Locus 13148

Sequence ID dm3.chrX
Location 4,673,735 – 4,673,830
Length 95
Max. P 0.970000
window18069 window18070

overview

Window 9

Location 4,673,735 – 4,673,830
Length 95
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 81.53
Shannon entropy 0.33765
G+C content 0.47826
Mean single sequence MFE -23.93
Consensus MFE -16.82
Energy contribution -17.77
Covariance contribution 0.95
Combinations/Pair 1.14
Mean z-score -1.71
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.76
SVM RNA-class probability 0.809748
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4673735 95 + 22422827
-----AUCCAGGACCAACCAUUUGGCCAAUCCCGCACCGUCUGUC-------AUUAACGUAAUUCAAUAACCUUCAUCUGGCCAGUUGGCCAUGAUGAUUGUUGAUU
-----.....((.((((....))))))..................-------...........(((((((...((((((((((....))))).)))))))))))).. ( -25.10, z-score =  -1.88, R)
>droSim1.chrX 3626432 95 + 17042790
-----GCCCAGGACCUCCCAUUUGGCCAAUCCCGCACCGUCUGUC-------AUUAACGUAAUUCAAUAACCUUCAUCUGGCCAGUUGUCCAUGAUGAUUGUUGAUU
-----((...(((....((....))....))).))..........-------...........(((((((...((((((((.(....).))).)))))))))))).. ( -16.90, z-score =   0.17, R)
>droSec1.super_4 4116781 95 - 6179234
-----GCCCAGGACCUCCCAUUUGGCCAAUCCCGCACCGUCUGUC-------AUUAACGUAAUUCAAUAACCUUCAUCUGGCCAGUUGGCCAUGAUGAUUGUUGAUU
-----((...(((....((....))....))).))..........-------...........(((((((...((((((((((....))))).)))))))))))).. ( -24.00, z-score =  -1.52, R)
>droEre2.scaffold_4690 2047914 95 + 18748788
-----UACCAGGUCCUCCCAUUUGGCCAAUCCCUCACCGUCUGCC-------AUUACUGUAAUUCAAUAACCUUCAUCUGGCCAGUUGGCCAUGAUGAUGGUUGAUU
-----.....((.((........))))..................-------...............(((((.((((((((((....))))).))))).)))))... ( -26.00, z-score =  -1.97, R)
>droYak2.chrX 17999207 102 - 21770863
-----UGGCAGGACCUCCCAUUCGGUCAAUCCCGUACCGUCUGUCGCCUGUCAUUAAUGUAAUUCAAUAACCUUCAUCUCGCCAGUUGGCCGUGAUGAUUGUUGAUU
-----(((((((......((..(((((......).))))..))...)))))))..........(((((((...(((((.((((....)).)).)))))))))))).. ( -29.40, z-score =  -2.69, R)
>droAna3.scaffold_13417 6937310 101 - 6960332
UCCCUUCUCCCACCCGCCACUUUCUCCGGCCAACCGUCGUCCGAC------CAUUAAUGUAAUUUAAUAACCUCCAUCUGGCCAGUCGGCCAUGAUGAUUGUUGAUU
...............(((.........)))((((.((((((....------.(((((......)))))..........(((((....))))).)))))).))))... ( -22.20, z-score =  -2.38, R)
>consensus
_____UCCCAGGACCUCCCAUUUGGCCAAUCCCGCACCGUCUGUC_______AUUAACGUAAUUCAAUAACCUUCAUCUGGCCAGUUGGCCAUGAUGAUUGUUGAUU
..........((.((........))))....................................(((((((...((((((((((....))))).)))))))))))).. (-16.82 = -17.77 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 4,673,735 – 4,673,830
Length 95
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 81.53
Shannon entropy 0.33765
G+C content 0.47826
Mean single sequence MFE -30.98
Consensus MFE -22.40
Energy contribution -22.35
Covariance contribution -0.05
Combinations/Pair 1.32
Mean z-score -2.25
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.82
SVM RNA-class probability 0.970000
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4673735 95 - 22422827
AAUCAACAAUCAUCAUGGCCAACUGGCCAGAUGAAGGUUAUUGAAUUACGUUAAU-------GACAGACGGUGCGGGAUUGGCCAAAUGGUUGGUCCUGGAU-----
.(((.....(((((.(((((....))))))))))..((((((((......)))))-------)))....))).((((((..(((....)))..))))))...----- ( -38.40, z-score =  -4.53, R)
>droSim1.chrX 3626432 95 - 17042790
AAUCAACAAUCAUCAUGGACAACUGGCCAGAUGAAGGUUAUUGAAUUACGUUAAU-------GACAGACGGUGCGGGAUUGGCCAAAUGGGAGGUCCUGGGC-----
.........(((((.(((.(....).))))))))..((((((((......)))))-------))).....((.(((((((..((....))..))))))).))----- ( -26.90, z-score =  -1.49, R)
>droSec1.super_4 4116781 95 + 6179234
AAUCAACAAUCAUCAUGGCCAACUGGCCAGAUGAAGGUUAUUGAAUUACGUUAAU-------GACAGACGGUGCGGGAUUGGCCAAAUGGGAGGUCCUGGGC-----
.........(((((.(((((....))))))))))..((((((((......)))))-------))).....((.(((((((..((....))..))))))).))----- ( -34.00, z-score =  -3.10, R)
>droEre2.scaffold_4690 2047914 95 - 18748788
AAUCAACCAUCAUCAUGGCCAACUGGCCAGAUGAAGGUUAUUGAAUUACAGUAAU-------GGCAGACGGUGAGGGAUUGGCCAAAUGGGAGGACCUGGUA-----
((((.(((.(((((.(((((....))))))))))..(((((((.....)))))))-------.......)))....)))).((((...((.....)))))).----- ( -29.60, z-score =  -1.47, R)
>droYak2.chrX 17999207 102 + 21770863
AAUCAACAAUCAUCACGGCCAACUGGCGAGAUGAAGGUUAUUGAAUUACAUUAAUGACAGGCGACAGACGGUACGGGAUUGACCGAAUGGGAGGUCCUGCCA-----
.........(((((.((.((....)))).)))))..((((((((......)))))))).((((((...(.((.(((......))).)).)...)))..))).----- ( -29.70, z-score =  -1.93, R)
>droAna3.scaffold_13417 6937310 101 + 6960332
AAUCAACAAUCAUCAUGGCCGACUGGCCAGAUGGAGGUUAUUAAAUUACAUUAAUG------GUCGGACGACGGUUGGCCGGAGAAAGUGGCGGGUGGGAGAAGGGA
..(((((..(((((.(((((....))))))))))..)))......((((..((((.------(((....))).))))((((.......))))..))))..))..... ( -27.30, z-score =  -1.00, R)
>consensus
AAUCAACAAUCAUCAUGGCCAACUGGCCAGAUGAAGGUUAUUGAAUUACAUUAAU_______GACAGACGGUGCGGGAUUGGCCAAAUGGGAGGUCCUGGGA_____
....(((..(((((.(((((....))))))))))..)))..................................(((((((..((....))..)))))))........ (-22.40 = -22.35 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:15:30 2011