Locus 7252

Sequence ID dm3.chr3L
Location 13,353,067 – 13,353,117
Length 50
Max. P 0.944087
window9984 window9985

overview

Window 4

Location 13,353,067 – 13,353,117
Length 50
Sequences 8
Columns 50
Reading direction forward
Mean pairwise identity 95.93
Shannon entropy 0.08432
G+C content 0.36500
Mean single sequence MFE -11.06
Consensus MFE -11.06
Energy contribution -10.95
Covariance contribution -0.11
Combinations/Pair 1.09
Mean z-score -1.58
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.50
SVM RNA-class probability 0.944087
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 13353067 50 + 24543557
AGCACAAAAGCAUUUGCAUUGCAAAUGCAACAUAAUGCACAACAACAACA
.(((.....((((((((...)))))))).......)))............ ( -11.20, z-score =  -1.91, R)
>droPer1.super_47 493803 50 - 592741
AGCACAAAAGCAUUUGCAUUGCAAAUGCAACAUAAUGCACAGCAACAACA
.(((.....((((((((...)))))))).......)))............ ( -11.20, z-score =  -1.30, R)
>dp4.chrXR_group6 7705272 50 - 13314419
AGCACAAAAGCAUUUGCAUUGCAAAUGCAACAUAAUGCACAGCAACAACA
.(((.....((((((((...)))))))).......)))............ ( -11.20, z-score =  -1.30, R)
>droYak2.chr3L 13449338 50 + 24197627
AGCACAAAAGCAUUUGCAUUGCAAAUGCAACAUAAUGCACAACAACAACA
.(((.....((((((((...)))))))).......)))............ ( -11.20, z-score =  -1.91, R)
>droEre2.scaffold_4784 13365117 50 + 25762168
AGCACAAAAGCAUUUGCAUUGCAAAUGCAACAUAAUGCACAGCAACAACG
.(((.....((((((((...)))))))).......)))............ ( -11.20, z-score =  -1.77, R)
>droSec1.super_0 5528073 50 + 21120651
AGUACAAAAGCAUUUGCAUUGCAAAUGCAACAUAAUGCACAACAACAACA
.........((((((((...))))))))...................... ( -10.10, z-score =  -1.23, R)
>droSim1.chr3L 12750660 50 + 22553184
AGCACAAAAGCAUUUGCAUUGCAAAUGCAACAUAAUGCACAACAACAACA
.(((.....((((((((...)))))))).......)))............ ( -11.20, z-score =  -1.91, R)
>droVir3.scaffold_13049 12785500 50 + 25233164
AGCACAAAAGCAUUUGCAUUGCAAAUGCAACAUAAUGCAAAAUAACAGGA
.(((.....((((((((...)))))))).......)))............ ( -11.20, z-score =  -1.27, R)
>consensus
AGCACAAAAGCAUUUGCAUUGCAAAUGCAACAUAAUGCACAACAACAACA
.(((.....((((((((...)))))))).......)))............ (-11.06 = -10.95 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,353,067 – 13,353,117
Length 50
Sequences 8
Columns 50
Reading direction reverse
Mean pairwise identity 95.93
Shannon entropy 0.08432
G+C content 0.36500
Mean single sequence MFE -13.49
Consensus MFE -12.69
Energy contribution -12.81
Covariance contribution 0.12
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.725175
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 13353067 50 - 24543557
UGUUGUUGUUGUGCAUUAUGUUGCAUUUGCAAUGCAAAUGCUUUUGUGCU
............((((...(..((((((((...))))))))..).)))). ( -13.50, z-score =  -1.40, R)
>droPer1.super_47 493803 50 + 592741
UGUUGUUGCUGUGCAUUAUGUUGCAUUUGCAAUGCAAAUGCUUUUGUGCU
............((((...(..((((((((...))))))))..).)))). ( -13.50, z-score =  -1.15, R)
>dp4.chrXR_group6 7705272 50 + 13314419
UGUUGUUGCUGUGCAUUAUGUUGCAUUUGCAAUGCAAAUGCUUUUGUGCU
............((((...(..((((((((...))))))))..).)))). ( -13.50, z-score =  -1.15, R)
>droYak2.chr3L 13449338 50 - 24197627
UGUUGUUGUUGUGCAUUAUGUUGCAUUUGCAAUGCAAAUGCUUUUGUGCU
............((((...(..((((((((...))))))))..).)))). ( -13.50, z-score =  -1.40, R)
>droEre2.scaffold_4784 13365117 50 - 25762168
CGUUGUUGCUGUGCAUUAUGUUGCAUUUGCAAUGCAAAUGCUUUUGUGCU
............((((...(..((((((((...))))))))..).)))). ( -13.50, z-score =  -0.93, R)
>droSec1.super_0 5528073 50 - 21120651
UGUUGUUGUUGUGCAUUAUGUUGCAUUUGCAAUGCAAAUGCUUUUGUACU
..........(((((.......((((((((...))))))))...))))). ( -13.40, z-score =  -1.41, R)
>droSim1.chr3L 12750660 50 - 22553184
UGUUGUUGUUGUGCAUUAUGUUGCAUUUGCAAUGCAAAUGCUUUUGUGCU
............((((...(..((((((((...))))))))..).)))). ( -13.50, z-score =  -1.40, R)
>droVir3.scaffold_13049 12785500 50 - 25233164
UCCUGUUAUUUUGCAUUAUGUUGCAUUUGCAAUGCAAAUGCUUUUGUGCU
............((((...(..((((((((...))))))))..).)))). ( -13.50, z-score =  -2.10, R)
>consensus
UGUUGUUGUUGUGCAUUAUGUUGCAUUUGCAAUGCAAAUGCUUUUGUGCU
............((((...(..((((((((...))))))))..).)))). (-12.69 = -12.81 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

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