Locus 5694

Sequence ID dm3.chr3L
Location 538,784 – 538,896
Length 112
Max. P 0.771696
window7821 window7822

overview

Window 1

Location 538,784 – 538,896
Length 112
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 88.33
Shannon entropy 0.19191
G+C content 0.53405
Mean single sequence MFE -35.30
Consensus MFE -27.38
Energy contribution -27.26
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.71
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.17
SVM RNA-class probability 0.575426
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 538784 112 + 24543557
GAGGAAAAUGGGGAAA-CCCACGAGAGGGGAGGGUGG---GAAAUCUAGGAAGAGGGCACCAGUAAAAUGUUGCAGUAAACGAUUUUCCAUUUCCCGCUGGGUCAGCGGGUCAUCG
........((((....-))))(((((.....((((((---((((((..........(((.((......)).))).(....)))))))))))))(((((((...))))))))).))) ( -37.10, z-score =  -1.88, R)
>droSim1.chr2R 8759622 112 + 19596830
GAGGAAAAUGGGGAAA-CUCACGAGAGGGGAGGGUGG---GAAAUCUAGGAAGAGGGCACCAGUAAAAUGCUGCAGUAAACGAUUUUCCAUUUCCCGCUGGGUCAGCGGGUCAUCC
..(((...((((....-)))).((.......((((((---((((((..........(((.((......)).))).(....)))))))))))))(((((((...))))))))).))) ( -34.40, z-score =  -1.04, R)
>droSec1.super_2 559494 112 + 7591821
GAGGAAAAUGGGGAAA-CUCACGAGAGGGGAGGGUGG---GAAAUCUAGGAAGAGGGCACCAGUAAAAUGUUGCAGUAAACGAUUUUCCAUUUCCCGCUGGGUCAGCGGGUCAUCG
........((((....-))))(((((.....((((((---((((((..........(((.((......)).))).(....)))))))))))))(((((((...))))))))).))) ( -34.10, z-score =  -1.51, R)
>droYak2.chr3L 519502 102 + 24197627
GAGGAAAGUGGGGAAA-CUCACGAGAGGGACGGGUGGUGGGAAAUCUAGGAAGAGGGCACC-------------AUUAAACGGUUUUCCAUUUCCCGCUGGGUCAGCGGGUCAUCG
((((((((((((....-)))))........((..(((((((...(((....)))...).))-------------))))..))..)))))....(((((((...)))))))...)). ( -38.60, z-score =  -2.75, R)
>droEre2.scaffold_4784 537371 100 + 25762168
GAGGAAAAUGGGGAAAACUCACGAGAGGGGUGGGUGG---GAAAUCUAGGAAGAGGGCACC-------------AUUAAACGGUUUUCCAUUUCCCGCUGGGUCAGCGGGUCAUCG
(((((((((.(.....((((.(....))))).(((((---(...(((....)))...).))-------------)))...).)))))))....(((((((...)))))))...)). ( -32.30, z-score =  -1.38, R)
>consensus
GAGGAAAAUGGGGAAA_CUCACGAGAGGGGAGGGUGG___GAAAUCUAGGAAGAGGGCACCAGUAAAAUG_UGCAGUAAACGAUUUUCCAUUUCCCGCUGGGUCAGCGGGUCAUCG
((.((((((((..((..(((.(....))))..((((........(((....)))...))))......................))..))))))(((((((...))))))))).)). (-27.38 = -27.26 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 538,784 – 538,896
Length 112
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 88.33
Shannon entropy 0.19191
G+C content 0.53405
Mean single sequence MFE -26.58
Consensus MFE -20.92
Energy contribution -20.96
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.92
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.64
SVM RNA-class probability 0.771696
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 538784 112 - 24543557
CGAUGACCCGCUGACCCAGCGGGAAAUGGAAAAUCGUUUACUGCAACAUUUUACUGGUGCCCUCUUCCUAGAUUUC---CCACCCUCCCCUCUCGUGGG-UUUCCCCAUUUUCCUC
......(((((((...)))))))....(((((((........(((.((......)).)))..........((...(---((((...........)))))-..))...))))))).. ( -27.70, z-score =  -1.55, R)
>droSim1.chr2R 8759622 112 - 19596830
GGAUGACCCGCUGACCCAGCGGGAAAUGGAAAAUCGUUUACUGCAGCAUUUUACUGGUGCCCUCUUCCUAGAUUUC---CCACCCUCCCCUCUCGUGAG-UUUCCCCAUUUUCCUC
(((...(((((((...)))))))((((((.(((((((.....)).(((((.....)))))..........))))).---..........(((....)))-.....))))))))).. ( -27.80, z-score =  -1.63, R)
>droSec1.super_2 559494 112 - 7591821
CGAUGACCCGCUGACCCAGCGGGAAAUGGAAAAUCGUUUACUGCAACAUUUUACUGGUGCCCUCUUCCUAGAUUUC---CCACCCUCCCCUCUCGUGAG-UUUCCCCAUUUUCCUC
......(((((((...)))))))....(((((((.....................((((...(((....)))....---.)))).....(((....)))-.......))))))).. ( -24.40, z-score =  -1.45, R)
>droYak2.chr3L 519502 102 - 24197627
CGAUGACCCGCUGACCCAGCGGGAAAUGGAAAACCGUUUAAU-------------GGUGCCCUCUUCCUAGAUUUCCCACCACCCGUCCCUCUCGUGAG-UUUCCCCACUUUCCUC
.((((.(((((((...)))))))((((((....))))))..(-------------((((...(((....))).....)))))..)))).(((....)))-................ ( -26.70, z-score =  -2.22, R)
>droEre2.scaffold_4784 537371 100 - 25762168
CGAUGACCCGCUGACCCAGCGGGAAAUGGAAAACCGUUUAAU-------------GGUGCCCUCUUCCUAGAUUUC---CCACCCACCCCUCUCGUGAGUUUUCCCCAUUUUCCUC
.((((.(((((((...)))))))....(((((((........-------------((((...(((....)))....---.))))(((.......))).))))))).))))...... ( -26.30, z-score =  -2.73, R)
>consensus
CGAUGACCCGCUGACCCAGCGGGAAAUGGAAAAUCGUUUACUGCA_CAUUUUACUGGUGCCCUCUUCCUAGAUUUC___CCACCCUCCCCUCUCGUGAG_UUUCCCCAUUUUCCUC
......(((((((...)))))))....((((((......................((((...(((....)))........)))).....(((....))).........)))))).. (-20.92 = -20.96 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:53:18 2011