Locus 5912

Sequence ID dm3.chr3L
Location 2,421,615 – 2,421,681
Length 66
Max. P 0.730434
window8132 window8133

overview

Window 2

Location 2,421,615 – 2,421,681
Length 66
Sequences 6
Columns 66
Reading direction forward
Mean pairwise identity 71.62
Shannon entropy 0.55749
G+C content 0.47047
Mean single sequence MFE -17.05
Consensus MFE -8.95
Energy contribution -7.95
Covariance contribution -0.99
Combinations/Pair 1.70
Mean z-score -0.97
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.17
SVM RNA-class probability 0.577090
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2421615 66 + 24543557
UUUGGCCAACAUUUUUGGGUGCACUCAUCCAUGAUUCGUGCACCAGCAGUCGACGACAAUAAUUCU
.(((((...((....))(((((((..(((...)))..)))))))....)))))............. ( -15.40, z-score =  -1.13, R)
>droEre2.scaffold_4784 2437614 66 + 25762168
UUUGGCUGGCGUUUUUGGGUGCACUCAUCCAUGAUUCGUGCACCACCAGUCGACGACAAUGAGUCU
.((((((((((....))(((((((..(((...)))..))))))).)))))))).(((.....))). ( -23.80, z-score =  -2.34, R)
>droYak2.chr3L 14683998 66 - 24197627
UUUGGCUGGCGUUUUUGGGUGCACUCAUCCAUGAUUCGUGCACCAGCAGUCGACGACAAUGAGUCU
.(((((((.((....))(((((((..(((...)))..)))))))..))))))).(((.....))). ( -21.10, z-score =  -1.20, R)
>droSec1.super_2 2447246 66 + 7591821
UUUGGCCAGCGUUUUUGGGUGCACUCAUCCAUGAUUCGUGCACCAGCAGUCGACGACAAUGAGUCU
...(((((.((((.((((((((((..(((...)))..)))))))..)))..))))....)).))). ( -18.60, z-score =  -0.68, R)
>droSim1.chr3L 1984418 66 + 22553184
UUUGGCCAGCGUUUUUGGGUGUACUCAUCCAUGAUUCGUGCACCAGCAGUCGCCGACAAUGAGACU
.(((((..(((..((((((((....)))))).))..)))((....))....))))).......... ( -16.90, z-score =  -0.25, R)
>droVir3.scaffold_10322 201855 52 + 456481
-------UGUGUCUAUUAGUAAACACAACUAUACACCAU-UGUUGGUCACUUCUAUUUAU------
-------(((((.((....)).))))).......((((.-...)))).............------ (  -6.50, z-score =  -0.19, R)
>consensus
UUUGGCCAGCGUUUUUGGGUGCACUCAUCCAUGAUUCGUGCACCAGCAGUCGACGACAAUGAGUCU
.................(((((((.............)))))))....(((...)))......... ( -8.95 =  -7.95 +  -0.99)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 2,421,615 – 2,421,681
Length 66
Sequences 6
Columns 66
Reading direction reverse
Mean pairwise identity 71.62
Shannon entropy 0.55749
G+C content 0.47047
Mean single sequence MFE -17.37
Consensus MFE -9.44
Energy contribution -9.17
Covariance contribution -0.27
Combinations/Pair 1.50
Mean z-score -1.06
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.730434
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2421615 66 - 24543557
AGAAUUAUUGUCGUCGACUGCUGGUGCACGAAUCAUGGAUGAGUGCACCCAAAAAUGUUGGCCAAA
............((((((....(((((((..(((...)))..))))))).......)))))).... ( -19.70, z-score =  -1.86, R)
>droEre2.scaffold_4784 2437614 66 - 25762168
AGACUCAUUGUCGUCGACUGGUGGUGCACGAAUCAUGGAUGAGUGCACCCAAAAACGCCAGCCAAA
.(((.....)))...(.((((((((((((..(((...)))..))))))).......))))).)... ( -22.51, z-score =  -2.18, R)
>droYak2.chr3L 14683998 66 + 24197627
AGACUCAUUGUCGUCGACUGCUGGUGCACGAAUCAUGGAUGAGUGCACCCAAAAACGCCAGCCAAA
.(((.....)))(.((......(((((((..(((...)))..)))))))......)).)....... ( -17.30, z-score =  -0.68, R)
>droSec1.super_2 2447246 66 - 7591821
AGACUCAUUGUCGUCGACUGCUGGUGCACGAAUCAUGGAUGAGUGCACCCAAAAACGCUGGCCAAA
.........((((.((......(((((((..(((...)))..)))))))......)).)))).... ( -17.90, z-score =  -0.63, R)
>droSim1.chr3L 1984418 66 - 22553184
AGUCUCAUUGUCGGCGACUGCUGGUGCACGAAUCAUGGAUGAGUACACCCAAAAACGCUGGCCAAA
.........(((((((......((((.((..(((...)))..)).))))......))))))).... ( -17.90, z-score =  -0.56, R)
>droVir3.scaffold_10322 201855 52 - 456481
------AUAAAUAGAAGUGACCAACA-AUGGUGUAUAGUUGUGUUUACUAAUAGACACA-------
------.............((((...-.)))).......((((((((....))))))))------- (  -8.90, z-score =  -0.46, R)
>consensus
AGACUCAUUGUCGUCGACUGCUGGUGCACGAAUCAUGGAUGAGUGCACCCAAAAACGCUGGCCAAA
......................(((((((..(((...)))..)))))))................. ( -9.44 =  -9.17 +  -0.27)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:57:38 2011