Locus 12279

Sequence ID dm3.chr3R
Location 27,049,020 – 27,049,077
Length 57
Max. P 0.977794
window16884 window16885

overview

Window 4

Location 27,049,020 – 27,049,077
Length 57
Sequences 5
Columns 59
Reading direction forward
Mean pairwise identity 93.32
Shannon entropy 0.11865
G+C content 0.44270
Mean single sequence MFE -17.32
Consensus MFE -15.64
Energy contribution -15.88
Covariance contribution 0.24
Combinations/Pair 1.08
Mean z-score -2.49
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.98
SVM RNA-class probability 0.977794
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27049020 57 + 27905053
GGUCCCGAAAAUGCCCGGGAUAAUUUAUUUAUGAGUGU--UUCUGCACUCGCAUUUAGA
.((((((........))))))..((((..(.(((((((--....))))))).)..)))) ( -17.90, z-score =  -3.00, R)
>droSim1.chr3R 26692190 57 + 27517382
GGUCCCGAAAAUGCCCGGGAUAACUUAUUUAUGAGUGU--UUCUGCACUCGCAUUUAGA
.((((((........))))))...........((((((--....))))))......... ( -17.50, z-score =  -2.83, R)
>droSec1.super_4 5866991 57 + 6179234
GGUCCCGAAAAUGCCCGGGAUAACUUAUUUAUGAGUGU--UUCUGCACUCGCAUUUAGA
.((((((........))))))...........((((((--....))))))......... ( -17.50, z-score =  -2.83, R)
>droYak2.chr3R 27985475 59 + 28832112
GGUCCCGAAAAUGCCCGGGAUAAUUUAUUUAUGAGAGUGGUUCCGCACUCGCAUUGAGA
.((((((........))))))......((.(((.(((((......))))).))).)).. ( -17.60, z-score =  -1.76, R)
>droEre2.scaffold_4820 9538312 59 - 10470090
GGUCCCGAAAAUGCCCGGGAUAAAUUAUUUACGAGAGUGAUUCUGCACUCGCAUUUAGA
.((((((........))))))...........(.(((((......))))).)....... ( -16.10, z-score =  -2.03, R)
>consensus
GGUCCCGAAAAUGCCCGGGAUAACUUAUUUAUGAGUGU__UUCUGCACUCGCAUUUAGA
.((((((........))))))..........(((((((......)))))))........ (-15.64 = -15.88 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 27,049,020 – 27,049,077
Length 57
Sequences 5
Columns 59
Reading direction reverse
Mean pairwise identity 93.32
Shannon entropy 0.11865
G+C content 0.44270
Mean single sequence MFE -15.20
Consensus MFE -12.48
Energy contribution -12.88
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.870253
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27049020 57 - 27905053
UCUAAAUGCGAGUGCAGAA--ACACUCAUAAAUAAAUUAUCCCGGGCAUUUUCGGGACC
.........(((((.....--.)))))............(((((((....))))))).. ( -14.80, z-score =  -2.62, R)
>droSim1.chr3R 26692190 57 - 27517382
UCUAAAUGCGAGUGCAGAA--ACACUCAUAAAUAAGUUAUCCCGGGCAUUUUCGGGACC
.........(((((.....--.)))))............(((((((....))))))).. ( -14.80, z-score =  -2.26, R)
>droSec1.super_4 5866991 57 - 6179234
UCUAAAUGCGAGUGCAGAA--ACACUCAUAAAUAAGUUAUCCCGGGCAUUUUCGGGACC
.........(((((.....--.)))))............(((((((....))))))).. ( -14.80, z-score =  -2.26, R)
>droYak2.chr3R 27985475 59 - 28832112
UCUCAAUGCGAGUGCGGAACCACUCUCAUAAAUAAAUUAUCCCGGGCAUUUUCGGGACC
.....(((.(((((......))))).)))..........(((((((....))))))).. ( -16.10, z-score =  -2.05, R)
>droEre2.scaffold_4820 9538312 59 + 10470090
UCUAAAUGCGAGUGCAGAAUCACUCUCGUAAAUAAUUUAUCCCGGGCAUUUUCGGGACC
.....(((.(((((......))))).)))..........(((((((....))))))).. ( -15.50, z-score =  -2.09, R)
>consensus
UCUAAAUGCGAGUGCAGAA__ACACUCAUAAAUAAAUUAUCCCGGGCAUUUUCGGGACC
.........(((((........)))))............(((((((....))))))).. (-12.48 = -12.88 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:59:10 2011