Locus 3362

Sequence ID 3L_DroMel_CAF1
Location 9,828,110 – 9,828,203
Length 93
Max. P 0.956881
window5253 window5254

overview

Window 3

Location 9,828,110 – 9,828,203
Length 93
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 96.63
Mean single sequence MFE -19.40
Consensus MFE -17.38
Energy contribution -18.12
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.90
SVM decision value 0.50
SVM RNA-class probability 0.760447
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9828110 93 + 23771897
AAGCGAAUGCCGUAACAUUCAGCCUGGUCAUCCAUUACUUCUCAAACGGCAGCAACAACAAAUGUAUUGCACUGCUGCUGCACGAAAAA-AAAA
..(((((((......))))).)).(((....)))............((((((((.((.(((.....)))...)).)))))).)).....-.... ( -18.60)
>DroSec_CAF1 122072 94 + 1
AAGCGAAUGCCGUAACAUUCAGCCUGGUCAUCCAUUACUUCUCAAACGGCAGCAACAAUAAAUGUAUUGCACUGCUGCUGCACGAAAAAAAAAA
..(((((((......))))).)).(((....)))............((((((((.(((((....)))))...)))))))).............. ( -20.90)
>DroSim_CAF1 125361 94 + 1
AAGCGAAUGCCGUAACAUUCAGCCUUGUCAUCCAUUACUUCUCAAACGGCAGCAACAAUAAAUGUAUUGCACUGCUGCUGCACGAAAAAAAAAA
..(((((((......))))).)).......................((((((((.(((((....)))))...)))))))).............. ( -19.40)
>DroYak_CAF1 135211 94 + 1
AAGCGAAUGCCGUAACAUUCAGCCUGGUCAUCCAUUACUUCUCCAACGGCAGCAACAACAAAUGCAUUGCACUGCUGCUGCACGAAAAAAAAAU
..(((((((......))))).)).(((....)))............((((((((.((.....(((...))).)).)))))).)).......... ( -18.70)
>consensus
AAGCGAAUGCCGUAACAUUCAGCCUGGUCAUCCAUUACUUCUCAAACGGCAGCAACAACAAAUGUAUUGCACUGCUGCUGCACGAAAAAAAAAA
..(((((((......))))).)).......................((((((((.(((((....)))))...)))))))).............. (-17.38 = -18.12 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 9,828,110 – 9,828,203
Length 93
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 96.63
Mean single sequence MFE -30.80
Consensus MFE -27.66
Energy contribution -27.48
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -3.02
Structure conservation index 0.90
SVM decision value 1.47
SVM RNA-class probability 0.956881
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9828110 93 - 23771897
UUUU-UUUUUCGUGCAGCAGCAGUGCAAUACAUUUGUUGUUGCUGCCGUUUGAGAAGUAAUGGAUGACCAGGCUGAAUGUUACGGCAUUCGCUU
((((-((...((.(((((((((..((((.....)))))))))))))))...))))))...(((....)))(((.((((((....))))))))). ( -30.40)
>DroSec_CAF1 122072 94 - 1
UUUUUUUUUUCGUGCAGCAGCAGUGCAAUACAUUUAUUGUUGCUGCCGUUUGAGAAGUAAUGGAUGACCAGGCUGAAUGUUACGGCAUUCGCUU
.((((((...((.((((((((((((.........))))))))))))))...))))))...(((....)))(((.((((((....))))))))). ( -30.20)
>DroSim_CAF1 125361 94 - 1
UUUUUUUUUUCGUGCAGCAGCAGUGCAAUACAUUUAUUGUUGCUGCCGUUUGAGAAGUAAUGGAUGACAAGGCUGAAUGUUACGGCAUUCGCUU
.((((((...((.((((((((((((.........))))))))))))))...))))))............((((.((((((....)))))))))) ( -29.20)
>DroYak_CAF1 135211 94 - 1
AUUUUUUUUUCGUGCAGCAGCAGUGCAAUGCAUUUGUUGUUGCUGCCGUUGGAGAAGUAAUGGAUGACCAGGCUGAAUGUUACGGCAUUCGCUU
((((((((..((.(((((((((..((((.....)))))))))))))))..))))))))..(((....)))(((.((((((....))))))))). ( -33.40)
>consensus
UUUUUUUUUUCGUGCAGCAGCAGUGCAAUACAUUUAUUGUUGCUGCCGUUUGAGAAGUAAUGGAUGACCAGGCUGAAUGUUACGGCAUUCGCUU
.....(((((((.((.((((((..((((((....)))))))))))).)).)))))))............((((.((((((....)))))))))) (-27.66 = -27.48 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:14 2006