Locus 3408

Sequence ID 3L_DroMel_CAF1
Location 9,988,771 – 9,988,902
Length 131
Max. P 0.782237
window5327 window5328

overview

Window 7

Location 9,988,771 – 9,988,870
Length 99
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 79.86
Mean single sequence MFE -17.26
Consensus MFE -8.84
Energy contribution -11.24
Covariance contribution 2.40
Combinations/Pair 1.00
Mean z-score -2.15
Structure conservation index 0.51
SVM decision value 0.56
SVM RNA-class probability 0.782237
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9988771 99 - 23771897
UAAUCAGCGCAAGCUGAUUCUCAAUUAAGAUCCAACCAAGAAAGCCAAAUACGGAGUGAAACGAAAUACGAUUCUUUUCGAAGAAUU-CAUUUAAAUAUA
.(((((((....)))))))................................(((((.(((.((.....)).))).))))).......-............ ( -17.80)
>DroSec_CAF1 41388 100 - 1
UAAUCAGCGCAAGCUGAUUCUCAAUUAAGAUCCAACCAAGAAAGCCAAAUGCGGAGUGAAAAGAAAUACAAUUCUUUUCGAAGAAUUUCAUUUAAAUAUA
.(((((((....)))))))....................((((.((......))..(((((((((......))))))))).....))))........... ( -21.50)
>DroSim_CAF1 50508 100 - 1
UAAUCAGCGCAAGCUGAUUCUCAAUUAAGAUCCAACCAAGAAAGCCAAAUACGGAGUGAAAAGAAAUACAAUUCUUUUCGAAGAAUUUAAUUUAAAUAUA
.(((((((....)))))))...(((((((.((............((......))..(((((((((......)))))))))..)).)))))))........ ( -22.10)
>DroEre_CAF1 43559 87 - 1
UAAUCAACGCAAGCUGAAUCUCAAUUAAGAUUUAACCAAGAAAACCAAAUACCGAGGGCAAAGUAAUACAAUUCUUG-------------CCUUACAAUG
...((..(....).(((((((......))))))).....)).............((((((((((......))).)))-------------))))...... ( -12.00)
>DroYak_CAF1 42205 99 - 1
UAAUCAACGCAAGCUGAUUCUCAUUUAAGGUUUAACUAGGAAUUCCAAAUACCCAGGUAAAAGUAACACAAUCCUCUGUGAA-AAUAUCAUUUAAAAAUA
.(((((.(....).)))))....((((((.....(((.((....))...(((....)))..)))..((((......))))..-.......)))))).... ( -12.90)
>consensus
UAAUCAGCGCAAGCUGAUUCUCAAUUAAGAUCCAACCAAGAAAGCCAAAUACGGAGUGAAAAGAAAUACAAUUCUUUUCGAAGAAUUUCAUUUAAAUAUA
.(((((((....)))))))......................................((((((((......))))))))..................... ( -8.84 = -11.24 +   2.40)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,988,794 – 9,988,902
Length 108
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 84.44
Mean single sequence MFE -24.10
Consensus MFE -15.18
Energy contribution -15.46
Covariance contribution 0.28
Combinations/Pair 1.15
Mean z-score -1.83
Structure conservation index 0.63
SVM decision value -0.04
SVM RNA-class probability 0.515251
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9988794 108 - 23771897
AG--------AAUGGAUUGGAGUGAGAAGGAUAAGUCGUCUAAUCAGCGCAAGCUGAUUCUCAAUUAAGAUCCAACCAAGAAAGCCAAAUACGGAGUGAAACGAAAUACGAUUCUU
..--------..((((((....((((((((((.....))))..(((((....))))))))))).....))))))...(((((..((......)).......((.....)).))))) ( -28.00)
>DroSec_CAF1 41412 108 - 1
AG--------AAAGGAGUGGAGUAAGAAGGAUAAGUUGUCUAAUCAGCGCAAGCUGAUUCUCAAUUAAGAUCCAACCAAGAAAGCCAAAUGCGGAGUGAAAAGAAAUACAAUUCUU
..--------..((((((...(((....((((.(((((...(((((((....)))))))..)))))...))))...........((......))............))).)))))) ( -24.80)
>DroSim_CAF1 50532 108 - 1
AG--------AAAGGAGUGGAAUGAGAAGGAUAAGUUGUCUAAUCAGCGCAAGCUGAUUCUCAAUUAAGAUCCAACCAAGAAAGCCAAAUACGGAGUGAAAAGAAAUACAAUUCUU
..--------...(((...((.((((((((((.....))))..(((((....))))))))))).))....)))....(((((..((......)).(((........)))..))))) ( -24.60)
>DroEre_CAF1 43570 108 - 1
AG--------GAAGGAUUGGAGUGAGCUGGAUAAGUUGUCUAAUCAACGCAAGCUGAAUCUCAAUUAAGAUUUAACCAAGAAAACCAAAUACCGAGGGCAAAGUAAUACAAUUCUU
..--------.((((((((...(((..(((((.....))))).)))..((....(((((((......)))))))..........((.........)))).........)))))))) ( -18.40)
>DroYak_CAF1 42228 116 - 1
AGUAGAAGUAGAAGGAGUGGAGUGAGAUGGAUAAGUUGUCUAAUCAACGCAAGCUGAUUCUCAUUUAAGGUUUAACUAGGAAUUCCAAAUACCCAGGUAAAAGUAACACAAUCCUC
............((((((((((((((((((((.....)))))((((.(....).))))))))))))........(((.((....))...(((....)))..)))..)))..)))). ( -24.70)
>consensus
AG________AAAGGAGUGGAGUGAGAAGGAUAAGUUGUCUAAUCAGCGCAAGCUGAUUCUCAAUUAAGAUCCAACCAAGAAAGCCAAAUACGGAGUGAAAAGAAAUACAAUUCUU
.............(((...((.((((((((((.....))))..(((((....))))))))))).))....)))........................................... (-15.18 = -15.46 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:26 2006