Locus 3217

Sequence ID dm3.chr2R
Location 3,521,876 – 3,521,994
Length 118
Max. P 0.982852
window4426 window4427

overview

Window 6

Location 3,521,876 – 3,521,994
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.15
Shannon entropy 0.18984
G+C content 0.31891
Mean single sequence MFE -23.68
Consensus MFE -20.33
Energy contribution -20.33
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.55
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.12
SVM RNA-class probability 0.982852
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3521876 118 + 21146708
--UUACUGAUAUCAGCAUUUCUGCCGAAAUCUAUUCGUUUGUUUGAACAACAGUCUGGCUUCUUGAUAGCCAUAUAAUAAAUAAUUCGAACAAACACAUUUGCAAAGUAUAAUUUGCAAA
--.....(((.((.(((....))).)).))).....(((((((((((........(((((.......)))))(((.....))).)))))))))))...((((((((......)))))))) ( -28.70, z-score =  -3.76, R)
>droSec1.super_1 1178864 110 + 14215200
---------UUACAGCAUUUCUGCCGAAAUCUAUUCGUUUGUUUGAACAACAAUCU-GCUGCUUGAAAGCCAUAUAAUAAAUAAUUCGAACAAACACCUAUGCAAAGUAUUAUUUGCAAA
---------....((.(((((....)))))))....(((((((((((.........-(((.......)))..(((.....))).))))))))))).....((((((......)))))).. ( -20.60, z-score =  -2.00, R)
>droSim1.chr2R 2247110 120 + 19596830
UUACUGAUAUCACAGCAUUUCUGCCGAAAUCUAUUCGUUUGUUUGAACAACAAUCUUGCUGCUUGAAAGCCAUAUAAUAAAUAAUUCGAACAAACACCUUUGCAAAGUAUAAUUUGCAAC
.....(((.((...(((....))).)).))).....(((((((((((.............(((....)))..............)))))))))))....(((((((......))))))). ( -21.73, z-score =  -1.90, R)
>consensus
________AUAACAGCAUUUCUGCCGAAAUCUAUUCGUUUGUUUGAACAACAAUCU_GCUGCUUGAAAGCCAUAUAAUAAAUAAUUCGAACAAACACCUUUGCAAAGUAUAAUUUGCAAA
.............((.(((((....)))))))....(((((((((((..........(((.......)))..(((.....))).))))))))))).....((((((......)))))).. (-20.33 = -20.33 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 3,521,876 – 3,521,994
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.15
Shannon entropy 0.18984
G+C content 0.31891
Mean single sequence MFE -29.03
Consensus MFE -22.47
Energy contribution -22.80
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.871473
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3521876 118 - 21146708
UUUGCAAAUUAUACUUUGCAAAUGUGUUUGUUCGAAUUAUUUAUUAUAUGGCUAUCAAGAAGCCAGACUGUUGUUCAAACAAACGAAUAGAUUUCGGCAGAAAUGCUGAUAUCAGUAA--
((((((((......))))))))..((((((((.((((.....((....(((((.......)))))....)).)))).))))))))....(((.((((((....)))))).))).....-- ( -34.70, z-score =  -4.27, R)
>droSec1.super_1 1178864 110 - 14215200
UUUGCAAAUAAUACUUUGCAUAGGUGUUUGUUCGAAUUAUUUAUUAUAUGGCUUUCAAGCAGC-AGAUUGUUGUUCAAACAAACGAAUAGAUUUCGGCAGAAAUGCUGUAA---------
..((((((......))))))((..((((((((.((((.....(((.....(((....)))...-.)))....)))).))))))))..)).....(((((....)))))...--------- ( -24.80, z-score =  -1.20, R)
>droSim1.chr2R 2247110 120 - 19596830
GUUGCAAAUUAUACUUUGCAAAGGUGUUUGUUCGAAUUAUUUAUUAUAUGGCUUUCAAGCAGCAAGAUUGUUGUUCAAACAAACGAAUAGAUUUCGGCAGAAAUGCUGUGAUAUCAGUAA
.(((((((......)))))))...((((((((.((((.....(((.....(((....))).....)))....)))).))))))))....(((..(((((....)))))....)))..... ( -27.60, z-score =  -1.20, R)
>consensus
UUUGCAAAUUAUACUUUGCAAAGGUGUUUGUUCGAAUUAUUUAUUAUAUGGCUUUCAAGCAGC_AGAUUGUUGUUCAAACAAACGAAUAGAUUUCGGCAGAAAUGCUGUAAU________
..((((((......)))))).....(((((((((................(((.......)))....(((((.....))))).)))))))))..(((((....)))))............ (-22.47 = -22.80 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:06:02 2011