Locus 3113

Sequence ID dm3.chr2R
Location 2,594,528 – 2,594,627
Length 99
Max. P 0.915746
window4275 window4276

overview

Window 5

Location 2,594,528 – 2,594,627
Length 99
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 65.54
Shannon entropy 0.55447
G+C content 0.33873
Mean single sequence MFE -19.15
Consensus MFE -9.20
Energy contribution -8.63
Covariance contribution -0.56
Combinations/Pair 1.20
Mean z-score -1.62
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.10
SVM RNA-class probability 0.890856
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2594528 99 + 21146708
CAGUUAUUAG--AAC------UCAACUGAGAUGAAAGACCAAUAUCGAAAGCCAAAAUUUCCAUGAAAGUGUAGGAUGUUGAUAAGAUUUAAGCUGCACUCCCAUAA
(((((.....--..(------((....))).........(((((((((((.......))))(((....)))...)))))))..........)))))........... ( -15.40, z-score =  -0.55, R)
>droEre2.scaffold_4929 6690194 106 - 26641161
CAGUAAUGAAAAUACCGACUAUUAAAUUUAUUGAAUUAUUAGAGCUCAAAGACAGACAUUCAAUGAAAGCGUAGGAUGCUGAUAAGAUUGAAAUUGCGCUCCCAUA-
((((((....((((.....))))....))))))........((((.(((...(((.(((((.(((....))).))))))))(......)....))).)))).....- ( -15.30, z-score =  -0.03, R)
>droSec1.super_1 258935 90 + 14215200
CAGUUAUUAGUUAGU------UUAAUAACUAAGAUGAAUGCGAGCUAAUGAGCAAACAUUCCAUGAAAGUGUAGGAUUUU-----------AGCUGCACUCCCAUAU
.(((((((((.....------))))))))).....(((((...(((....)))...))))).(((..(((((((......-----------..)))))))..))).. ( -22.30, z-score =  -2.85, R)
>droSim1.chr2R 1414600 101 + 19596830
CAGUUAUUAGUUAGU------UUAAUAACUAAGAUGAAUGCGAGCUAAAGAGCAAACAUUCCAUGAAAGUGUAGGAUGUUGAUAAGAUUUAAACUGCACUCCCAUAU
.(((((((((.....------))))))))).....(((((...(((....)))...))))).(((..(((((((....((((......)))).)))))))..))).. ( -23.60, z-score =  -3.04, R)
>consensus
CAGUUAUUAGUUAAC______UUAAUAACUAAGAAGAAUGAGAGCUAAAAAGCAAACAUUCCAUGAAAGUGUAGGAUGUUGAUAAGAUUUAAACUGCACUCCCAUAU
..............................................................(((..(((((((...................)))))))..))).. ( -9.20 =  -8.63 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,594,528 – 2,594,627
Length 99
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 65.54
Shannon entropy 0.55447
G+C content 0.33873
Mean single sequence MFE -19.71
Consensus MFE -8.30
Energy contribution -9.73
Covariance contribution 1.44
Combinations/Pair 1.32
Mean z-score -1.99
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.25
SVM RNA-class probability 0.915746
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2594528 99 - 21146708
UUAUGGGAGUGCAGCUUAAAUCUUAUCAACAUCCUACACUUUCAUGGAAAUUUUGGCUUUCGAUAUUGGUCUUUCAUCUCAGUUGA------GUU--CUAAUAACUG
(((((..((((.((...................)).))))..))))).....((((..((((((...(((.....)))...)))))------)..--))))...... ( -15.41, z-score =   0.30, R)
>droEre2.scaffold_4929 6690194 106 + 26641161
-UAUGGGAGCGCAAUUUCAAUCUUAUCAGCAUCCUACGCUUUCAUUGAAUGUCUGUCUUUGAGCUCUAAUAAUUCAAUAAAUUUAAUAGUCGGUAUUUUCAUUACUG
-(((.(((((.(((.((((((......(((.......)))...)))))).........))).))))).)))...................(((((.......))))) ( -14.10, z-score =   0.41, R)
>droSec1.super_1 258935 90 - 14215200
AUAUGGGAGUGCAGCU-----------AAAAUCCUACACUUUCAUGGAAUGUUUGCUCAUUAGCUCGCAUUCAUCUUAGUUAUUAA------ACUAACUAAUAACUG
.((((..((((.((..-----------......)).))))..))))((((((..(((....)))..))))))....(((((((((.------......))))))))) ( -25.30, z-score =  -4.61, R)
>droSim1.chr2R 1414600 101 - 19596830
AUAUGGGAGUGCAGUUUAAAUCUUAUCAACAUCCUACACUUUCAUGGAAUGUUUGCUCUUUAGCUCGCAUUCAUCUUAGUUAUUAA------ACUAACUAAUAACUG
.((((..((((.((...................)).))))..))))((((((..(((....)))..))))))....(((((((((.------......))))))))) ( -24.01, z-score =  -4.08, R)
>consensus
AUAUGGGAGUGCAGCUUAAAUCUUAUCAACAUCCUACACUUUCAUGGAAUGUUUGCCCUUUAGCUCGCAUUCAUCAUAGUAAUUAA______ACUAACUAAUAACUG
.((((..((((.((...................)).))))..))))((((((..(((....)))..))))))................................... ( -8.30 =  -9.73 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:03:56 2011