>input_sequence_78862
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-----------------------------------------------------------ATGGCCAGGCGATGGCTCACG
TCGGACGCGAGCGCGCCCCCTCCGTCGCAGCATTCTGGGTGGGACGTGAACCGGTCGGCCGTGAAGGTTGCCATCGTCGG
CAACGTGGTCGTCGTGCTGCTCTTCTTCGTCGCCATCGTCTGGCGCCTCTTCTTCTCGGGGAGAGCTCAAGAAGGCGCCG
---------GCGGCGGTGGGGCGGTCATTGCGCCCTCCTCCGGGGAGAGCTCGCCGTGCGCGTCGCCTCGGGCTAAAGGG
CTCAGGAAGGAGGACCTCATGTCGCTGCCGGTGTACGTCCACCGCGCCTCGGCGGAGGACGGCGGCAAGGTGGAGTGCGC
GGTGTGCATCTGCGAGCTCAGAGACGGCGACACCGGCCGGCGGCTGCCGAGGTGCGGGCACCGCTTCCACGCCGAGTGTG
TCGACAGGTGGTTCCGCTCGCACGCTACGTGTCCACTCTGCCGCGCTCTTGTGGCGGACGGCGGCTGA------------
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>chr4D_1_TraesCS4D01G170000
CCGGCCAAACATAAAGGAAAAAA-AGGATCACTATCCGCGTACCGGCCTTGTGGGGACTGTGAAGCGTGTGATGGTATAT
TT-TTTTCATTTGGATGAAGGAA--AAAATGTCTTTGTCATGATTGATCCATATTTTTTGCTTA-T-TTTTTGAACATAG
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----------TACAAACGTAGATGCTCATACATAAGC--ATACCCTCATCCTTATGTACGCACGCACACTCTATCTCT--
-----ATGAACACCTTCGAGAGACTGAGCCGGCACATCATCTTTTTTTTTACGACTAGGCACATCATCTTAAGATTGTCG
AAGTCGTCACATTCATAAATTTGTTCAGGGAAGGT-GTACAATGCATTAGAAAATAACCCGAAGGAAGATACACTGTAGT
AGTGAAAAGTCG---------TATCCCTCTTTGAACAAAGAGATTTTCACCTCGTACCGAGGATGGTTGAAGTAACCGGA
GAAAAGCATGTCGATCAGTCATCGGGATGCTCAAACTGGCCGGGGGGAAGCATGCCGAATAATATGAC------------
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---------------------------------------------------GAGGATACAGGTTGATGAGGCAACACCAC
CAGACACCAGGATGACCGCGCAATGTTGCTATGCAATTTCGTTGTCAGTAGCCTGGAGCAGGAAACACAGA---------
--------------------------------------------------------------------TAGATTGGAGAC
GTCAAGTTTCGTGGCAGAACAATTTCAGTTTGGGTAGGCGACAATCTCTGACCTGCAGTTGCGCTGCCACGGTACAGACG
GATCAAAGGTCCTCGGCGCCGGCACGGCACGAGTGAAGCAGCTGCAACTACTAGGTCC---TACAAGTTGCCGGCTATCG
GCGGCTTTT-AAATAAGCATGCTAGAGTGTCGTCGTTTCCAGTGGTGACGGCGACGCGCGTGTCCATTCCATTGTCGCAA
CCTCCTTCGTTTCATCCTTCGCCACTCAATAAATGTTCGTTGCTGTCATACATGTCGTGCCAAACCAACCCATAACTAAG
CACCTCTTGACTCCCGTGCTTCCTGCCGGAGTCTCCGTTGATAAACCACCAAGCCATTGATGGCCAGGCGATGGCTCACG
TCGGACGCGAGCGCGCCCCCTCCGTCGCAGCATTCTGGGTGGGACGTGAACCGGTCGGCCGTGAAGGTTGCCATCGTCGG
CAACGTGGTCGTCGTGCTGCTCTTCTTCGTCGCCATCGTCTGGCGCCTCTTCTTCTCGGGGAGAGCTCAAGAAGGCGCCG
---------GCGGCGGTGGGGCGGTCATTGCGCCCTCCTCCGGGGAGAGCTCGCCGTGCGCGTCGCCTCGGGCTAAAGGG
CTCAGGAAGGAGGACCTCATGTCGCTGCCGGTGTACGTCCACCGCGCCTCGGCGGAGGACGGCGGCAAGGTGGAGTGCGC
GGTGTGCATCTGCGAGCTCAGAGACGGCGACACCGGCCGGCGGCTGCCGAGGTGCGGGCACCGCTTCCACGCCGAGTGTG
TCGACAGGTGGTTCCGCTCGCACGCTACGTGTCCACTCTGCCGCGCTCTTGTGGCGGACGGCGGCTGATCCGGTGAGGTC
GACCCTGATCGGTGATCCATAAGCACTAGTGATTTTCTTGTTCATGTTAACC------TTTTGACGAAACCAATGTCGTT
CGCTATACCACTTCCCTATTGACGTGTATCCACAAGCACATGCTCGACATTCAGGGTGCAGATTCTCAA-----AAAGAA
AGAAAGAC-ATTCAGGGTTCAGGCCCATCCCAATAC---------------ATGAAGGGCCAGTTCTTTTCGCGCAAGAT
TTTATAAAATTAAAATTCTGAAAAACTTCCCACAGAATCTGCTTCTCACAGAAACTGTCATTCAACTTTTTTCTGAGATA
GCAGATTGTGGTACGAGTTTTTTGTCACTGAAACTGTTTGCTATACTACTTCCTTATTGATGTGTACCCACAAGCTCATG
TTCGACATTCAGGGTTCAGATTCTAAAAAGAAAGATTCAGGGTTCAGGCCTTTCTCCACACGTCAAATACTTTCTCTGTT
TCAAAATATAATGCATATTTTATTTCAAAAGAAATTTTATACATCTACGAAGAGACACGTAAACTTCCTGACAATAACCC
TCCTC---------------------------------------------------------------------------
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---------------CCCCCTCCCCCCGGCCGAATTTCAGGCGGTAGGGCTGTCCCGCCCTTATCTACAATCATATTTCT
CCACGTGGCACATAGATCTAGCATTGCTCATTTTATTTTCTAAAAGTCAAATATGTCTACAATTAATCAAGTTTAAACAC
AAAACATCAACA-CGACAACACAAACTAGTAGATAATATAAAATTAGTATCATTAGAGTATCTACAGCCGGACTTGGCAA
ATCCGGCCG-TCAAACGCCCGCAGACGCGCCCAGGAGCGTGTGTGGGCACTGACCGGGCACCCTTCAAATAATGTAATCC
ATATCCGAACACCTTAATTATCATATCTCAAATCCATACAAACTCATGCAACTACGTCGATGCACACACATCGTCCGGCT
ACTCCATCAGTACTAACTAAACATGCCATCGGACTATCAAAATTTGGCATGTTTGACTATGGTGGAG
>chr4A_1
CCGGCCAAACATAAAGGAAAAAAGA---TCACTATCTGCGTACCGGCCTTGTGGGGACTGTGAAGCGTGTGATGGTATAT
TTGTTTTCATTTTGATGAAGGAA--AAAATGTCTTTGTCGTGATTGATCTATAATTTTTGCTTATT-TTTTTGAACATAG
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----------TACAAACGTAGATGCTCATACATAAGTACATATATTCATCTCTATGTACGCATGCACACTCTATCTCT--
-----ACGAGCACCTTCGAAAGACTGAGCCGACATATTATT---------------------------TTAAAATTGTCG
AAGTCGTCACATTCATAAATTTTGTTCAAGGA------ACAATGCATTATAAAATAACCAGAAGGACGATGCACTGTAGT
GAAAAAGTCGAAGTCACCTATTATCCCTTTTTTAAAC---AGATTTTCACCTCGTAAGGAGGATGGTTGAAGTAACCGGA
GAAAAGCATGGCAATCAGTCATGGGGATGCTCAAATTGGCC-GGGGGAAGCATACCGAATAATATGATACTTCCTTTATT
TACTTATACAAAACCACTATGGAAAAATACACTTTACATTTATATAAGGCCATCAACACTAATCGAGACAAAAGTTAATG
ATATTTTTTTGAACTAACAGTCTATTTTATACTTACATGCATGCAGTCATAATGACACATCAATCAACTTTCAATCCCTT
CTTTGCATGCATGTATTGTACTATTAATGATACCACTAAACGAAAAGAAAAATGAGTTTATAAGGCAAGACATTAAATTT
TATCTTGATATTTATAATATGAGTTTGTGGTCTTATATATAAAAATGGAGGGAGTATACAGATTGATGAGGCAACACCAC
CCGGCACCAGGATGACCGCGCAATGTTGCTATGCAA--------------------------------------------
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>chr4B_3
--GGCCAAACATAAAGGAAAAAAGAGGATCACTATCTCTGTACCGGCCTTGTGGGGACTGTGAAGCGTGTGATGGTATAT
TT-TTTTCATTTTGACGAAGGAAAAAAAATGTCTTTGTCGTGATTGATCCATAATTTTTGCTTA-TATTTTTGAACATAA
TACATATGTGAGTTATTTACGCAAAACCATCACACTTGAGTCTAGAGTAACAACTTCGTGCCGCATTTAGGCCAGGACAC
AAAGAACCACCAACTCTGCGTCTAACCTATAACGTCGAGCACTGATAGTCGAAATTACTCACGAAAACAGCGAAACCGAC
GGATAGGGCCCACATGTCAAGACGATGTGGCATGCCTATCTGGACAATTTGCTGAGGTGGACGTAGGTCCCATCCGCCAT
CCTCAAGTACCTCCTCCTTCCTTCTCTTTGTCTTTTTTTCGCTCTTCAACCAGCGAACACAGCGGACCTCGCCAGTGGCC
ATGCTCAGGCTGGACCCATGCCTCCGCCGCCATGGTCGGCCACCACGGTCGTCCCCGCCGGCAGCCCAATGCCTGACGAG
GCGATGCGTCCTCCGCCATCAACCTCCTCCTCTCGTCCAAGCCGCTCCGGCGATGCGCGCCTCGCCCCGAGCAGCACCAC
TCGGGCCGCTTGCCTTGCCGGCTGCCACTCGCTCCGGATGTGGATGTCCGCGACCCCGCTGCCCTGGATCTGGTGCCCAG
GACCTGTACGGCGTCCGCATCGGCCGCCGGCGTCCACACCCCATGGAGCCCACAACAGCTCCTCCCCGATCCGCGGTCAC
CGCCGGCCTTCTTTCTCATGGCCAGAGACCACTCCAAGCCCCACCACCTTGTCTGGGAGCCCCGGAATGCCTCCCTGAGC
ACCCCTACTGGAGTTCTTGGACCCGGACGTCCAAAATTGGCCATGCCACGGTCGTCTTCTCCACCTCCGACCACCACCGT
GCCACCATCTCCTGCTCAGGTGAATCTCTGCGCCTCGCATCTAGTCCCTAGGCTTCGACGCGTCCTCTTGATGCCTTTGC
CGCCAACACCGGCAAGCTGCGAGTCCTCAAGCCGTCTTCCTCGCCTCACCATGCTTTGTCGGCCGCTGCCGCTCACGAGG
ACGTTGCTCTAGTGCTACCTCGCCGCGTTCGAGCACACATACGTGCTCAAGGTGAGCCCCTCGCCCCTTCCCCATGCCAT
GGCGCGTTGTGCCTTCTTCAGTGACCAGAGGATGAACGCACGGAAGGTGCTCGATGGAATGCCCGATAGAGAGAATGTTG
TGAAGAAGATGACCCTCTAGTCATTGACATTTGGAGCCCAAGTCTCATTTGCCACATCAGTCGGTCAAAGTTTTTGGTCT
TTGCCATGTCAGCCCGACAAGTGGGGCCAACCTGTCAGTTTCACTGTTTTCGTGAGCTTATCAGAAAATCAGTGTTCCGC
GTTATAGGTTAGGGCGCAGAGTTGGTGGTTTTTTGTGCCCTGTCAAGTTGTTACCCTAGCCCCAACTATGGTGTTTTGGG
TAAATAACTCTACAAACGTAGATG-TCAAACATAAGCATATACACTCATCCCTATATACGCACGCACACTCTATGACTCT
ATCCCATGAGCAACTTCAAGAAACTGAGCCGGCACATCATC---------------------------TTAAGACTGACG
GAGTTGCCACATTCATAAATTTTATGCAGAGAAGGCGTACAATGCATTAGAAAATAACCAGAAGGAAGATACACTGTAGT
GAAAAAGTCGAAGTCACGTATTATTCCTATTTGAACTCAGAGACTTTCACCTCGTACGGAGGATGGTTGAAGTAACCGGA
GAAAAGCATGGCGATCAGTCATCGAGATGCTCAAACTGGCCGGGGGGAAGCATGCCGAAAAATATGATA-----------
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--------------------------------------------------------TACAGGTTGATGAGGCAACACCAC
CCGGCACCAGGATGACTGCGCAATGTTGCTATGCAATTTCGTTGTTAGTAGTCTGGAGTACAGAAATTTCCTCCGTTTTA
AAATAGACGACTCAATTTTATTTTAGTTTTAGTATAAAATTAGATTATCTATTTTAGAACGGAGAGAGTATATTGGAGAC
GTCA----------------------AGTTTGGGTAGGCGACAATCTCCGACCTGCAGTTGCGATGCCACGGTACAGACG
GATC-AAGGTCCTCGGCGCCGGCACGGCACGAGTGAAGCAGCTGCAACTACTAGGTCC---TACAAGTTGCCGGCTATCG
GCGGCTTTT-AAATAAGCATGCTAGAGTATCGTCGTTTCCAGTGGGGTCGGCGATGCGCGTGTCCATTCCATTGTCGCAA
CCTCCTTCATTTCATCCTTCGCCACTCAATAAATGTTCGTTGTTGTCATACTTGTCGTGCCAAACCAACCCATAACTAAG
CACCTCCTGACTCCCGTGCTTCCTGCCGGAGTCTCCGTTGATAAACC---AAGCCATTGATGGCCAGGCGATGGCTCACG
TCTGACGCGAGCGCGGCCCCTCCGTCGCAGCATTCCGGGTGGGACGTGAACCGGTCGGTCGTGAAGGTCGCCATCGTCGG
CAACGTGGTCGTCGTGCTGCTCTTCTTCGTCGCCATCGTCTGGCGTCTCTTCTTCTCGGGGAGAGCTCAAGAAGGCGCCA
CGGCTCCCGGCGGCGGTGGGGTGGTCATTGCGCCCTCCTCCAGGGAGAGCTCGCCGTGCGCGTCGCCTCGGGCTAAAGGG
CTCAGGAAGGAGGACCTCACGTCGCTGTCGGTGTACGTCCACCGCGCGTCGGCAGAGGACGGCGGCAAGGTGGAGTGCGC
GGTGTGCATCTGCGAGCTCAGAGACGGCGACACCGGCCGGCGCCTGCCGAGGTGCGGACACCGCTTCCACGCCGAGTGTG
TCGACAGGTGGTTCCGCTCGCACGCTATGTATCCACTCTGCCGCGCTCTTGTGGCGGACGGCGGCTGATCCGGTGAGGTC
GACCCTCATCGGTGATCGATAAGCACAAGTGATTTTCTTGTTCATGGTAACC------TTTTGATGAAACCAATGTCGTT
CGCT----------------------------------------------------------------------------
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>chr4A_591
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------------------------------------------------TAGCCTGGAGCAGGGAACACAGA---------
--------------------------------------------------------------------TAGATTGGAGAC
ATCAAGTTTCGTGGCAGAACAATTTTAGTTTGGGTAGGCGACAATCTCCGACCTGCAGTTGCGATGCCACGGTAGAGACG
GATCAAAGGTCCTCGGCGCCGGCACGGCACCAGTGAAGCAGCTGCAACTACTAGGTAGGAGTACAAGTTGTCGGCTATCG
GCGGCTTTTTAAATAACCATTGTAGAGTATCGTCGTTTCCAGTGTTGACGGCGATGGGCACGTCCATTCCATTGTCGCAA
CCTCCTTCGTTTCATCCTTCGCCACTGAATAAATGTTCGTTGCTGTCATACATGTCGTGCCAAACCAACCCATAAATGTT
CGTTTCATCCT--------------CCGGAGTCTC-------------CCAAGCAATTAATGGCCAGGCGATGGCTCACG
TCGGACGCCAGCGCGCCCTCTCCGGCGCAGCATTCCGGGTGGGACGTGAACCGGTCGGCCGTCAAGGTTGCCATCGTCGG
CAACGTGGTCGTCGTGCTGCTCTTCTTCGTCGCCATCGTTTGGCGCCTCTTCTTCTCGGGGAGAGCTCAAGAAGGCGCCG
CGGCTCCCGGCGGCGGTGGGGCGGTCATTGCGCCCTCCTCCGGGGAGAGCTCGCCGTGCGCGTCGCCTCGGGCTAAAGGG
CTCAGGAAGGAGGACCTCATGTCGTTGCCGGTGTACGTCCACCGCGCGTCCGTTGAGGACGGCGGCAAGGTGGAGTGCGC
GGTGTGCATCTGCGAGCTCAGAGACGGCGACATCGGCCGGCGCCTGCCGAGGTGCGGGCACCGCTTCCACTCCGAGTGTG
TCGACAGGTGGTTCCGCTCACACGCTACGTGTCCACTCTGCCGCGCTCTTGTGGCAGACGGCGGCTGATCCGGTGAGGTC
CGGTGAGGTCCACC---------------------------TCATGTTAACCTTTTGATTTTGATTAAGCCAATGTCGTT
CGCTATACCACTTCCCTCTTGACGTGTATCCACAAGCACATACTCGACATTCAGGGTGCAGATTCTCATCTCAGAAAGAA
AGAAAGACGATTCACGGTTCAGGCCCATCCCAACACATGAACTCCCGATAGATGAAGGGCCAGTTCTTTTCGCGTAAGAT
TTTACAAAATTAAAATTCTGAAAAACTCTCCACAGAATCCGCTTCTAAGAGAAACTGTCGTTCAACT-------------
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>chr4B_1564
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-----------------------------------------------------------------------------GTT
CGCTATACCACTTCCCTATTGACGTGTATCCACAAGCACATGCTCGACATTCAGGGTGCAGACTCTCAA-----AAAGAA
AGAAAGAC-ATTCAGGGTTCAGGCCCATCCCAACACATGAACTCCCAATACATGAAGGGCCAGTTCTTTTCGTGCAAGAT
TTTATAAAATTAAAATTCTGAAAAACTTCCCACAGAATCTGCTTCTCACAGAAACTGTCATTCAACTTTTTTATGAGATA
GCAGATTGTGGTACGAGTTTTTTGTCACTGAAACTGTTTGCTATACTACTTCCTTATTGATGTGTACCTACAAGCTCATG
TTCGACATTCAGGGTTCAGATTCTAAAAAGAAAGATTCAGGGTTCATGCCCTTCTCCACACGTCAAATACTTTCTCTGTT
CCAAAATATAATATATATTTTATTTCAAA-GAAATTTTATACATCTACGAAGAGGTACGTAAACTTCCTGAGACTAGTTA
CAATGGGTAGTAACTTAGACTAGTAACATGCATATGTTACTATCTCTATAGTGGAGTAGAGTAACATATATGTGGTGTCT
TCATTTATTAGATTGTAGGCTCATCTTGTCTTGGTTTGTGTGATGTTACAGTAACTAGTTATGTTACCACATGCCTCTCT
TTTCTCATTAATTACTCGTCACATCATCTATTTTATCTAAAGATGTGTGACGTTATCACCTATGTTACTCCCACTGGTTG
TCTGACAATAAAATGCCCCCACCCCCGGCGCGAATTTCAGGCCGTGGAGTTGTCCCACCCTTATCTTCAATCATATTTCT
CCAAATGGCATGTAGATCTAGCATTGCTC-TTTTATTTTTTAAAAGTCAAATATGTCTACAATTACTCACGTTTAAACAC
AAAACATCAACATCGATAACACAAACTAGTAGATAATATAGAATTAGGATCATTAGAGCATTTACAGCCGAACTTGGCAA
ATCCGGCCCCTCAAACGCCCGCAGTCGTGCCCAGGCGCGTCTGTGGGCACTGACCGGGCACCCTTCAAATAATGTAATCC
ACATTCGAACACCTTAGTTATCATATCTCAAATACATACAAATCCATGCAACTACGTCGATGTACACACATCGCCCGACT
ACTCCATTAGTACTAACTAAACATGCCATCGGACTACCAAAATTTGCCATGTTTGGCTATTGTGGAG
>SNPs
------------------------------------S-------------------------------------------
------------S--------------------------S-------------S--------------------------
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-------------------------------------------S-------S----------------------------
---------S-------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSS------------
----------------------SS-SSS--S-S-S------------------------S--------------------
SSSS--SSSSSS----------------S-------SS-------------------S----------------------
----------S--------------------------------------------------------S------------
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------------------------------------------------------S-------------------------
-S-S-----------------------------------------S----------------S-----------------
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-------------------------S----------------------S--------------S----------------
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----------------------------S-------------------------S-------------------------
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------S----------------------------------------S--------------------------------
-----------------------------------S--------------------------------------------
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-----------------------------------------------S-----S--------------------------
------------------------------------------S-------------------------------------
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-----------------S--------S-------------------------------------S---------------
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---------------------------------S----------------------------------------------
------------------------------------------------------------------------S-------
--------------------------------------------------------------------S-----------
----------------------------------------------S---S-----------------------------
S-----------SS---------------S------------------------SS---------------S-S--SSSS
SSS-S---------------------------------------------------------------------------
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--------------------S-----S-SS------------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-----------S----------------S--------SS------------------S----------S---S--
-------S----------------------------S---------S--------S----S------
>forward_1644
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------------------------TGAGCCGGCACATCATCTTT------------------------------------
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>reverse_3345
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----------------------------------------------------------------CGAAACCAATGTCGTT
CGCT----------------------------------------------------------------------------
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