Locus 13018

Sequence ID dm3.chrX
Location 3,878,810 – 3,878,917
Length 107
Max. P 0.987639
window17890 window17891

overview

Window 0

Location 3,878,810 – 3,878,917
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 66.04
Shannon entropy 0.48518
G+C content 0.56594
Mean single sequence MFE -28.67
Consensus MFE -13.46
Energy contribution -14.13
Covariance contribution 0.67
Combinations/Pair 1.13
Mean z-score -2.66
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.29
SVM RNA-class probability 0.987639
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3878810 107 + 22422827
GCGCGAAUUAUGAGCCAUAAUUUGUGUUAGCGCCAAGUGUCGCCCAUCCCCAACACCACCACUCCCCCCUCUCCCCCCCCCUGUCAGCUGGCUGGAGAAGCGCAAUC
((((((((((((...))))))))))))..((((...((((.(........).)))).............(((((..((..(.....)..))..))))).)))).... ( -27.00, z-score =  -2.67, R)
>droSec1.super_4 3339985 98 - 6179234
GCGCGAAUUAUGAGUCAUAAUUUGUGUUAGCGCCAAGUGUCGCCCAUACCCAACACCAAC---------CCCCCCGCCCCCAGCCAGCUGACUGGAGAAACGCAAUC
((((((((((((...))))))))))))..(((....((((.(........).))))....---------..........((((.(....).)))).....))).... ( -20.60, z-score =  -1.70, R)
>droWil1.scaffold_180588 1227005 104 + 1294757
GCGCGAGUUAUGUGCCAUAAUUUGUGUAAGCGCCAAGUGGCGCCCUUAU--AGUACUCACUCCCUUCGCAGCCGUACCCCAACGCUUUCAGUUAGCUGGCUGCGAU-
((((((((((((...))))))))))))..(((((....)))))......--..............((((((((((......))(((.......))).)))))))).- ( -38.40, z-score =  -3.61, R)
>consensus
GCGCGAAUUAUGAGCCAUAAUUUGUGUUAGCGCCAAGUGUCGCCCAUACCCAACACCAAC_C_C__C_CACCCCCACCCCCAGCCAGCUGGCUGGAGAAACGCAAUC
((((((((((((...))))))))))))..(((....((((............)))).......................((((........)))).....))).... (-13.46 = -14.13 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 3,878,810 – 3,878,917
Length 107
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 66.04
Shannon entropy 0.48518
G+C content 0.56594
Mean single sequence MFE -37.17
Consensus MFE -19.72
Energy contribution -21.30
Covariance contribution 1.58
Combinations/Pair 1.35
Mean z-score -2.13
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.81
SVM RNA-class probability 0.969110
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3878810 107 - 22422827
GAUUGCGCUUCUCCAGCCAGCUGACAGGGGGGGGGAGAGGGGGGAGUGGUGGUGUUGGGGAUGGGCGACACUUGGCGCUAACACAAAUUAUGGCUCAUAAUUCGCGC
..((.(.(((((((..((..((....))..)).))))))).).))(((.((((((..((....(....).))..)))))).))).(((((((...)))))))..... ( -35.70, z-score =  -1.04, R)
>droSec1.super_4 3339985 98 + 6179234
GAUUGCGUUUCUCCAGUCAGCUGGCUGGGGGCGGGGGG---------GUUGGUGUUGGGUAUGGGCGACACUUGGCGCUAACACAAAUUAUGACUCAUAAUUCGCGC
....((....((((((((....))))))))(((.....---------((((((((..(((...(....))))..))))))))...(((((((...)))))))))))) ( -35.50, z-score =  -2.40, R)
>droWil1.scaffold_180588 1227005 104 - 1294757
-AUCGCAGCCAGCUAACUGAAAGCGUUGGGGUACGGCUGCGAAGGGAGUGAGUACU--AUAAGGGCGCCACUUGGCGCUUACACAAAUUAUGGCACAUAACUCGCGC
-.((((((((.(((.......)))((......)))))))))).(.((((..((.((--(((((((((((....))))))).......)))))).))...)))).).. ( -40.31, z-score =  -2.95, R)
>consensus
GAUUGCGCUUCUCCAGCCAGCUGACUGGGGGCGGGGGAG_G__G_G_GUUGGUGUUGGGUAUGGGCGACACUUGGCGCUAACACAAAUUAUGGCUCAUAAUUCGCGC
...(((.(((((((.(((..(.....)..))).))))))).......((((((((((((....(....).))))))))))))...(((((((...))))))).))). (-19.72 = -21.30 +   1.58)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:13:04 2011