Locus 10049

Sequence ID dm3.chr3R
Location 10,850,304 – 10,850,387
Length 83
Max. P 0.818804
window13812 window13813

overview

Window 2

Location 10,850,304 – 10,850,387
Length 83
Sequences 4
Columns 83
Reading direction forward
Mean pairwise identity 92.57
Shannon entropy 0.11957
G+C content 0.42169
Mean single sequence MFE -15.96
Consensus MFE -14.54
Energy contribution -14.60
Covariance contribution 0.06
Combinations/Pair 1.07
Mean z-score -1.63
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.818804
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10850304 83 + 27905053
GGCAAACACGCCCAUUCAAAAGGAAAAGAAUGGGAUACUAGCAGGCAAAUAUACUAGUACAUACUGAUCUCUAGACACAGGCA
.((.......(((((((..........))))))).((((((............))))))....(((.((....))..))))). ( -16.50, z-score =  -1.85, R)
>droSim1.chr3R 16911281 83 - 27517382
GGCAAACACGCCCAUUCAAAAAGAAAAGAAUGGGAUACUAGCAGGCAAAUAUACUAGUACAUACUGAUCUCUAGACACACGCA
.((.......(((((((..........))))))).((((((............)))))).....................)). ( -15.60, z-score =  -2.23, R)
>droSec1.super_0 10033841 83 - 21120651
GGCAAACACGCCCAUUCAAAAAGAAAAGAAUGGGAUACUAGCAGGCAAAUAUACUAGUACAUUCUGAUCUGUAGACACACGCA
.((.......(((((((..........)))))))...(((.(((((((((.((....)).))).)).)))))))......)). ( -16.40, z-score =  -1.81, R)
>droYak2.chr3R 13264083 83 - 28832112
GGCAAACACGCCCAUUCAAAAGGAAAGGAAUGGGAUACCAGCAAGCAAAUGUACUAGUGUAUACAGAUCUCUACACACACGCA
.((.......(((((((..........)))))))......))..((...(((((....))))).((....))........)). ( -15.32, z-score =  -0.64, R)
>consensus
GGCAAACACGCCCAUUCAAAAAGAAAAGAAUGGGAUACUAGCAGGCAAAUAUACUAGUACAUACUGAUCUCUAGACACACGCA
.((.......(((((((..........))))))).((((((............)))))).....................)). (-14.54 = -14.60 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 10,850,304 – 10,850,387
Length 83
Sequences 4
Columns 83
Reading direction reverse
Mean pairwise identity 92.57
Shannon entropy 0.11957
G+C content 0.42169
Mean single sequence MFE -20.07
Consensus MFE -17.62
Energy contribution -17.50
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -1.64
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.722890
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10850304 83 - 27905053
UGCCUGUGUCUAGAGAUCAGUAUGUACUAGUAUAUUUGCCUGCUAGUAUCCCAUUCUUUUCCUUUUGAAUGGGCGUGUUUGCC
...(((.(((....))))))...(((((((((........)))))))))(((((((..........))))))).......... ( -20.20, z-score =  -2.04, R)
>droSim1.chr3R 16911281 83 + 27517382
UGCGUGUGUCUAGAGAUCAGUAUGUACUAGUAUAUUUGCCUGCUAGUAUCCCAUUCUUUUCUUUUUGAAUGGGCGUGUUUGCC
(((.((.(((....)))))))).(((((((((........)))))))))(((((((..........))))))).......... ( -19.10, z-score =  -1.48, R)
>droSec1.super_0 10033841 83 + 21120651
UGCGUGUGUCUACAGAUCAGAAUGUACUAGUAUAUUUGCCUGCUAGUAUCCCAUUCUUUUCUUUUUGAAUGGGCGUGUUUGCC
.((((.((((...(((..((((((((((((((........))))))))...))))))..)))....).))).))))....... ( -20.10, z-score =  -1.80, R)
>droYak2.chr3R 13264083 83 + 28832112
UGCGUGUGUGUAGAGAUCUGUAUACACUAGUACAUUUGCUUGCUGGUAUCCCAUUCCUUUCCUUUUGAAUGGGCGUGUUUGCC
.((((((((((((....))))))))))...(((...((((....)))).(((((((..........))))))).)))...)). ( -20.90, z-score =  -1.27, R)
>consensus
UGCGUGUGUCUAGAGAUCAGUAUGUACUAGUAUAUUUGCCUGCUAGUAUCCCAUUCUUUUCCUUUUGAAUGGGCGUGUUUGCC
.((....................(((((((((........)))))))))(((((((..........))))))).......)). (-17.62 = -17.50 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:16:25 2011