Locus 7408

Sequence ID dm3.chr3L
Location 14,639,422 – 14,639,483
Length 61
Max. P 0.878672
window10203 window10204

overview

Window 3

Location 14,639,422 – 14,639,483
Length 61
Sequences 5
Columns 69
Reading direction forward
Mean pairwise identity 88.89
Shannon entropy 0.18370
G+C content 0.58888
Mean single sequence MFE -19.12
Consensus MFE -16.90
Energy contribution -17.10
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.04
SVM RNA-class probability 0.878672
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14639422 61 + 24543557
UGCAUAUCGCCGGAUGAGGAACCCACAGCUCCUUGCUGCUGCCUCCCUGGUUACUGGAUCC--------
........(((((..((((......((((.....))))...)))).)))))..........-------- ( -16.00, z-score =  -0.34, R)
>droEre2.scaffold_4784 14609604 69 + 25762168
UGCAUAUCGCCGGAUGAGGAACCCGCAGCUCCUUGCUGCUGCCUCCUUGGUUCCUGAAUCCCUGAAUCC
.((.....)).((((.(((((((.(((((........)))))......)))))))..))))........ ( -22.60, z-score =  -2.94, R)
>droYak2.chr3L 14728007 69 + 24197627
UGCAUAUCGCCGGAUGAGGAACCCCCAGCUCCUGGCUGCUGCCUCCUUGGUUCCUGAAUCCCUGUAUCC
.((.....)).((((.(((((((..((((........)))).......)))))))..))))........ ( -19.00, z-score =  -1.13, R)
>droSec1.super_0 6764759 61 + 21120651
UGCAUAUCGCCGGAUGAGGAACCCACAGCUCCUUGCUGCUGCCUCCCUGGUUCCUGAAUCC--------
.((.....)).((((.(((((((((((((.....)))).)).......)))))))..))))-------- ( -19.01, z-score =  -2.17, R)
>droSim1.chr3L 13970026 61 + 22553184
UGCAUAUCGCCGGAUGAGGAACCCACAGCUCCUUGCUGCUGCCUCCCUGGUUCCUGAAUCC--------
.((.....)).((((.(((((((((((((.....)))).)).......)))))))..))))-------- ( -19.01, z-score =  -2.17, R)
>consensus
UGCAUAUCGCCGGAUGAGGAACCCACAGCUCCUUGCUGCUGCCUCCCUGGUUCCUGAAUCC________
.((.....)).((((.(((((((..((((........)))).......)))))))..))))........ (-16.90 = -17.10 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 14,639,422 – 14,639,483
Length 61
Sequences 5
Columns 69
Reading direction reverse
Mean pairwise identity 88.89
Shannon entropy 0.18370
G+C content 0.58888
Mean single sequence MFE -21.10
Consensus MFE -20.04
Energy contribution -20.32
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -0.87
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.583556
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14639422 61 - 24543557
--------GGAUCCAGUAACCAGGGAGGCAGCAGCAAGGAGCUGUGGGUUCCUCAUCCGGCGAUAUGCA
--------((((((........))((((..(((((.....))))).....)))))))).((.....)). ( -17.20, z-score =   0.47, R)
>droEre2.scaffold_4784 14609604 69 - 25762168
GGAUUCAGGGAUUCAGGAACCAAGGAGGCAGCAGCAAGGAGCUGCGGGUUCCUCAUCCGGCGAUAUGCA
((((..((((((((.....((.....))..(((((.....))))))))))))).)))).((.....)). ( -23.60, z-score =  -1.54, R)
>droYak2.chr3L 14728007 69 - 24197627
GGAUACAGGGAUUCAGGAACCAAGGAGGCAGCAGCCAGGAGCUGGGGGUUCCUCAUCCGGCGAUAUGCA
........((((..(((((((..((.(((....))).....))...))))))).)))).((.....)). ( -20.90, z-score =  -0.32, R)
>droSec1.super_0 6764759 61 - 21120651
--------GGAUUCAGGAACCAGGGAGGCAGCAGCAAGGAGCUGUGGGUUCCUCAUCCGGCGAUAUGCA
--------((((..(((((((.........(((((.....))))).))))))).)))).((.....)). ( -21.90, z-score =  -1.47, R)
>droSim1.chr3L 13970026 61 - 22553184
--------GGAUUCAGGAACCAGGGAGGCAGCAGCAAGGAGCUGUGGGUUCCUCAUCCGGCGAUAUGCA
--------((((..(((((((.........(((((.....))))).))))))).)))).((.....)). ( -21.90, z-score =  -1.47, R)
>consensus
________GGAUUCAGGAACCAGGGAGGCAGCAGCAAGGAGCUGUGGGUUCCUCAUCCGGCGAUAUGCA
........((((..(((((((.........(((((.....))))).))))))).)))).((.....)). (-20.04 = -20.32 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:26:23 2011