Locus 10388

Sequence ID dm3.chr3R
Location 13,539,479 – 13,539,626
Length 147
Max. P 0.886549
window14289 window14290

overview

Window 9

Location 13,539,479 – 13,539,592
Length 113
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 78.26
Shannon entropy 0.37639
G+C content 0.40639
Mean single sequence MFE -19.44
Consensus MFE -13.00
Energy contribution -13.64
Covariance contribution 0.64
Combinations/Pair 1.06
Mean z-score -1.51
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.734329
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 13539479 113 + 27905053
ACCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGAAAAAAUCAUAUCACGUGCUUCUCCAUUGGGGCCAACAAACCAAGCAAA------CCAAACCAAACACCAA
.(((((..........((((((.(((...))).))))))....((((((..........))))))..........))))).................------................ ( -18.00, z-score =  -1.64, R)
>droSim1.chr3R 19564094 110 - 27517382
UCCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGA---AAUCAUAUCACGUGCUUCUCCAUUGGGGCCAAUAAACCAAGCAAA------CCAAACCAAAAACCAA
.(((((..........((((((.(((...))).))))))....((((((---.......))))))..........))))).................------................ ( -18.20, z-score =  -1.93, R)
>droSec1.super_12 1500224 110 - 2123299
ACCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGA---AAUCAUAUCACGUGCUUCUCCAUUGGGGCCAAUAAACCAAGCAAA------CCAAACCAAAAACCAA
.(((((..........((((((.(((...))).))))))....((((((---.......))))))..........))))).................------................ ( -18.60, z-score =  -1.94, R)
>droYak2.chr3R 2115847 116 + 28832112
ACCCCACUAAUGAAACAAUUAACCGGUUUAUAUUUAAUUCAAAACGUGA---AAUCACAUCACGUGCUUCUCCUUUGGGGCCAAUAAACCAGGCAAAAAAAAACCAAACCAAAAACCAA
...((..((((......))))...(((((((............((((((---.......))))))(((((......)))))..))))))).)).......................... ( -19.70, z-score =  -1.61, R)
>droAna3.scaffold_12911 3255130 89 - 5364042
GCCUCGCCAAUAAAACAAUUAACCGGUUUCCGUUUAAAUGGAAACGUGA---AGUCGCAUCACGUGCACCGAGCGGGCCGGCCAUCAACCAA---------------------------
(((.(((.(((......)))...((((((((((....))))))((((((---.......))))))..)))).)))))).((.......))..--------------------------- ( -22.70, z-score =  -0.41, R)
>consensus
ACCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGA___AAUCAUAUCACGUGCUUCUCCAUUGGGGCCAAUAAACCAAGCAAA______CCAAACCAAAAACCAA
.((((...........((((((.((.....)).))))))....((((((..........))))))...........))))....................................... (-13.00 = -13.64 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 13,539,516 – 13,539,626
Length 110
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 90.69
Shannon entropy 0.14581
G+C content 0.40460
Mean single sequence MFE -18.55
Consensus MFE -16.45
Energy contribution -17.20
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.08
SVM RNA-class probability 0.886549
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13539516 110 + 27905053
UUCAAAACGUGAAAAAAUCAUAUCACGUGCUUCUCCAUUGGGGCCAACAAACCAAGCAAA------CCAAACCAAACACCAACUUCAAGCGCAUUAUCGCUUGACACAACUGAUAG
.(((..((((((..........))))))(((((......)))))................------..................(((((((......)))))))......)))... ( -19.30, z-score =  -2.07, R)
>droSim1.chr3R 19564131 106 - 27517382
UUCAAAACGUGAA---AUCAUAUCACGUGCUUCUCCAUUGGGGCCAAUAAACCAAGCAAA------CCAAACCAAAAACCAACUUCAAGCGCAUUAUCGCUUGACACAACUGAUA-
.(((..((((((.---......))))))((((....((((....)))).....))))...------..................(((((((......)))))))......)))..- ( -20.20, z-score =  -2.35, R)
>droSec1.super_12 1500261 106 - 2123299
UUCAAAACGUGAA---AUCAUAUCACGUGCUUCUCCAUUGGGGCCAAUAAACCAAGCAAA------CCAAACCAAAAACCAACUUCAAGCGCUUUAUCGCUUGACACAACUGAUA-
.(((..((((((.---......))))))((((....((((....)))).....))))...------..................(((((((......)))))))......)))..- ( -20.20, z-score =  -2.35, R)
>droYak2.chr3R 2115884 108 + 28832112
UUCAAAACGUGAA---AUCACAUCACGUGCUUCUCCUUUGGGGCCAAUAAACCAGGCAAAAAAAAACCAAACCAAAAACCAACUUCAA----CUUAUCGCUUGACACAACUGAUA-
.(((..((((((.---......))))))(((((......)))))........(((((...............................----......))))).......)))..- ( -14.49, z-score =  -0.60, R)
>consensus
UUCAAAACGUGAA___AUCAUAUCACGUGCUUCUCCAUUGGGGCCAAUAAACCAAGCAAA______CCAAACCAAAAACCAACUUCAAGCGCAUUAUCGCUUGACACAACUGAUA_
.(((..((((((..........))))))(((((......)))))........................................(((((((......)))))))......)))... (-16.45 = -17.20 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:23:04 2011