Locus 6196

Sequence ID dm3.chr3L
Location 4,549,953 – 4,550,004
Length 51
Max. P 0.960527
window8514 window8515

overview

Window 4

Location 4,549,953 – 4,550,004
Length 51
Sequences 4
Columns 51
Reading direction forward
Mean pairwise identity 91.75
Shannon entropy 0.13096
G+C content 0.33833
Mean single sequence MFE -10.55
Consensus MFE -11.20
Energy contribution -11.32
Covariance contribution 0.13
Combinations/Pair 1.18
Mean z-score -1.20
Structure conservation index 1.06
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.68
SVM RNA-class probability 0.960527
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4549953 51 + 24543557
UAUUGGUUAAGCUUGAUUGAGCUGCUAAGAAAGCUUUCUCAAGUACUUUAA
..........((((((..(((((........)))))..))))))....... ( -13.60, z-score =  -1.76, R)
>droYak2.chr3L 5123640 50 + 24197627
UAUUGGUGAAACUUGAUUGAGCUGAUA-GAAAGCUUUCUUAAGUACUGUAG
..........((((((..(((((....-...)))))..))))))....... ( -10.80, z-score =  -1.88, R)
>droSec1.super_2 4532675 50 + 7591821
UAUUGGUUAAACUCGAUUGAGCUGCUA-GAAAGCUUUCUCAAGUACUUUAA
..........(((.((..(((((....-...)))))..)).)))....... (  -8.90, z-score =  -0.59, R)
>droSim1.chr3L 4081569 50 + 22553184
UAUUGGUUAAACUCGAUUGAGCUGCUA-GAAAGCUUUCUCAAGUACUUUAA
..........(((.((..(((((....-...)))))..)).)))....... (  -8.90, z-score =  -0.59, R)
>consensus
UAUUGGUUAAACUCGAUUGAGCUGCUA_GAAAGCUUUCUCAAGUACUUUAA
..........((((((..(((((........)))))..))))))....... (-11.20 = -11.32 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,549,953 – 4,550,004
Length 51
Sequences 4
Columns 51
Reading direction reverse
Mean pairwise identity 91.75
Shannon entropy 0.13096
G+C content 0.33833
Mean single sequence MFE -7.30
Consensus MFE -7.15
Energy contribution -7.40
Covariance contribution 0.25
Combinations/Pair 1.10
Mean z-score -0.78
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.569649
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4549953 51 - 24543557
UUAAAGUACUUGAGAAAGCUUUCUUAGCAGCUCAAUCAAGCUUAACCAAUA
...((((..(((((...(((.....)))..)))))....))))........ (  -8.60, z-score =  -0.83, R)
>droYak2.chr3L 5123640 50 - 24197627
CUACAGUACUUAAGAAAGCUUUC-UAUCAGCUCAAUCAAGUUUCACCAAUA
.....(.((((.....((((...-....)))).....))))..)....... (  -3.00, z-score =   0.02, R)
>droSec1.super_2 4532675 50 - 7591821
UUAAAGUACUUGAGAAAGCUUUC-UAGCAGCUCAAUCGAGUUUAACCAAUA
(((((.(..(((((...(((...-.)))..)))))...).)))))...... (  -8.80, z-score =  -1.16, R)
>droSim1.chr3L 4081569 50 - 22553184
UUAAAGUACUUGAGAAAGCUUUC-UAGCAGCUCAAUCGAGUUUAACCAAUA
(((((.(..(((((...(((...-.)))..)))))...).)))))...... (  -8.80, z-score =  -1.16, R)
>consensus
UUAAAGUACUUGAGAAAGCUUUC_UAGCAGCUCAAUCAAGUUUAACCAAUA
.......((((((...((((........))))...)))))).......... ( -7.15 =  -7.40 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:02:58 2011