Locus 2823

Sequence ID dm3.chr2L
Location 22,985,063 – 22,985,183
Length 120
Max. P 0.999442
window3893 window3894

overview

Window 3

Location 22,985,063 – 22,985,161
Length 98
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 60.30
Shannon entropy 0.56562
G+C content 0.55255
Mean single sequence MFE -45.53
Consensus MFE -25.15
Energy contribution -27.40
Covariance contribution 2.25
Combinations/Pair 1.41
Mean z-score -2.97
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.89
SVM RNA-class probability 0.999442
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22985063 98 - 23011544
-GACUGGGGCUUCAGUCCUCGAGCCAGGCGGACCAUAUAUGACGGACUCAUGGCACCUUGUGUGCUGUUUGGUGCCCCGGUAUGGAACAA-GUAGCUGCC------------
-.((((((((.((((((((((.....((....)).....))).))))..(((((((.....))))))).))).)))))))).........-.........------------ ( -31.00, z-score =   0.77, R)
>droVir3.scaffold_9500 4936 112 + 5668
UGACUGGGGCCUAAGCAGACGUGCUGUCCGCACCAUCUAUGAGGGUCUGUUUGUUGCAUGUGCAGCAUAUGGAUCGUCUGUAUGGUGCAAGGCGGUCACGACUGUGGUCGGC
.......((((...((((.(((((((((.(((((((.((.((.(((((((.((((((....)))))).))))))).)))).)))))))..))))).)))).))))))))... ( -51.80, z-score =  -3.44, R)
>droGri2.scaffold_15040 117682 111 - 162499
-GACUGGGGCCUCAGCAGAACUGCUGCUCGCGCCGUAUACGAUGGUCUAUUUGUUGCCUGUGCAACUUAUGGAUCGUCGGUAUGGUGUAAAGUAGUUUCGACUGUUGUAGGC
-.......((((((((((....((((((.(((((((((.(((((((((((..(((((....)))))..))))))))))))))))))))..)))))).....)))))).)))) ( -53.80, z-score =  -6.25, R)
>consensus
_GACUGGGGCCUCAGCAGACGUGCUGCCCGCACCAUAUAUGACGGUCUAUUUGUUGCAUGUGCAACAUAUGGAUCGUCGGUAUGGUGCAA_GUAGUUACGACUGU_GU_GGC
.(((((((((...((((....))))))))(((((((((.(((.(((((((..(((((....)))))..))))))).))))))))))))....)))))............... (-25.15 = -27.40 +   2.25) 

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 4

Location 22,985,074 – 22,985,183
Length 109
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 55.56
Shannon entropy 0.64008
G+C content 0.55802
Mean single sequence MFE -43.11
Consensus MFE -20.79
Energy contribution -23.37
Covariance contribution 2.57
Combinations/Pair 1.38
Mean z-score -2.45
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.31
SVM RNA-class probability 0.998277
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22985074 109 - 23011544
---GCUGGCGCGUGUGCUUCGAGCCGACUGGGGCUUCAGUCCUCGAGCCAGGCGGACCAUAUAUGACGGACUCAUGGCACCUUGUGUGCUGUUUGGUGCCCCGGUAUGGAAC
---.....(((.((.(((.((((..((((((....))))))))))))))).)))..((((((((((.....))))((((((.............))))))...))))))... ( -40.52, z-score =   0.12, R)
>droVir3.scaffold_9500 4960 112 + 5668
GCAAGUGCGUCGUAUUUUGAGGUCUGACUGGGGCCUAAGCAGACGUGCUGUCCGCACCAUCUAUGAGGGUCUGUUUGUUGCAUGUGCAGCAUAUGGAUCGUCUGUAUGGUGC
...((..((((........((((((.....)))))).....))))..))....(((((((.((.((.(((((((.((((((....)))))).))))))).)))).))))))) ( -47.32, z-score =  -3.18, R)
>droGri2.scaffold_15040 117706 92 - 162499
--------------------GAAGUGACUGGGGCCUCAGCAGAACUGCUGCUCGCGCCGUAUACGAUGGUCUAUUUGUUGCCUGUGCAACUUAUGGAUCGUCGGUAUGGUGU
--------------------..........((((...((((....))))))))(((((((((.(((((((((((..(((((....)))))..)))))))))))))))))))) ( -41.50, z-score =  -4.30, R)
>consensus
_____UG___CGU_U__U__GAACUGACUGGGGCCUCAGCAGACGUGCUGCCCGCACCAUAUAUGACGGUCUAUUUGUUGCAUGUGCAACAUAUGGAUCGUCGGUAUGGUGC
..............................((((...((((....))))))))(((((((((.(((.(((((((..(((((....)))))..))))))).)))))))))))) (-20.79 = -23.37 +   2.57) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:58:44 2011