>input_sequence_82732
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------ATGGGCTGCTGGTGGGAGCGCCTCGTGCTGCC
GGTGCGCAGGGCGTGGCTCGGCGTCGCCTCCCGCTTCGGCGTGCGCCAGTCCGGTAAGGCCGCGCGCCGCTAGCTCGCCG
TTTCCCGACGTGCTGCAGAGGCTT--------------------CCTAGGCTGACTCCGGCGTTGCTTTTTGGTTGCTTG
TTGATTTGCAGGGCTGTGGAGGCTCCGGCAGGAGGTGAGCACGTGCGAGTACGAGGACGTGCGCGTGATGTGGGAGATGC
TGAGCCGCACCGCGACGGCGCCGCCGCCGCCGGCGGCCAGGCGCCACAGCAGGTTCCGGCAGCCGAGGCCGTGGGCCGAC
AGGCTCCGCCTCTGCCGGGACATCTAG-----------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------
>chr4A_1_TraesCS4A01G049100
CCGGATAAGCTCACGACCATGCCCCAGTTTTGTGGTGACCCCGTCAATCTAAATTGCTGTGTCAGCTCAACAACCTAGAG
ATGCTCATAAAAATCGAATGTATGTGCATGTCTACATTCATAGAAGTGAGTATGTGTTTGTAAGTGAGCCTATGTGACAT
TG----------------------CGCACCACCCCGAAGCGCCAATACAGTCAGACATTTGGTTACCAGAAAGTTATCTA
ACATTTGCAGTGGAAAGACCTAGATTCATCCAACGGAGATCCACGGGAGCTTTAAAATAACCATCGCAGCTCATCTTCAG
CCATCAACGGTGTCACGGTGACCCCATTCCTCTA-CCTCGAGCTCTGCCGCTGCGCCACGGATGCCGAGTGACGAGGCGG
TGCATCGTCATCGCTCGACGATGAATAGTACGAAATATCTGA-AAAACCAATCATCAACGAATAAAAATCAGTGTTGATG
AATAAGAAAA----------------------------------------------------------------------
--------------------------------------------------------------------------------
------TATCTGGAAAACCCGTCAGCACCAAATAAAAAATCTCGCCGTTGCGAGTTACTAGTAGCAGCAGCTGACAAGGA
CCCAATTGCTGAGCTGAGCTCGCGCGGGCGACCTAATTCCATCCACTGACACGCCCCGTACGTAACCACCGCTCAACCGC
CCGCCACATACCCGCA-------------------------CTCCCACGGGCCCCGCTTTATCAGGACCCCGCGCCTACG
TGTGGGTGGGTGTGGCACGCCGCCTACGGCATTCCGGCACGTCCCGGCCGCCCCCCGTTAACAAACCCCCGCCACCCGCG
TCCGCTACCCCGTCGCTTGCACCGCGGGCCCGCCATAGACCACCGCGCG---------CGTCAGTGCCCTGGAAAATCGA
AGCATCGGTGCGTGC--------------------------CCCCGCGTGTACAAATACGAGCGCCCAGAAGACGACCGG
AGGCCCCGGTGTCATAACCCGGGAGTGCCAAGAGGACTGGGTAGAAGGGAAGGGGAGCCTCCGAGGGTCTGGTCTTGTTG
CCTACGGCGGTGCAA--------ATCTGACGACCGCCCGCCGCCGGCGATGGGCTGCTGGTGGGAGCGCCTCGTGCTGCC
GGTGCGCAGGGCGTGGCTCGGCGTCGCCTCCCGCTTCGGCGTGCGCCAGTCCGGTAAGGCCGCGCGCCGCTAGCTCGCCG
TTTCCCGACGTGCTGCAGAGGCTT--------------------CCTAGGCTGACTCCGGCGTTGCTTTTTGGTTGCTTG
TTGATTTGCAGGGCTGTGGAGGCTCCGGCAGGAGGTGAGCACGTGCGAGTACGAGGACGTGCGCGTGATGTGGGAGATGC
TGAGCCGCACCGCGACGGCGCCGCCGCCGCCGGCGGCCAGGCGCCACAGCAGGTTCCGGCAGCCGAGGCCGTGGGCCGAC
AGGCTCCGCCTCTGCCGGGACATCTAGACCAGGACCGTCGACCGGGGGCCGCCGCGCGCTTGCTTGCTTGCGGCTTACTG
CTTGGTCTTGGTGGCCTGGTTAAT-TAGCTTCTTGATCTGTATTGACCT-CCCTTCCCTTCCATGGGTTCTCGATCTTTT
TCCTCTGCTACCGCCGCTGTATGTATGCAC---GCTGCTTGGGGCTCTGAGGTGTACTCCATTCCTCCCCGTGTATCCGG
TCGATCCGCTTGTAGATGGGTGATACCTCTGGGGTATGTGAATGAACAGAGCTGTTCCGTTCGAATACATCTTACACGAC
TCCTTTCTTCTTTGCC-----TGCAAACTTTGATCTACCACAAATATTTA------------------------------
--TGTTCTGCAGTCTGTTTGTTCATGCTTCAGATAGACAAACCAGCCTGTTTGTTCAGGCTTCAGATA--GGCAAAACCT
AGTATCAGCAGGGTGGTGCCCTCGAGTTCAGAGAACTCGTCAGGTTTGATGCTCCACCGG-ACTGGAATATCCTAGACCC
AGTTGTTGGTTGGAAAGTTATTTCTGCCGACCTGCCAATTAATTAGCAGCACCAAGATTT-GACGTCTCAG-------TC
CTGACCCGTCCGTCTCAATACGAGCTCGATCCGCCGTGCTGTGGTTTTCATTGCCCATCATCAACGCCTCCGGTGATCCG
ATCACCACACCACACACGGACACTGTACCGGACGCAAAACAACCGATAATAATTGCCT-----------CCAACCAATAT
CTACCTTGACAATCTCCCGTGAACCGCACTTCAACTAACCTA---AGATGGCCACTAGGACTGTCGACCAAGCAATGTGA
GTTAGAGGGTGCTTGGATACAAGGGACTATTTTTAGTCTGACTAAAAATAGTCTCTTTTAGAGGCTAAAGTTCCAAGCAC
CCCTGACTAAAGAGAGGCTAGGACTAGTCTTGAGGCTAAAATCTTTTAGTCATGGGAAACCTACTAAAATATGTATTAGC
TCTCTCTCTCCTCATTTAATTCCTCTCCTTAGTTCTGGATTGGAGGGTTTGGAG
>chr4D_3
--GGATCAACTCAGGACCATGCCACGGTTTTGTGGTGCCTTCGTCAATCTAAGCTGTTGTGTGAGCTCAGTAACTTAGAG
GTGCTCATAAAGATCAAATGTACGTGCATGT--ACGTTCATAGAA----GTATGTGTGTATAAATGAGCGTCTATGGTAG
TATCGTGTTAAAAGAAAATCATGACGCACCATCCCGAAGCGCCAATACAGTCAGACATTTGGTTAGCAGAGAGTTATCTA
ACATCCGCAGTCGAAAGACCTAGATTCATCCAACAGTGATGCACCGGAGCTTTAAAATAACCATCGCAGCTCATCTTTAG
CCATCAACGT--------TGACCAAATTACTCTACCCTCGAGCTCTGCCGTTGCGCCACACATGCCGAGTGACGAGGCAG
TGCATCGTCATGGATCGACGATGAATAA---GAAATATCTGG-AAAACCCATCATCAACAAATAAAAATCAGTGTTGATG
AATAAGAAATACTCCCTCCGTTCCTAAATATAAGTCTTTGTAGAGTTTTCACTATAAACCACATACGGATGTATATAGAT
GCATTTTAAGTGTAGATTCATTCATTTTGCACCGTATGTAGTCCACCTAGTGAAATCTCTACAAAGACTTACATTTAGGA
ACGGAGTATCTGGAAAACCCGTCAGCAACAAATAAAAAATCTCGCCGTTGCGAATTACTAGCAGCAGCAGGTGACAAGGA
CCCAA-----GAGCTGGGCTCGCGCGGGCGACCTAACTCCATCCACTGGCACGCCCCGTACGTAACCACCGCTCAACCGC
CCGCCACATACCCCCACTGACAGCAGTGCGGATATGTGAATCTGCCAGGGGCCGCGCTTTATCAGGACCCCGCGCCTACG
T----------GTGGCACGCCGCCTACGGCATTCCGGCACGTGCCGGCCGCCCCCCGTTAACAAACTCCCACCACCCGCG
TCCGCTACCCCGTCGCTTGCACCACGGCCCCACCATAGACCACCGCGTCGGTCCGGAACGTCAGTGTCCTGGAAAATCGA
AGCATCGGCGCGTGCGTGCGTGCCCGGGCTTCCACCCCC-GCCCCGCGTGTACAAATACGAGCGCCCAGAAGAGGGCCGG
AGACCCCGGTGTCATAACC-GGCAGTGCGAAGAGGACTGACTA-----GAAGCGGTGCCTCTGAGGGTCTGGTCTT-TTG
TCTACGGCGGTGCATATCTGAGTATCTGACGACCGCCCGCCGCCGGCGATGGGCTGCTGGTGGGAGCGCCTCGTGCTGCC
GGTGCGAAGGGCGTGGCTCGGCGTCGCCTCCCGCTTCGGTGTGCGCCAGTCCGGTAAGGCCGCCCGCCGCTAGCTCACCG
TTCAGCCACATGCTGCAGAGGCTTCCCTCGTCGGTCCACCTAGTCCTGGGCTGACTCCGGCGTCGCTGGTTGCTTTTTTG
G----TTGCAGGGCTGTGGAGGCTCCGGCAGGAGGTGAGCACGTGCGAGTACGAGGACGTGCGCGTGATGTGGGAGATGC
TGAGCCGCACCGCGTCGGCGCCGCCGGCGCCGGCGACCAGGCGCCACAGCAGCTTCCGGCAGCCGCGGCCGTGGGCCGAC
AGGCTCCGCCTCTGCCGGGACATCTAGACTGGGACCGTCGACCGGGGGCCGCCGCTTGCTTGCTTGCTTGCGGCTTACTG
CTTGGTCTTG-TGTCCTGGTTAATCTAGCTTCTTGATCTGTATTGACCTTCCCTTCCCTTCCATGGGTTCTCGATCTTTT
TCCTCTGCTACCGCCGC----TGTATGTAC---GCTGCTTGGGGCTCTGAGGTGTACTCCATTCCTCCCCGTGTATCCGG
TCGATCCGCATGTAGATGGGTGATACCTCTGGGGTATGTGAATGAACAGAGCTGTTTCGTTCGAATACATATTACACGTC
TCCTTTCTTCTTTGCTTTCCTTGCACACTTTGATCTACTAGAAATATTCAGCATGCGAATGAAAACTTCAGTCAATCCTT
TGTGTTCCGCAGC--------------------------------CCTGTTTGTTCAGGCTTCAGATATAGACAAACCCT
ACTATCAGCAA---GGTGCCCTCGGGTTCAGGGAACTCATCAGGTTTGATGCTCCACTGG-ACTGGAATATCCTAGACCC
AGTTGTTGGTTGGAAAGTTATTTCTGCCGACCTACCAATTAATTAGTAGCACCAAGATTTTGACGTCTCAGTCCTGACTC
CTGACCCGTCCGTCTCCATACGAGCCCGATGCGCCGTGCTGTAGTTTTCATTGCCCATCATCAACGCCTCCGGTGATCCG
ATCACCACACCACACA--GACACTGTACCGGACGCAAAACAACCGATAATAATTGCCT-----------CCAACCAATAT
CTATC-TGACAATCTCCCGTGAACCGCACTTCAACTAACCTA---AGATGACTGCAATGGCTGTCGACCAAGGAAT----
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------
>chr4B_166
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
---------------------------ACCACCCCGAAGCGCCAATACAGTCAGGCATTTGGTTACCAGAAAGTTATCTA
ACATTTGCAGTCGAAAGACCTAGATTCATCCAACAGCGATGCACGGGAGCTTTAAAATAACCATCGCAGCTCATCTTTAG
CCATCAAGGGTGTCACGGTGACCCCATTGCTCTA-CCTCGAGCTCTGCCGCAGCGCCACACATGCCGGGTGACGAGGCAG
CGCATCGTCATCGATCGACGATGAGTAG---GAAATATCACGCAAAACCCATCATCAACAAATAAAAATCAGTGTTG---
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------CGAGTTACTCCTAT---CAGCTGACAAGGA
CCCAA-----GAGCTGAGCTCGCGCGGGCGACCTAACTCCATCCACTGACACGCCCCGTACGTAACC-------------
----------------------------------------------------------------------------TACG
TGTGGCA-----TGGCACGCCGCCTACGGCATTCCGGCACGTGCCGGCCGCCCCCGGTTAACAAACTCCCACCACCCGCG
TCCGCTACCCTGTCGCTTGCACCGCGGCCCCACCATAGACCACCGCGCCGGCCCGCAACGTCAGTGCCCTGGAAAATCGA
AGCATCGGTGCGTGCGTGCGTGCCCGGGCTTCCACCCCCCGCCCCGCGTGTACAAATACGAGCTCCGAGCAGAGGACCGA
AGGCCCCGGTGTCATAACC-GGGAGCGCGAAGAGGACTGACTA-----GAAGGGGAGCCTCCGAGGGTCTGGTCTT-TTG
TCTACGGCGGTGCAA--------ATCTGACGACCGCCCGCTGCCGGCGATGGGCTGCTGGTGGGAGCGCCTCGTACTGCC
GGTGCGCAGGGCGTGGCTCGGCGTCGCCTCCCGCTTCGGTGTGCGCCAGTCCGGTAAGGCCGCGCGCCGCTAGCTCACCG
TTCCGCGACATGCTGCAGAGGCTT--------------------CCTAGGCTGACTCCGGCGTCGCTGGTTGCTTTTT-G
G----TTGCAGGGCTGTGGAGGCTCCGGCAGGAGGTGAGCACGTGCGAGTACGAGGACGTGCGCGTGATGTGGGAGATGC
TGAGCCGCACCGCGTCCGCGCCGCCGCCGCCGCCGGCAAGGCGCCACAGCAGGTTCCGGCAGCCGCGGCCGTGGGCCGAC
AGGCTCCGCCTCTGCCGGGACATCTAGGCTAGGACCGTCGACCGGGGGCCGCCGCGC----GCTTGCTTGCGGCTTACTG
CTTGGTCTTGATGTCCTGGTTAAT-TAGCTTCTTGATCTGTATTGACCTTCCCTTCCAT------GGCTCTCGATCTTTT
TCCTCTGCTACTGCCAC----TGTATGTATGCTGCTGCTTGGGGCTCTGAGGTGTACTCCATTCCTCCCCGTGTATCCGG
TCGATCTGCATGTAGATGGGTGATACCTCTGGGGTATGTGAATGAACAGAGCTGTTTCGTTCGAATACATCTTACACGAC
TCCTTTCTTCTTTGCTT-----GCGAACTTTGATCTGCTACAAATATTTAGCATGCGAACGTAAACTTCAGTTAAACCTT
TGTGTTCTGCAGCCTGTTTGTTCATGCTTCAGATAGACACACCAGCCTGTTCGTTCAGGCTTCAGATG--GTCAAAACGT
ACAACCAGCAG---GGTGCCCTCGAGTTCAGAGAACTCATCAGGTTTGATGCTCCTAGAGCACTAGAATATCCTAGACCC
AGTTGTTGGTTGGAAAGTTATTTCTGCCGACCTGCCAATTAATTAGTAGCACCAAGATTT-GACGTCTCAG-------TC
CTGACCCGTCCGTCTCAATACGAGCTCGATGCGCCGTGCTGTGGTTTTCATTGCCCATCAAAGCA---TCCGGTGATCCG
ATCACCACACCACACACAGACACTGTACCGGACGCAAAACAACCGATAATAATTGCCTCTCTTTTCTCCCCAACCAATAT
CTATCTTGACAATCTCCCTTGAACCGCACTTCAGCTAACCTAGTAAGATGACTGCAACGGCTGTCGACCAAGCAATATGA
GTTAG---------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------
>SNPs
SS----S-S----S---------S-S-----------S-SS-----------SS--S-----S------SS---S-----
S----------S---S------S--------SS--S---------SSSS--------S-S---S-----S-S-S--SS-S
-S------------------------------------------------------------------------------
-----------S----------------------S-S---S------------------------------------S--
----------------------------S------------------------------SS-----------------S-
-------------S--------------SSS----------S-------S---------S--------------------
---------S----------------------------------------------------------------------
--------------------------------------------------------------------------------
---------------------------S----------------------------------------------------
-----SSSSS--------------------------S-------------------------------------------
-------------S-----------------------------S---S-----S--------------------------
-----SSSSSS-------------------------------S-----------------------S---S---------
---------------------------S---S----------------S-------------------------------
-------------------------------------------------------------------------S------
-------------------S--------S----------SS--SSSSS----------------------------S---
S-------------------------------------------------------------------------------
---------------------------------------S------------------------------------S---
--S-S----S-----------------------------------------------------S---SS---S--SS---
SSSSS---------------------------------------------------------------------------
--------------S--------------------------------------------------S--------------
-----------------------------S--------------------------------------------------
----------S--S------------------------------------------------------------------
-----------------SSSS------S----------------------------------------------------
---------S----------------------------------------------S-----------------------
---------------S----------------------S-----------------------------------------
------------S--------------------------S-------------------------------S--------
-S---------SSS------------------------S------------------S----------------------
----------------------------------------------S---------------------------------
------------------------------S-------------------------------------------------
-----------------S--------------------------------------------------------------
---S----------------------------------------------S-SS-S-S-S----------------S---
-----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_38
------------------ATGCCCCAGTTTTGTGGTGA------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------
>reverse_1441
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
TTGATTTGCAGGGCTGTGGA------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------
>forward_1165
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-------------------------TGCCAAGAGGACTGGGTAGA-----------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------
>reverse_2548
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-------------------------------------------------------------------AAGTTCCAAGCAC
CCCTGAC-------------------------------------------------------------------------
------------------------------------------------------
