Locus 610

Sequence ID dm3.chr2L
Location 4,265,603 – 4,265,680
Length 77
Max. P 0.979053
window807 window808

overview

Window 7

Location 4,265,603 – 4,265,680
Length 77
Sequences 5
Columns 81
Reading direction forward
Mean pairwise identity 86.77
Shannon entropy 0.23300
G+C content 0.52546
Mean single sequence MFE -27.84
Consensus MFE -22.60
Energy contribution -23.44
Covariance contribution 0.84
Combinations/Pair 1.05
Mean z-score -2.31
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.70
SVM RNA-class probability 0.962000
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 4265603 77 + 23011544
UCUGUGUAGACUGUUAGUCUGCAAGUCUCCUGUUCCUUUUGGACGUUUG----ACGCACUGCCAGGAGGUCCUUGCAGUGC
....(((((((.....))))))).(((...(((.((....)))))...)----))(((((((.(((....))).))))))) ( -31.70, z-score =  -3.54, R)
>droSim1.chr2L 4186156 77 + 22036055
UCUGUGUAGACUGUUAGUCUGCAAGUCUCCUGUUCCUUUUGGAUGCUUG----ACGCACUGCCAGGAGGUCCUUGCAGUGC
....(((((((.....))))))).(((....(((((....))).))..)----))(((((((.(((....))).))))))) ( -31.60, z-score =  -3.40, R)
>droSec1.super_5 2363734 77 + 5866729
UCUGUGUAGACUGUUAGUCUGCAAGUCUCCUGUUCCUUUUGGAUGCUUG----ACGCACUGCCAGGAGGUCCUUGCAGUGC
....(((((((.....))))))).(((....(((((....))).))..)----))(((((((.(((....))).))))))) ( -31.60, z-score =  -3.40, R)
>droYak2.chr2L 4293735 77 + 22324452
UCUGUGUAGUCUGUUAGUCUGCAAAUCUCUGGUUCUUUUUGAAAGCUUG----ACGCACUGCCAGGCGCUCCUUGCAGUGC
....(((((.(.....).)))))....((.(((((.....))..))).)----).(((((((.(((....))).))))))) ( -20.80, z-score =  -0.48, R)
>droEre2.scaffold_4929 4342109 73 + 26641161
GCUGUGUAGACUCUUAGUCU--------CCUGCUCCUUUUGGAUGCUUGCCUGACGCACUGCCAGGCGGUCCUUGCAGUGC
((...(.((((.....))))--------.).(((((....))).))..)).....(((((((.(((....))).))))))) ( -23.50, z-score =  -0.73, R)
>consensus
UCUGUGUAGACUGUUAGUCUGCAAGUCUCCUGUUCCUUUUGGAUGCUUG____ACGCACUGCCAGGAGGUCCUUGCAGUGC
....(((((((.....)))))))..........(((....)))............(((((((.(((....))).))))))) (-22.60 = -23.44 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 4,265,603 – 4,265,680
Length 77
Sequences 5
Columns 81
Reading direction reverse
Mean pairwise identity 86.77
Shannon entropy 0.23300
G+C content 0.52546
Mean single sequence MFE -26.56
Consensus MFE -20.54
Energy contribution -20.78
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -2.67
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.979053
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 4265603 77 - 23011544
GCACUGCAAGGACCUCCUGGCAGUGCGU----CAAACGUCCAAAAGGAACAGGAGACUUGCAGACUAACAGUCUACACAGA
(((((((.(((....))).)))))))((----(...(.(((....)))...)..))).((.((((.....)))).)).... ( -27.10, z-score =  -2.81, R)
>droSim1.chr2L 4186156 77 - 22036055
GCACUGCAAGGACCUCCUGGCAGUGCGU----CAAGCAUCCAAAAGGAACAGGAGACUUGCAGACUAACAGUCUACACAGA
(((((((.(((....))).)))))))..----...((((((....)))..((....)))))((((.....))))....... ( -28.20, z-score =  -3.19, R)
>droSec1.super_5 2363734 77 - 5866729
GCACUGCAAGGACCUCCUGGCAGUGCGU----CAAGCAUCCAAAAGGAACAGGAGACUUGCAGACUAACAGUCUACACAGA
(((((((.(((....))).)))))))..----...((((((....)))..((....)))))((((.....))))....... ( -28.20, z-score =  -3.19, R)
>droYak2.chr2L 4293735 77 - 22324452
GCACUGCAAGGAGCGCCUGGCAGUGCGU----CAAGCUUUCAAAAAGAACCAGAGAUUUGCAGACUAACAGACUACACAGA
(((((((.(((....))).)))))))((----(..((..((.............))...)).)))................ ( -19.62, z-score =  -0.69, R)
>droEre2.scaffold_4929 4342109 73 - 26641161
GCACUGCAAGGACCGCCUGGCAGUGCGUCAGGCAAGCAUCCAAAAGGAGCAGG--------AGACUAAGAGUCUACACAGC
(((((((.(((....))).)))))))((.((((..((.(((....)))))((.--------...))....))))))..... ( -29.70, z-score =  -3.46, R)
>consensus
GCACUGCAAGGACCUCCUGGCAGUGCGU____CAAGCAUCCAAAAGGAACAGGAGACUUGCAGACUAACAGUCUACACAGA
(((((((.(((....))).)))))))............(((....))).............((((.....))))....... (-20.54 = -20.78 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:15:54 2011