Locus 11775

Sequence ID dm3.chr3R
Location 23,681,131 – 23,681,226
Length 95
Max. P 0.997744
window16181 window16182

overview

Window 1

Location 23,681,131 – 23,681,226
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 87.41
Shannon entropy 0.20178
G+C content 0.44134
Mean single sequence MFE -32.48
Consensus MFE -24.49
Energy contribution -26.55
Covariance contribution 2.06
Combinations/Pair 1.03
Mean z-score -3.12
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.35
SVM RNA-class probability 0.988991
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23681131 95 + 27905053
CUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUGCUGUUCCUGCUGCUGCUGUGUGCGAUAUGAAAAAUGCAAAG
..((((......))))(((((..(((((((((((((((((((.....((....))......)))))))))))).)))).))).....)))))... ( -33.50, z-score =  -2.71, R)
>droSim1.chr3R 23402985 95 + 27517382
CUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUGCUGUUGCUGUUGCUGCUGUGUGCGAUAUGAAAAAUGCAAAG
..((((......))))(((((......(((((((((((((((....)))))))))))))))((((((........))))))......)))))... ( -37.20, z-score =  -3.70, R)
>droSec1.super_22 318525 89 + 1066717
CUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUGCUGUU------GCUGCUGUGUGCGAUAUGAAAAAUGCAAAG
..((((......))))(((((......(((((((((((((((....)))))))))))))------))(((.....))).........)))))... ( -33.70, z-score =  -3.37, R)
>droYak2.chr3R 6026685 74 - 28832112
CUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCU---------------------GCUGCUGUGUGCGAUAUGAAAAAUGCAAAG
..((((......))))(((((..((((((((((((((((....)---------------------)))))))).)))).))).....)))))... ( -25.50, z-score =  -2.72, R)
>consensus
CUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUGCUGUU______GCUGCUGUGUGCGAUAUGAAAAAUGCAAAG
..((((......))))(((((..(((((((((((((((((((.....((....))......)))))))))))).)))).))).....)))))... (-24.49 = -26.55 +   2.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 23,681,131 – 23,681,226
Length 95
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 87.41
Shannon entropy 0.20178
G+C content 0.44134
Mean single sequence MFE -30.57
Consensus MFE -23.83
Energy contribution -23.96
Covariance contribution 0.13
Combinations/Pair 1.00
Mean z-score -3.75
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.17
SVM RNA-class probability 0.997744
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23681131 95 - 27905053
CUUUGCAUUUUUCAUAUCGCACACAGCAGCAGCAGGAACAGCAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAG
.(((((((.....(((.((((.(((((((((((.(......)....((....))))))))))))))))))))..))))))).............. ( -33.90, z-score =  -3.71, R)
>droSim1.chr3R 23402985 95 - 27517382
CUUUGCAUUUUUCAUAUCGCACACAGCAGCAACAGCAACAGCAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAG
.(((((((.....(((.((((.(((((((((.(.((....))....((....))).))))))))))))))))..))))))).............. ( -30.60, z-score =  -3.17, R)
>droSec1.super_22 318525 89 - 1066717
CUUUGCAUUUUUCAUAUCGCACACAGCAGC------AACAGCAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAG
.(((((((....(.....((.....)).((------(((((((.((((......)))).)))))))))).....))))))).............. ( -30.30, z-score =  -3.61, R)
>droYak2.chr3R 6026685 74 + 28832112
CUUUGCAUUUUUCAUAUCGCACACAGCAGC---------------------AGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAG
.(((((((.....(((.((((.((((((((---------------------(....))))))))))))))))..))))))).............. ( -27.50, z-score =  -4.52, R)
>consensus
CUUUGCAUUUUUCAUAUCGCACACAGCAGC______AACAGCAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAG
.(((((((.....(((.((((.((((((((..........((....)).........)))))))))))))))..))))))).............. (-23.83 = -23.96 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:49:23 2011