Locus 9216

Sequence ID dm3.chr3R
Location 4,972,576 – 4,972,724
Length 148
Max. P 0.636245
window12629 window12630

overview

Window 9

Location 4,972,576 – 4,972,692
Length 116
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 99.14
Shannon entropy 0.01459
G+C content 0.51034
Mean single sequence MFE -37.92
Consensus MFE -36.96
Energy contribution -36.56
Covariance contribution -0.40
Combinations/Pair 1.06
Mean z-score -1.06
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.518495
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 4972576 116 - 27905053
AACGUGCCCGGUGCAGUGAACACGGUUCGCUCUUCUGGGAAGUAUAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAGUAUCUGACAGAUACAUAUGCUCGUGCUGCCUACAAACU
.(((..(((((...(((((((...)))))))...))))).(((((((((((((((((.....))).)))))))....(((((.....))))))))))))))).............. ( -38.70, z-score =  -1.36, R)
>droSim1.chr3R 11175766 116 + 27517382
AACGUGCCCGGUGCAGUGAACACGGUUCGCUCUUCUGGGAAGUAUAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAGUAUCUGACAGAUACAUAUGCUCGUGCUGCCUACAAACU
.(((..(((((...(((((((...)))))))...))))).(((((((((((((((((.....))).)))))))....(((((.....))))))))))))))).............. ( -38.70, z-score =  -1.36, R)
>droSec1.super_0 4211433 116 + 21120651
AACGUGCCCGGUGCAGUGAACACGGUUCGCUCUUCUGGGAAGUAUAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAGUAUCUGACAGAUACAUAUGCUCGUGCUGCCUACAAACU
.(((..(((((...(((((((...)))))))...))))).(((((((((((((((((.....))).)))))))....(((((.....))))))))))))))).............. ( -38.70, z-score =  -1.36, R)
>droYak2.chr3R 9019913 116 - 28832112
AACGUGCCCGGUGCAGUGAACACGGUUCGUUCUUCUGGGAAGUACAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAGUAUCUGACAGAUACAUAUGCUCGUGCUGCCUACAAACU
((((.(((..(((.......)))))).))))....((((.(((((..((((((((((.....))).)))))))....(((((.....)))))........))))).))))...... ( -34.50, z-score =  -0.02, R)
>droEre2.scaffold_4770 1117025 116 + 17746568
AACGUGCCCGGUGCAGUGAACACGGUUCGCUCUUCUGGGAAGUACAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAGUAUCUGACAGAUACAUAUGCUCGUGCUGCCUACAAACU
...((((((((...(((((((...)))))))...))))).(((((..((((((((((.....))).)))))))....(((((.....)))))........)))))...)))..... ( -39.00, z-score =  -1.23, R)
>consensus
AACGUGCCCGGUGCAGUGAACACGGUUCGCUCUUCUGGGAAGUAUAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAGUAUCUGACAGAUACAUAUGCUCGUGCUGCCUACAAACU
...((((((((...(((((((...)))))))...))))).(((((..((((((((((.....))).)))))))....(((((.....)))))........)))))...)))..... (-36.96 = -36.56 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 4,972,614 – 4,972,724
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 99.09
Shannon entropy 0.01539
G+C content 0.53818
Mean single sequence MFE -37.94
Consensus MFE -37.40
Energy contribution -37.24
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.05
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.636245
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 4972614 110 - 27905053
GUGACAAGUAUCUGGCAGAUACACUUGGCCCAAACGUGCCCGGUGCAGUGAACACGGUUCGCUCUUCUGGGAAGUAUAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAG
.......(((((.....)))))..((((((...(((((.(((((..(((((((...)))))))((((...)))).....))))).)))))..(((....))))))))).. ( -38.30, z-score =  -1.22, R)
>droSim1.chr3R 11175804 110 + 27517382
GUGACAAGUAUCUGGCAGAUACACUUGGCCCAAACGUGCCCGGUGCAGUGAACACGGUUCGCUCUUCUGGGAAGUAUAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAG
.......(((((.....)))))..((((((...(((((.(((((..(((((((...)))))))((((...)))).....))))).)))))..(((....))))))))).. ( -38.30, z-score =  -1.22, R)
>droSec1.super_0 4211471 110 + 21120651
GUGACAAGUAUCUGGCAGAUACACUUGGCCCAAACGUGCCCGGUGCAGUGAACACGGUUCGCUCUUCUGGGAAGUAUAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAG
.......(((((.....)))))..((((((...(((((.(((((..(((((((...)))))))((((...)))).....))))).)))))..(((....))))))))).. ( -38.30, z-score =  -1.22, R)
>droYak2.chr3R 9019951 110 - 28832112
GUGACAAGUAUCUGGCAGAUACACUUGGCCCAAACGUGCCCGGUGCAGUGAACACGGUUCGUUCUUCUGGGAAGUACAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAG
.......(((((.....)))))..((((((...(((((.(((((.....((((...))))((.((((...)))).))..))))).)))))..(((....))))))))).. ( -36.50, z-score =  -0.61, R)
>droEre2.scaffold_4770 1117063 110 + 17746568
GUGACAAGUAUCUGGCAGAUACACUUGGCCCAAACGUGCCCGGUGCAGUGAACACGGUUCGCUCUUCUGGGAAGUACAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAG
.......(((((.....)))))..((((((...(((((.(((((..(((((((...)))))))((((...)))).....))))).)))))..(((....))))))))).. ( -38.30, z-score =  -0.98, R)
>consensus
GUGACAAGUAUCUGGCAGAUACACUUGGCCCAAACGUGCCCGGUGCAGUGAACACGGUUCGCUCUUCUGGGAAGUAUAUGCCGGCUACGUGUAACGUGAGUUGGCCAAAG
.......(((((.....)))))..((((((...(((((.(((((..(((((((...)))))))((((...)))).....))))).)))))..(((....))))))))).. (-37.40 = -37.24 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:00:04 2011