Locus 11450

Sequence ID dm3.chr3R
Location 21,276,764 – 21,276,828
Length 64
Max. P 0.910208
window15740 window15741

overview

Window 0

Location 21,276,764 – 21,276,828
Length 64
Sequences 6
Columns 64
Reading direction forward
Mean pairwise identity 80.10
Shannon entropy 0.39946
G+C content 0.34222
Mean single sequence MFE -10.61
Consensus MFE -6.21
Energy contribution -7.13
Covariance contribution 0.92
Combinations/Pair 1.36
Mean z-score -2.06
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.21
SVM RNA-class probability 0.910208
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 21276764 64 + 27905053
AUUCAAGCUUUCAUCGCACUUUAUUACUAUUUAUCAACACAAUUUAGUGCAGAAAGCGAUUAUA
......((((((...(((((..(((...............)))..))))).))))))....... ( -12.96, z-score =  -3.41, R)
>droSim1.chr3R 21104938 64 + 27517382
AUUCAAGCUUUCAUCGCACUUUAUUACUAUUUAUCAACACAAUUUAGUGCAGAAAGCUAUUAUA
.....(((((((...(((((..(((...............)))..))))).)))))))...... ( -13.66, z-score =  -4.16, R)
>droSec1.super_13 62635 64 + 2104621
AUUCAAGCUGUCAUCGCACUUUAUUACUAUUUAUCAACACAAUUUAGUGCAGAAAGCGAUUAUA
......(((.((...(((((..(((...............)))..))))).)).)))....... (  -9.46, z-score =  -1.35, R)
>droYak2.chr3R 3623873 64 - 28832112
AUUCAAGCUUUCAUCGCACUUUUUCACUAUUUAUCAACACAAUUUAGUGCAGAAAGCGAUUAUA
......((((((...(((((.........................))))).))))))....... ( -12.01, z-score =  -3.72, R)
>droEre2.scaffold_4820 3701714 63 - 10470090
GUGCGAGUUUUCAUCGCAGUU-GCUACUACUUAUCAACACAAUUGAGGGCAGAAAGCGAUUAUA
..((((.......))))((((-(((.((.(((.((((.....))))))).))..)))))))... ( -12.90, z-score =  -0.72, R)
>droAna3.scaffold_13340 14494146 64 - 23697760
AUCCCAUCUCUCAGCGCACGACAAAAUUAGUUUUCCACACAAUUUCACAGCCGGAACGAUUACA
...........................(((((((((................)))).))))).. (  -2.69, z-score =   1.00, R)
>consensus
AUUCAAGCUUUCAUCGCACUUUAUUACUAUUUAUCAACACAAUUUAGUGCAGAAAGCGAUUAUA
......((((((...(((((.........................))))).))))))....... ( -6.21 =  -7.13 +   0.92)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 1

Location 21,276,764 – 21,276,828
Length 64
Sequences 6
Columns 64
Reading direction reverse
Mean pairwise identity 80.10
Shannon entropy 0.39946
G+C content 0.34222
Mean single sequence MFE -13.93
Consensus MFE -7.30
Energy contribution -7.75
Covariance contribution 0.45
Combinations/Pair 1.47
Mean z-score -2.00
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.64
SVM RNA-class probability 0.770768
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 21276764 64 - 27905053
UAUAAUCGCUUUCUGCACUAAAUUGUGUUGAUAAAUAGUAAUAAAGUGCGAUGAAAGCUUGAAU
.......((((((((((((..((((((((....)))).))))..))))))..))))))...... ( -16.00, z-score =  -3.09, R)
>droSim1.chr3R 21104938 64 - 27517382
UAUAAUAGCUUUCUGCACUAAAUUGUGUUGAUAAAUAGUAAUAAAGUGCGAUGAAAGCUUGAAU
......(((((((((((((..((((((((....)))).))))..))))))..)))))))..... ( -16.40, z-score =  -3.37, R)
>droSec1.super_13 62635 64 - 2104621
UAUAAUCGCUUUCUGCACUAAAUUGUGUUGAUAAAUAGUAAUAAAGUGCGAUGACAGCUUGAAU
.......(((.((((((((..((((((((....)))).))))..))))))..)).)))...... ( -12.50, z-score =  -1.42, R)
>droYak2.chr3R 3623873 64 + 28832112
UAUAAUCGCUUUCUGCACUAAAUUGUGUUGAUAAAUAGUGAAAAAGUGCGAUGAAAGCUUGAAU
.......((((((((((((..(((((........))))).....))))))..))))))...... ( -15.30, z-score =  -3.20, R)
>droEre2.scaffold_4820 3701714 63 + 10470090
UAUAAUCGCUUUCUGCCCUCAAUUGUGUUGAUAAGUAGUAGC-AACUGCGAUGAAAACUCGCAC
.......(((..((((..(((((...)))))...)))).)))-...((((((....).))))). ( -13.70, z-score =  -1.66, R)
>droAna3.scaffold_13340 14494146 64 + 23697760
UGUAAUCGUUCCGGCUGUGAAAUUGUGUGGAAAACUAAUUUUGUCGUGCGCUGAGAGAUGGGAU
.....((((((((((.(..((((((.((.....))))))))..).....)))).)).))))... (  -9.70, z-score =   0.76, R)
>consensus
UAUAAUCGCUUUCUGCACUAAAUUGUGUUGAUAAAUAGUAAUAAAGUGCGAUGAAAGCUUGAAU
.......((((((((((((..(((((........))))).....))))))..))))))...... ( -7.30 =  -7.75 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:43:14 2011