Locus 4276

Sequence ID dm3.chr2R
Location 11,818,973 – 11,819,024
Length 51
Max. P 0.998940
window5859 window5860

overview

Window 9

Location 11,818,973 – 11,819,024
Length 51
Sequences 5
Columns 53
Reading direction forward
Mean pairwise identity 75.29
Shannon entropy 0.43588
G+C content 0.50588
Mean single sequence MFE -14.41
Consensus MFE -10.64
Energy contribution -10.88
Covariance contribution 0.24
Combinations/Pair 1.23
Mean z-score -1.00
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.729582
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 11818973 51 + 21146708
CUAGAUAAGCAACGCUCGCUGAACGUGUGUGUGCGUGCGUCGCUUUGUUUC--
..((((((((.((((.(((...((....))..))).)))).)).)))))).-- ( -16.20, z-score =  -1.21, R)
>droSim1.chr2R 10557619 51 + 19596830
CUAGCUAAGCAACGCUCGCUGAACGUGUGUGUGCGUGCGUCGCUUUGUUUC--
..(((.((((.((((.(((...((....))..))).)))).)))).)))..-- ( -17.70, z-score =  -1.57, R)
>droSec1.super_1 9319189 51 + 14215200
CUAGCUAAGCAACGCUCGCUGAACGUGUGUGUGCGUGCGUCGCUUUGUUUC--
..(((.((((.((((.(((...((....))..))).)))).)))).)))..-- ( -17.70, z-score =  -1.57, R)
>droEre2.scaffold_4845 8550148 51 - 22589142
CUAUCUAAGCAACGCUCGCUGAACGUGUGUGUGCGUGCGUCGCUUUGUUUC--
......((((.((((.(((...((....))..))).)))).))))......-- ( -15.70, z-score =  -1.67, R)
>droGri2.scaffold_15245 17884872 51 - 18325388
GCGGCCAGUCAACAAU--UUGAAGAUUUUUUUUUGUUCAUGGAGUCAACUUAC
((..(((...(((((.--..............)))))..))).))........ (  -4.76, z-score =   1.03, R)
>consensus
CUAGCUAAGCAACGCUCGCUGAACGUGUGUGUGCGUGCGUCGCUUUGUUUC__
......((((.((((.(((...((....))..))).)))).))))........ (-10.64 = -10.88 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 11,818,973 – 11,819,024
Length 51
Sequences 5
Columns 53
Reading direction reverse
Mean pairwise identity 75.29
Shannon entropy 0.43588
G+C content 0.50588
Mean single sequence MFE -16.00
Consensus MFE -13.52
Energy contribution -13.56
Covariance contribution 0.04
Combinations/Pair 1.33
Mean z-score -3.10
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.56
SVM RNA-class probability 0.998940
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 11818973 51 - 21146708
--GAAACAAAGCGACGCACGCACACACACGUUCAGCGAGCGUUGCUUAUCUAG
--......(((((((((.(((..((....))...))).)))))))))...... ( -18.10, z-score =  -3.88, R)
>droSim1.chr2R 10557619 51 - 19596830
--GAAACAAAGCGACGCACGCACACACACGUUCAGCGAGCGUUGCUUAGCUAG
--......(((((((((.(((..((....))...))).)))))))))...... ( -18.10, z-score =  -3.22, R)
>droSec1.super_1 9319189 51 - 14215200
--GAAACAAAGCGACGCACGCACACACACGUUCAGCGAGCGUUGCUUAGCUAG
--......(((((((((.(((..((....))...))).)))))))))...... ( -18.10, z-score =  -3.22, R)
>droEre2.scaffold_4845 8550148 51 + 22589142
--GAAACAAAGCGACGCACGCACACACACGUUCAGCGAGCGUUGCUUAGAUAG
--......(((((((((.(((..((....))...))).)))))))))...... ( -18.10, z-score =  -4.17, R)
>droGri2.scaffold_15245 17884872 51 + 18325388
GUAAGUUGACUCCAUGAACAAAAAAAAAUCUUCAA--AUUGUUGACUGGCCGC
((.(((..((....((((............)))).--...))..))).))... (  -7.60, z-score =  -1.02, R)
>consensus
__GAAACAAAGCGACGCACGCACACACACGUUCAGCGAGCGUUGCUUAGCUAG
........(((((((((.(((.............))).)))))))))...... (-13.52 = -13.56 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:26:02 2011