Locus 6281

Sequence ID dm3.chr3L
Location 5,242,909 – 5,243,027
Length 118
Max. P 0.860200
window8634 window8635

overview

Window 4

Location 5,242,909 – 5,243,027
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 95.76
Shannon entropy 0.07363
G+C content 0.38030
Mean single sequence MFE -16.79
Consensus MFE -15.99
Energy contribution -15.87
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.60
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.860200
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5242909 118 + 24543557
AAAUUCGCAUAAAAAUAAUAAAGCUUUUGCCACAUAACUCCCUAAUUUAUGCGAAUGCCCCUCUCUCAGAAGGUGUCAACUUUAUGAUAUAAUCCCAGCCAACAUGAAGCUAAUCCCC
..(((((((((((.........((....))....((......)).)))))))))))((((.((.....)).)).))...(((((((................)))))))......... ( -16.79, z-score =  -1.44, R)
>droSim1.chr3L 4761943 118 + 22553184
AAAUUCGCAUAAAAAUAAUAAAGCUUUUGCCACAUAACUCCCUAAUUUAUGCGAAUGCCCCUCUCUCAGAAGGUGUCAACUUUAUGAUAUAAUCCCAGCCAACAUGAAGCUAAUCCCC
..(((((((((((.........((....))....((......)).)))))))))))((((.((.....)).)).))...(((((((................)))))))......... ( -16.79, z-score =  -1.44, R)
>droSec1.super_2 5195781 117 + 7591821
AAAUUCGCAUAAAAAUAAUAAAGCGUUUGCCACAUAACUCCCUAAUUUAUGCGA-UGCCCCUCUCUCAGAAGGUGUCAACUUUAUGAUAUAAUCCUAGCCAACAUAAAGCUAAUCCCC
......(((((((.........((....))....((......)).)))))))((-((((..((.....)).))))))..(((((((................)))))))......... ( -15.29, z-score =  -1.04, R)
>droYak2.chr3L 5807497 118 + 24197627
AAAUUCGCAUAAAAAUAAUAAAGCUUUUGCCACAUAACUCCCUAAUUUAUGCGAAUGCCCCUCCCUCUAAAGGUGUCAACUUUAUGAUAUAAUCCCAGCGAACAUGAAGCUAAUCCCC
..(((((((((((.........((....))....((......)).)))))))))))................((((((......))))))......(((.........)))....... ( -16.40, z-score =  -1.62, R)
>droEre2.scaffold_4784 7938164 118 + 25762168
AAAUUCGCAUAAAAAUAAUAAAGCUUUUGCCACAUAACUGCCUAAUUUAUGCGAAUGCCCCUCCCUCAAAAGGUGCCAACUUUAUGAUAUAAUCCCAACGAACAUGAAGCUAAUCCCC
..(((((((((((.........((....))..((....)).....)))))))))))((.(((........))).))...(((((((................)))))))......... ( -18.69, z-score =  -2.48, R)
>consensus
AAAUUCGCAUAAAAAUAAUAAAGCUUUUGCCACAUAACUCCCUAAUUUAUGCGAAUGCCCCUCUCUCAGAAGGUGUCAACUUUAUGAUAUAAUCCCAGCCAACAUGAAGCUAAUCCCC
..(((((((((((.........((....))....((......)).)))))))))))((.(((........))).))...(((((((................)))))))......... (-15.99 = -15.87 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 5,242,909 – 5,243,027
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 95.76
Shannon entropy 0.07363
G+C content 0.38030
Mean single sequence MFE -28.82
Consensus MFE -26.12
Energy contribution -26.16
Covariance contribution 0.04
Combinations/Pair 1.09
Mean z-score -1.53
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.39
SVM RNA-class probability 0.672618
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5242909 118 - 24543557
GGGGAUUAGCUUCAUGUUGGCUGGGAUUAUAUCAUAAAGUUGACACCUUCUGAGAGAGGGGCAUUCGCAUAAAUUAGGGAGUUAUGUGGCAAAAGCUUUAUUAUUUUUAUGCGAAUUU
........((....(((..(((..(((...)))....)))..)))(((((.....)))))))(((((((((((....((((((.(......).))))))......))))))))))).. ( -30.70, z-score =  -1.93, R)
>droSim1.chr3L 4761943 118 - 22553184
GGGGAUUAGCUUCAUGUUGGCUGGGAUUAUAUCAUAAAGUUGACACCUUCUGAGAGAGGGGCAUUCGCAUAAAUUAGGGAGUUAUGUGGCAAAAGCUUUAUUAUUUUUAUGCGAAUUU
........((....(((..(((..(((...)))....)))..)))(((((.....)))))))(((((((((((....((((((.(......).))))))......))))))))))).. ( -30.70, z-score =  -1.93, R)
>droSec1.super_2 5195781 117 - 7591821
GGGGAUUAGCUUUAUGUUGGCUAGGAUUAUAUCAUAAAGUUGACACCUUCUGAGAGAGGGGCA-UCGCAUAAAUUAGGGAGUUAUGUGGCAAACGCUUUAUUAUUUUUAUGCGAAUUU
........((....(((..(((..(((...)))....)))..)))(((((.....))))))).-(((((((((.(((((.(((........))).))))).....))))))))).... ( -28.70, z-score =  -1.70, R)
>droYak2.chr3L 5807497 118 - 24197627
GGGGAUUAGCUUCAUGUUCGCUGGGAUUAUAUCAUAAAGUUGACACCUUUAGAGGGAGGGGCAUUCGCAUAAAUUAGGGAGUUAUGUGGCAAAAGCUUUAUUAUUUUUAUGCGAAUUU
........(((((.((((.(((..(((...)))....))).))))(((....)))..)))))(((((((((((....((((((.(......).))))))......))))))))))).. ( -28.00, z-score =  -1.50, R)
>droEre2.scaffold_4784 7938164 118 - 25762168
GGGGAUUAGCUUCAUGUUCGUUGGGAUUAUAUCAUAAAGUUGGCACCUUUUGAGGGAGGGGCAUUCGCAUAAAUUAGGCAGUUAUGUGGCAAAAGCUUUAUUAUUUUUAUGCGAAUUU
........(((((.(.((((..(((....(..((......))..))))..)))).).)))))(((((((((((....(((....)))(((....)))........))))))))))).. ( -26.00, z-score =  -0.60, R)
>consensus
GGGGAUUAGCUUCAUGUUGGCUGGGAUUAUAUCAUAAAGUUGACACCUUCUGAGAGAGGGGCAUUCGCAUAAAUUAGGGAGUUAUGUGGCAAAAGCUUUAUUAUUUUUAUGCGAAUUU
........((....(((..(((..(((...)))....)))..)))(((((.....)))))))(((((((((((....((((((.(......).))))))......))))))))))).. (-26.12 = -26.16 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:04:37 2011