Locus 2178

Sequence ID X_DroMel_CAF1
Location 5,900,237 – 5,900,348
Length 111
Max. P 0.662840
window3532 window3533

overview

Window 2

Location 5,900,237 – 5,900,348
Length 111
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 93.03
Mean single sequence MFE -34.14
Consensus MFE -28.58
Energy contribution -28.98
Covariance contribution 0.40
Combinations/Pair 1.11
Mean z-score -1.30
Structure conservation index 0.84
SVM decision value 0.07
SVM RNA-class probability 0.568223
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5900237 111 + 22224390
AGGCAAAUGAG------AGGCAGGCGGCAGUGGCAAGCUCAUCUUGCACGCAAUCAAACUCCGAAUGAUUUGAAGCGCAAAAUUUAAAUUGUUUUGCCAGCCGACGGUUUCACCUGG
..........(------((((.(((((((((((((((.....))))).)))...........(((..(((((((........)))))))..))))))).)))....)))))...... ( -31.70)
>DroSec_CAF1 16928 111 + 1
AGGCAAAUGAG------AGGCAGGCAGCGGUGGCAAGCUCAUCUUGCACGCAAUCAAACUCCGAAUGAUUUGAAGCGCAAAAUUUAAAUUGUUUUGCCAGCCGAGGGUUUCACCUGG
...........------.(((.(((((((...(((((.....))))).)))...........(((..(((((((........)))))))..))))))).))).(((......))).. ( -32.00)
>DroSim_CAF1 14279 111 + 1
AGGCAAAUGAG------AGGCAGGCAGCGGUGGCAAGCUCAUCUUGCACGCAAUCAAACUCCGAAUGAUUUGAAGCGCAAAAUUUAAAUUGUUUUGCCAGCCGCGGGUUUCACCUGG
...........------.(((.(((((((...(((((.....))))).)))...........(((..(((((((........)))))))..))))))).))).((((.....)))). ( -33.60)
>DroEre_CAF1 17051 110 + 1
AGGCAAAUGAG------CGGCAGGCAGCGGUGGCAAGCUCAUCUUGCACGCAAUCAAACUCCAAAUGAUUUGAAGCGCAAAAUUAAAAUUGUUUUGCCAGCCGCGGGUUUCACC-CA
..........(------((((..((.(((...(((((.....))))).)))..(((((.((.....))))))).))(((((((.......)))))))..)))))(((.....))-). ( -37.00)
>DroYak_CAF1 17212 117 + 1
AGGCAAAUGAGAGGCGGCGGCAGGCAGCGGUGGCAAGCUCAUCUUGCACGCAAUCAAACUCGGAAUGAUUUGAAGCGCAAAAUUUAAAUUGUUUUGCCAGCCGAGGGUUUCACCCCA
..........(((((..((((.(((.(((...(((((.....))))).)))..........((((..(((((((........)))))))..))))))).))))...)))))...... ( -36.40)
>consensus
AGGCAAAUGAG______AGGCAGGCAGCGGUGGCAAGCUCAUCUUGCACGCAAUCAAACUCCGAAUGAUUUGAAGCGCAAAAUUUAAAUUGUUUUGCCAGCCGAGGGUUUCACCUGG
..................(((.(((((((...(((((.....))))).)))...........(((..(((((((........)))))))..))))))).)))..(((.....))).. (-28.58 = -28.98 +   0.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,900,237 – 5,900,348
Length 111
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 93.03
Mean single sequence MFE -33.10
Consensus MFE -27.88
Energy contribution -28.36
Covariance contribution 0.48
Combinations/Pair 1.04
Mean z-score -1.35
Structure conservation index 0.84
SVM decision value 0.27
SVM RNA-class probability 0.662840
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5900237 111 - 22224390
CCAGGUGAAACCGUCGGCUGGCAAAACAAUUUAAAUUUUGCGCUUCAAAUCAUUCGGAGUUUGAUUGCGUGCAAGAUGAGCUUGCCACUGCCGCCUGCCU------CUCAUUUGCCU
.(((((((....((.(((.((((................((((.((((((........))))))..))))(((((.....)))))...))))))).))..------.)))))))... ( -31.70)
>DroSec_CAF1 16928 111 - 1
CCAGGUGAAACCCUCGGCUGGCAAAACAAUUUAAAUUUUGCGCUUCAAAUCAUUCGGAGUUUGAUUGCGUGCAAGAUGAGCUUGCCACCGCUGCCUGCCU------CUCAUUUGCCU
..(((..((......(((.((((................((((.((((((........))))))..))))(((((.....)))))......)))).))).------....))..))) ( -31.10)
>DroSim_CAF1 14279 111 - 1
CCAGGUGAAACCCGCGGCUGGCAAAACAAUUUAAAUUUUGCGCUUCAAAUCAUUCGGAGUUUGAUUGCGUGCAAGAUGAGCUUGCCACCGCUGCCUGCCU------CUCAUUUGCCU
..(((..((....(.(((.((((................((((.((((((........))))))..))))(((((.....)))))......)))).))).------)...))..))) ( -31.50)
>DroEre_CAF1 17051 110 - 1
UG-GGUGAAACCCGCGGCUGGCAAAACAAUUUUAAUUUUGCGCUUCAAAUCAUUUGGAGUUUGAUUGCGUGCAAGAUGAGCUUGCCACCGCUGCCUGCCG------CUCAUUUGCCU
.(-((..((....(((((.((((................((((.((((((........))))))..))))(((((.....)))))......)))).))))------)...))..))) ( -37.20)
>DroYak_CAF1 17212 117 - 1
UGGGGUGAAACCCUCGGCUGGCAAAACAAUUUAAAUUUUGCGCUUCAAAUCAUUCCGAGUUUGAUUGCGUGCAAGAUGAGCUUGCCACCGCUGCCUGCCGCCGCCUCUCAUUUGCCU
.((((((.......((((.((((................((((.((((((........))))))..))))(((((.....)))))......)))).)))).)))))).......... ( -34.00)
>consensus
CCAGGUGAAACCCUCGGCUGGCAAAACAAUUUAAAUUUUGCGCUUCAAAUCAUUCGGAGUUUGAUUGCGUGCAAGAUGAGCUUGCCACCGCUGCCUGCCU______CUCAUUUGCCU
.(((((((.......(((.(((.................((((.((((((........))))))..))))(((((.....))))).......))).)))........)))))))... (-27.88 = -28.36 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:02 2006