Locus 6000

Sequence ID dm3.chr3L
Location 2,979,366 – 2,979,456
Length 90
Max. P 0.952859
window8255 window8256

overview

Window 5

Location 2,979,366 – 2,979,456
Length 90
Sequences 6
Columns 91
Reading direction forward
Mean pairwise identity 85.50
Shannon entropy 0.28357
G+C content 0.46910
Mean single sequence MFE -28.62
Consensus MFE -20.99
Energy contribution -22.35
Covariance contribution 1.36
Combinations/Pair 1.08
Mean z-score -2.32
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.59
SVM RNA-class probability 0.952859
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2979366 90 + 24543557
UCUGGAUCCCCAGUCACGCUGUGCGUGCUAGAAUGGUCAACAGUUUUAUUGUCCGGCAAAGGACUCUGGAAACAAAUGUUGAUUUCU-GCG
.((((....))))..((((...))))((.((((..((((((((((((...((((......))))....)))))...)))))))))))-)). ( -27.70, z-score =  -1.92, R)
>droSim1.chr3L 2511586 90 + 22553184
UCUGGAUCCCCAGUCACGCUGUGCGUGCUGGAAUGGUCAACAGUUUUAUUGUCCGGCAAAGGACUCUGGAAACAAAUGUUGAUUUCU-GCG
...(((...((((.(((((...)))))))))...(((((((((((((...((((......))))....)))))...)))))))))))-... ( -29.60, z-score =  -2.17, R)
>droSec1.super_2 2983342 90 + 7591821
UCUGUAUCCCCAGUCACGCUGUGCGUGCUGGAAUGGUCAACAGUUUUAUUGUCCGACAAAGGACUCUGGAAACAAAUGUUGAUUUCU-GCG
...(((...((((.(((((...)))))))))...(((((((((((((...((((......))))....)))))...))))))))..)-)). ( -29.80, z-score =  -3.01, R)
>droYak2.chr3L 15236919 91 - 24197627
UCUGGAUUCCCAGUCACGCUGUGCGUGCUGGAAUGGUCAACAGUUUUAUUGUCCGGCAAAGGACUCUAGAAACAAAUGUUGAUUUUCAGCG
.(((((...((((.(((((...)))))))))...((((((((.(((((..((((......))))..))))).....))))))))))))).. ( -32.20, z-score =  -3.33, R)
>droEre2.scaffold_4784 2994293 90 + 25762168
UCUGGAUCCCCAGGCACGCAGCGCGUGCAGGAAUGGUCAACAGUUUUAUUGUCCGGCAAAGGACUCUAGAAACAAAUGUUGAUUUCU-GCG
.((((....))))((((((...)))))).((((..(((((((.(((((..((((......))))..))))).....)))))))))))-... ( -32.20, z-score =  -2.80, R)
>droAna3.scaffold_13337 14164528 81 - 23293914
---------CCAUUCACACGGUUCGUGCCGGAAUGGUGAGGAUUUUUAUUGUCCGACAAUGGACUCUUCAAGCAAUUGUUGAUUUUUGAA-
---------((((((...((((....))))))))))((((((..(((((((.....))))))).))))))....................- ( -20.20, z-score =  -0.70, R)
>consensus
UCUGGAUCCCCAGUCACGCUGUGCGUGCUGGAAUGGUCAACAGUUUUAUUGUCCGGCAAAGGACUCUGGAAACAAAUGUUGAUUUCU_GCG
.........((((.(((((...)))))))))...((((((((.(((((..((((......))))..))))).....))))))))....... (-20.99 = -22.35 +   1.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 2,979,366 – 2,979,456
Length 90
Sequences 6
Columns 91
Reading direction reverse
Mean pairwise identity 85.50
Shannon entropy 0.28357
G+C content 0.46910
Mean single sequence MFE -24.52
Consensus MFE -18.20
Energy contribution -19.37
Covariance contribution 1.17
Combinations/Pair 1.16
Mean z-score -1.79
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.72
SVM RNA-class probability 0.797119
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2979366 90 - 24543557
CGC-AGAAAUCAACAUUUGUUUCCAGAGUCCUUUGCCGGACAAUAAAACUGUUGACCAUUCUAGCACGCACAGCGUGACUGGGGAUCCAGA
.((-((((.((((((((((....))))((((......))))........))))))...)))).))((((...))))..((((....)))). ( -23.60, z-score =  -1.16, R)
>droSim1.chr3L 2511586 90 - 22553184
CGC-AGAAAUCAACAUUUGUUUCCAGAGUCCUUUGCCGGACAAUAAAACUGUUGACCAUUCCAGCACGCACAGCGUGACUGGGGAUCCAGA
...-.....((((((((((....))))((((......))))........))))))...(((((((((((...))))).))))))....... ( -25.50, z-score =  -1.70, R)
>droSec1.super_2 2983342 90 - 7591821
CGC-AGAAAUCAACAUUUGUUUCCAGAGUCCUUUGUCGGACAAUAAAACUGUUGACCAUUCCAGCACGCACAGCGUGACUGGGGAUACAGA
...-...........(((((.(((...((((......))))...................(((((((((...))))).))))))).))))) ( -26.00, z-score =  -2.05, R)
>droYak2.chr3L 15236919 91 + 24197627
CGCUGAAAAUCAACAUUUGUUUCUAGAGUCCUUUGCCGGACAAUAAAACUGUUGACCAUUCCAGCACGCACAGCGUGACUGGGAAUCCAGA
..(((....((((((...((((.((..((((......))))..))))))))))))...(((((((((((...))))).))))))...))). ( -29.00, z-score =  -3.31, R)
>droEre2.scaffold_4784 2994293 90 - 25762168
CGC-AGAAAUCAACAUUUGUUUCUAGAGUCCUUUGCCGGACAAUAAAACUGUUGACCAUUCCUGCACGCGCUGCGUGCCUGGGGAUCCAGA
...-.....((((((...((((.((..((((......))))..))))))))))))..((((((((((((...))))))..))))))..... ( -25.50, z-score =  -1.11, R)
>droAna3.scaffold_13337 14164528 81 + 23293914
-UUCAAAAAUCAACAAUUGCUUGAAGAGUCCAUUGUCGGACAAUAAAAAUCCUCACCAUUCCGGCACGAACCGUGUGAAUGG---------
-(((((.(((.....)))..)))))..((((......))))..............((((((..(((((...)))))))))))--------- ( -17.50, z-score =  -1.42, R)
>consensus
CGC_AGAAAUCAACAUUUGUUUCCAGAGUCCUUUGCCGGACAAUAAAACUGUUGACCAUUCCAGCACGCACAGCGUGACUGGGGAUCCAGA
.........((((((...((((.....((((......))))....))))))))))...(((((((((((...))))).))))))....... (-18.20 = -19.37 +   1.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:59:21 2011