Locus 13848

Sequence ID dm3.chrX
Location 9,540,875 – 9,540,967
Length 92
Max. P 0.995415
window19060 window19061

overview

Window 0

Location 9,540,875 – 9,540,967
Length 92
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 76.39
Shannon entropy 0.45566
G+C content 0.42550
Mean single sequence MFE -24.82
Consensus MFE -17.44
Energy contribution -17.34
Covariance contribution -0.10
Combinations/Pair 1.43
Mean z-score -2.37
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.80
SVM RNA-class probability 0.995415
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9540875 92 + 22422827
AAAGAGAGGUGAGCGAUGCUAUGCGUCAUCGUAUUUAUGAUCCUCACCUCUUUCCCAGCGA-UCACGUUUGUUUAUCUCGCCUCUUUCUACGA
..(((((((((((....((...((((.(((((......((........)).......))))-).))))..))....)))))))))))...... ( -26.32, z-score =  -2.72, R)
>droSim1.chrX 7593013 93 + 17042790
AAAGAGAGGUGAGCGAUGCUAUGCGUCAUCGUAUUUAUGAUCCUCACCUCUUUCACAGCAAAUCACGUUUGUUUAUCUCGCCUCUUUCUACGA
..(((((((((((.(((((...)))))(((((....))))).)))))))))))...(((((((...))))))).................... ( -24.70, z-score =  -2.46, R)
>droSec1.super_15 304552 92 + 1954846
AAAGAGAGGUGAGCGAUGCUAUGCGUCAUCGUAUUUAUGAUCCUCACCUCUUUCACAGCGA-UCACGUUGGUUUAUCUCGCCUCUUUCUACGA
..(((((((((((....((((.((((.(((((......((........)).......))))-).))))))))....)))))))))))...... ( -27.82, z-score =  -2.47, R)
>droEre2.scaffold_4690 13171431 92 - 18748788
AAAGAGAGGUGAGCGAUGCUAUGCGUCAUCGUAUUUAUGAUCCUCACCUCUGUUCCAGCGA-UCAUGUUUGUUUAUCUCGCGUCUUUCUACGA
.((.(((((((((.(((((...)))))(((((....))))).))))))))).))...((((-..(((......))).))))............ ( -26.50, z-score =  -2.00, R)
>droYak2.chrX 18131413 92 + 21770863
AAAGAGAGGUGAGCGAUGGUAUGCGUCAUCGUAUUUAUGAUCCUCACCUCUUUCCCAGCGA-UCACGUUUGUUUAUCUCGCGUCUUUCUACGA
..(((((((((((.(((.(((((((....))))..))).))))))))))))))....((((-...............))))............ ( -28.06, z-score =  -2.53, R)
>triCas2.ChLG3 19966696 78 - 32080666
---AAAAUGUGGGCAAAAAAAUGUGUAGUC-UACU-GUGUCUUUUGUUUAAACUAGGAUGA----GAUUAUUAAAUUUUGUGCCGUU------
---........((((..(((((..((((((-(...-..(((((..((....)).))))).)----))))))...))))).))))...------ ( -15.50, z-score =  -2.05, R)
>consensus
AAAGAGAGGUGAGCGAUGCUAUGCGUCAUCGUAUUUAUGAUCCUCACCUCUUUCACAGCGA_UCACGUUUGUUUAUCUCGCCUCUUUCUACGA
..(((((((((((.(((...(((((....))))).....))))))))))))))....((((................))))............ (-17.44 = -17.34 +  -0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 9,540,875 – 9,540,967
Length 92
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 76.39
Shannon entropy 0.45566
G+C content 0.42550
Mean single sequence MFE -21.28
Consensus MFE -11.89
Energy contribution -14.08
Covariance contribution 2.20
Combinations/Pair 1.21
Mean z-score -1.43
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.39
SVM RNA-class probability 0.676607
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9540875 92 - 22422827
UCGUAGAAAGAGGCGAGAUAAACAAACGUGA-UCGCUGGGAAAGAGGUGAGGAUCAUAAAUACGAUGACGCAUAGCAUCGCUCACCUCUCUUU
......((((((((((.....((....))..-)))))......((((((((...........(((((.(.....))))))))))))))))))) ( -25.20, z-score =  -1.68, R)
>droSim1.chrX 7593013 93 - 17042790
UCGUAGAAAGAGGCGAGAUAAACAAACGUGAUUUGCUGUGAAAGAGGUGAGGAUCAUAAAUACGAUGACGCAUAGCAUCGCUCACCUCUCUUU
......(((((((((((....((....))..))))))......((((((((...........(((((.(.....))))))))))))))))))) ( -23.30, z-score =  -1.20, R)
>droSec1.super_15 304552 92 - 1954846
UCGUAGAAAGAGGCGAGAUAAACCAACGUGA-UCGCUGUGAAAGAGGUGAGGAUCAUAAAUACGAUGACGCAUAGCAUCGCUCACCUCUCUUU
......((((((((((.....((....))..-)))))......((((((((...........(((((.(.....))))))))))))))))))) ( -24.60, z-score =  -1.30, R)
>droEre2.scaffold_4690 13171431 92 + 18748788
UCGUAGAAAGACGCGAGAUAAACAAACAUGA-UCGCUGGAACAGAGGUGAGGAUCAUAAAUACGAUGACGCAUAGCAUCGCUCACCUCUCUUU
......(((((.((((...............-)))).......((((((((...........(((((.(.....))))))))))))))))))) ( -22.76, z-score =  -1.48, R)
>droYak2.chrX 18131413 92 - 21770863
UCGUAGAAAGACGCGAGAUAAACAAACGUGA-UCGCUGGGAAAGAGGUGAGGAUCAUAAAUACGAUGACGCAUACCAUCGCUCACCUCUCUUU
((.(((...((((((...........)))).-)).))).)).(((((((((...........(((((........)))))))))))))).... ( -25.40, z-score =  -2.00, R)
>triCas2.ChLG3 19966696 78 + 32080666
------AACGGCACAAAAUUUAAUAAUC----UCAUCCUAGUUUAAACAAAAGACAC-AGUA-GACUACACAUUUUUUUGCCCACAUUUU---
------...((((.((((..........----........((((.......))))..-.(((-...)))....)))).))))........--- (  -6.40, z-score =  -0.95, R)
>consensus
UCGUAGAAAGACGCGAGAUAAACAAACGUGA_UCGCUGGGAAAGAGGUGAGGAUCAUAAAUACGAUGACGCAUAGCAUCGCUCACCUCUCUUU
......(((((.((((.....((....))...)))).......((((((((...........(((((........)))))))))))))))))) (-11.89 = -14.08 +   2.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:29:02 2011