Locus 3079

Sequence ID dm3.chr2R
Location 2,064,450 – 2,064,511
Length 61
Max. P 0.995549
window4224 window4225

overview

Window 4

Location 2,064,450 – 2,064,511
Length 61
Sequences 3
Columns 61
Reading direction forward
Mean pairwise identity 88.52
Shannon entropy 0.16147
G+C content 0.29672
Mean single sequence MFE -10.07
Consensus MFE -8.92
Energy contribution -9.03
Covariance contribution 0.11
Combinations/Pair 1.10
Mean z-score -2.99
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.68
SVM RNA-class probability 0.994265
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 2064450 61 + 21146708
UCGUUUUAUCAUUUUUCUUCUCAUUUAUUAUGGACACGCCAAAAUUAUUUUGAUGUUUCCG
...............................(((.(((.((((.....)))).))).))). (  -6.80, z-score =  -1.36, R)
>droSim1.chr2R 959658 60 + 19596830
UCGUUUUAUCAUGUUUUU-CUCUUUUUUUAUAGAUACGCCAAAAUUAUUUUGGCGUUUCCG
..................-.............((.((((((((.....)))))))).)).. ( -11.80, z-score =  -4.25, R)
>droSec1.super_26 707110 61 + 826190
UCGUUUUAUCAUGUUUUUUCUCAUUUUUAAUUGAUACGCCAAAAUUAUUUUGGCGUUUCCG
................................((.((((((((.....)))))))).)).. ( -11.60, z-score =  -3.35, R)
>consensus
UCGUUUUAUCAUGUUUUUUCUCAUUUUUUAUAGAUACGCCAAAAUUAUUUUGGCGUUUCCG
................................((.((((((((.....)))))))).)).. ( -8.92 =  -9.03 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 2,064,450 – 2,064,511
Length 61
Sequences 3
Columns 61
Reading direction reverse
Mean pairwise identity 88.52
Shannon entropy 0.16147
G+C content 0.29672
Mean single sequence MFE -10.97
Consensus MFE -10.20
Energy contribution -10.53
Covariance contribution 0.34
Combinations/Pair 1.18
Mean z-score -2.92
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.82
SVM RNA-class probability 0.995549
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 2064450 61 - 21146708
CGGAAACAUCAAAAUAAUUUUGGCGUGUCCAUAAUAAAUGAGAAGAAAAAUGAUAAAACGA
.(((.((..((((.....))))..)).)))............................... (  -7.40, z-score =  -0.97, R)
>droSim1.chr2R 959658 60 - 19596830
CGGAAACGCCAAAAUAAUUUUGGCGUAUCUAUAAAAAAAGAG-AAAAACAUGAUAAAACGA
.(((.((((((((.....)))))))).)))............-.................. ( -13.20, z-score =  -4.43, R)
>droSec1.super_26 707110 61 - 826190
CGGAAACGCCAAAAUAAUUUUGGCGUAUCAAUUAAAAAUGAGAAAAAACAUGAUAAAACGA
..((.((((((((.....)))))))).))................................ ( -12.30, z-score =  -3.37, R)
>consensus
CGGAAACGCCAAAAUAAUUUUGGCGUAUCAAUAAAAAAUGAGAAAAAACAUGAUAAAACGA
.(((.((((((((.....)))))))).)))............................... (-10.20 = -10.53 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:03:14 2011