Locus 6400

Sequence ID dm3.chr3L
Location 6,371,572 – 6,371,668
Length 96
Max. P 0.726463
window8806 window8807

overview

Window 6

Location 6,371,572 – 6,371,668
Length 96
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 84.43
Shannon entropy 0.26126
G+C content 0.51042
Mean single sequence MFE -25.74
Consensus MFE -21.67
Energy contribution -21.30
Covariance contribution -0.37
Combinations/Pair 1.10
Mean z-score -1.14
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.536677
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6371572 96 + 24543557
CUACCUACAUAUCUGCUGAUGGUGAGAU--GUGGUGAUGUUGAUGGAAAGCGGAAGAGGGGGCUUUCCCGGGUCCGAAAGGGUAGGGAAUAGGAAUAG
((((((.(((((((((.....)).))))--))).................((((...((((....))))...))))...))))))............. ( -27.40, z-score =  -1.36, R)
>droSim1.chr3L 5870528 80 + 22553184
CUACCUACAUAUCUGCUGAUGGUGA------UG------------GAAAGCGGAAGAGGGGGCUUUCCCGGGUCCGAAAGGGUAGGGAAUAGGAAUAG
...((((....((((((........------..------------...))))))..........(((((...(((....)))..)))))))))..... ( -23.32, z-score =  -0.85, R)
>droSec1.super_2 6335925 92 + 7591821
CUACCUACAUAUCUGCUGAUGGUGA------UGACGAUGGUGAUGGAAAGCGGAAGAGGGGGCUUUCCCGGGUCCGAAAGGGUAGGGAAUAGGAAUAG
...((((....((((((.....(.(------(.((....)).)).)..))))))..........(((((...(((....)))..)))))))))..... ( -25.90, z-score =  -1.04, R)
>droEre2.scaffold_4784 9062357 97 + 25762168
CUACCUACACAUCUGCUGAUGGUGAUGGUGAAGUUGAUGUUGAUGAAAAGCGGAAGAGGGG-CUUUUCCGGCUCCGAAAGGGUAGGGAAUUGGAAUAG
...((((((((((.(((..............))).)))))........((((((((((...-))))))).)))((....)))))))............ ( -26.34, z-score =  -1.31, R)
>consensus
CUACCUACAUAUCUGCUGAUGGUGA______UG_UGAUGUUGAUGGAAAGCGGAAGAGGGGGCUUUCCCGGGUCCGAAAGGGUAGGGAAUAGGAAUAG
((((((.((((((....))).)))..........................((((...((((....))))...))))...))))))............. (-21.67 = -21.30 +  -0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 6,371,572 – 6,371,668
Length 96
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 84.43
Shannon entropy 0.26126
G+C content 0.51042
Mean single sequence MFE -17.00
Consensus MFE -13.12
Energy contribution -13.38
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.726463
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6371572 96 - 24543557
CUAUUCCUAUUCCCUACCCUUUCGGACCCGGGAAAGCCCCCUCUUCCGCUUUCCAUCAACAUCACCAC--AUCUCACCAUCAGCAGAUAUGUAGGUAG
.............(((((....((....))(((((((..........)))))))............((--((.((..........)).)))).))))) ( -17.00, z-score =  -1.75, R)
>droSim1.chr3L 5870528 80 - 22553184
CUAUUCCUAUUCCCUACCCUUUCGGACCCGGGAAAGCCCCCUCUUCCGCUUUC------------CA------UCACCAUCAGCAGAUAUGUAGGUAG
.............(((((.....((.....(((((((..........))))))------------).------...))....(((....))).))))) ( -17.10, z-score =  -1.58, R)
>droSec1.super_2 6335925 92 - 7591821
CUAUUCCUAUUCCCUACCCUUUCGGACCCGGGAAAGCCCCCUCUUCCGCUUUCCAUCACCAUCGUCA------UCACCAUCAGCAGAUAUGUAGGUAG
.............(((((.....((.....(((((((..........)))))))....)).......------.........(((....))).))))) ( -17.10, z-score =  -1.45, R)
>droEre2.scaffold_4784 9062357 97 - 25762168
CUAUUCCAAUUCCCUACCCUUUCGGAGCCGGAAAAG-CCCCUCUUCCGCUUUUCAUCAACAUCAACUUCACCAUCACCAUCAGCAGAUGUGUAGGUAG
.............(((((....((....))((((((-(.........))))))).....................((((((....)))).)).))))) ( -16.80, z-score =  -1.85, R)
>consensus
CUAUUCCUAUUCCCUACCCUUUCGGACCCGGGAAAGCCCCCUCUUCCGCUUUCCAUCAACAUCA_CA______UCACCAUCAGCAGAUAUGUAGGUAG
.............(((((....((((...(((......)))...))))..................................(((....))).))))) (-13.12 = -13.38 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:07:01 2011