Locus 7698

Sequence ID dm3.chr3L
Location 16,650,862 – 16,651,004
Length 142
Max. P 0.998752
window10593 window10594 window10595

overview

Window 3

Location 16,650,862 – 16,650,976
Length 114
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 90.17
Shannon entropy 0.13343
G+C content 0.34602
Mean single sequence MFE -34.43
Consensus MFE -31.11
Energy contribution -30.23
Covariance contribution -0.88
Combinations/Pair 1.17
Mean z-score -4.16
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.47
SVM RNA-class probability 0.998752
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16650862 114 + 24543557
UCAGAACCGUGGUUGCUAAUUAGAGAUUCUUAAACAUGGCAUGGUUUGGAAAACGUCAAAUAUUGAAUAUUCAUGC---AUGUGUUUGAGUAUUCAAGAAGUUAAGUAGCCAUGCUG
.(((...((((((((((((((...((..(((((((((((((((((((((......))))))..........)))))---.))))))))))...))....)))).))))))))))))) ( -30.70, z-score =  -2.47, R)
>droSim1.chr3L 15981705 115 + 22553184
UCAGAACCCUGAUUGCUAAUUAGGGAUUCUUAAAGA--GCUUGGCUUGUAAAACGUCAAAUAUUGAAUAUUCAUAUGCUAUGUGUUUGAGUAUUCAAAAAGUUAAGUAGCCAAGCUG
..(((((((((((.....))))))).)))).....(--((((((((.....(((........(((((((((((.((((...)))).)))))))))))...)))....))))))))). ( -36.90, z-score =  -5.03, R)
>droSec1.super_0 8728772 112 + 21120651
UCAGAACCCUGAUUGCUGAUUAGGGAUUCUUAAAGA--GCUUGGCUUGUAAAACGUCAAAUAUUGAAUAUUCAUAU---AUGUGUUUGAGUAUUCAAAAAGUUAAGUAGCCAAGCUG
..((((((((((((...)))))))).)))).....(--((((((((.....(((........(((((((((((.((---....)).)))))))))))...)))....))))))))). ( -35.70, z-score =  -4.99, R)
>consensus
UCAGAACCCUGAUUGCUAAUUAGGGAUUCUUAAAGA__GCUUGGCUUGUAAAACGUCAAAUAUUGAAUAUUCAUAU___AUGUGUUUGAGUAUUCAAAAAGUUAAGUAGCCAAGCUG
..((((((((((((...)))))))).))))........((((((((.....(((........(((((((((((.((.......)).)))))))))))...)))....)))))))).. (-31.11 = -30.23 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,650,862 – 16,650,976
Length 114
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 90.17
Shannon entropy 0.13343
G+C content 0.34602
Mean single sequence MFE -24.71
Consensus MFE -21.06
Energy contribution -21.06
Covariance contribution 0.00
Combinations/Pair 1.07
Mean z-score -2.80
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.11
SVM RNA-class probability 0.982547
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16650862 114 - 24543557
CAGCAUGGCUACUUAACUUCUUGAAUACUCAAACACAU---GCAUGAAUAUUCAAUAUUUGACGUUUUCCAAACCAUGCCAUGUUUAAGAAUCUCUAAUUAGCAACCACGGUUCUGA
.((((((((...........(((((((.(((..(....---)..))).)))))))..((((........))))....)))))))).............((((.(((....))))))) ( -20.90, z-score =  -1.67, R)
>droSim1.chr3L 15981705 115 - 22553184
CAGCUUGGCUACUUAACUUUUUGAAUACUCAAACACAUAGCAUAUGAAUAUUCAAUAUUUGACGUUUUACAAGCCAAGC--UCUUUAAGAAUCCCUAAUUAGCAAUCAGGGUUCUGA
.(((((((((....(((((.(((((((.(((.............))).))))))).....)).))).....))))))))--).....((((.((((.((.....)).)))))))).. ( -26.52, z-score =  -3.04, R)
>droSec1.super_0 8728772 112 - 21120651
CAGCUUGGCUACUUAACUUUUUGAAUACUCAAACACAU---AUAUGAAUAUUCAAUAUUUGACGUUUUACAAGCCAAGC--UCUUUAAGAAUCCCUAAUCAGCAAUCAGGGUUCUGA
.(((((((((....(((((.(((((((.(((.......---...))).))))))).....)).))).....))))))))--).....((((.((((.((.....)).)))))))).. ( -26.70, z-score =  -3.69, R)
>consensus
CAGCUUGGCUACUUAACUUUUUGAAUACUCAAACACAU___AUAUGAAUAUUCAAUAUUUGACGUUUUACAAGCCAAGC__UCUUUAAGAAUCCCUAAUUAGCAAUCAGGGUUCUGA
..((((((((....(((.(((((((((.(((.............))).))))))).....)).))).....))))))))........(((((((..............))))))).. (-21.06 = -21.06 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,650,902 – 16,651,004
Length 102
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 84.64
Shannon entropy 0.20976
G+C content 0.35685
Mean single sequence MFE -26.73
Consensus MFE -20.04
Energy contribution -18.93
Covariance contribution -1.10
Combinations/Pair 1.15
Mean z-score -1.81
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.24
SVM RNA-class probability 0.609890
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16650902 102 + 24543557
AUGGUUUGGAAAACGUCAAAUAUUGAAUAUUCAUGC---AUGUGUUUGAGUAUUCAAGAAGUUAAGUAGCCAUGCUGAGCA---AGCGGAAAUCAAUCC---------GUUUUAAUU
..(((.(((...((........(((((((((((.((---....)).)))))))))))........))..))).)))....(---((((((......)))---------))))..... ( -26.59, z-score =  -2.72, R)
>droSim1.chr3L 15981743 117 + 22553184
UUGGCUUGUAAAACGUCAAAUAUUGAAUAUUCAUAUGCUAUGUGUUUGAGUAUUCAAAAAGUUAAGUAGCCAAGCUGAGCAGCAAGCGGAAGUCAACCCUUGGGCACCGUUUUAAUU
((((((.....(((........(((((((((((.((((...)))).)))))))))))...)))....))))))(((....)))((((((..(((........))).))))))..... ( -28.60, z-score =  -1.35, R)
>droSec1.super_0 8728810 111 + 21120651
UUGGCUUGUAAAACGUCAAAUAUUGAAUAUUCAUAU---AUGUGUUUGAGUAUUCAAAAAGUUAAGUAGCCAAGCUGAGUG---AGCGGAAGUCAACCCUUGGGCACAGUUUUAAUU
((((((.....(((........(((((((((((.((---....)).)))))))))))...)))....))))))((((..((---(.(....)))).((....))..))))....... ( -25.00, z-score =  -1.36, R)
>consensus
UUGGCUUGUAAAACGUCAAAUAUUGAAUAUUCAUAU___AUGUGUUUGAGUAUUCAAAAAGUUAAGUAGCCAAGCUGAGCA___AGCGGAAGUCAACCCUUGGGCAC_GUUUUAAUU
((((((.....(((........(((((((((((.((.......)).)))))))))))...)))....))))))(((........)))((........)).................. (-20.04 = -18.93 +  -1.10)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:31:47 2011