Locus 7003

Sequence ID dm3.chr3L
Location 11,414,995 – 11,415,071
Length 76
Max. P 0.962043
window9637 window9638

overview

Window 7

Location 11,414,995 – 11,415,071
Length 76
Sequences 5
Columns 84
Reading direction forward
Mean pairwise identity 87.12
Shannon entropy 0.21782
G+C content 0.55276
Mean single sequence MFE -26.30
Consensus MFE -19.52
Energy contribution -20.36
Covariance contribution 0.84
Combinations/Pair 1.05
Mean z-score -2.40
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.30
SVM RNA-class probability 0.923365
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11414995 76 + 24543557
---AACAGCUGCGGGCUGCGAAAUGAGAUGAAAUCGAAUCGCUGACGACUC-----ACUCGACCGCAGCUGGAAUCGGAAUUGG
---..(((((((((...((((..(((.......)))..))))...(((...-----..))).)))))))))............. ( -26.50, z-score =  -2.94, R)
>droAna3.scaffold_13337 5697009 84 + 23293914
GGCAGCUGCCGCCGACUGCCAAAUGAGAUGAAAUCGAAUCGCUGACGGCCCGGCCCACUCGACCGCAGCUGGAAAUGCGGAUGA
(((....)))((((...(((....(.(((........))).)....))).))))....(((.(((((........))))).))) ( -25.60, z-score =  -0.21, R)
>droEre2.scaffold_4784 11421022 76 + 25762168
---AACAGCUGCGGGCUGCGAAAUGAGAUGAAAUCGAAUCGCUGACGACUC-----ACUCGGCCGCAGCUGGAAUUGGAAUUGG
---..(((((((((.(.((((..(((.......)))..))))(((....))-----)...).)))))))))............. ( -26.50, z-score =  -2.70, R)
>droSec1.super_0 3624107 76 + 21120651
---AACAGCUGCGGGCUGCGAAAUGAGAUGAAAUCGAAUCUCUGACGACUC-----ACUCGACCGCAGCUGGAAUCGGAAUUGG
---..(((((((((....(((...(((((........)))))(((....))-----).))).)))))))))............. ( -26.40, z-score =  -3.18, R)
>droSim1.chr3L 10809361 76 + 22553184
---AACAGCUGCGGGCUGCGAAAUGAGAUGAAAUCGAAUCGCUGACGACUC-----ACUCGACCGCAGCUGGAAUCGGAAUUGG
---..(((((((((...((((..(((.......)))..))))...(((...-----..))).)))))))))............. ( -26.50, z-score =  -2.94, R)
>consensus
___AACAGCUGCGGGCUGCGAAAUGAGAUGAAAUCGAAUCGCUGACGACUC_____ACUCGACCGCAGCUGGAAUCGGAAUUGG
.....(((((((((...((((..(((.......)))..))))...(((..........))).)))))))))............. (-19.52 = -20.36 +   0.84)

alignment

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secondary structure

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dotplot

Postscript

Window 8

Location 11,414,995 – 11,415,071
Length 76
Sequences 5
Columns 84
Reading direction reverse
Mean pairwise identity 87.12
Shannon entropy 0.21782
G+C content 0.55276
Mean single sequence MFE -26.34
Consensus MFE -20.76
Energy contribution -21.24
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -2.45
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.70
SVM RNA-class probability 0.962043
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11414995 76 - 24543557
CCAAUUCCGAUUCCAGCUGCGGUCGAGU-----GAGUCGUCAGCGAUUCGAUUUCAUCUCAUUUCGCAGCCCGCAGCUGUU---
.............(((((((((.((((.-----((((((....))))))(((...)))....))))....)))))))))..--- ( -25.90, z-score =  -2.97, R)
>droAna3.scaffold_13337 5697009 84 - 23293914
UCAUCCGCAUUUCCAGCUGCGGUCGAGUGGGCCGGGCCGUCAGCGAUUCGAUUUCAUCUCAUUUGGCAGUCGGCGGCAGCUGCC
.............(((((((.(((((.((...(((..((....))..)))...(((.......))))).))))).))))))).. ( -28.40, z-score =   0.20, R)
>droEre2.scaffold_4784 11421022 76 - 25762168
CCAAUUCCAAUUCCAGCUGCGGCCGAGU-----GAGUCGUCAGCGAUUCGAUUUCAUCUCAUUUCGCAGCCCGCAGCUGUU---
.............((((((((((((((.-----((((((....))))))(((...)))....))))..).)))))))))..--- ( -26.00, z-score =  -3.54, R)
>droSec1.super_0 3624107 76 - 21120651
CCAAUUCCGAUUCCAGCUGCGGUCGAGU-----GAGUCGUCAGAGAUUCGAUUUCAUCUCAUUUCGCAGCCCGCAGCUGUU---
.............(((((((((.(..((-----(((......(((((........)))))..))))).).)))))))))..--- ( -25.50, z-score =  -2.95, R)
>droSim1.chr3L 10809361 76 - 22553184
CCAAUUCCGAUUCCAGCUGCGGUCGAGU-----GAGUCGUCAGCGAUUCGAUUUCAUCUCAUUUCGCAGCCCGCAGCUGUU---
.............(((((((((.((((.-----((((((....))))))(((...)))....))))....)))))))))..--- ( -25.90, z-score =  -2.97, R)
>consensus
CCAAUUCCGAUUCCAGCUGCGGUCGAGU_____GAGUCGUCAGCGAUUCGAUUUCAUCUCAUUUCGCAGCCCGCAGCUGUU___
.............(((((((((.(.........((((((....))))))(((...)))..........).)))))))))..... (-20.76 = -21.24 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:18:33 2011