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MatrixPlot 1.2: Fasta format for nucleotides

Introduction Data format User matrix Mutual Nucl Mutual Prot Dist matrix

For the fasta format each line has to begin with a ">" followed by the sequence name (no spaces allowed). The sequence is displayed on the following lines. The letters for nucleotide sequences are A, C, G , U, T and - to indicate gaps. The letters are always to be specified to the Inform program. (The sequences here are from Samuelsson and Zwieb, Nucl. Acids Res. 27 pp 169-170, 1999.)


>MET.JAN.
GGUGUGCAUGGcua-gGCCgGGGGGuuGGGCG-UCCCCuguaaCCCGa-a-auCGC
CCuuaugCGGGGGCc-g-aaaaCUUGGGggcGGCAUGUCcucCAGUCCUUCCU---UCCCA
GAcUCCUcgaugagGUCUCGuCcCGUGGgGCUcggCG-guGGGGG-agCAUCUCC
UguagGGGAGAUGuaacCCCCU-uu-acCUGCCgaaccCCGccaggCCCggaaGGGagcaaCGGu
aGGCAGgacg-ucGGCgcUCACGgGggugCGGGACggagaAGGAaUCUGGGggcg--
-AGGGA-GGACUGgagGACAUGCCcacCCCAAGGa-agCCAUGCACACCacuuuu
>MET.VOL.
--------UGGcua-gGCUgGGAGGuuAGGCG-UCUCCuguaaCUUGa-a-auCG
CCU-u-ugCGAGAGCc-g-aaaaCUUGGGggcGGCAuAAGuucCCAAAUUUCAU---UC
UUAAUUAGUAugucgacGUUUCGuCcUUUGGgGUaaGAug-guAAGAG-ac
uCUCUUUCuuaaGAAAGAGucaaaCUCUUuuc-guAuUUCgaaacCCGccaggCCCggaaGGG
agcaaCGGuaGAAuUuacU-uCgACgcUCAAGgGguagCGGGGCugagUACU
AAUUAAGGcaaa---AUGAG-AUUUGGu-gCUUuUGUCcacCCCAAGg
a-agCCA--------------
>MET.FER
--------AGGcua-gGCCgGGGGGuuAGGGG-UCCCCuguaaGC
GCa-a-auCCCCUauaugGCGCGGCc-g-aaGCCCAGGAggcGGCAAGACc-gCCA
GACAUCGG--cCUGAGGGUUAaAcaaugaaGCCUCGuCcCACAGgGCC-AUCG-guG
GCGA-ggGUCCAGCUggagGGCUGGACcuaaUCGCCuuu-gcUGCGGg-aac
GGGucaggCCCggaaGGGagcagCCCuaCCGCAgaCGgAUGGUgcUUGUGgG
ucaaCGGGGUggagUcUAACCCUCAGauca---CCGGU-GUCUGGu-gG
UCUUGUCcacUCCUGGGCgugCCU--------------
>MET.THE.
-------UGGGcua-gACCgGAGGGuuAGGGG-UCCUCuguaaGCGC
a-a-auCCCCUauacgGCGCGGUc-g-aaGUUCAGGGgacGGCuGAUCg-aCUGUU
UAUCGG--cCCUGCUGAUUGGugucgaaGCCUCGuccCGCAGgAUC-AGUG-guGAUGG-ggCCC
UGACUggagGGUCAGGGuaaaCCAUCuua-guCAUGGg-aacGGGucaggCC
UggaaAGGagcagCCCuaCCAUGgaCAgCUGAUgcUUGCGgauuaaCGGGGUggag
CCAGUCAGCGGGauca---CCGGU-AAAUGGa-aGGUCuGUCaacCCCUGA
ACgugCCCA-------------
>MET.ACE.
----UGAUGAGcua-gUCCgGGUAGccCGGCG-UUACCuguaaCCCGa-a-a
uCGCCGauaugCGGGGGAc-g-aaGCCaauGGaag-aUGcGUCa-aaGGGAU
UcCAG--cCUGuGAUCUCaacugagaaACCCCGuCcUGCuugGAU-GaUG-ca
GGUAUgugGACUUGcUggaaAaCAGGUCc-ucAUACCcua-acUGCGGaaaccG
GUcgaggCCCggaaGGGagcagACUcaCUGUGggCAacCGUCgcuuGCGgGg
ucgCGGGGUggagaaGAGAUUcCAGucua---CUGaA-AUCUCc--caGAUaC
AcgaCCugcGGUgugCUCAUCA-----------
>HAL.HAL.
--------GGAcua-gGCCgGGCGGuuUGGCU-CCGCCcgacaCCCGugag
acAGUCAuc-agCGGGGGCc-g-aacac-CGGGcgc-GUCCGaCc--gCCgCGGU
CGG--cCCCGGaaGCCaacggu-aaGCCUCGuCcGUCGGgGAC-GGCG-guCCGCg-gc
GuGCGCCCgcagGGGCGUuCcgucGUGG-uuc-gaCGGUGgcaacCCGccaggCACgga
aGUGagcagCGGacCACCGaaCGcCCGUCgcUCGACgGgucgCGGGGUggaga
aGGCgaCCGGGacuac--CCGGC-CGGGa---acGcCGGGCuacCCCGa---cug
UCCac------------
>ARC.FUL.
-----GGUGGGcua-gGCCgGGGGGuuCGGCG-UCCCCuguaaCCCGa-a-acC
GCCGauacgCGGGGGCc-g-aaGCC-gaGGGgagGCCUGUCa-agCGGGCGGCag--
cGGUUCCAGGCACcgcagagUCCUCGuCcCGGAGgGCC-GGCG-guUAUGgcCGGG
CuGCCCggagGGGCuGUCCGc-CAUA-uua-gcCGGGGggaacGGCccagg
CCCggaaGGGagcagGCUaaCCCCGgaCGaCCGGCgcUUCCGgGggugCGGG
GAggagGUGCCUGGGGCUucaa---GCCGC-CCGua----aGGCAGGUcgaC
CCgaGGCgugCCCACC-----------
>PYR.HOR.
--GGCGGCGGGcua-gGCCgGGGGGuuCGGCG-UCCCCuguaaCCGGa-a-acCG
CCGauaugCCGGGGCc-g-aaGCCCGAGGggc-GGuuCCCg-aaGCCGCCUCUgga
aGCCAGGGCCgAacgaugagUCCUCGuCcCGCGGgGUG-cCCG-guGGGGG-aGGCAC
GGCUgaagGGCCGUGCUaa-CCCCCuuu-ggGCCCCaaaccCCGcaaggCCCggaaGGGa
gcagCGGuaGGGGCcaCGGagCACgcUCGCGgGggugCGGGGAugaggUaGGC
CCUGGUgaaa---GGAGG-CGGUgg---aGGGuuCCcaCCCUCGGGCgugCCCGCCGCC--------
>THE.CEL.
--GGCGGCGGGcua-gGCCgGGGGGuuCGGCG-UCCCCuguaaCCGGa-a-acCG
UCGauacgCCGGGGCc-g-aaGCCCGGGGggc-GGuuCCCg-aaGCCGUUCCCgga
aGCCGGGGCacaacggugauCCCUCGuCcCACGGgGCC-GGCG-guGGGCg
-gGGUCCGGCUggagGGCCGGGCUaacGCCC-uuu-gcCCGCCgaaccCCGucaggCCCg
gaaGGGagcagCGGuaGGCGGgaCGuUCGGCgcUCGUGgGguagCGGGGGugagc-g
aGCCCCGGUggaa---GGGGA-CGGUgg---aGGGucCCcacCCCCGGGCgcgCCCGCCGCC--------
>PYR.OCC.
--------CGGguaggGCC-GGGGGcuCGCCC-UCCCCcgagcCCCGa-a-au
GGGCGuaaugCGGGGGCcaguaaCCCGCACGucg-GCCGUAGu--GGUCCAGG
GCA--gaCCCGGCCGacccau-ga-CcCCCGuCcCGCGGgGCC-GGCG-gcGCGG
a-GCC-CCCUCCggagGGAGGGaGGCuaCCGCccuu-acCGGGGgaaccAGGccaggCC
CggaaGGGagcaaCCUaaCCCCGgaCGcCCGGCguUCGCGgGgccaCGGG-Gugag
gcaaCGGCCGGGcccc--cUGCCC-UGGGCC--cCUACGGCu-ggCGUGCGGGg-gCCGc-------------
>SUL.SO-A
---AUGGUCAGguaggGUGgAGGGUcuCGCCA-GCCCUuaua-CCCAc-a---UGGCG
caacgUGGGCACcaguaaCUCCUAUGc---uAUAAUac-cUGCUCUUCGAg--aUCCCA
GUCUaacuau-ga-UcAUCGcCcGACGGgGCG-aGAUaguCGUGGgUUCCCUUUCUggag
GGAGAGGGAAuuCCACG-uu-gaCCGGGggaacCGGccaggCCCggaaGGGagcaaCCGu
gCCCGGcuAU-CCG-CguUCGUCgGucucCGAU-Aggagg-aAGACUGGGGguaaa
ucUCGGG-GAGUA----aggGUUAU-ggCAUAGGGGa-gCUGACCAU---------
>SUL.SO-B
---GGGGUCAGggaggGUGGGGGaucuCGCCaaucCCUauua-CCCGc-a-a--GG
CGuaaugCGGGCACcaguaaCUCCUACCc---uAUGGUgucuCCUAUcuguag--g
UCCCAGUggagcgau-ga-agcCUGcCcAGCggggcU-UGGCgguCAUGGgCUUUCUC
UCCggagGGAGAGAAAGuaCCAUG-auag-CUGGGggaauCGGcgaggCCCggaaGGGa
gcagCCGugCCUGGacGC-CAG-cguucGCUgGucaaCAGc-cagagu-gaAACUGGGG
uaaa--cCUAUAgAUAGGu---agG-CCAU-ggGGUAGGGGg-uCUGGCCCCau-------




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