Locus 13184

Sequence ID dm3.chrX
Location 4,819,781 – 4,819,939
Length 158
Max. P 0.997506
window18131 window18132 window18133

overview

Window 1

Location 4,819,781 – 4,819,899
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.55
Shannon entropy 0.18366
G+C content 0.59957
Mean single sequence MFE -50.67
Consensus MFE -40.66
Energy contribution -39.67
Covariance contribution -0.99
Combinations/Pair 1.11
Mean z-score -2.12
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.874316
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4819781 118 - 22422827
UCACAGGCGCUGGAAAAUCUUAACCGCC-GGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCAGUCGAGCGGAA-GGAGGGACUUGUUUGAGUCCAACUACAGGAUACUGGGGGGCC
.....((((((((((((((..(.(((.(-(((((...)))))).))).)..)))))))))))))).(((...(....-)...((((((....))))))..(..(((....)))..)))). ( -50.70, z-score =  -3.52, R)
>droSim1.chrX 3726445 117 - 17042790
UCACCGGCGCUGGAGUUUCUUAACCGCC-GGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACGCUGGGGCC--
...(((((((((((((..(((..(((.(-(((((...)))))).)))((((..(((((.(((....)))))))))))).)))..))))(((((...)))))..)))..))))))....-- ( -53.10, z-score =  -1.99, R)
>droSec1.super_4 4252150 117 + 6179234
UCACCGGCGCUGGAGUUUCUUAACCGCCGGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCC-ACUACAGGACACUGGGGCC--
.....(((.(..((((..(((..(((.(((((......))))).)))((((..(((((.(((....)))))))))))).)))..))).......((((-......)))).)..).)))-- ( -48.20, z-score =  -0.84, R)
>consensus
UCACCGGCGCUGGAGUUUCUUAACCGCC_GGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACACUGGGGCC__
(((((((.((((((((.((..(.(((.(.(((((...)))))).))).)..)).)))))))).))))).))...........((((((....))))))..(..(((....)))..).... (-40.66 = -39.67 +  -0.99)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 4,819,821 – 4,819,939
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.30
Shannon entropy 0.16070
G+C content 0.57689
Mean single sequence MFE -52.80
Consensus MFE -43.60
Energy contribution -45.27
Covariance contribution 1.67
Combinations/Pair 1.05
Mean z-score -3.16
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.57
SVM RNA-class probability 0.992794
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4819821 118 + 22422827
-CCUUCCGCUCGACUGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCC-GGCGGUUAAGAUUUUCCAGCGCCUGUGAAGCGCCAGGAGCGAACUUGUUGGAGUCAAACUACAGGCUA
-(((..((((..((.(.((((((((((((..((((..((((((...)))))-)..))))..)))))))))))).).))..))))..)))......(((((.(........).)))))... ( -46.10, z-score =  -2.60, R)
>droSim1.chrX 3726483 119 + 17042790
CCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCC-GGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUGUUGGAGUCAAACUACAGGCUA
.(((((((((..((((..((.((((..((..(((((.((((((...)))))-).)))))..))..)))).))..))))..)))))))))....(((((((.(........).))))))). ( -60.00, z-score =  -4.45, R)
>droSec1.super_4 4252187 120 - 6179234
CCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGAUUGUUGGAGUCAAACUUCAGGCUA
.(((((((((..((((..((.((((..((..(((((.((((((...))).))).)))))..))..)))).))..))))..)))))))))(((.......((((((.....))))))))). ( -52.31, z-score =  -2.43, R)
>consensus
CCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCC_GGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUGUUGGAGUCAAACUACAGGCUA
.(((((((((..((((..((.((((..((..(((((.((((((...))))).).)))))..))..)))).))..))))..)))))))))....(((((((.(........).))))))). (-43.60 = -45.27 +   1.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 4,819,821 – 4,819,939
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.30
Shannon entropy 0.16070
G+C content 0.57689
Mean single sequence MFE -51.70
Consensus MFE -43.09
Energy contribution -42.10
Covariance contribution -0.99
Combinations/Pair 1.14
Mean z-score -3.72
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.12
SVM RNA-class probability 0.997506
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4819821 118 - 22422827
UAGCCUGUAGUUUGACUCCAACAAGUUCGCUCCUGGCGCUUCACAGGCGCUGGAAAAUCUUAACCGCC-GGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCAGUCGAGCGGAAGG-
...(((...((((((((..........(((.....))).......((((((((((((((..(.(((.(-(((((...)))))).))).)..))))))))))))))))))))))...)))- ( -50.80, z-score =  -4.30, R)
>droSim1.chrX 3726483 119 - 17042790
UAGCCUGUAGUUUGACUCCAACAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCC-GGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGG
.(((....((((((.......)))))).)))(((((.((((.(((((.((((((((.((..(.(((.(-(((((...)))))).))).)..)).)))))))).))))).)))).))))). ( -54.10, z-score =  -3.98, R)
>droSec1.super_4 4252187 120 + 6179234
UAGCCUGAAGUUUGACUCCAACAAUCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGG
.(((..((...(((....)))...))..)))(((((.((((.(((((.((((((((.((..(.(((.(((((......))))).))).)..)).)))))))).))))).)))).))))). ( -50.20, z-score =  -2.87, R)
>consensus
UAGCCUGUAGUUUGACUCCAACAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCC_GGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGG
.(((..((...(((....)))...))..)))(((((.((((.(((((.((((((((.((..(.(((.(.(((((...)))))).))).)..)).)))))))).))))).)))).))))). (-43.09 = -42.10 +  -0.99)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:16:21 2011