Locus 12003

Sequence ID dm3.chr3R
Location 25,038,034 – 25,038,117
Length 83
Max. P 0.721745
window16496 window16497

overview

Window 6

Location 25,038,034 – 25,038,117
Length 83
Sequences 5
Columns 83
Reading direction forward
Mean pairwise identity 98.55
Shannon entropy 0.02609
G+C content 0.42169
Mean single sequence MFE -17.32
Consensus MFE -16.66
Energy contribution -16.70
Covariance contribution 0.04
Combinations/Pair 1.06
Mean z-score -1.38
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.721745
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25038034 83 + 27905053
CAAUGGUUUUUAUUUUCUCCAUUUUUCGUAUUUCUUUCAGCGAUCCUCUCGCUGUUUUUGGACUGUUUAGACAGGCCGGCCAA
...(((((.............................((((((.....)))))).....((.((((....)))).))))))). ( -18.00, z-score =  -1.82, R)
>droSim1.chr3R 24708911 83 + 27517382
CAAUGGUUUUUAUUUUCCCCAUUUUUCGUAUUUCUUUCAGCGAUCCUCUCGCUGUUUUUGGACUGUUUAGACAGGCCGGCCAA
...(((((.............................((((((.....)))))).....((.((((....)))).))))))). ( -18.00, z-score =  -1.63, R)
>droSec1.super_4 3900850 83 + 6179234
CAAUGCUUUUUAUUUUCCCCAUUUUUCGUAUUUCUUUCAGCGAUCCUCUCGCUGUUUUUGGACUGUUUAGACAGGCCGGCCAA
....(((..............................((((((.....)))))).....((.((((....)))).)))))... ( -15.30, z-score =  -0.99, R)
>droYak2.chr3R 7372549 83 - 28832112
CAAUGGUUUUUAUUUUCCCCAUUUUUCGUAUUUCUUUCAGCGAUCCUCUCGCUGUUUUUGGACUGUUUAGACAGGCCGGCCAA
...(((((.............................((((((.....)))))).....((.((((....)))).))))))). ( -18.00, z-score =  -1.63, R)
>droEre2.scaffold_4820 7477514 83 - 10470090
CAAUGGUUUUUAUUUUCCCCAUUUUUCGUAUUUCUUUCGGCGAUCCUCUCGCUGUUUUUGGACUGUUUAGACAGGCCGGCCAA
...(((((.............................((((((.....)))))).....((.((((....)))).))))))). ( -17.30, z-score =  -0.81, R)
>consensus
CAAUGGUUUUUAUUUUCCCCAUUUUUCGUAUUUCUUUCAGCGAUCCUCUCGCUGUUUUUGGACUGUUUAGACAGGCCGGCCAA
...(((((.............................((((((.....)))))).....((.((((....)))).))))))). (-16.66 = -16.70 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 25,038,034 – 25,038,117
Length 83
Sequences 5
Columns 83
Reading direction reverse
Mean pairwise identity 98.55
Shannon entropy 0.02609
G+C content 0.42169
Mean single sequence MFE -17.88
Consensus MFE -16.56
Energy contribution -16.96
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.719668
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25038034 83 - 27905053
UUGGCCGGCCUGUCUAAACAGUCCAAAAACAGCGAGAGGAUCGCUGAAAGAAAUACGAAAAAUGGAGAAAAUAAAAACCAUUG
(((...((.((((....)))).)).....((((((.....)))))).........)))..(((((............))))). ( -17.90, z-score =  -2.21, R)
>droSim1.chr3R 24708911 83 - 27517382
UUGGCCGGCCUGUCUAAACAGUCCAAAAACAGCGAGAGGAUCGCUGAAAGAAAUACGAAAAAUGGGGAAAAUAAAAACCAUUG
(((...((.((((....)))).)).....((((((.....)))))).........)))..(((((............))))). ( -19.20, z-score =  -2.00, R)
>droSec1.super_4 3900850 83 - 6179234
UUGGCCGGCCUGUCUAAACAGUCCAAAAACAGCGAGAGGAUCGCUGAAAGAAAUACGAAAAAUGGGGAAAAUAAAAAGCAUUG
....((((.((((....)))).)).....((((((.....)))))).................)).................. ( -17.30, z-score =  -1.24, R)
>droYak2.chr3R 7372549 83 + 28832112
UUGGCCGGCCUGUCUAAACAGUCCAAAAACAGCGAGAGGAUCGCUGAAAGAAAUACGAAAAAUGGGGAAAAUAAAAACCAUUG
(((...((.((((....)))).)).....((((((.....)))))).........)))..(((((............))))). ( -19.20, z-score =  -2.00, R)
>droEre2.scaffold_4820 7477514 83 + 10470090
UUGGCCGGCCUGUCUAAACAGUCCAAAAACAGCGAGAGGAUCGCCGAAAGAAAUACGAAAAAUGGGGAAAAUAAAAACCAUUG
(((((.((.((((....)))).))........(....)....))))).............(((((............))))). ( -15.80, z-score =  -0.55, R)
>consensus
UUGGCCGGCCUGUCUAAACAGUCCAAAAACAGCGAGAGGAUCGCUGAAAGAAAUACGAAAAAUGGGGAAAAUAAAAACCAUUG
(((...((.((((....)))).)).....((((((.....)))))).........)))..(((((............))))). (-16.56 = -16.96 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:53:48 2011