Locus 2415

Sequence ID dm3.chr2L
Location 18,870,026 – 18,870,076
Length 50
Max. P 0.973782
window3322 window3323

overview

Window 2

Location 18,870,026 – 18,870,076
Length 50
Sequences 7
Columns 57
Reading direction forward
Mean pairwise identity 83.23
Shannon entropy 0.30214
G+C content 0.42642
Mean single sequence MFE -14.37
Consensus MFE -10.79
Energy contribution -11.50
Covariance contribution 0.71
Combinations/Pair 1.00
Mean z-score -1.64
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.66
SVM RNA-class probability 0.777482
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18870026 50 + 23011544
------AGAAACAG-GCUGCUCGUGGCUUCUAGGAAAAUUUGUCAAUUUUCCUGGAA
------.......(-((((....)))))((((((((((((....)))))))))))). ( -16.10, z-score =  -2.52, R)
>droPer1.super_1 3700207 57 + 10282868
GGGGAGAGACACAGCAGAGCGCGUGACUUCUUGGAAAAUUUGUCAUUUUUCCUGGAA
((((((...(((.((.....))))).))))))((((((........))))))..... ( -12.30, z-score =   0.26, R)
>dp4.chr4_group3 2229606 57 + 11692001
GGGGAGGGACACAGCAGAGCGCGUGACUUCUUGGAAAAUUUGUCAUUUUUCCUGGAA
.((((((..(((.((.....))))).))))))((((((........))))))..... ( -14.60, z-score =  -0.52, R)
>droSim1.chr2L 18560318 50 + 22036055
------AGAAACAG-GCAGCUCGUGUCUUCUAGGAAAAUUUGUCAAUUUUCCUGGAA
------......((-(((.....)))))((((((((((((....)))))))))))). ( -15.70, z-score =  -2.78, R)
>droSec1.super_7 2497153 50 + 3727775
------AGAAACAG-GCAGCUCGUGUCUUCUAGGAAAAUUUGUUAAUUUUCCUGGAA
------......((-(((.....)))))((((((((((((....)))))))))))). ( -16.40, z-score =  -3.27, R)
>droYak2.chr2R 5385967 50 + 21139217
------AGAAACAG-GCGGCUCGUGACUUCUAGGAAAAUUUGUCCAUUUUCCUGGAA
------.((..(..-..)..))......(((((((((((......))))))))))). ( -12.50, z-score =  -0.84, R)
>droEre2.scaffold_4845 17182750 50 - 22589142
------AGGAACAU-UCAGCUCGUGACUUCUAGGAAAAUUUGUCAAUUUUCCUGGAA
------........-.............((((((((((((....)))))))))))). ( -13.00, z-score =  -1.81, R)
>consensus
______AGAAACAG_GCAGCUCGUGACUUCUAGGAAAAUUUGUCAAUUUUCCUGGAA
............................((((((((((((....)))))))))))). (-10.79 = -11.50 +   0.71)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 18,870,026 – 18,870,076
Length 50
Sequences 7
Columns 57
Reading direction reverse
Mean pairwise identity 83.23
Shannon entropy 0.30214
G+C content 0.42642
Mean single sequence MFE -10.96
Consensus MFE -10.59
Energy contribution -10.77
Covariance contribution 0.19
Combinations/Pair 1.12
Mean z-score -1.63
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.90
SVM RNA-class probability 0.973782
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18870026 50 - 23011544
UUCCAGGAAAAUUGACAAAUUUUCCUAGAAGCCACGAGCAGC-CUGUUUCU------
(((.(((((((((....))))))))).)))((.....))...-........------ ( -11.50, z-score =  -2.03, R)
>droPer1.super_1 3700207 57 - 10282868
UUCCAGGAAAAAUGACAAAUUUUCCAAGAAGUCACGCGCUCUGCUGUGUCUCUCCCC
.....((((((........)))))).(((.(.(((((.....)).))).)))).... ( -10.20, z-score =  -0.94, R)
>dp4.chr4_group3 2229606 57 - 11692001
UUCCAGGAAAAAUGACAAAUUUUCCAAGAAGUCACGCGCUCUGCUGUGUCCCUCCCC
(((..((((((........))))))..)))(.(((((.....)).))).)....... (  -9.00, z-score =  -0.62, R)
>droSim1.chr2L 18560318 50 - 22036055
UUCCAGGAAAAUUGACAAAUUUUCCUAGAAGACACGAGCUGC-CUGUUUCU------
(((.(((((((((....))))))))).))).....((((...-..))))..------ ( -11.50, z-score =  -1.97, R)
>droSec1.super_7 2497153 50 - 3727775
UUCCAGGAAAAUUAACAAAUUUUCCUAGAAGACACGAGCUGC-CUGUUUCU------
(((.(((((((((....))))))))).))).....((((...-..))))..------ ( -10.60, z-score =  -2.09, R)
>droYak2.chr2R 5385967 50 - 21139217
UUCCAGGAAAAUGGACAAAUUUUCCUAGAAGUCACGAGCCGC-CUGUUUCU------
(((.((((((((......)))))))).)))............-........------ ( -10.10, z-score =  -0.75, R)
>droEre2.scaffold_4845 17182750 50 + 22589142
UUCCAGGAAAAUUGACAAAUUUUCCUAGAAGUCACGAGCUGA-AUGUUCCU------
(((.(((((((((....))))))))).))).....((((...-..))))..------ ( -13.80, z-score =  -3.04, R)
>consensus
UUCCAGGAAAAUUGACAAAUUUUCCUAGAAGUCACGAGCUGC_CUGUUUCU______
(((.(((((((((....))))))))).))).....((((......))))........ (-10.59 = -10.77 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:50:47 2011