Locus 4278

Sequence ID 3R_DroMel_CAF1
Location 11,404,076 – 11,404,191
Length 115
Max. P 0.999558
window6953 window6954

overview

Window 3

Location 11,404,076 – 11,404,191
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.70
Mean single sequence MFE -29.72
Consensus MFE -26.74
Energy contribution -27.34
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.47
Structure conservation index 0.90
SVM decision value 3.72
SVM RNA-class probability 0.999558
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11404076 115 + 27905053
AUCGAGGCAGUAACACAACAAUUAUUGUUAUUAUUGCUUGGGAACUGCAGCACAUCUCGAGUCUGAGAAAC-----GAUUCACCCUCGACCGAAUCCUCACACUAAGUAUUUCCCCUCGA
.((((((((((((.((((......))))..)))))))..(((((.(((........(((((..((((....-----..))))..)))))..((....)).......))).)))))))))) ( -30.30)
>DroSec_CAF1 151726 115 + 1
AUCGAGGCAGUAACACAACAAUUAUUGUUAUUAUUGCUUGGGAACUGCAGCACAUCUCGAGUCUGAGAAAC-----GAUUCACCCUCGACCGAAUCCUCACUCUAAGUAUUUCCCCUCAA
...((((((((((.((((......))))..)))))))..(((((.(((........(((((..((((....-----..))))..)))))..((....)).......))).)))))))).. ( -27.70)
>DroSim_CAF1 143201 115 + 1
AUCGAGGCAGUAACACAACAAUUAUUGUUAUUAUUGCUUGGGAACUGCAGCACUUCUCGAGUCUGAGAAAC-----GAUUCACCCUCGACCGAAUCCUCACUCUAAGUAUUUCCCCUCGA
.((((((((((((.((((......))))..)))))))..(((((.(((........(((((..((((....-----..))))..)))))..((....)).......))).)))))))))) ( -30.30)
>DroEre_CAF1 139779 114 + 1
AUCGAGGCAGUAACACAACAAUUAUUGUUAUUA-UGCUUGGGAACUGCAGCAUAUCUCGAGUCUGAGAAGC-----GAUUCACCCUCGCCCGAAUCCCCACUCUAAGUAUUUCCCCUCGA
.((((((((((((((..........))))))..-)))..(((((.(((.((...(((((....))))).))-----(((((..........)))))..........))).)))))))))) ( -28.40)
>DroYak_CAF1 142943 120 + 1
AUCGAGGCAGUAACACAACAAUUAUUGUUAUUAUUGCUUGGGAACUGCAGCAUAUCUCGAGUUUGAGAAACGACACGACUCACCCUCGACCGAAUCCUCACUCUAAGUAUUUCCCCUCGA
.((((((((((((.((((......))))..)))))))..(((((.(((........(((((..((((...........))))..)))))..((....)).......))).)))))))))) ( -31.90)
>consensus
AUCGAGGCAGUAACACAACAAUUAUUGUUAUUAUUGCUUGGGAACUGCAGCACAUCUCGAGUCUGAGAAAC_____GAUUCACCCUCGACCGAAUCCUCACUCUAAGUAUUUCCCCUCGA
.((((((((((((.((((......))))..)))))))..(((((.(((......(((((....)))))........(((((..........)))))..........))).)))))))))) (-26.74 = -27.34 +   0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,404,076 – 11,404,191
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.70
Mean single sequence MFE -34.50
Consensus MFE -30.18
Energy contribution -29.82
Covariance contribution -0.36
Combinations/Pair 1.08
Mean z-score -1.52
Structure conservation index 0.87
SVM decision value 1.01
SVM RNA-class probability 0.899377
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11404076 115 - 27905053
UCGAGGGGAAAUACUUAGUGUGAGGAUUCGGUCGAGGGUGAAUC-----GUUUCUCAGACUCGAGAUGUGCUGCAGUUCCCAAGCAAUAAUAACAAUAAUUGUUGUGUUACUGCCUCGAU
((((((((((...((((((.((((((((((.(....).))))))-----....)))).))).))).((.....)).)))))..(((.(((((.((((....))))))))).)))))))). ( -34.90)
>DroSec_CAF1 151726 115 - 1
UUGAGGGGAAAUACUUAGAGUGAGGAUUCGGUCGAGGGUGAAUC-----GUUUCUCAGACUCGAGAUGUGCUGCAGUUCCCAAGCAAUAAUAACAAUAAUUGUUGUGUUACUGCCUCGAU
((((((((((.......(((.((.((((((.(....).))))))-----.)).)))((((.......)).))....)))))..(((.(((((.((((....))))))))).)))))))). ( -30.70)
>DroSim_CAF1 143201 115 - 1
UCGAGGGGAAAUACUUAGAGUGAGGAUUCGGUCGAGGGUGAAUC-----GUUUCUCAGACUCGAGAAGUGCUGCAGUUCCCAAGCAAUAAUAACAAUAAUUGUUGUGUUACUGCCUCGAU
((((((((((.(((((.(((((((((((((.(....).))))))-----....)))..))))...)))))......)))))..(((.(((((.((((....))))))))).)))))))). ( -34.10)
>DroEre_CAF1 139779 114 - 1
UCGAGGGGAAAUACUUAGAGUGGGGAUUCGGGCGAGGGUGAAUC-----GCUUCUCAGACUCGAGAUAUGCUGCAGUUCCCAAGCA-UAAUAACAAUAAUUGUUGUGUUACUGCCUCGAU
((((((..............(((((((((((((((.......))-----)).((((......))))....))).))))))))((((-((((((......))))))))))....)))))). ( -37.50)
>DroYak_CAF1 142943 120 - 1
UCGAGGGGAAAUACUUAGAGUGAGGAUUCGGUCGAGGGUGAGUCGUGUCGUUUCUCAAACUCGAGAUAUGCUGCAGUUCCCAAGCAAUAAUAACAAUAAUUGUUGUGUUACUGCCUCGAU
((((((((((.......((((....))))..(((((..((((.((...))...))))..)))))............)))))..(((.(((((.((((....))))))))).)))))))). ( -35.30)
>consensus
UCGAGGGGAAAUACUUAGAGUGAGGAUUCGGUCGAGGGUGAAUC_____GUUUCUCAGACUCGAGAUGUGCUGCAGUUCCCAAGCAAUAAUAACAAUAAUUGUUGUGUUACUGCCUCGAU
((((((((((.(((.....)))((.((....(((((..(((.............)))..)))))...)).))....)))))..(((.(((((.((((....))))))))).)))))))). (-30.18 = -29.82 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:25 2006