Locus 2097

Sequence ID dm3.chr2L
Location 16,277,875 – 16,277,928
Length 53
Max. P 0.941300
window2883 window2884

overview

Window 3

Location 16,277,875 – 16,277,928
Length 53
Sequences 7
Columns 53
Reading direction forward
Mean pairwise identity 70.84
Shannon entropy 0.54522
G+C content 0.51826
Mean single sequence MFE -9.40
Consensus MFE -4.23
Energy contribution -5.17
Covariance contribution 0.94
Combinations/Pair 1.14
Mean z-score -2.00
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.47
SVM RNA-class probability 0.941300
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16277875 53 + 23011544
UAUCAUCCCUCACUUAAAAGGCCGUUCGUUCCACCGGCCUUUUGCGAAACACG
............(.((((((((((..........)))))))))).)....... ( -13.20, z-score =  -3.34, R)
>droPer1.super_8 3242770 51 + 3966273
UCUCACCGGCCAGCCAAAAGCCCUUCAGCUUCAGCGUCUUCUCAACAUGCG--
.......((....))..((((......))))..((((.........)))).-- (  -5.80, z-score =   0.37, R)
>dp4.chr4_group2 590485 51 - 1235136
UCUCACCGGCCAGCCAAAAGCCCUUCAGCUUCAGCGUCUUCUCAACAUGCG--
.......((....))..((((......))))..((((.........)))).-- (  -5.80, z-score =   0.37, R)
>droEre2.scaffold_4929 7974356 53 + 26641161
UAUCAUCCCUCACUAACAAGGCCGUUCGUUCUACCGGCCUUUUACAAAACACG
.................(((((((..........)))))))............ (  -9.80, z-score =  -3.62, R)
>droYak2.chr2L 3275893 53 - 22324452
UAUCCUUUCUCACUAACAAGGCCGUUCGUUCUACCGGCCUUUUACGAAUCACG
.................(((((((..........)))))))............ (  -9.80, z-score =  -2.59, R)
>droSec1.super_5 5003138 53 + 5866729
UAUCAUCCCUCGCUUACAAGGCCGUUCGUUCCACCGGCCUUUUACGAAACACG
.........(((..((.(((((((..........))))))).)))))...... ( -11.40, z-score =  -2.56, R)
>droSim1.chr2L 15986922 53 + 22036055
UAUCAUCCCUCACUUACAAGGCCGUUCGUUCCACCGGCCUUUUACGAAACACG
............(.((.(((((((..........))))))).)).)....... ( -10.00, z-score =  -2.67, R)
>consensus
UAUCAUCCCUCACUUACAAGGCCGUUCGUUCCACCGGCCUUUUACGAAACACG
.................(((((((..........)))))))............ ( -4.23 =  -5.17 +   0.94)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 16,277,875 – 16,277,928
Length 53
Sequences 7
Columns 53
Reading direction reverse
Mean pairwise identity 70.84
Shannon entropy 0.54522
G+C content 0.51826
Mean single sequence MFE -15.74
Consensus MFE -6.51
Energy contribution -7.13
Covariance contribution 0.62
Combinations/Pair 1.54
Mean z-score -1.85
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.815280
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16277875 53 - 23011544
CGUGUUUCGCAAAAGGCCGGUGGAACGAACGGCCUUUUAAGUGAGGGAUGAUA
(((.(((((((((((((((..........)))))))))..)))))).)))... ( -21.50, z-score =  -3.96, R)
>droPer1.super_8 3242770 51 - 3966273
--CGCAUGUUGAGAAGACGCUGAAGCUGAAGGGCUUUUGGCUGGCCGGUGAGA
--...............(((((.(((..(((...)))..)))...)))))... ( -11.00, z-score =   0.86, R)
>dp4.chr4_group2 590485 51 + 1235136
--CGCAUGUUGAGAAGACGCUGAAGCUGAAGGGCUUUUGGCUGGCCGGUGAGA
--...............(((((.(((..(((...)))..)))...)))))... ( -11.00, z-score =   0.86, R)
>droEre2.scaffold_4929 7974356 53 - 26641161
CGUGUUUUGUAAAAGGCCGGUAGAACGAACGGCCUUGUUAGUGAGGGAUGAUA
(((.(((..(..(((((((..........)))))))....)..))).)))... ( -15.90, z-score =  -2.82, R)
>droYak2.chr2L 3275893 53 + 22324452
CGUGAUUCGUAAAAGGCCGGUAGAACGAACGGCCUUGUUAGUGAGAAAGGAUA
.....((((((((((((((..........))))))).))).))))........ ( -13.20, z-score =  -1.68, R)
>droSec1.super_5 5003138 53 - 5866729
CGUGUUUCGUAAAAGGCCGGUGGAACGAACGGCCUUGUAAGCGAGGGAUGAUA
(((.((((((..(((((((..........)))))))....)))))).)))... ( -20.70, z-score =  -3.60, R)
>droSim1.chr2L 15986922 53 - 22036055
CGUGUUUCGUAAAAGGCCGGUGGAACGAACGGCCUUGUAAGUGAGGGAUGAUA
(((.(((((...(((((((..........))))))).....))))).)))... ( -16.90, z-score =  -2.59, R)
>consensus
CGUGUUUCGUAAAAGGCCGGUGGAACGAACGGCCUUGUAAGUGAGGGAUGAUA
..((((((....(((((((..........)))))))........))))))... ( -6.51 =  -7.13 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:44:42 2011