Locus 4248

Sequence ID dm3.chr2R
Location 11,679,283 – 11,679,333
Length 50
Max. P 0.972570
window5820 window5821

overview

Window 0

Location 11,679,283 – 11,679,333
Length 50
Sequences 4
Columns 52
Reading direction forward
Mean pairwise identity 87.58
Shannon entropy 0.19448
G+C content 0.42596
Mean single sequence MFE -14.73
Consensus MFE -12.77
Energy contribution -12.40
Covariance contribution -0.37
Combinations/Pair 1.27
Mean z-score -2.31
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.87
SVM RNA-class probability 0.972570
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11679283 50 + 21146708
ACUGUCCCAAACGGGUGGGGAAACUACUAUGGAAUGGACAGUUUUAAGCA--
(((((((......(((((.....))))).......)))))))........-- ( -15.22, z-score =  -1.89, R)
>droSim1.chr2R 10416409 50 + 19596830
ACUGUCCCAAACAGAAGGGGAAACUACUAUGGAAUGGACAGUUUUAAGCA--
(((((((....((....((....))....))....)))))))........-- ( -15.20, z-score =  -2.71, R)
>droSec1.super_1 9172875 52 + 14215200
ACUGUCCCAAACAGAAGGGGAAACUACUAUGGAAUGGACAGUUUUAAACACA
(((((((....((....((....))....))....))))))).......... ( -15.20, z-score =  -2.79, R)
>droYak2.chr2R 3831727 50 - 21139217
ACUGUCCUAAAUGGGAGGGGAAAAUACCAUGGAAUGGGCAGUUUUAAGAA--
(((((((...((((............)))).....)))))))........-- ( -13.30, z-score =  -1.85, R)
>consensus
ACUGUCCCAAACAGAAGGGGAAACUACUAUGGAAUGGACAGUUUUAAGCA__
(((((((....((....((....))....))....))))))).......... (-12.77 = -12.40 +  -0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 11,679,283 – 11,679,333
Length 50
Sequences 4
Columns 52
Reading direction reverse
Mean pairwise identity 87.58
Shannon entropy 0.19448
G+C content 0.42596
Mean single sequence MFE -9.69
Consensus MFE -8.74
Energy contribution -9.30
Covariance contribution 0.56
Combinations/Pair 1.15
Mean z-score -1.36
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.61
SVM RNA-class probability 0.760080
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11679283 50 - 21146708
--UGCUUAAAACUGUCCAUUCCAUAGUAGUUUCCCCACCCGUUUGGGACAGU
--........(((((((........((.(.....).)).......))))))) (  -8.26, z-score =  -0.55, R)
>droSim1.chr2R 10416409 50 - 19596830
--UGCUUAAAACUGUCCAUUCCAUAGUAGUUUCCCCUUCUGUUUGGGACAGU
--........(((((((.....((((.((......)).))))...))))))) ( -12.30, z-score =  -2.31, R)
>droSec1.super_1 9172875 52 - 14215200
UGUGUUUAAAACUGUCCAUUCCAUAGUAGUUUCCCCUUCUGUUUGGGACAGU
..........(((((((.....((((.((......)).))))...))))))) ( -12.30, z-score =  -2.29, R)
>droYak2.chr2R 3831727 50 + 21139217
--UUCUUAAAACUGCCCAUUCCAUGGUAUUUUCCCCUCCCAUUUAGGACAGU
--........((((.((.....((((............))))...)).)))) (  -5.90, z-score =  -0.28, R)
>consensus
__UGCUUAAAACUGUCCAUUCCAUAGUAGUUUCCCCUCCCGUUUGGGACAGU
..........(((((((.....((((.((......)).))))...))))))) ( -8.74 =  -9.30 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:25:31 2011