>input_sequence_69546
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------------------------------------ACACCATGCAGCTCCTACCGGCCTTCATCTTCGCCCTAGC
CCTAGTCCTTATGGCGTCAGCTGCGGCAACGGAGACGATCCACCTCAAGTTCTACATGCATGACATCGTCACCGGCGGGC
CATCGAGTCCAGCAACAGCGGTGCAAGTCATCAAAGGTGTGGTGCCGCTGGCCAACGACCCCACCACCTACTTCGGCGAC
ATGTACGTCATCGACGACCTGCTGACGGAGGGCCCAGACGCGGCGTCCCCCGCCGTCGGCAGGGCACAGGGGTTCTTCCA
GTTCGCGTCGATGACAGAGTACGCGCTGCTGCTCACTGCCAATTTCGTGTTCACGGCAGGGAGTCAAAACGGCAGCTCCG
TGGCCGTACTCTCCAGGGACGTCATCTTCGACAGTGTCAGGGAGTTGCCGATCGTAGGCGGCACTGGCGGCCTCCGTGGT
GCGACTGGGTACGGTCTGCTCCGGACACACTCGGTCAACACCACCACCAGGAACGCGGTGCTCACGATTGATATGTACCT
CCGCGTGTAGGTGCATGCAGACCCTAGGTCTGAACTTACTTTCATGCATCTGGTGGGTGCTTGCATAAAAGAAGCATCTA
CGATTAATTTGTGTCAT------------TGTGTGTGTGTGTGTGTGTCATGGTCCGGAATGTCTTCAGCATGTCAGTGC
GTCCGATTTATTTGTGTAGCTTCCAGGTGTAAGTGTTATAATGTGAGTTCATGATTGATGGGGATTTTTATTAAAATAAA
TGAGGTACAACAGT------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------
>chr2A_1_TraesCS2A01G053600
AACTTAGACCTACTTTGTGCATCGACCAAGGTGACTTAATGAAGGTTTGGATGAAATCATGAAACAATATGATGTAATGA
AGATATTTGTTGCCCGCATTCCATATCAGTTTCAGTTGTTCCGCTTGAAGTTGGCCCTACCTCTACATACTACCATCGCA
GCAAGCTCACCCTCGGCTCAGCTTCTAGATGCGATACATATGAGCATTGGAAAAGGCCATTGAAAGACATTGATACATAT
ATTCAATATTTGAACAAACTTAGATGATTATTTGATCCCCAAAGAAATCAGTAGAGAACATGTTTTGAGTATACGAAGTT
GTTACCTTCAATTATGCACCAGAATAAGATTGAAAAGGTCTTGAACATTCAACCATGAATGTATCAGATAAGGCGGCATT
CAAACCATGACTAGCTTGCATACCATTAAATTACATACGTCAATCTCATTGGGAAGATTTTGCATACTATATATACAGAA
ACATAATTTGCAGAACTTAGATAAATAAAACACCTACAAAATTAAAGTAACAAGAAATGAACATCACCTAGAAAATTACA
GTTCAATCAATTACACTCGGGCACTGGGGCTCATTCGCTATTCCTTGTACGAAAAATACAGTGCCCATTCTTCGTGATGT
AACTCATCAATAATCATGGCTGCCCAAGTAGTTGACATGCCCAACAGTTGACTTCACATCACTTGCATAGATGCCTCCTC
ATCATTTTGCACTCTACTTCACCGTCCAGCTCATCATTGGCTGTATTTATAGTTGCACTATTCAATTATTGTTCTATTTC
TTAAGATTAGATACATGATACTCAAGTACACCTTTGTGTAAAAATGAATTCACTTATCATGGGCACATGTTCCCGGCTGC
TTTGCCGCCGGGTCCTTTCCAGTTTGCCTATATAAAGGGTTCGAGGCAGAGCGTATACAGATAGAGTCAATGCACGCACA
TCTGTCCTATACATCCTAGTACAAACCATGGCCATCAGGCACACCATGCAGCTCCTACCGGCCTTCATCTTCGCCCTAGC
CCTAGTCCTTATGGCGTCAGCTGCGGCAACGGAGACGATCCACCTCAAGTTCTACATGCATGACATCGTCACCGGCGGGC
CATCGAGTCCAGCAACAGCGGTGCAAGTCATCAAAGGTGTGGTGCCGCTGGCCAACGACCCCACCACCTACTTCGGCGAC
ATGTACGTCATCGACGACCTGCTGACGGAGGGCCCAGACGCGGCGTCCCCCGCCGTCGGCAGGGCACAGGGGTTCTTCCA
GTTCGCGTCGATGACAGAGTACGCGCTGCTGCTCACTGCCAATTTCGTGTTCACGGCAGGGAGTCAAAACGGCAGCTCCG
TGGCCGTACTCTCCAGGGACGTCATCTTCGACAGTGTCAGGGAGTTGCCGATCGTAGGCGGCACTGGCGGCCTCCGTGGT
GCGACTGGGTACGGTCTGCTCCGGACACACTCGGTCAACACCACCACCAGGAACGCGGTGCTCACGATTGATATGTACCT
CCGCGTGTAGGTGCATGCAGACCCTAGGTCTGAACTTACTTTCATGCATCTGGTGGGTGCTTGCATAAAAGAAGCATCTA
CGATTAATTTGTGTCAT------------TGTGTGTGTGTGTGTGTGTCATGGTCCGGAATGTCTTCAGCATGTCAGTGC
GTCCGATTTATTTGTGTAGCTTCCAGGTGTAAGTGTTATAATGTGAGTTCATGATTGATGGGGATTTTTATTAAAATAAA
TGAGGTACAACAGTCTCGTTTGTTTACTGTGGTTGAAATCTTCGATGT--------------------------------
----GGCGTGCTGGTGAGGATGTGTCACAGCTGGAATATGGTGTATATGGTACGGGGCGATGCAAGAATATCGGTTTTTA
TAGGATGTGCATTTCCACATTTTCTTACAAAACCCCCTATCTATGCGAGATAAAAGG---AATTAAAGGGTTTTTGTAAA
CATGGGTGCATTGTGACAAAAATCAAG---------------------------AAAGTCTGACACTTTGTGCCTTCAAA
AATGCACAAATTTATATAGGTGGTTCAGTTTTATGTGTTGGAACGACATCTGTGGAGCTTGTGAC-AAAAATAAAATTAC
TGCTCAAACATTTGAGCACTCATTTTGTTTTCTTTTTGTCAGGAGCCCCTCAGCTCAGATATCATTTCGCCTTCGAATTT
TGCAAGCACCAAAAACATTTGCGCATCTTTATATCCAGTAACTTTCATAATAAAACAAAAACATTTTGTCCG-ATTTCAG
TGTTGAAGCTGCGTGCAATGCACCCAGGTTCAGCTACAACTTCTCCATTAATGGTGCCACCAGGCAATAAAATGGAGTTC
TACGCAATATTTGTGGCAACCTCATATTTCTTAAGACCTACTAGTCCTCTGTTTTTTTAACCAAGATAGTTTGCACGTTA
TTATATCCTCCTCATAGCG----TCATGAATTAGGATTCAGAAGTCAGAACGAATTACATTGTTGAGGGATATTTTGTTA
CGCACATCGGATACTTATTAGTCAGGTTAATTTATCAAACTAAAGGAGAGCTGACGTAGATATCTAGGTTAGTAATGTGA
AGTCAACTGTTAGAAAT----------------GTCAACTAACTTGGGCATCCCCGATGAGTTAGGTCATGAAGAATCTT
CATTTTATTTTAGTTTTTTCACATGGCTGTGCCTATTTCTCATAGAGGCGATATAGAATTCCAAATCTATTTAGATATCA
TATATATATATATATATATATATATATATATATATATATAATTTCACCTACAACAAATTATG
>chr2B_559
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------------CA
GTTCAATCAATTATACTCGGGAACTAGGGCT-ATTCCCTATTCCTTGTACGAAAAATACAGGGCCCATTCTTAATGATGT
AACTCATCAATAATCATGGCTGCCCAAGTAGTTGACATGCCCAACAGTTGACTTCACATAACTTACATAGATGCCTCCTC
ATCATTT-GCGCTCTAATTCACCGTCCACCTCATCATGGCTGCCCGTAGTAGATGCACTATTCAATTATTGTTCTTTTTT
TTAATATTAGAAAGATGAGACTCAAATACACCTTTGTGTAAAAATGAATGCACTTAACATGGGCGCACGTTCCCGGCTGC
TTTGCCGCCGGGTCCTTTCCAGTTTTCCTATATAAAGGGTACGAGGCAGAGCGTGTAACCATAGAATCAGCTCATGCACA
TATGTCCAATACATCCTAGTACAAGCCATGGCCATCAAGCACACCATGCAGCTCCTACCAGCCTTGGTCTTCGCTCTAGC
CCTTGTCCTTAGGGCATCAGCAGATGCAACGGAGACGATCCACCTCAAGTTCTACATGCATGACATCATCACTGGCGGGC
CGTCGACTCCAGCAACAGCTGTGCAAGTCATCAAAGGTGTGGTGCCGCTGGCCAACGACCCCACCACCCACTTCGGTGAC
ATGTATGTCATCGACGACCTGCTGACGGAGGGGCCGGACGCAGCGTCCCCCGCCGTCGGCAGGGCACAGGGCTTCTTCCA
GTTCGCGTCGATGACGGAGTACGCGCTGCTGCTCACTGCCAACTTCGTGTTCACGGCAGGGAGCCATAACGGGAGCTCTG
TGGCCGTGCTCTCAAGGGACGTCATCTTCGATACCGTCAGGGAGCTCCCGATCGTGGGCGGCACTGGCGGGCTCCGTGGT
GCGACCGGGTACGGTCTGCTCCGGACACACTCCGCCAACACCACCACCAGGAACGCGGTGCTCAAGATTGATATGTACCT
GCGCGTGTAGGTGCAT----ACCATAGGTCTGAACATATTTCCATGCATCTGATGGGTGCTTGCATAAAAAAA-CATCCA
CGATTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTATGGTCTGGGATGTCTTCAGCATGTCAGTGC
GTCCGATTTATATGTTTAGGTTCCAGGTCGAAGTGT--TAATGCGAGTTCATGATTGATGGAGATTTTTGTTAAAATAAA
TGAGGTACAACAGTCTCGTTTGTTTGCTGTCATTGAAATTTTCCTTCACTCTTTGGGAGGAACAAGAGGCCCGATCTTTG
AAAACATGGGT-------------GCACAGCCGGAACATCGTGTATATAGTACGGGGCAATGCAAGAATTTCGG------
--------------CCAGATTTGCTTACAAAACCACCCAATTATGCGAGATAAAAGGAATAATTAAAGGGCTTTTGAAAA
CATGGGTGCATTGCACCATTGATGAACAGT-----------------------AAAATTCTCACATTTTGTGCCTTCAAA
GGTGCACAAATTTATTAAGGTGCTTGAATTTTGTATGTCGGAATGTCATCTGTGGACCTTGTGACAAAAAATCAAATTAG
TGCTCGAACTTTTGGGCACTCATTTTGTTTTCCTTTTGTCAGGAGCCCCTCAGG-----TCTCATTTCGCCTTCAAATTT
TGCAAGCACCTAAAACATTTTTGCATCTTCAAATCCAATAAGTTTCATAAAAAAATG----CATTTTGTTCAAATTTTGC
TGTTCACCATGGGTGCAATGCAACCAGCTTCGGCTAGAACTTCTCCATTGATGGTGCTAACAGGCAATAAACTGGAGTTC
TCCAC-ATAGTTATGGCAACCTCATCTCTCTTAAGACCTACTTTGCAC-------------------------------A
TTATATCCTCGTCGTACCGTAGTTCATGAATTAGGATTCAGAAGTCAGAACGAATTACATTGTTGAGGGATATTCTGTTA
TGCACATCGGAAGCTTGCTAGTCAGGTTAATTTATCAAACTAAAGGACAGCTGATGTAGATATCTAGGTTAGTGATGTGA
AGTCAACTGTTAGAAATGTCAACTTGTTCTTACGTCAACTAACTTGGGCATCCCAGATGAGTTACGTCATAAAGAATCTT
CATTGTATTTTAATTTTT--------------------------------------------------------------
--------------------------------------------------------------
>chrUn_607
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------------------------------------------GTACGAAAAATACAGGGCCCATTCTTCATGATGT
AACTCATCAATAATCATGGCTGCCCAAGTAGTT----------------GACTTCACATAACTTACATAGATGCCTCCTC
ATCATTT-GCGCTCTAATTCACCGTCCACCTTATCATGGCTGCCCAT-GTAGATGCACTATTCAATTATTGTTCTATGTT
TTAATATTAGAAAGATGAGACTCAAATACACCTTTGTGTAAAAATGAATGCACTTATCGTGGGCGCACGTTCCCTGCTGC
TTTGCCGCC-GGTCCTTTCCAGTTTGCCTATATAAAGGGTTCGAGCCAGAGCATGTAAACATAGAATCAACTCATGCACA
TCTGCCCTATACATCCTAGTACAAGCCATGGCCGTCAAGCACACCATGCAGCTCCTACCAGCCTTTGTCTTCGCCCTAGC
CCTTGTCCTTAGGGCATCAGCAGCAGCAGCGGAGACGATCCACCTCAAGTTCTACATGCATGACATCGTGACTGGC----
-----AGCCCAGCAACAGCAGTGCAAGTCATCAAAGGCGTGGTGCCGCTGGCAAACGACCCCACCACCTACTTCGGCGAC
ATGTATGTCATCGACGACCTGCTGACGGAGGGGCCGGACGCAGCGTCCCCCGCCGTCGGCAGGGCACAGGGCTTCTTCCA
GTTCGCGTCGATGACGGAGTACGCGCTGCTGCTCACTGCCAACTTCGTGTTCACGGCGGGGAGCCATAACGGGAGCTCTG
TGGCCGTGCTCTCAAGGGACGTCATCTTCGATACCGTCAGGGAGCTGCCGATCGTGGGCGGCACTGGCGGGCTCCGTGGT
GCGACCGGGTACGGTCTGCTCCGGACACACTCCGCCAACACCACCACCAGGAACGCGGTGCTCAAGATTGATATGTACCT
GCGCGTGTAGGTGCA----GACCATAGGTCTGAACTTACTTTCATGCATCTGGTGGGTGCTTGCATAAAAGAAGCATCGA
CGATT------------------TGTGTGTGTGTGTGTGTGTGTGTGTTATGGCCCGGGATGTCTTCAGCATGTCAGCGC
GTCTGATTTTTTTGTTTAGCTTCCTGGTCGAAGTGT--TAATGCGAGTTCATGATTGATGGAGATTTTTATTAAAATAAA
TGAGGTACAACAGTCTCGTTTGTTTTCTGTCGTAGACATTTTCCTCCACTCTCTGCGAGGCACAAGAGGCCCCATAATTG
AACCGGCATGCCGGTGAGGACGTGGCACAGCCTGAACATCGTGTATATGGTACGGGGCGATGCAAGAATATCGGTTTTTA
TAGGACGTGCATTTCCAGATTTTCTTACAAAAACCCCTATTTATACCAGATAAAAGG---AATTAAAGGGTTTTTGTAAA
CATGGCTGCAATGCACCATCGATGAACAGCAAAATTAAAAACCAAACGATCAAAAAAGTCTGACACTTTGTGCCTTCAAA
GATGCACAAATTATTT-AGTTGCTTGAGTTTTATATGTTCGAATGACATCTGTGGAACTTCTGATAAAAAATCAAATTAG
TGCTCAAACTTTTGAGCACTCATTTTGTTTTCATTTTGTCAGGAGCCCCTTG-----GATCTTATTTCGCCTTCAAATTT
TGTAAGCACCTAAAACATTTGTGCATCTTCAAATCCAGTAAGTTTCATAAAAA--TG----CATTTTGTTTG-ATTTTAC
TGTTCAACATGGGTGCAATGCAACCAGCTTCAGCTACAACTTCCCCATTGATGGTGCCAACAGGCAATAAACTGTAGTTC
TC-AC-ATATTTATGGCAACCTCATCTTTCTTAAGACCTACTTTGCTCG-------------------------------
TTATATCCTCGTCATACCGCAGTTCATGAATTAGGATTCAGAAGTCAGAACGAATTACATTGTTGAGGGATATTCTGTTA
TGCACATTGGATGCCTGCTAGTCAGGTTAGTTTATCAAACTAAAGGAGCGCTGATGTAGATATCTAGGTTAGTGATGTGA
AGTCAACGGTTAGAAATGTCAACTT----------------ACTTGGGCATCCCCGATGAGTTACGTCATCAAGAATCTT
CATTATATTTTAGTTTTT--------------------------------------------------------------
--------------------------------------------------------------
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--
-------------S-------S---S-----S----S------------------------S-----------S------
-----------------------------------------------------------S----S---------------
-------S--S-----S-----------S--------S-SSSSSSS-SS---S--------------------------S
----S------S-S----S------S-----------------------S--------------S--S------------
------------------------------------------------------S--S-S-----S----SS--S-----
------------------------S------------S---------------------S-----SS-------------
---S-------S---S-----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---------------SSS----S------------------------------------------------------S-
-----SS-S-----SSS-------------------------------S---------S---------------------
---------------S------------SS------SS-----S-----------------S------------------
-------------------------S----S--------S---SS-SS--------------------------------
-----------S--------S---S------S----S--S----------------------------------------
-----S-----------S----------------------S---------------------------------------
-------------SSS--SSS--S--S-----------------------------------------------------
S--------------SS-----S--S--------S--------S------------S---------------S------S
---------S----------------------S--------------------SSSS---S-------------S-----
----------S----------S-------S-S---------S--------S----SSSSSS--------S-------S-S
----S--SS--S----------S----S---------------------S---------S-----------S--------
-S-S-S------S------------S----------------SSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-
----------S-----S---------------------------------------------------------S-----
S-----------S---SS------------------------------------S------------------S------
----------------------------------------------------------------S-----S---------
----S-------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_142
--------------------------------------------------------------------------------
------------------------------------------GCTTGAAGTTGGCCCTACCT------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------
>reverse_1852
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-----------TGGTGAGGATGTGTCACAGC-------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------
