Locus 1973

Sequence ID X_DroMel_CAF1
Location 5,390,524 – 5,390,712
Length 188
Max. P 0.525454
window3212 window3213

overview

Window 2

Location 5,390,524 – 5,390,634
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.11
Mean single sequence MFE -30.54
Consensus MFE -20.79
Energy contribution -21.35
Covariance contribution 0.56
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.68
SVM decision value -0.02
SVM RNA-class probability 0.525454
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5390524 110 + 22224390
----UGUUGGUGUG------GGUGUCCUUCUCGAAAGUCUAUAAUUGGAAAAUUUUACACACUCGAACAUCAAUUUCAACAGCAGCAUGCAGCAUGCCAGUUGAAAUGUUGAAAUGCCAA
----..(((((...------(((((.....((((..((.((.((((....)))).)).))..))))))))).(((((((((.((((..((.....))..))))...)))))))))))))) ( -28.80)
>DroSec_CAF1 71653 103 + 1
----UGUGGGUGUG------GGUGUCCUUCUCGAAAGUCUAUAAUUGGACAAUUUUACACACUCGAACAUCAAUUUCAACAGCAG-------CAUGCCAGUUGAAAUGUUGAAAUGCCAG
----..((((((((------..(((((....(....).........)))))......)))))))).......(((((((((.(((-------(......))))...)))))))))..... ( -30.22)
>DroSim_CAF1 59384 114 + 1
----UGUUGGUGUGG--GUGGGUGUCCUUCUCGAAAGUCUAUAAUUGGAAAAUUUUACACACUCGAACAUCAAUUUCAACAGCAGCAUGCAGCAUGCCAGUUGAAAUGUUGAAAUGCCAG
----...(((((((.--.(((((((......(....)((((....)))).........)))))))..)))..(((((((((.((((..((.....))..))))...))))))))))))). ( -32.00)
>DroYak_CAF1 65190 120 + 1
UGUGUGUUUGUGUGGGAGUGAGAGUCCUUCUCGAAAGUCUAUAAUUGGAAAAUUUUACACACUCGAACAUCAAUUUCAACAGCAGCAUGCAGCAUGCCAGUUGAAAUGCUGAAAUGCCAG
((.(((((((.(((...((((((.(((....(....).........)))...)))))).))).)))))))))((((((((.(((((.....)).)))..))))))))((......))... ( -31.12)
>consensus
____UGUUGGUGUG______GGUGUCCUUCUCGAAAGUCUAUAAUUGGAAAAUUUUACACACUCGAACAUCAAUUUCAACAGCAGCAUGCAGCAUGCCAGUUGAAAUGUUGAAAUGCCAG
....((((((((((.................(....)((((....))))........))))))..))))(((((((((((.(((((.....)).)))..))))))))..)))........ (-20.79 = -21.35 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,390,594 – 5,390,712
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.02
Mean single sequence MFE -34.05
Consensus MFE -29.90
Energy contribution -30.53
Covariance contribution 0.63
Combinations/Pair 1.03
Mean z-score -1.34
Structure conservation index 0.88
SVM decision value -0.04
SVM RNA-class probability 0.513401
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5390594 118 + 22224390
AGCAGCAUGCAGCAUGCCAGUUGAAAUGUUGAAAUGCCAAUCGAUAUGCGGAUAAUGGGACGGGGGCAUCAGUGGGUUAAUUACGUGCCAGCUAU--AUAUUUUAAUUGGCAGCGAUCAU
.((.....)).((.(((((((((((((((....(((((..(((.(((.......)))...))).))))).(((.(((.........))).)))..--)))))))))))))))))...... ( -32.40)
>DroSec_CAF1 71723 110 + 1
AGCAG-------CAUGCCAGUUGAAAUGUUGAAAUGCCAGUCGAUAUGCGGAUAAUGGGACAGGGGCAUCAGUGGGUUAAU-GUGUGCCAGCGAU--AUAUUUUAAUUGGCAGCGAUCAU
....(-------(.((((((((((((((((((..((((.(((..(((.......))).)))...)))))))((.(((....-....))).))...--)))))))))))))))))...... ( -33.50)
>DroSim_CAF1 59458 118 + 1
AGCAGCAUGCAGCAUGCCAGUUGAAAUGUUGAAAUGCCAGUCGAUAUGCGGAUAAUGGGACGGGGGCAUCAGUGGGUUAAUUACGUGCCAGCGAU--AUAUUUUAAUUGGCAGCGAUCAU
.((.....)).((.(((((((((((((((.......(((.(((.....)))....)))..((..(((((..((((.....)))))))))..))..--)))))))))))))))))...... ( -35.60)
>DroYak_CAF1 65270 120 + 1
AGCAGCAUGCAGCAUGCCAGUUGAAAUGCUGAAAUGCCAGUCGAUAUGCGGAUAAUAGGCCGGGGGCAUCAGUGGGUUAAUUACGUGCCAGCGAUAUAUAUUUUAAUUGGCAGCGAUCUU
.((.....)).((.(((((((((((((((......))..((((...(.(((........))).)(((((..((((.....)))))))))..))))....)))))))))))))))...... ( -34.70)
>consensus
AGCAGCAUGCAGCAUGCCAGUUGAAAUGUUGAAAUGCCAGUCGAUAUGCGGAUAAUGGGACGGGGGCAUCAGUGGGUUAAUUACGUGCCAGCGAU__AUAUUUUAAUUGGCAGCGAUCAU
.((.((.....)).((((((((((((((((((..((((.(((..(((.......))).)))...)))))))((.(((.........))).)).....)))))))))))))))))...... (-29.90 = -30.53 +   0.63)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:14 2006