Locus 5970

Sequence ID dm3.chr3L
Location 2,849,815 – 2,849,877
Length 62
Max. P 0.977606
window8212 window8213

overview

Window 2

Location 2,849,815 – 2,849,877
Length 62
Sequences 5
Columns 62
Reading direction forward
Mean pairwise identity 96.77
Shannon entropy 0.05461
G+C content 0.51935
Mean single sequence MFE -20.36
Consensus MFE -20.60
Energy contribution -20.36
Covariance contribution -0.24
Combinations/Pair 1.06
Mean z-score -1.93
Structure conservation index 1.01
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.98
SVM RNA-class probability 0.977606
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2849815 62 + 24543557
UGUUGCCAUCUAGCUGAUUUUAUGGCCAGCAGAGCCACACGUGAUACACAUCCAGCUGGAUG
......((((((((((......(((((....).))))...(((...)))...)))))))))) ( -20.60, z-score =  -2.46, R)
>droEre2.scaffold_4784 2875873 62 + 25762168
UGUUGCCGUCUAGCUGAUUUUAUGGCCAGCGGUGCCACACGUGAUUCACAUCCAGCUGGAUG
......((((((((((......(((((....).))))...(((...)))...)))))))))) ( -20.10, z-score =  -1.37, R)
>droYak2.chr3L 15114704 62 - 24197627
UGUUGCCGUCUAGCUGAUUUUAUGGCCAGCGGAGCCACACGUGAUUCACAUCCAGCUGGAUG
......((((((((((......(((((....).))))...(((...)))...)))))))))) ( -20.10, z-score =  -1.60, R)
>droSec1.super_2 2870209 62 + 7591821
UGUUGCCAUCUAGCUGAUUUUAUGGCCAGCGGAGCCACACGUGAUACACAUCCAGCUGGAUG
......((((((((((......(((((....).))))...(((...)))...)))))))))) ( -20.50, z-score =  -2.12, R)
>droSim1.chr3L 2402919 62 + 22553184
UGUUGCCAUCUAGCUGAUUUUAUGGCCAGCGGAGCCACACGUGAUACACAUCCAGCUGGAUG
......((((((((((......(((((....).))))...(((...)))...)))))))))) ( -20.50, z-score =  -2.12, R)
>consensus
UGUUGCCAUCUAGCUGAUUUUAUGGCCAGCGGAGCCACACGUGAUACACAUCCAGCUGGAUG
......((((((((((......(((((....).))))...(((...)))...)))))))))) (-20.60 = -20.36 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 2,849,815 – 2,849,877
Length 62
Sequences 5
Columns 62
Reading direction reverse
Mean pairwise identity 96.77
Shannon entropy 0.05461
G+C content 0.51935
Mean single sequence MFE -20.74
Consensus MFE -19.80
Energy contribution -20.40
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.82
SVM RNA-class probability 0.826822
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2849815 62 - 24543557
CAUCCAGCUGGAUGUGUAUCACGUGUGGCUCUGCUGGCCAUAAAAUCAGCUAGAUGGCAACA
((((.(((((((((((...)))))((((((.....))))))....)))))).))))...... ( -22.10, z-score =  -1.95, R)
>droEre2.scaffold_4784 2875873 62 - 25762168
CAUCCAGCUGGAUGUGAAUCACGUGUGGCACCGCUGGCCAUAAAAUCAGCUAGACGGCAACA
......((((.(((((...))))).)))).((((((((..........))))).)))..... ( -18.20, z-score =  -0.80, R)
>droYak2.chr3L 15114704 62 + 24197627
CAUCCAGCUGGAUGUGAAUCACGUGUGGCUCCGCUGGCCAUAAAAUCAGCUAGACGGCAACA
..((.(((((((((((...)))))((((((.....))))))....)))))).)).(....). ( -19.20, z-score =  -1.18, R)
>droSec1.super_2 2870209 62 - 7591821
CAUCCAGCUGGAUGUGUAUCACGUGUGGCUCCGCUGGCCAUAAAAUCAGCUAGAUGGCAACA
((((.(((((((((((...)))))((((((.....))))))....)))))).))))...... ( -22.10, z-score =  -1.97, R)
>droSim1.chr3L 2402919 62 - 22553184
CAUCCAGCUGGAUGUGUAUCACGUGUGGCUCCGCUGGCCAUAAAAUCAGCUAGAUGGCAACA
((((.(((((((((((...)))))((((((.....))))))....)))))).))))...... ( -22.10, z-score =  -1.97, R)
>consensus
CAUCCAGCUGGAUGUGUAUCACGUGUGGCUCCGCUGGCCAUAAAAUCAGCUAGAUGGCAACA
((((.(((((((((((...)))))((((((.....))))))....)))))).))))...... (-19.80 = -20.40 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:58:45 2011