Locus 9356

Sequence ID dm3.chr3R
Location 6,219,169 – 6,219,259
Length 90
Max. P 0.976984
window12822 window12823

overview

Window 2

Location 6,219,169 – 6,219,259
Length 90
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 72.71
Shannon entropy 0.50966
G+C content 0.50256
Mean single sequence MFE -17.57
Consensus MFE -9.48
Energy contribution -10.37
Covariance contribution 0.89
Combinations/Pair 1.18
Mean z-score -1.78
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.47
SVM RNA-class probability 0.941099
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6219169 90 + 27905053
AAUA--UAUAAUAGAAGCGCAUA----CACCUUAUCAGCCGACCGACAAGCCCAAGGUCGACGAUCAGGCGAGAGCCAGACCAGACCGGUCCAGCC
....--............((...----..........(.(((((...........))))).).....(((....))).((((.....))))..)). ( -20.80, z-score =  -2.23, R)
>droSim1.chr3R 12339216 90 - 27517382
AAUA--UAUAAUAGAAGCAUAUU----CACCUUAUCAGCCGACCGACAAGCCCAAGGUCGUCGAUCAGGCGAGAGCCAGACCAGAGCAGUCCAGCC
....--...............((----(.(((.(((.(.(((((...........))))).)))).))).))).((..(((.......)))..)). ( -18.30, z-score =  -2.00, R)
>droSec1.super_0 5394417 83 - 21120651
AAUA--UAUAAUAGAAGCAUAUU----CACCUUAUCAGCCGACCGACAAGCCCAAGGUC-------AGGCGAGAGCCAGACCAGAGCAGUCCAGCC
....--..........((.....----...(((.((........)).))).....((((-------.(((....))).))))...))......... ( -16.90, z-score =  -2.72, R)
>droYak2.chr3R 10245001 93 + 28832112
AGUAA-UAGAAUAGAAGCAUAUA--CACACCUUAUCAGCCGACCGACAAACCCAAGGUCGUCGAUCAGGCGAGAGCCAGACCAGUCCAGUCCAGCC
.....-..........((.....--............(.(((((...........))))).)(.((.(((....))).)).)...........)). ( -16.60, z-score =  -1.62, R)
>droEre2.scaffold_4770 2345349 93 - 17746568
AGUA--UAUAAUAGAAGCAUAUAAACACACCUUAUCA-CCGACCGACAAACCCAAGGUCGUCGAUCAGGCGAGAGCCAGACCAGACCAGUCCAGCC
....--..........((...............(((.-.(((((...........)))))..)))..(((....))).(((.......)))..)). ( -17.90, z-score =  -2.83, R)
>droWil1.scaffold_181089 12279869 79 - 12369635
GACAUUUAUCUUAUCGACUUG------AAUUGCAUAUAUCUGCCUACA---UCAAGGUCAU---UUGAGGGUGAAAGAGGGGAGGCGGGUC-----
(((.....(((..((..((((------(...(((......))).....---))))).((((---(....)))))..))..))).....)))----- ( -14.90, z-score =   0.71, R)
>consensus
AAUA__UAUAAUAGAAGCAUAUA____CACCUUAUCAGCCGACCGACAAGCCCAAGGUCGUCGAUCAGGCGAGAGCCAGACCAGACCAGUCCAGCC
.......................................(((((...........))))).......(((....))).(((.......)))..... ( -9.48 = -10.37 +   0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 6,219,169 – 6,219,259
Length 90
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 72.71
Shannon entropy 0.50966
G+C content 0.50256
Mean single sequence MFE -27.67
Consensus MFE -15.28
Energy contribution -17.78
Covariance contribution 2.50
Combinations/Pair 1.15
Mean z-score -2.01
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.96
SVM RNA-class probability 0.976984
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6219169 90 - 27905053
GGCUGGACCGGUCUGGUCUGGCUCUCGCCUGAUCGUCGACCUUGGGCUUGUCGGUCGGCUGAUAAGGUG----UAUGCGCUUCUAUUAUA--UAUU
(((..((((.....))))..)))..(((((.((((((((((...........))))))).))).)))))----.................--.... ( -32.20, z-score =  -1.79, R)
>droSim1.chr3R 12339216 90 + 27517382
GGCUGGACUGCUCUGGUCUGGCUCUCGCCUGAUCGACGACCUUGGGCUUGUCGGUCGGCUGAUAAGGUG----AAUAUGCUUCUAUUAUA--UAUU
(((..((((.....))))..)))...(((.(((((((((((...)).))))))))))))(((((((((.----.....)))).)))))..--.... ( -31.40, z-score =  -2.73, R)
>droSec1.super_0 5394417 83 + 21120651
GGCUGGACUGCUCUGGUCUGGCUCUCGCCU-------GACCUUGGGCUUGUCGGUCGGCUGAUAAGGUG----AAUAUGCUUCUAUUAUA--UAUU
((((((...((((.((((.(((....))).-------))))..))))...))))))...(((((((((.----.....)))).)))))..--.... ( -28.10, z-score =  -2.45, R)
>droYak2.chr3R 10245001 93 - 28832112
GGCUGGACUGGACUGGUCUGGCUCUCGCCUGAUCGACGACCUUGGGUUUGUCGGUCGGCUGAUAAGGUGUG--UAUAUGCUUCUAUUCUA-UUACU
(((..((((.....))))..)))...(((.(((((((((((...)).))))))))))))(((((..(((.(--(....))...)))..))-))).. ( -31.00, z-score =  -2.10, R)
>droEre2.scaffold_4770 2345349 93 + 17746568
GGCUGGACUGGUCUGGUCUGGCUCUCGCCUGAUCGACGACCUUGGGUUUGUCGGUCGG-UGAUAAGGUGUGUUUAUAUGCUUCUAUUAUA--UACU
(((..((((.....))))..))).(((((.(((((((((((...)).)))))))))))-)))...(((((((..(((......))).)))--)))) ( -34.00, z-score =  -3.43, R)
>droWil1.scaffold_181089 12279869 79 + 12369635
-----GACCCGCCUCCCCUCUUUCACCCUCAA---AUGACCUUGA---UGUAGGCAGAUAUAUGCAAUU------CAAGUCGAUAAGAUAAAUGUC
-----...........................---.((((.((((---.....(((......)))...)------))))))).............. (  -9.30, z-score =   0.43, R)
>consensus
GGCUGGACUGGUCUGGUCUGGCUCUCGCCUGAUCGACGACCUUGGGCUUGUCGGUCGGCUGAUAAGGUG____UAUAUGCUUCUAUUAUA__UAUU
(((..((((.....))))..)))..(((((.(((..(((((...........)))))...))).)))))........................... (-15.28 = -17.78 +   2.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:02:45 2011