Locus 4232

Sequence ID dm3.chr2R
Location 11,556,647 – 11,556,715
Length 68
Max. P 0.995751
window5796 window5797

overview

Window 6

Location 11,556,647 – 11,556,715
Length 68
Sequences 3
Columns 72
Reading direction forward
Mean pairwise identity 93.06
Shannon entropy 0.09854
G+C content 0.47631
Mean single sequence MFE -19.73
Consensus MFE -19.95
Energy contribution -19.73
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -2.61
Structure conservation index 1.01
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.84
SVM RNA-class probability 0.995751
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11556647 68 + 21146708
AACGAUGUUUCCGUUUGGGAAAGUCGUCUGCCUCUGCUCGUGCAGGCAGCAUAC----UAAAUUCUCUUAUC
.(((((.(((((....))))).)))))((((((..((....)))))))).....----.............. ( -19.10, z-score =  -2.35, R)
>droSim1.chr2R 10288338 72 + 19596830
AACGAUGUUUCCGUUCGGAAAAGUCGUCUGCCUCUGCUCGUGCAGGCAGCACACUCACUAAAUUCUCUUAUC
.(((((.(((((....))))).)))))((((((..((....))))))))....................... ( -20.50, z-score =  -3.14, R)
>droSec1.super_1 9049759 72 + 14215200
AACGAUGUUUCCGUUUGGAAAAGUCGUCUGCCUCUGCUCGUGCAGGCAGCACACUCAGUAAAUUCUCUUAUC
.(((((.(((((....))))).)))))((((((..((....))))))))....................... ( -19.60, z-score =  -2.35, R)
>consensus
AACGAUGUUUCCGUUUGGAAAAGUCGUCUGCCUCUGCUCGUGCAGGCAGCACACUCA_UAAAUUCUCUUAUC
.(((((.(((((....))))).)))))((((((..((....))))))))....................... (-19.95 = -19.73 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 11,556,647 – 11,556,715
Length 68
Sequences 3
Columns 72
Reading direction reverse
Mean pairwise identity 93.06
Shannon entropy 0.09854
G+C content 0.47631
Mean single sequence MFE -19.63
Consensus MFE -18.27
Energy contribution -18.60
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.61
SVM RNA-class probability 0.954727
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11556647 68 - 21146708
GAUAAGAGAAUUUA----GUAUGCUGCCUGCACGAGCAGAGGCAGACGACUUUCCCAAACGGAAACAUCGUU
..............----...((((..((((....)))).))))(((((.(((((.....)))))..))))) ( -17.50, z-score =  -2.16, R)
>droSim1.chr2R 10288338 72 - 19596830
GAUAAGAGAAUUUAGUGAGUGUGCUGCCUGCACGAGCAGAGGCAGACGACUUUUCCGAACGGAAACAUCGUU
..................((.((((..((((....)))).)))).))((..(((((....)))))..))... ( -20.30, z-score =  -1.72, R)
>droSec1.super_1 9049759 72 - 14215200
GAUAAGAGAAUUUACUGAGUGUGCUGCCUGCACGAGCAGAGGCAGACGACUUUUCCAAACGGAAACAUCGUU
..............(((..(((((.....)))))..))).....(((((..(((((....)))))..))))) ( -21.10, z-score =  -2.42, R)
>consensus
GAUAAGAGAAUUUA_UGAGUGUGCUGCCUGCACGAGCAGAGGCAGACGACUUUUCCAAACGGAAACAUCGUU
.....................((((..((((....)))).))))(((((..(((((....)))))..))))) (-18.27 = -18.60 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:25:12 2011