Locus 9090

Sequence ID dm3.chr3R
Location 4,023,108 – 4,023,214
Length 106
Max. P 0.707691
window12470 window12471

overview

Window 0

Location 4,023,108 – 4,023,214
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 93.11
Shannon entropy 0.11792
G+C content 0.47170
Mean single sequence MFE -31.92
Consensus MFE -29.17
Energy contribution -29.49
Covariance contribution 0.32
Combinations/Pair 1.13
Mean z-score -1.41
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.684211
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 4023108 106 + 27905053
CAGUGCAAGAACCGACUGUUCGAAGGAACAACAUCAUCAUCAUCAUCAGAAUUGACAAUUGGUGCCGCUGUUCCUGUUGGUGGUUUUACCUUUGUUGUUCCUGUGG
........((((.....))))..((((((((((...(((...((....))..))).....((((((((((.......)))))))...)))..)))))))))).... ( -26.30, z-score =   0.07, R)
>droSim1.chr3R 10282988 106 - 27517382
CAGUGCAAGAACCGACUGUUCGAAGGAACAACAUCAUCAUCAUCAUCAGCAUUGACAAUUGGUGCCGCUGUUCCUGUUGGUGAUUUUACCUUUGUUGUUCCUGUGG
........((((.....))))..((((((((((........((((((((((..((((..((....)).))))..))))))))))........)))))))))).... ( -31.79, z-score =  -1.76, R)
>droSec1.super_0 3315007 106 - 21120651
CAGUGCAAGAACCGACUGUUCGAAGGAACAACAUCAUCAUCAUCAUCAGCAUUGACAAUUGGUGCCGCUGUUCCUGUUGGUGAUUUUACCUUUGUUGUUCCUGUGG
........((((.....))))..((((((((((........((((((((((..((((..((....)).))))..))))))))))........)))))))))).... ( -31.79, z-score =  -1.76, R)
>droYak2.chr3R 8097287 106 + 28832112
CAGUGCAAGAACUGACUGUUCGAAGGAACAACAUCAUCGUCGUCAUCAUCAUUGACAAUCGGUGCCGCUGUUCCUGCUGGUGGCACUACCUUGGUUGUUCCUGUGG
((((......))))......((.(((((((((.........((((.......))))....(((((((((((....)).)))))))))......))))))))).)). ( -36.60, z-score =  -2.12, R)
>droEre2.scaffold_4770 191488 106 - 17746568
CAGUGCAAGAACUGACUGUUCGAAGGAACGACAUCAUCAUCUUCAUCAUCAUUGACAAUCGGAGCCGCUGUUCCUGUUGGUGGCUCUACCUUGGUUGUUCCUGUGG
((((......))))......((.(((((((((.............(((....)))(((..((((((((((.......))))))))))...)))))))))))).)). ( -33.10, z-score =  -1.49, R)
>consensus
CAGUGCAAGAACCGACUGUUCGAAGGAACAACAUCAUCAUCAUCAUCAGCAUUGACAAUUGGUGCCGCUGUUCCUGUUGGUGGUUUUACCUUUGUUGUUCCUGUGG
........((((.....))))..((((((((((........((((((((((..((((..((....)).))))..))))))))))........)))))))))).... (-29.17 = -29.49 +   0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 4,023,108 – 4,023,214
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 93.11
Shannon entropy 0.11792
G+C content 0.47170
Mean single sequence MFE -29.54
Consensus MFE -28.12
Energy contribution -28.20
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -1.19
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.47
SVM RNA-class probability 0.707691
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 4023108 106 - 27905053
CCACAGGAACAACAAAGGUAAAACCACCAACAGGAACAGCGGCACCAAUUGUCAAUUCUGAUGAUGAUGAUGAUGUUGUUCCUUCGAACAGUCGGUUCUUGCACUG
...(((((((......(((......)))...((((((((((.((.((((..(((....)))..))..)).)).)))))))))).(((....))))))))))..... ( -29.70, z-score =  -1.60, R)
>droSim1.chr3R 10282988 106 + 27517382
CCACAGGAACAACAAAGGUAAAAUCACCAACAGGAACAGCGGCACCAAUUGUCAAUGCUGAUGAUGAUGAUGAUGUUGUUCCUUCGAACAGUCGGUUCUUGCACUG
...(((((((......(((......)))...((((((((((.((.((((..(((....)))..))..)).)).)))))))))).(((....))))))))))..... ( -29.70, z-score =  -1.42, R)
>droSec1.super_0 3315007 106 + 21120651
CCACAGGAACAACAAAGGUAAAAUCACCAACAGGAACAGCGGCACCAAUUGUCAAUGCUGAUGAUGAUGAUGAUGUUGUUCCUUCGAACAGUCGGUUCUUGCACUG
...(((((((......(((......)))...((((((((((.((.((((..(((....)))..))..)).)).)))))))))).(((....))))))))))..... ( -29.70, z-score =  -1.42, R)
>droYak2.chr3R 8097287 106 - 28832112
CCACAGGAACAACCAAGGUAGUGCCACCAGCAGGAACAGCGGCACCGAUUGUCAAUGAUGAUGACGACGAUGAUGUUGUUCCUUCGAACAGUCAGUUCUUGCACUG
...(((((((......(((......))).(.((((((((((.((.((.((((((.......)))))))).)).)))))))))).).........)))))))..... ( -33.60, z-score =  -1.82, R)
>droEre2.scaffold_4770 191488 106 + 17746568
CCACAGGAACAACCAAGGUAGAGCCACCAACAGGAACAGCGGCUCCGAUUGUCAAUGAUGAUGAAGAUGAUGAUGUCGUUCCUUCGAACAGUCAGUUCUUGCACUG
...(((((((..........(((((.(...........).))))).((((((((....)))(((((..((((....)))).)))))..))))).)))))))..... ( -25.00, z-score =   0.29, R)
>consensus
CCACAGGAACAACAAAGGUAAAACCACCAACAGGAACAGCGGCACCAAUUGUCAAUGCUGAUGAUGAUGAUGAUGUUGUUCCUUCGAACAGUCGGUUCUUGCACUG
...(((((((......(((......)))...((((((((((.((.((.((((((.......)))))))).)).))))))))))...........)))))))..... (-28.12 = -28.20 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:57:49 2011