Locus 14877

Sequence ID dm3.chrX
Location 16,028,404 – 16,028,500
Length 96
Max. P 0.818368
window20489 window20490

overview

Window 9

Location 16,028,404 – 16,028,500
Length 96
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 86.92
Shannon entropy 0.18023
G+C content 0.54193
Mean single sequence MFE -39.80
Consensus MFE -28.43
Energy contribution -29.77
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.73
SVM RNA-class probability 0.799645
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16028404 96 + 22422827
-----------GGCUAGAAGGAAAUAUCCGGGCUAGGAGUGAUUGGCUCCUGCCCAAGCGAAUGGCAGCUGAAAGGUUUCCUAGCGAGCAGCUGCUGAUCGAGAAUG
-----------.(((....(((....)))((((.((((((.....)))))))))).)))((.(((((((((....(((....)))...))))))))).))....... ( -39.20, z-score =  -2.61, R)
>droSec1.super_47 86082 107 + 216421
GGCUGGAUGUGACCAAGAAGGAAAUAUCCGGGCUAGGAGUGAUUGGCUCCAGCCCAAGCGAAUGACAGCUGAAAGGUUUCCUAGGGAGCAGCUGCUGAACGAGGAUG
.(((((((((..((.....))..))))))(((((.(((((.....)))))))))).)))......((((.(....(((((....)))))..).)))).......... ( -40.70, z-score =  -2.83, R)
>droSim1.chrX 12366338 107 + 17042790
GGCUGGAUGUGGCCAAGAAUGAAAUAUCCGGGCUAGGAGUGAUUGGCUCCUUCCCAAGCGAAUGGCAGCUGAAAGGUUUCCUAGGGAGCAGCUGCUGAACGAGGAUG
((((......))))..........((((((((..((((((.....)))))).)))...((..((((((((.....(((((....)))))))))))))..)).))))) ( -39.50, z-score =  -1.65, R)
>consensus
GGCUGGAUGUGGCCAAGAAGGAAAUAUCCGGGCUAGGAGUGAUUGGCUCCUGCCCAAGCGAAUGGCAGCUGAAAGGUUUCCUAGGGAGCAGCUGCUGAACGAGGAUG
........................(((((((((.((((((.....))))))))))...((..(((((((((..(((...)))......)))))))))..)).))))) (-28.43 = -29.77 +   1.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 16,028,404 – 16,028,500
Length 96
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 86.92
Shannon entropy 0.18023
G+C content 0.54193
Mean single sequence MFE -31.93
Consensus MFE -26.31
Energy contribution -26.53
Covariance contribution 0.23
Combinations/Pair 1.09
Mean z-score -1.91
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.818368
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16028404 96 - 22422827
CAUUCUCGAUCAGCAGCUGCUCGCUAGGAAACCUUUCAGCUGCCAUUCGCUUGGGCAGGAGCCAAUCACUCCUAGCCCGGAUAUUUCCUUCUAGCC-----------
.......((...(((((((.......(....)....)))))))...))(((.(((((((((.......))))).))))(((....)))....))).----------- ( -32.90, z-score =  -2.42, R)
>droSec1.super_47 86082 107 - 216421
CAUCCUCGUUCAGCAGCUGCUCCCUAGGAAACCUUUCAGCUGUCAUUCGCUUGGGCUGGAGCCAAUCACUCCUAGCCCGGAUAUUUCCUUCUUGGUCACAUCCAGCC
............(((((((.......(....)....))))))).....(((.(((((((((.......)))).)))))((((....((.....))....))))))). ( -33.10, z-score =  -2.33, R)
>droSim1.chrX 12366338 107 - 17042790
CAUCCUCGUUCAGCAGCUGCUCCCUAGGAAACCUUUCAGCUGCCAUUCGCUUGGGAAGGAGCCAAUCACUCCUAGCCCGGAUAUUUCAUUCUUGGCCACAUCCAGCC
............(((((((.......(....)....))))))).....(((.(((.(((((.......))))).(((.(((........))).)))....)))))). ( -29.80, z-score =  -0.99, R)
>consensus
CAUCCUCGUUCAGCAGCUGCUCCCUAGGAAACCUUUCAGCUGCCAUUCGCUUGGGCAGGAGCCAAUCACUCCUAGCCCGGAUAUUUCCUUCUUGGCCACAUCCAGCC
.((((.((....(((((((.......(....)....)))))))....))...(((((((((.......))))).))))))))......................... (-26.31 = -26.53 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:48:36 2011