Locus 8616

Sequence ID dm3.chr3RHet
Location 1,944,534 – 1,944,591
Length 57
Max. P 0.712209
window11831 window11832

overview

Window 1

Location 1,944,534 – 1,944,591
Length 57
Sequences 3
Columns 59
Reading direction forward
Mean pairwise identity 81.92
Shannon entropy 0.24903
G+C content 0.36574
Mean single sequence MFE -10.57
Consensus MFE -9.05
Energy contribution -9.17
Covariance contribution 0.11
Combinations/Pair 1.17
Mean z-score -1.31
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.712209
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 1944534 57 + 2517507
UAAAUUUGUU-GCCCAGCAUAGCUUAUUGGGACUCAAUCAUGGAUUUCAACA-AUAGCU
......((((-....)))).((((..(((..(..((....))..)..)))..-..)))) (  -8.90, z-score =   0.16, R)
>droSec1.super_42 95275 59 - 298440
UACAUUUUUUUACCCAGCAGAGCUAGCUGGGACUCAAAGACAGAUUUUAACAGAUAGUU
............((((((.......))))))............................ ( -11.40, z-score =  -2.19, R)
>droSim1.chr2h_random 3030368 59 + 3178526
UAAAUUUUUUUACCCAGCAGAGGUAGCUGGGACUCAAAGACAGAUUUUAACAGAUAGUU
............((((((.......))))))............................ ( -11.40, z-score =  -1.89, R)
>consensus
UAAAUUUUUUUACCCAGCAGAGCUAGCUGGGACUCAAAGACAGAUUUUAACAGAUAGUU
............((((((.......))))))............................ ( -9.05 =  -9.17 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 1,944,534 – 1,944,591
Length 57
Sequences 3
Columns 59
Reading direction reverse
Mean pairwise identity 81.92
Shannon entropy 0.24903
G+C content 0.36574
Mean single sequence MFE -10.30
Consensus MFE -8.49
Energy contribution -8.60
Covariance contribution 0.11
Combinations/Pair 1.17
Mean z-score -1.33
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.20
SVM RNA-class probability 0.588877
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 1944534 57 - 2517507
AGCUAU-UGUUGAAAUCCAUGAUUGAGUCCCAAUAAGCUAUGCUGGGC-AACAAAUUUA
.....(-(((((...((((.(....(((........)))...))))))-)))))..... (  -8.30, z-score =   0.54, R)
>droSec1.super_42 95275 59 + 298440
AACUAUCUGUUAAAAUCUGUCUUUGAGUCCCAGCUAGCUCUGCUGGGUAAAAAAAUGUA
.....................(((....((((((.......))))))....)))..... ( -11.30, z-score =  -1.90, R)
>droSim1.chr2h_random 3030368 59 - 3178526
AACUAUCUGUUAAAAUCUGUCUUUGAGUCCCAGCUACCUCUGCUGGGUAAAAAAAUUUA
.....................(((....((((((.......))))))....)))..... ( -11.30, z-score =  -2.64, R)
>consensus
AACUAUCUGUUAAAAUCUGUCUUUGAGUCCCAGCUAGCUCUGCUGGGUAAAAAAAUUUA
............................((((((.......))))))............ ( -8.49 =  -8.60 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:48:55 2011