Locus 10098

Sequence ID dm3.chr3R
Location 11,273,404 – 11,273,462
Length 58
Max. P 0.641081
window13884 window13885

overview

Window 4

Location 11,273,404 – 11,273,462
Length 58
Sequences 14
Columns 58
Reading direction forward
Mean pairwise identity 71.86
Shannon entropy 0.65702
G+C content 0.54698
Mean single sequence MFE -16.43
Consensus MFE -8.08
Energy contribution -7.94
Covariance contribution -0.14
Combinations/Pair 1.67
Mean z-score -0.72
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.641081
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 11273404 58 + 27905053
AGUCAUUGCCGAAACUCAGCUGGCACUGGGCGUCCAGGGAGUAGAUCUCUCCAGGCAG
......((((((..(((((......)))))..))...((((.......)))).)))). ( -18.10, z-score =  -0.28, R)
>droSim1.chr3R 17312153 58 - 27517382
AGUCAUUGCCGAAACUCAGCUGGCACUGGGCGUCCAGGGAGUAAAUCUCUCCAGGCAG
......((((((..(((((......)))))..))...((((.......)))).)))). ( -18.10, z-score =  -0.82, R)
>droSec1.super_0 10445255 58 - 21120651
AGUCAUUGCCGAAACUCAGCUGGCACUGGGCGUCCAGGGAGUAUAUCUCUCCAGGCAG
......((((((..(((((......)))))..))...((((.......)))).)))). ( -18.10, z-score =  -0.77, R)
>droYak2.chr3R 13674901 58 - 28832112
AGUCGUUGCCGAAACUCAGCUGGCACUGGGCGUCCAGGGAGUAGAUCUCUCCGGGCAG
.(((..(((((.........)))))...)))((((.(((((.....))))).)))).. ( -20.10, z-score =  -0.41, R)
>droEre2.scaffold_4770 10800232 58 + 17746568
AGUCAUUGCCGAAACUCAGCUGGCACUGGGCGUCCAGGGAGUAGAUCUCCCCGGGCAG
.(((..(((((.........)))))...)))((((.(((((.....))))).)))).. ( -24.20, z-score =  -1.86, R)
>droAna3.scaffold_13340 12859268 58 + 23697760
UCGAGUUGCCGAAAAUCAACUGGCACUGGUGGGUUAGGGAGUAGAUCUCGCCAGGCAG
...(((((........))))).((.((((((((((........)))).)))))))).. ( -17.40, z-score =  -0.94, R)
>dp4.chr2 24439716 58 - 30794189
UCUGGUUGCCGUAAAUCAGCUCGCACUGGUUGUCCAGCGAGUAGAUCUCGCCCGGCAG
......(((((...(((.((((((..(((....))))))))).)))......))))). ( -20.30, z-score =  -1.91, R)
>droPer1.super_0 11644380 58 - 11822988
UCUGGUUGCCGUAAAUCAGCUCGCACUGGUUGUCCAGCGAGUAGAUCUCGCCCGGCAG
......(((((...(((.((((((..(((....))))))))).)))......))))). ( -20.30, z-score =  -1.91, R)
>droWil1.scaffold_181089 10809720 55 - 12369635
---UAUUACUGUAUAUCAAUUGACAUUGGCUAUCAAGGGAGUAGAUUUCACCCGGUAG
---...(((((....(((((....))))).......(((((.....))).))))))). (  -6.50, z-score =   0.97, R)
>droVir3.scaffold_13047 5919055 58 - 19223366
UCUGGUUGCCAUGUAUCAGCUGGCAUUGGUGGUCCAGCGAGUAAAUCUCACCGGGCAG
.(..((.((((.((....))))))))..)..((((.(.(((.....))).).)))).. ( -17.80, z-score =  -0.62, R)
>droMoj3.scaffold_6540 23614456 58 - 34148556
UCUGGUUGCCAUGUAUCAGACGACACUGAUGGUCCAGCGAAUAAAUCUCUCCUGGCUG
.((((..((((....((((......))))))))))))..................... ( -10.30, z-score =   0.68, R)
>droGri2.scaffold_14906 4390836 58 + 14172833
UCUGGUUGCCAUGUAUCAGCUGACACUGGUGAUCCAGAGAGUAGAUCUCACCGGGCAG
((((((..(((.((.((....)).)))))..).)))))(((.....)))......... ( -17.60, z-score =  -0.46, R)
>anoGam1.chr2R 53520604 58 + 62725911
AUCCAUUGCCAAACACCAGCUCGCACUGCUUGUCGUUGGUGAACUUUUCUCCCGCCAG
.....(..((((..((.(((.......))).))..))))..)................ ( -11.00, z-score =  -0.87, R)
>triCas2.ChLG6 4155970 58 + 13544221
AACCAAUCCCGAAUUCUAGUUCGCAUUGUUUGUCGGCUUCGAAGUUCUCUCCUGGUAG
.((((.....(((((..(((..(((.....)))..)))....))))).....)))).. ( -10.20, z-score =  -0.91, R)
>consensus
ACUCAUUGCCGAAAAUCAGCUGGCACUGGUCGUCCAGGGAGUAGAUCUCUCCAGGCAG
......((((....(((((......)))))........(((.....)))....)))). ( -8.08 =  -7.94 +  -0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,273,404 – 11,273,462
Length 58
Sequences 14
Columns 58
Reading direction reverse
Mean pairwise identity 71.86
Shannon entropy 0.65702
G+C content 0.54698
Mean single sequence MFE -16.09
Consensus MFE -6.79
Energy contribution -7.42
Covariance contribution 0.63
Combinations/Pair 1.71
Mean z-score -0.93
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.02
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr3R 11273404 58 - 27905053
CUGCCUGGAGAGAUCUACUCCCUGGACGCCCAGUGCCAGCUGAGUUUCGGCAAUGACU
.((((.((.(((.....)))))..((.((.((((....)))).)).))))))...... ( -16.60, z-score =  -0.34, R)
>droSim1.chr3R 17312153 58 + 27517382
CUGCCUGGAGAGAUUUACUCCCUGGACGCCCAGUGCCAGCUGAGUUUCGGCAAUGACU
.((((.((.(((.....)))))..((.((.((((....)))).)).))))))...... ( -16.60, z-score =  -0.72, R)
>droSec1.super_0 10445255 58 + 21120651
CUGCCUGGAGAGAUAUACUCCCUGGACGCCCAGUGCCAGCUGAGUUUCGGCAAUGACU
.((((.((.(((.....)))))..((.((.((((....)))).)).))))))...... ( -16.60, z-score =  -0.81, R)
>droYak2.chr3R 13674901 58 + 28832112
CUGCCCGGAGAGAUCUACUCCCUGGACGCCCAGUGCCAGCUGAGUUUCGGCAACGACU
.(((((((.(((.....))).)))((.((.((((....)))).)).))))))...... ( -17.00, z-score =  -0.47, R)
>droEre2.scaffold_4770 10800232 58 - 17746568
CUGCCCGGGGAGAUCUACUCCCUGGACGCCCAGUGCCAGCUGAGUUUCGGCAAUGACU
.(((((((((((.....)))))))((.((.((((....)))).)).))))))...... ( -23.90, z-score =  -2.17, R)
>droAna3.scaffold_13340 12859268 58 - 23697760
CUGCCUGGCGAGAUCUACUCCCUAACCCACCAGUGCCAGUUGAUUUUCGGCAACUCGA
.(((((((((((.....)))....((......))))))...(.....)))))...... ( -10.00, z-score =   0.36, R)
>dp4.chr2 24439716 58 + 30794189
CUGCCGGGCGAGAUCUACUCGCUGGACAACCAGUGCGAGCUGAUUUACGGCAACCAGA
.(((((....(((((..((((((((....)))..)))))..))))).)))))...... ( -22.80, z-score =  -3.00, R)
>droPer1.super_0 11644380 58 + 11822988
CUGCCGGGCGAGAUCUACUCGCUGGACAACCAGUGCGAGCUGAUUUACGGCAACCAGA
.(((((....(((((..((((((((....)))..)))))..))))).)))))...... ( -22.80, z-score =  -3.00, R)
>droWil1.scaffold_181089 10809720 55 + 12369635
CUACCGGGUGAAAUCUACUCCCUUGAUAGCCAAUGUCAAUUGAUAUACAGUAAUA---
.(((.(((.(.......).)))((((((.....))))))..........)))...--- (  -7.40, z-score =   0.09, R)
>droVir3.scaffold_13047 5919055 58 + 19223366
CUGCCCGGUGAGAUUUACUCGCUGGACCACCAAUGCCAGCUGAUACAUGGCAACCAGA
(((.((((((((.....))))))))........(((((.........)))))..))). ( -19.70, z-score =  -2.88, R)
>droMoj3.scaffold_6540 23614456 58 + 34148556
CAGCCAGGAGAGAUUUAUUCGCUGGACCAUCAGUGUCGUCUGAUACAUGGCAACCAGA
..((((..(.((((.....(((((......)))))..))))..)...))))....... ( -13.00, z-score =  -0.08, R)
>droGri2.scaffold_14906 4390836 58 - 14172833
CUGCCCGGUGAGAUCUACUCUCUGGAUCACCAGUGUCAGCUGAUACAUGGCAACCAGA
.((((.(((((..((((.....))))))))).(((((....)))))..))))...... ( -18.80, z-score =  -1.28, R)
>anoGam1.chr2R 53520604 58 - 62725911
CUGGCGGGAGAAAAGUUCACCAACGACAAGCAGUGCGAGCUGGUGUUUGGCAAUGGAU
...((.(((.(..(((((....((........))..)))))..).))).))....... ( -11.60, z-score =   0.88, R)
>triCas2.ChLG6 4155970 58 - 13544221
CUACCAGGAGAGAACUUCGAAGCCGACAAACAAUGCGAACUAGAAUUCGGGAUUGGUU
..(((((....(((.(((.....((.((.....)))).....))))))....))))). (  -8.50, z-score =   0.36, R)
>consensus
CUGCCCGGAGAGAUCUACUCCCUGGACAACCAGUGCCAGCUGAUUUUCGGCAACGAGU
.(((((((.(((.....))).)))......((((....))))......))))...... ( -6.79 =  -7.42 +   0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:17:27 2011