Locus 6708

Sequence ID dm3.chr3L
Location 9,079,893 – 9,080,004
Length 111
Max. P 0.991371
window9232 window9233

overview

Window 2

Location 9,079,893 – 9,080,004
Length 111
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 81.08
Shannon entropy 0.26247
G+C content 0.54354
Mean single sequence MFE -33.01
Consensus MFE -25.01
Energy contribution -26.90
Covariance contribution 1.89
Combinations/Pair 1.04
Mean z-score -2.08
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.21
SVM RNA-class probability 0.910035
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9079893 111 + 24543557
GCAAUCGAGGAUACCAGCCGCCUAAUGAGUUAAACGGAGGCUAUCAGCCUCCCAAUGAGUUAAAUGGAGCCUACCCGGCACCUUCUCAGUUAAACGGAGGCUACCAGCCUC
......((((.....((((.((......(((.(((((((((.....))))))...((((......((.(((.....))).))..))))))).))))).)))).....)))) ( -37.00, z-score =  -2.53, R)
>droEre2.scaffold_4784 20797092 111 - 25762168
GCAAUCGAGGCUACCAGCCACCUUCCCAGUUAAAUGGAGGCUACCAGCCACCUUCUCAGCCAAACGGAGGCUACCAGCCACCCUCUCAGCCAAACGGAGGCUAUCAGCCAC
........((((...((((.((...(((......))).((((...((((.((.............)).))))...))))................)).))))...)))).. ( -32.02, z-score =  -1.62, R)
>droSec1.super_0 1342834 111 + 21120651
GCAAUCGAGGCUACCAACCUCCUAAUGAGUUAAACGGAGCCUACCAACCUCCUUCUCAGUUGAACGGAGGCUACAAGCCACCUUCUCAGUUUAACGAAGGCUACCAGCCUC
......((((((......(((.....)))......(((((((.....((((((((......))).)))))....((((..........)))).....))))).)))))))) ( -30.00, z-score =  -2.10, R)
>consensus
GCAAUCGAGGCUACCAGCCACCUAAUGAGUUAAACGGAGGCUACCAGCCUCCUUCUCAGUUAAACGGAGGCUACCAGCCACCUUCUCAGUUAAACGGAGGCUACCAGCCUC
......((((((...((((.((.............((((((.....)))))).............((.(((.....))).)).............)).))))...)))))) (-25.01 = -26.90 +   1.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 9,079,893 – 9,080,004
Length 111
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 81.08
Shannon entropy 0.26247
G+C content 0.54354
Mean single sequence MFE -46.47
Consensus MFE -38.19
Energy contribution -38.53
Covariance contribution 0.34
Combinations/Pair 1.17
Mean z-score -2.71
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.47
SVM RNA-class probability 0.991371
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9079893 111 - 24543557
GAGGCUGGUAGCCUCCGUUUAACUGAGAAGGUGCCGGGUAGGCUCCAUUUAACUCAUUGGGAGGCUGAUAGCCUCCGUUUAACUCAUUAGGCGGCUGGUAUCCUCGAUUGC
((((.((.(((((...((((((.((((..((.(((.....))).)).............((((((.....))))))......))))))))))))))).)).))))...... ( -44.20, z-score =  -2.29, R)
>droEre2.scaffold_4784 20797092 111 + 25762168
GUGGCUGAUAGCCUCCGUUUGGCUGAGAGGGUGGCUGGUAGCCUCCGUUUGGCUGAGAAGGUGGCUGGUAGCCUCCAUUUAACUGGGAAGGUGGCUGGUAGCCUCGAUUGC
(.(((((.(((((.((..(..(.((((.(((.(((((.(((((.((.(((......))))).))))).)))))))).)))).)..)...)).))))).))))).)...... ( -48.40, z-score =  -2.15, R)
>droSec1.super_0 1342834 111 - 21120651
GAGGCUGGUAGCCUUCGUUAAACUGAGAAGGUGGCUUGUAGCCUCCGUUCAACUGAGAAGGAGGUUGGUAGGCUCCGUUUAACUCAUUAGGAGGUUGGUAGCCUCGAUUGC
(((((((.(((((((((((((((......((.(.((..((((((((.(((......)))))))))))..)).).)))))))))......)))))))).)))))))...... ( -46.80, z-score =  -3.69, R)
>consensus
GAGGCUGGUAGCCUCCGUUUAACUGAGAAGGUGGCUGGUAGCCUCCGUUUAACUGAGAAGGAGGCUGGUAGCCUCCGUUUAACUCAUUAGGAGGCUGGUAGCCUCGAUUGC
(((((((.(((((.((.......((((..((.(((.....))).)).............((((((.....))))))......))))...)).))))).)))))))...... (-38.19 = -38.53 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:12:57 2011