Locus 14135

Sequence ID dm3.chrX
Location 11,398,374 – 11,398,484
Length 110
Max. P 0.967902
window19450 window19451

overview

Window 0

Location 11,398,374 – 11,398,484
Length 110
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 83.92
Shannon entropy 0.21949
G+C content 0.35257
Mean single sequence MFE -28.30
Consensus MFE -22.04
Energy contribution -22.60
Covariance contribution 0.56
Combinations/Pair 1.12
Mean z-score -2.54
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.79
SVM RNA-class probability 0.967902
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11398374 110 + 22422827
--UUAUAUACCCUUUAAUAGGGUACUUCAGACAUGGACAAAGCUUGGCACUGCCCUUUCUUGUUGGAAACGAAGCAUUUCUAUGCUUACCAAUCAAUAAAAAUGUUAGAAAU----
--.....((((((.....)))))).(((.(((((((.((..((...))..)).))....(((((((.....((((((....)))))).....)))))))..))))).)))..---- ( -25.10, z-score =  -1.98, R)
>droSec1.super_36 120229 109 + 449511
--UUAUAUACCCUUUAAUAGGGUAUUUCAGACAUGGACAAAGCUUGGCCAUGCCCUUUGUUGUUGGAAACGAAGCAUUUCUAUGCUUACCAAUCAAUAAAU-UGUCCGAAAU----
--....(((((((.....)))))))........(((((((.....(((...))).(((((((((((.....((((((....)))))).)))).))))))))-))))))....---- ( -32.30, z-score =  -3.89, R)
>droYak2.chrX 11012965 116 - 21770863
UUAUAUAUACCCUUUAAUAAGGUAUUUCAGACAUGGGCAAGGGUUGGCAAUGUCCCUUGUUGUUGGAAACGACACAUUUCUUUGCUUACCAAUUAUUAAAACUGUUAGAAACAAAU
............((((((((((((....(((.(((((((((((..........))))))))((((....)))).))).))).....))))..))))))))................ ( -27.50, z-score =  -1.77, R)
>consensus
__UUAUAUACCCUUUAAUAGGGUAUUUCAGACAUGGACAAAGCUUGGCAAUGCCCUUUGUUGUUGGAAACGAAGCAUUUCUAUGCUUACCAAUCAAUAAAA_UGUUAGAAAU____
.......((((((.....)))))).(((.((((..(((((((...(((...))))))))))(((((.....((((((....)))))).))))).........)))).)))...... (-22.04 = -22.60 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 11,398,374 – 11,398,484
Length 110
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 83.92
Shannon entropy 0.21949
G+C content 0.35257
Mean single sequence MFE -29.80
Consensus MFE -20.73
Energy contribution -21.07
Covariance contribution 0.34
Combinations/Pair 1.10
Mean z-score -2.64
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.46
SVM RNA-class probability 0.939739
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11398374 110 - 22422827
----AUUUCUAACAUUUUUAUUGAUUGGUAAGCAUAGAAAUGCUUCGUUUCCAACAAGAAAGGGCAGUGCCAAGCUUUGUCCAUGUCUGAAGUACCCUAUUAAAGGGUAUAUAA--
----..(((..((((.....(((.((((.((((((....)))))).....)))))))....((((((.((...)).))))))))))..)))(((((((.....)))))))....-- ( -30.10, z-score =  -2.75, R)
>droSec1.super_36 120229 109 - 449511
----AUUUCGGACA-AUUUAUUGAUUGGUAAGCAUAGAAAUGCUUCGUUUCCAACAACAAAGGGCAUGGCCAAGCUUUGUCCAUGUCUGAAAUACCCUAUUAAAGGGUAUAUAA--
----..((((((((-.(((.(((.((((.((((((....)))))).....))))))).)))(((((.(((...))).))))).))))))))(((((((.....)))))))....-- ( -37.00, z-score =  -4.78, R)
>droYak2.chrX 11012965 116 + 21770863
AUUUGUUUCUAACAGUUUUAAUAAUUGGUAAGCAAAGAAAUGUGUCGUUUCCAACAACAAGGGACAUUGCCAACCCUUGCCCAUGUCUGAAAUACCUUAUUAAAGGGUAUAUAUAA
.(((((((....(((((.....)))))..)))))))...((((((((((((..(((.((((((..........))))))....)))..))))).((((....))))).)))))).. ( -22.30, z-score =  -0.38, R)
>consensus
____AUUUCUAACA_UUUUAUUGAUUGGUAAGCAUAGAAAUGCUUCGUUUCCAACAACAAAGGGCAUUGCCAAGCUUUGUCCAUGUCUGAAAUACCCUAUUAAAGGGUAUAUAA__
......(((..(((..........((((.((((((....)))))).....)))).......(((((..(.....)..))))).)))..)))(((((((.....)))))))...... (-20.73 = -21.07 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:34:24 2011