Locus 12931

Sequence ID dm3.chrX
Location 3,379,943 – 3,380,054
Length 111
Max. P 0.818749
window17780 window17781

overview

Window 0

Location 3,379,943 – 3,380,054
Length 111
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 70.68
Shannon entropy 0.52517
G+C content 0.61080
Mean single sequence MFE -45.58
Consensus MFE -22.02
Energy contribution -23.82
Covariance contribution 1.80
Combinations/Pair 1.38
Mean z-score -1.61
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.818749
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3379943 111 + 22422827
-----UGGUGUUCAAGAAGUGCGCUAGAUUUGCGGACUCUUCAGAAUCGGCGGAGAUCCAGCAGGACGGCAAGGAGCAACUGCCUGAGAGGCAAGACUCGCUGGAUGCCAAGGAAU
-----.(((....((((.((.(((.......))).))))))....)))(((....(((((((.....((((.(......)))))...(((......)))))))))))))....... ( -36.20, z-score =  -0.33, R)
>droSim1.chrX 2457411 111 + 17042790
-----UGGUGUCCAAGGAGUGCGCGAGACUUGCGGACUCUUCAGGAUCGGCGGGGAUCCAGCCGGACGGCAAGAAGCAGCUGCCGGAGCGGGAUGACUCGCUGGAUGCCAAGGAAU
-----((((((((.((((((.(((((...))))).)))))).......((((((.((((..((((.((((........))))))))....))))..))))))))))))))...... ( -52.50, z-score =  -3.09, R)
>droSec1.super_4 2895177 111 - 6179234
-----UGGUGUCCAAGGAGUGCGCGAGACUUGCGGACUCUUCAGGAUCGGCGGGGAUCCAGCAGGACGGCAAGAAGCAGAUGCCGGAGCGGGAUGACUCGCUGGAUGCCAAGGAAU
-----((((((((.((((((.(((((...))))).)))))).......((((((.((((.((....(((((.........)))))..)).))))..))))))))))))))...... ( -48.10, z-score =  -2.89, R)
>droYak2.chrX 16769657 114 - 21770863
--UGGUGGUGUCCAAGGAGUCUGGGGGAUCUGCGGAAUCUGCAGAAUCGGCAGCGCUGCAGCAGGACGGCAAGGAGCAGCUGCCGGAGCGGAAGGACUCGCUGGCAGCCAAGGAAU
--...((((..(((..((((((......(((((((...))))))).(((((((((((.(.((......))..).))).)))))))).......))))))..)))..))))...... ( -46.70, z-score =  -1.05, R)
>droAna3.scaffold_13248 3633574 108 + 4840945
AGGGGAAGCGGCCAGCCAAGGCAUCUGCCU--CUGGCGGUCCUGCGUCCGGGGAGUCGUCACAGGAUGCCAAAGCGAAGCAGCCAAAGGGCGAAG------UGGCUGCAAAGGAAU
.......(((((((((((((((....))))--.)))).(((((((((((...((....))...))))))....((......))...)))))....------)))))))........ ( -44.40, z-score =  -0.69, R)
>consensus
_____UGGUGUCCAAGGAGUGCGCGAGACUUGCGGACUCUUCAGAAUCGGCGGAGAUCCAGCAGGACGGCAAGGAGCAGCUGCCGGAGCGGGAAGACUCGCUGGAUGCCAAGGAAU
.....(((((((((..((((((......(((((.((.((....)).)).)))))......))....(((((.........)))))..........))))..)))))))))...... (-22.02 = -23.82 +   1.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 3,379,943 – 3,380,054
Length 111
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 70.68
Shannon entropy 0.52517
G+C content 0.61080
Mean single sequence MFE -38.10
Consensus MFE -15.72
Energy contribution -18.40
Covariance contribution 2.68
Combinations/Pair 1.29
Mean z-score -1.75
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.38
SVM RNA-class probability 0.668652
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3379943 111 - 22422827
AUUCCUUGGCAUCCAGCGAGUCUUGCCUCUCAGGCAGUUGCUCCUUGCCGUCCUGCUGGAUCUCCGCCGAUUCUGAAGAGUCCGCAAAUCUAGCGCACUUCUUGAACACCA-----
.......((((...(((((...(((((.....))))))))))...)))).....(((((((....((.(((((....))))).))..))))))).................----- ( -33.30, z-score =  -1.29, R)
>droSim1.chrX 2457411 111 - 17042790
AUUCCUUGGCAUCCAGCGAGUCAUCCCGCUCCGGCAGCUGCUUCUUGCCGUCCGGCUGGAUCCCCGCCGAUCCUGAAGAGUCCGCAAGUCUCGCGCACUCCUUGGACACCA-----
.....((((((((((((((((......))))((((((.......))))))....)))))))....)))))(((....((((.(((.......))).))))...))).....----- ( -37.80, z-score =  -1.13, R)
>droSec1.super_4 2895177 111 + 6179234
AUUCCUUGGCAUCCAGCGAGUCAUCCCGCUCCGGCAUCUGCUUCUUGCCGUCCUGCUGGAUCCCCGCCGAUCCUGAAGAGUCCGCAAGUCUCGCGCACUCCUUGGACACCA-----
.....((((((((((((((((......))))(((((.........)))))....)))))))....)))))(((....((((.(((.......))).))))...))).....----- ( -37.60, z-score =  -2.21, R)
>droYak2.chrX 16769657 114 + 21770863
AUUCCUUGGCUGCCAGCGAGUCCUUCCGCUCCGGCAGCUGCUCCUUGCCGUCCUGCUGCAGCGCUGCCGAUUCUGCAGAUUCCGCAGAUCCCCCAGACUCCUUGGACACCACCA--
......(((.((((((.(((((.........(((((((.(((.(..((......)).).))))))))))..(((((.......))))).......))))).)))).)))))...-- ( -40.70, z-score =  -2.35, R)
>droAna3.scaffold_13248 3633574 108 - 4840945
AUUCCUUUGCAGCCA------CUUCGCCCUUUGGCUGCUUCGCUUUGGCAUCCUGUGACGACUCCCCGGACGCAGGACCGCCAG--AGGCAGAUGCCUUGGCUGGCCGCUUCCCCU
........(((((((------..........)))))))...((((((((.(((((((.((......))..)))))))..)))))--)(((....((....))..)))))....... ( -41.10, z-score =  -1.78, R)
>consensus
AUUCCUUGGCAUCCAGCGAGUCAUCCCGCUCCGGCAGCUGCUCCUUGCCGUCCUGCUGGAUCCCCGCCGAUCCUGAAGAGUCCGCAAGUCUCGCGCACUCCUUGGACACCA_____
.......((..(((((.((((........((((((((..((.....))....)))))))).....((.(((((....))))).))...........)))).)))))..))...... (-15.72 = -18.40 +   2.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:11:32 2011