Locus 5332

Sequence ID dm3.chr2R
Location 19,547,884 – 19,548,015
Length 131
Max. P 0.872942
window7309 window7310

overview

Window 9

Location 19,547,884 – 19,548,015
Length 131
Sequences 4
Columns 131
Reading direction forward
Mean pairwise identity 80.60
Shannon entropy 0.29101
G+C content 0.38629
Mean single sequence MFE -31.17
Consensus MFE -21.10
Energy contribution -22.73
Covariance contribution 1.62
Combinations/Pair 1.06
Mean z-score -1.86
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.718051
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19547884 131 + 21146708
UGCUCAUGUGUAUUUGUUUAAUUUAUAUCUAGAGUCUAGAGUCUGAUAUAAAUAUUAAAAUAAGUAUAAGAAGCGGCGCACAGCUACGUCUGCCCGCCUAUGUGCAUAAAAUAUCACAAGCAACAGGCGGC
.(((....(((((((((((.(((((((((.(((.(....).))))))))))))....)))))))))))...)))((((.((......)).))))(((((...(((..............)))..))))).. ( -35.34, z-score =  -2.00, R)
>droSec1.super_9 2827329 131 + 3197100
UGCUCAUGUGUAUUUGUUUAAUUUAUAUCUAGAGUCUAGAGUCUGAUAUAAAUAUUAAAAUAAGUAUAAGAAGCGGCGCACAGCUACGCCCCCCCGCCUAUGUGCAUAAAAUACCACAAGCAACAGGCGGC
.(((....(((((((((((.(((((((((.(((.(....).))))))))))))....)))))))))))...)))((((........))))...((((((...(((..............)))..)))))). ( -37.64, z-score =  -3.26, R)
>droYak2.chr2R 19524163 113 + 21139217
UGCUCAUGUGUAUUUGUUUAAUUUAUAUCUAGAGUCUAGAGUCUGAUAUAAAUAUUAAAAUAAGAAUAAGAAGCAGCGCAUAGCUACGUCCAC--GUCCACGAGCAACAGGCGGC----------------
(((((.(((.(((((.....(((((((((.(((.(....).))))))))))))....)))))...))).).)))).(((...(((.(((....--....)))))).....)))..---------------- ( -24.10, z-score =  -0.52, R)
>droEre2.scaffold_4845 20910042 111 + 22589142
UGCUCAUGUGUAUUUGUUUAAUUUAUAUCUAGAGUCUAGAGUCUGAUAUAAAUAUUAAAAUAAGAAUAAGAAGCAGCGCAUAG--ACGGCUAC--GUCCACGAGCAACAGGCGGC----------------
(((((((((((...(((((..((((((((.(((.(....).)))))))))))((((........))))..))))))))))).(--(((....)--)))...))))).........---------------- ( -27.60, z-score =  -1.65, R)
>consensus
UGCUCAUGUGUAUUUGUUUAAUUUAUAUCUAGAGUCUAGAGUCUGAUAUAAAUAUUAAAAUAAGAAUAAGAAGCAGCGCACAGCUACGUCCAC__GCCCACGAGCAAAAAACAGC________________
(((((((((((((((((((.(((((((((.(((.(....).))))))))))))....)))))))))))....(.(((.....))).)...........))))))))......................... (-21.10 = -22.73 +   1.62)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,547,884 – 19,548,015
Length 131
Sequences 4
Columns 131
Reading direction reverse
Mean pairwise identity 80.60
Shannon entropy 0.29101
G+C content 0.38629
Mean single sequence MFE -31.62
Consensus MFE -20.40
Energy contribution -21.65
Covariance contribution 1.25
Combinations/Pair 1.12
Mean z-score -2.24
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.872942
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19547884 131 - 21146708
GCCGCCUGUUGCUUGUGAUAUUUUAUGCACAUAGGCGGGCAGACGUAGCUGUGCGCCGCUUCUUAUACUUAUUUUAAUAUUUAUAUCAGACUCUAGACUCUAGAUAUAAAUUAAACAAAUACACAUGAGCA
.(((((((((((..((((....))))))).))))))))(((((.(..((.....))..).)))......(((((....((((((((((((........))).))))))))).....))))).......)). ( -32.00, z-score =  -1.41, R)
>droSec1.super_9 2827329 131 - 3197100
GCCGCCUGUUGCUUGUGGUAUUUUAUGCACAUAGGCGGGGGGGCGUAGCUGUGCGCCGCUUCUUAUACUUAUUUUAAUAUUUAUAUCAGACUCUAGACUCUAGAUAUAAAUUAAACAAAUACACAUGAGCA
.(((((((((((.((........)).))).))))))))((.((((((....)))))).)).(((((...(((((....((((((((((((........))).))))))))).....)))))...))))).. ( -38.10, z-score =  -2.15, R)
>droYak2.chr2R 19524163 113 - 21139217
----------------GCCGCCUGUUGCUCGUGGAC--GUGGACGUAGCUAUGCGCUGCUUCUUAUUCUUAUUUUAAUAUUUAUAUCAGACUCUAGACUCUAGAUAUAAAUUAAACAAAUACACAUGAGCA
----------------.........((((((((((.--..(((.(((((.....))))).)))...)).(((((....((((((((((((........))).))))))))).....)))))..)))))))) ( -29.20, z-score =  -2.63, R)
>droEre2.scaffold_4845 20910042 111 - 22589142
----------------GCCGCCUGUUGCUCGUGGAC--GUAGCCGU--CUAUGCGCUGCUUCUUAUUCUUAUUUUAAUAUUUAUAUCAGACUCUAGACUCUAGAUAUAAAUUAAACAAAUACACAUGAGCA
----------------.........((((((((((.--(((((((.--...)).))))).)).......(((((....((((((((((((........))).))))))))).....)))))..)))))))) ( -27.20, z-score =  -2.76, R)
>consensus
________________GCCACCUGAUGCACAUAGAC__GUAGACGUAGCUAUGCGCCGCUUCUUAUACUUAUUUUAAUAUUUAUAUCAGACUCUAGACUCUAGAUAUAAAUUAAACAAAUACACAUGAGCA
.........................((((((((((((.((((......)))).))))............(((((....((((((((((((........))).))))))))).....)))))..)))))))) (-20.40 = -21.65 +   1.25)

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 22:46:12 2011