Locus 7199

Sequence ID dm3.chr3L
Location 12,923,193 – 12,923,306
Length 113
Max. P 0.830690
window9905 window9906

overview

Window 5

Location 12,923,193 – 12,923,306
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 95.55
Shannon entropy 0.07689
G+C content 0.52593
Mean single sequence MFE -37.53
Consensus MFE -31.98
Energy contribution -32.58
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.569693
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12923193 113 + 24543557
UUUUGGAGACUCCACCCAGGCAGCUGGGGACAUACACGGAAAAGGUGUUGCUAAUCAAGCAACAAAGUUAGUCCCGUGGACAAAGUAAGCCGGUGGCAAAAAGGAGCCGGUGG
....(....).(((((..(((...((....))..(((((......(((((((.....))))))).........)))))..........)))...(((........)))))))) ( -36.26, z-score =  -1.20, R)
>droSim1.chr3L 12302457 112 + 22553184
UUUUGGAGACUCCACC-AGGCAGCUGGGGACAUACACGGAAAAGGUGUUGCUAAUCAAGCAACAAAGUUAGUCCCGGGGACAAAGUAAGCCGGUGGCAAAAAGGAGCCGGUGG
....(....).(((((-.(((.(((.(((((..((.(......).(((((((.....)))))))..))..)))))(....)..)))..)))...(((........)))))))) ( -38.40, z-score =  -2.13, R)
>droSec1.super_0 5098457 112 + 21120651
UCUUGGAGACUCCACC-AGGCAGCUGGGGACAUACACGGAAAAGGUGUUGCUAAUCAAGCAACAAAGUUAGUCCCGGGGACAAAGUAAGCCGGUGGCAAAAAGGAGCCGGUGG
....(....).(((((-.(((.(((.(((((..((.(......).(((((((.....)))))))..))..)))))(....)..)))..)))...(((........)))))))) ( -38.40, z-score =  -1.91, R)
>droYak2.chr3L 13002913 111 + 24197627
UUUUUGAGACUGCACC-AGGCAGCUGGGG-CAAACACGAGAAAGGUGUUGCUAAUCAAGCAACAAAGUUAGUCCCGGGGACAAAGUAAGCCGGUGGCAAAAUGGAGCCGGUGG
.(((((...((((...-..))))((((((-(.(((.(......).(((((((.....)))))))..))).)))))))...)))))...((((((..(.....)..)))))).. ( -37.80, z-score =  -1.87, R)
>droEre2.scaffold_4784 12932497 111 + 25762168
UUUUUGAGACUCCACC-AGGCAGCUGGGG-CAUACACGAAAAAGGUGUUGCUAAUCAAGCAACAAAGUUAGUCCCGGGGACAAAGUAAGCCGGUGGCAAGAAGGAGCCGGUGG
...........(((((-.(((.(((((((-(..((.(......).(((((((.....)))))))..))..)))))(....)..)))..)))...(((........)))))))) ( -36.80, z-score =  -1.67, R)
>consensus
UUUUGGAGACUCCACC_AGGCAGCUGGGGACAUACACGGAAAAGGUGUUGCUAAUCAAGCAACAAAGUUAGUCCCGGGGACAAAGUAAGCCGGUGGCAAAAAGGAGCCGGUGG
...........(((((..(((.(((.(((((..((.(......).(((((((.....)))))))..))..)))))(....)..)))..)))...(((........)))))))) (-31.98 = -32.58 +   0.60)

alignment

Postscript

secondary structure

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dotplot

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Window 6

Location 12,923,193 – 12,923,306
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 95.55
Shannon entropy 0.07689
G+C content 0.52593
Mean single sequence MFE -32.22
Consensus MFE -29.62
Energy contribution -29.82
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.830690
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12923193 113 - 24543557
CCACCGGCUCCUUUUUGCCACCGGCUUACUUUGUCCACGGGACUAACUUUGUUGCUUGAUUAGCAACACCUUUUCCGUGUAUGUCCCCAGCUGCCUGGGUGGAGUCUCCAAAA
((((((((........)))..(((((.....(((.(((((((.......(((((((.....)))))))....))))))).))).....)))))....)))))........... ( -36.00, z-score =  -2.44, R)
>droSim1.chr3L 12302457 112 - 22553184
CCACCGGCUCCUUUUUGCCACCGGCUUACUUUGUCCCCGGGACUAACUUUGUUGCUUGAUUAGCAACACCUUUUCCGUGUAUGUCCCCAGCUGCCU-GGUGGAGUCUCCAAAA
((((((((..((....(((...))).............(((((.......((((((.....))))))(((......).))..))))).))..))).-)))))........... ( -31.30, z-score =  -1.61, R)
>droSec1.super_0 5098457 112 - 21120651
CCACCGGCUCCUUUUUGCCACCGGCUUACUUUGUCCCCGGGACUAACUUUGUUGCUUGAUUAGCAACACCUUUUCCGUGUAUGUCCCCAGCUGCCU-GGUGGAGUCUCCAAGA
((((((((..((....(((...))).............(((((.......((((((.....))))))(((......).))..))))).))..))).-)))))........... ( -31.30, z-score =  -1.26, R)
>droYak2.chr3L 13002913 111 - 24197627
CCACCGGCUCCAUUUUGCCACCGGCUUACUUUGUCCCCGGGACUAACUUUGUUGCUUGAUUAGCAACACCUUUCUCGUGUUUG-CCCCAGCUGCCU-GGUGCAGUCUCAAAAA
.....(((........)))...(((.......)))...((((((.....(((((((.....)))))))..............(-(.((((....))-)).))))))))..... ( -29.90, z-score =  -1.38, R)
>droEre2.scaffold_4784 12932497 111 - 25762168
CCACCGGCUCCUUCUUGCCACCGGCUUACUUUGUCCCCGGGACUAACUUUGUUGCUUGAUUAGCAACACCUUUUUCGUGUAUG-CCCCAGCUGCCU-GGUGGAGUCUCAAAAA
((((((((........)))...(((.(((...((((...))))......(((((((.....)))))))..........))).)-))..........-)))))........... ( -32.60, z-score =  -1.91, R)
>consensus
CCACCGGCUCCUUUUUGCCACCGGCUUACUUUGUCCCCGGGACUAACUUUGUUGCUUGAUUAGCAACACCUUUUCCGUGUAUGUCCCCAGCUGCCU_GGUGGAGUCUCCAAAA
((((((((........)))..(((((......((((...))))......(((((((.....)))))))....................)))))....)))))........... (-29.62 = -29.82 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:22:18 2011