>input_sequence_85979
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-----------------------------------------------------ATGTCGGGGGCACAGGGAGCGCACCCG
GTCGGGGAGACGACGCCGACGACGTACGGGTCGGTGGGCGGCGGGGAGAACCGCACGCGCACGGACCTGCGGTCGCGGGA
GGACCAGGGCAACATCCAGATCGATAAGGTGCAGGACAAGGTGGAGGACGCCGCGTCGCGCAAGGTCGACGACAGCGCCT
TCGCCGCCAGGAAGGAACCGGGCCAGGCCGGCGACGCCGGGGCGACCGGCACCGGCGCGTGA------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------------
>chr3A_1_TraesCS3A01G237000
TCATGTATTAACTACATTTTATTGTGTCACTTGTGTTTACTCTTTTTTTAATGCAAGTTTACAGCTACTCGGAATTCCTA
ATTGTAGACTCAACTATCTTGACCTACCGATGATCTAATTTGTGGCATTATTACCTTAATAAAATATTTGCATTTAATTT
TCTTTTTATATAGGGGTATAAGTTCTTACCAAATGTACTCAAATATACTGTTACTGAAAAATGCAAATATTTTCAACACG
AACATGGTTTTAAATAGGTCTTTGCGCCATTTGGCGCAACTGGTCATCTAGTAGTTGGAAAGTATCATGGGTTAGGCGTG
ACGCTAATAAAGTTGCTCACTTATTAGCTACGGAAACAGTGTTAAATGAATTATGTAAGGTGTGGCGGCATGTGCCTTCA
GATTTCATTTTGCAGACTGTTTCAGACGAGATCCCTTCGTGAATGGTTAAATAAAAGTGTGGGTTGAGTTTAAAAAAAAA
AAGCTTAGCGGGCCGTGGACGCGAGGGATAATCACCAATGTATTTCTGCTGCTGGGTTCAACTTTGCAGAATCGGCCACA
GGCCAATGTGGTTTTCGCGGGCACGCCGACCATTATCATCCTAGACGCGGATCCGGCTTGCCTGCAGCACGGAGTTTTTT
TCTCAACAAAAAAAAAAATGCAGCACGGAGTTGATGTTTATCCATTA---CTCGGCGAAACGCACACGCTCTCTGCAGTA
CGGAGCCTCGAGCGTCCAGGTGCGCGCCGCAGCGGACACGAGTCCGATCTAGACG-CCCGCGCAGATATATCCGAGCCAT
GTGTCACGCGGACACCACCCGCGTCACACCACGTCCCCATGCCACGCGCCGATACCGCGCCGCTGGCGCTCGCCGCAGCT
CAGC--TATTTAAACGCCGGCCCGCTGCCGCCGGACCACACCGGAGCCGAGCAGGAAGA-----GCACGTCGAGTCAGCC
AGCAGCGA--GCATATATACATACGCGTGCGAAGTGCAGTGAAGGCAGGCAGGATGTCGGGGGCACAGGGAGCGCACCCG
GTCGGGGAGACGACGCCGACGACGTACGGGTCGGTGGGCGGCGGGGAGAACCGCACGCGCACGGACCTGCGGTCGCGGGA
GGACCAGGGCAACATCCAGATCGATAAGGTGCAGGACAAGGTGGAGGACGCCGCGTCGCGCAAGGTCGACGACAGCGCCT
TCGCCGCCAGGAAGGAACCGGGCCAGGCCGGCGACGCCGGGGCGACCGGCACCGGCGCGTGATCTGGGTTCT---CTGTG
GCACCCTGCCGCGCGCG------------------------------------------GGTGCGTTGTG-TTGTGTAGC
GAGTTGTGTTCTGTAAAAGAGTCTCTGCGTGCGAGCTCACAATAATAAGAA---CTGCTTCTCAGTTTGCTTAGCAAGAC
CATTAATTTTCTGTTCGTGCAAACACTCTGCTATCTTTTTAGATTAGATAGG-----CTGCAAATGTTCAGATCAACCCG
GGCGAGACCGATAGATTCCTGTGGAAATGGGATAGATTCCTGTGGAAATGGAATGCAGCCGGGACGCACTATGCTAGCTA
GTAAGGGCCG--CTACGGAAGTGCTAGGCACCAATGAATTCTAGAAATGTAGAGGAGGTGCGGTTTTGTCTACAGAGGAG
TAGGTCTCGAAGAACGTGAGCGGCGATCCCATTGAGATGCCGAGAGTGGCCGGACTTGCCCATCGCTCCGAGGAGGCGAG
GAGCGGGGACAATGCTAAGCGGAGAGGAGCGAGGCGGCAGGTTGGGAAGTGAATGTGGCGATGTTTCAAGAGTGGTACAT
GCGGCAGTATATAGTACATGGCACCTAGTCCACACGGAGTAAGAGCATCTCCAGCCACGTCGATTATGCGTTTCCAGGAG
ACCAATTATGCGTTTCCAAGAGCCCAATTTTTATCAATTGGGCCCGAAATTAGCGCCGTCGGACCCAGGCCAAACTGGAG
CTTGGAGGAATTGTTGCTCGAGGGAATTGTTTTTGGTGTGAAAAAACGGCGGGTCCGGAGTCAGCGACCCTGCACATTGT
TGTCCTCATTGCTCAGTTTTCTGCGGGAAATCAATGCCAAAGTTGCCGGCGGTTAGTCTTTTATTGATTTCTCACAGAAG
GTGCAATGTGGCGACACGCATTCTCCCGTCACGCGTACATACGTTTACCGTTCCGGGCTGTTATAAAAGCCGCCTTCTCC
TTCATCGATGGACACACTTGCCCCGCAGCCTCTCTTTCTTGCCGCCGACGCTCTCTCTTCCCCTCTTTCCCCGTTTAG
>chr3B_482
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-AGCTTAGAGGGCCGTGGACGCGAGGGATAGTAACCAATGTATTTCTGCTGCTGGGTTCAACTTTGCAGAATCGACCACA
TTCCAATGTGGTTTCGGCGGGCACGCCGACCATTATCATCCTACGCGGCAGCTGACCCC---------------------
----------------------------AGTTGATGTTTATCCATTATTACTCGCCGAAACGCACACGCGCTCTGCAGCA
CGAAGCCTCGAGCGTCCAGCTGCGCGCGGCAGCGGACACGAGTCCAATCTAGACGCCCCGGGCAGATATATCCGAGCCAT
GTGTCACGCGGACACCACCCGCGTCACACCACGTCCCCATGCCACGCGCCGAGACCGCGCCGCTCGCGCTCGCCGCAGCC
CAGC--TATTTATACGCCGGCCCGCTGCCGCTGGACCACACAGGAGCCGAGCAGG---A-----GCACGTCGAATCAGCC
AGGAGCAA--GCATATATACATACGTGTGTGCGGTGTAGTGAAGGCAGGCAGGATGTCGGGGGCACAGGGGGCGCACCCG
GTCGGGGAGACGACGCCGACGACGTACGGGTCGGTGGGCGGCGGGGAGAACCGCACGCGCACGGACCTGCGGTCGCGGGA
GGACCAGGGCAACATCCAGATCGAGAAGGTGCAGGACAAGGTGGAGGACGCCGCGTCGCGCAAGATCGACGACAGCGCCT
TCGCTGCCAGGAAGGAGCCGGGCCAGGCCGGCGACGCCGGGGCGACCGGCACCGGCGCGTGATCTGGGTTCTGT-----G
GCGCCCTGCCGCGCGCGCTCGTTGCACGACCAC-------GGTCGCTGCATTTGCGCGCGGTGCGTTGTC-TTGTGTAGC
GAGTTTTGTTCTGTAAAAGAGTCT--GCGTGTGAGCTCGCAATAAT---AA---CTGCTTCTCAGTGTGCTTAGCAAGAT
CATTAATTTTCTGTTCGTGCAAACACTATGCTATCTTTTT--ATTAGATTAGATACACTGCAAGTGTTCAGATCAACCCG
GGCGAGACCGATAGATTC--------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------------
>chr3D_543
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------TTTGCAGAAACGACCACA
GGCCAATGTGGTTTTGGCGGGCACGCCGACCATTATCATCCTAGACGCCAGCTGACCCC---------------------
---------------------------GAGTTGATGTTTATCCATTA---CTCGGCGAAACGCACACGCTCTCTGCAGCA
CGAAGCCTCGAGCGTCCAGCTGCGCGCGACAGCGGACACGAGTCCAATCTAGACGCCCCGCGCAGATATATCCGAGCCAT
GTGTCACGCGGACACCACCCGCGTCACACCACGTCCCCATGCCACGCGCCGATACCGCGCCGCTCGCGCTCGCTGCAGCC
CAGCTATATTTATACGCCGGCCCGCTGCCGCCAGACAACACCGGAGCCGAGCAGG---AAGAGCGCACGTCGAATCAGCC
AGGAGCAAGCGCATATATACATACGTGTGTGCGGTGTAGTGAAGACAGGCAGGATGTCGGGGGCACAGGGGGCGCACCCG
GTCGGGGAGACGACGCCGACGACGTACGGGTCGGTGGGCGGCGGGGAGAACCGCACGCGCACGGACCTGAGGTCGCGGGA
GGACCAGGGCAACATCCAGATCGAGAAGGTGCAGGACAAGGTGGAGGATGCCGCGTCGCGCAAGGTCGACGACAGCGCCT
TCGCTGCCAGGAAGGAGCCGGGCCAGGCCGGCGACGCCGGGGCAACCGGCACCGGCGCGTGATCTGGGTTCTGTTCTGTG
GCGCCCTGCCGGGCGCGCGCGTCGCACGATCTTCGATCTGGGTCGCTGCATTTGCGCGCGGCGCGTTGTGTTTGTGTAGC
GAGTTGTGTTCTGTAAAAGAGTCT--GCGTGTGAGCTCGCAATAAT---AAGAACTGCTTGTCAGTTTGCTTAGCAAGAC
CATGAATTTTCTGTTCGTGCAAACACTCTGCCATCTTTTTAGATTAGATTAGATACACTGCAAGTGTTCAGATCAACACG
GGCGAGACTGATGGATTCGA---------------------GTGGAAATGGAATGCAGCCGGGACGCACTATGCTAGCTG
TAGCAAAGGCCACTATGGAAGAGCTGGGCACCAATGAATTGTAGAAATGTAGA---------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------------
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
S-------S---------------------S-S-----------------------------------------S-----
---------------S--------------------------------SSSSSSSS-SSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSS---------------------------------------------------S-
--S----------------S-------S-----------------S----------------------------------
----------------------------------------------------------------S--------------S
------------S------------------------------------------SSS---------------S------
--S---S------------------S---S-SS---S---------------------------------S---------
--------------------------------------------------------------------------------
------------------------S-------------------------------------------------------
----S-----------S---------------------------------------------------------------
--S-----------------------------------------------------------------------------
------------------------SS-----S------S-------SSS-------------------------------
-------------------------------------------------SS------------S----------------
------------------SSSSSSSSSSSSSSSSSSSSSSS--------------------------------------S
SSSSSSSSSS-----S-----S---S--------------S------------SSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_292
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------GGCGCAACTGGTCATCTAGT----------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------------
>reverse_1704
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-----------------------CGATCCCATTGAGATGCCGA-------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------------
