAGGAGCAAGAAGGGGGAGAGGGACGCCAAGCCCATGAGCTACAGCCTCCGCGGCTTC
GACGAGGTCGAGAGGATCAAGGCCAAGCTGGAGGACGAGTGCCCGCTGACCGTGTCGTGCGCAGACATCATCATCATGGC
CGCGCGGGACGCCGTGTACCTGGTAATTTAAGCAGATCGATAATCCCCCCTTTCATGGCAA-CCATGGATTTTCTCAAGC
TTTCTTTTTAGCTGACCAA---ACTGCCTCGTTG----TTCCAGACCAACGGGCCACGGTTCCCGGTGGAGACCGGACGC
CGGGACGGCAAGGTGTCCTCATGCCTCGACGCCGAGAACGACCTGGCGCCGCCGAACGCCAACATTGTGGACCTGAAGAC
CTACTTCAGCGTGAAGAACCTGTCGTGGAAGGACCTCGTCGTCTTGTCAGGGAGCCACACGATCGGGAGGGCGCAGTGCA
ACGCGTTCGCGCCGGACCGGCTCTACAACAACAGCGGCAAAGGGGTGCAGGACCCGACGCTGGACAAGGCGTACGCTCCG
GAGCTGCGGGAGAGGTGCGAGCCAGGCAACGAGAAAGACGAGACGCCCGTGGACATGGACCCCAAGAGCCCCTACGAGTT
CGACCTCAGCTACTACCGGGACGTGCTCAGCAACAGGACCCTGTTCGTCTCCGACCAGGCGCTGCTCGACGACAAGTTGA
CGAGGGACTACGTGGCGAGGATGGCGGCCGCCGAGTCGACGGAGGAGTACTTCCATGACTACGCCACCGCCATGATCAAC
ATGGGCAGGATGGAGGTGCTCACCGGCGACAACGGGGAGATCAGGAAAATCTGCAGCGCGTACGTTCACTAATCGACCCG
GTGGTTGGTCGATGTGAGTTGGTGGCTTGGTGCAAGTGCTTCGTCATGTGGACGGGGTCACGACGGCCGGTGTGGCCGCC
AGCCGCAAGGCACTTGCATTATTCTAGGGGTGGTTAGAGAATTG--------ACACCGCCACGCGGCGAATCTTCCTCTG
TTTGTATGTAAAAAAAGTCGTCTCTTTGTTCTTGACCGAGTGCCCTTTGAGATTTGGCGAGTTGTAATTATATTTTTTTC
GCTTAATTAACTAGTCACCTGCAGAAAGTATGAATACATTGCTGAGAGTATTTCAATCAGAGCCATCGGTAGCTTAA---
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>chr3D_115
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----------------------------------TGGCCGTCAGATTTTAGAACTGGGTTCTGTTAAAAACAGTACTGTA
CTTTGACCTTGACAAGTCCTAGTTTGCGTAAACGGCGATAACCGGCAGGTGGAGTAGCTCACCACGAAGAACTGTATGCC
TGCACAGCCTGTCC--------------------ACTACCCCTGGTCAGCACATCCACCAGAGACCAGTTAAAATGCATG
CGCCTGAATATTTGTTTGTTCATTTGGTCAGCTCATTTTCCATTAGATGCTCGCATACCTCTACAAATGCATCGATCGGT
TCGTTAATATTGCCTTCATATATGCACTGCCATGTTCAACTGTTCATGGATGTGCAGAAAAGCTATCTCGCAGTCGGCCG
A----GGCGTGTGAACGGCGTGCGTTGACAAGTGCAAAAGCCCGCATCCACGACCGCCGTCCAGTCCAGACGCGGAACCA
ATCTGCTCGGCGCACTCGCGCCCCCTGGTCCAGTCTCATCTCATGTGCCGCGTGAAATGGGGG-AATTTTTGTTCCGTTC
TGCTCCGCCTTTGCGCGTAGCCTCCAACACCCCATTCCCATTCCC----------A-----GCTAGCCAGCCATTGTCCG
CCTCAGTTTTTAACTAACTTGCGAATTCCGAGCTTCTCGACAGCGATCGCCAACCCACCCGTGCCTCTCCAACTCTTTCT
TTATTCTCGCCATTCCGG------GGTTTTCATGCGCGGGCGGTCGACGCCGGCCAGCAAATTTAA------TCTC----
---CTTCCCCTTCCGCGAGTTCCCGGCTGACCCGAAGCCGAGAT-AGTTTCAACGCTTCTTGAGCTTCTGCTTCCCCTCG
TCACGACCAAGCAACCTCG----TCGACAACTCGATTCGGCTCTGTTCCTCCGGTCCGGCCGGATGGCATTGGACGTGCT
CCTCAGGCTGCTGATCCTCGCGGCCGTCGCGAGCGCCATGCCGATGCCGGGCGCCGCGGATCCCGCCGGCGCCGGGCTCG
CCATCGGGTTCTACGACAAGACGTGCCCGAAAGCCGAGGAGCTGGTGCTCGAGGAGATGCGGGACATCGTCCACGAGGAC
AGGACCCTCGGCCCGGCGCTGCTGCGGCTTCTCTTCCACGACTGCTTCGTCAGGGTGCGTGTTGCGCTGCTCT-TT----
TGCCGTGCCGCGTCGCGTGCACGAGCCGTCTGGATATGTTTTGCTTAACCTGAACTGGATGCGTGGTTTGCAGGGGTGCG
ACGGGTCGATCATGCTGAAATCGAGGAGCAAGAAGGGGGAGAGGGACGCCAAGCCCATGAGCTACAGCCTCCGCGGCTTC
CACGAGGTCGAGAGGATCAAGGCCAAGCTGGAGGACGAGTGCCCGCTCACCGTCTCCTGCGCAGACATCATCATCATGGC
CGCGCGGGATGCCGTGTACCTGGTAATTCAAGCAGATCGATAATCCCCCCCCTTCATCGGCTCCATGGATTTTCTCAAGC
TTTCTTGTTACCTGACCAA---ACCGCCTCCTTG----TTCCAGACCAACGGGCCACGGTTCCCGGTGGAGACCGGACGC
CGGGACGGCAAGGTGTCGTCGTGCGTCGACGCCGAGAACGACCTGGCGCCGCCGAACGCCAACATTGTGGACCTCAAGAC
CTACTTCAGCGTGAAGAACCTGTCGTGGAAGGACCTTGTCGTGCTGTCGGGGAGCCACACGATCGGGAGGGCGCAGTGCA
ACGCGTTCGCGCCGGACCGGCTCTACAACAACAGCGGCAAAGGGGTGCAGGACCCGACGCTGGACAAGGCGTACGCACCG
GAGCTGCGGGAGAGGTGCGAGCCAGGCAACGAGAAAGACGAGACGCGCGTGGACATGGACCCCAAGAGCCCCTACGAGTT
CGACCTCAGCTACTACCGGGACGTGCTCAGCAACAGGACTCTCTTCGTCTCCGACCAGGCGCTGCTCGACGACAAGTTGA
CGAGGGACTACGTGGCGAGGATGGCGGCCGCCGAGTCGACGGAGGAGTACTTCCATGACTACGCCGCCGCCATGATCAAC
ATGGGCAGGATGGAGGTGCTCACCGGCGACAACGGGGAGATCAGGAAAATCTGCAGCGCGTACGTTGACTAATCGACCCG
GTGGTTGGTCGATGTGAGTTGGTGGCTTGGTGCAAGTGTTTCGTCATGTGGACGGGGTCACGACGGCCGGTGTGGCCGCC
AGCCGCAAGGCACTTGCATTATTCTAGGGGTGGTTAGAGAATTG--------ACACCGCCACGCGGCGAATCTTCCTCTG
TTTGTATGT-AAAAAAGTCATCTCTTTGTTCTTGACCGAGTGCCCTTTGAGATTTGGCGAGTTGCAATTATATTTTTTTC
GCTTAATTAACTAGTCACCTGCAGAAAGTATGAATACATTGCTGAGAGTATTTCAATCAGAGCCCTCGGTAGCTTAACTT
AAGTGAGAGATTATCTTTTGAGGGATT-AAGTGCTACTAGTATCTAACAGATCCTACCCGCAAAAAAAAGTATCTAACAG
ATCCCTCAAATGTTTAGTTTCTTAAAAATATGGATTTTGATTCCTTAAAACTCAACCTCCAAGCCTATTTTT--------
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>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------------S------S---------S-----------------S
---------------------------------S----------------------------------------------
-S-S---------------------------------S------------------------------------------
-----------------------------------S--S------------SSS--------------------------
-----------------------------------------S-----S--------------------------------
-SSSS---------------------------S-------------------------S---------------------
---------------------------------------------S----------------------------S-----
---------------------------------------S----------------SSSSS-------------------
--------------------------------------------------------------------------------
------------------SSSSSS-----------S---------------------------------S------SSSS
SSS---------------------------------------S-S-----------S--------------------S--
-------------------S-SS-----S---------------------------------------------------
----------------------------------------------------S--S----S-------S-----------
--------------S----------------------------------S------------------------------
S------------------------------------------------------------S----------SS--SSSS
-------------------------S---------------S-------S------------------------------
---------------------------------------------------S---S------------------------
--S--------------------S--------------------------------------------------------
--------------------------------------S------------------S-------------------S--
----S-------------SSSS------------SSSS-------S------------------------------S---
------------------SS----S-----------------------------S----------S-----------S--
------------------------------------S--S---------------------------------------S
SS------------------------------------SS------------------------------------S---
--------------------------S---S--S-------S----S---S-----------------------------
-----------------------------------S--------------------------------------S--S--
-----------------------------------------------------S-S------------------------
----------------------------S-------------------S------------------------S--S---
-S----------------------SSSSS-SSSSSS-SSS----------------------------------S-----
--------------------------------------------SSSSSSSS------------------------SS--
-S-------------------------------------------S---------------S----------S-----SS
S--------------S--S------------------------S----------S-S-----------S--------S--
---S-S--S------------------S----------SS-------SSSSSSSS-SSSSSSSSS-SSSS----------
---------------------------SS----------------S---S----------S-----------SSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_606
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--------------------------CCTCCAGTCCAGTCTCATGC----------------------------------
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>reverse_2269
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----------------------------TGCCTCCATCGATCGTCATG--------------------------------
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