Locus 5686

Sequence ID dm3.chr3L
Location 504,201 – 504,291
Length 90
Max. P 0.977579
window7811 window7812

overview

Window 1

Location 504,201 – 504,291
Length 90
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.59
Shannon entropy 0.30431
G+C content 0.56696
Mean single sequence MFE -34.53
Consensus MFE -25.52
Energy contribution -25.90
Covariance contribution 0.38
Combinations/Pair 1.07
Mean z-score -1.98
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.22
SVM RNA-class probability 0.912431
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 504201 90 + 24543557
------CCAAUCUCGAUCGCCAUCUUCCCCGGCUGCCAAU----CCAUUUGGUCUGUGGCCAGUAGCUGU----GGGGCUUGAUUGCGUCGAUCGGUUUGUGUG----------------
------.(((.(.((((((.(.....((((((((((....----((((.......))))...))))))).----)))((......))).))))))).)))....---------------- ( -30.80, z-score =  -1.44, R)
>droSim1.chr2R 8723128 86 + 19596830
------CCAAUCUCGAUCGCCAUCUUCCCCGGCUGCCACU----CCAUUUGGUCUGUGGCCAGUAGCUGU----GGGGCUUGAUUGCGUCGAUCGGUUUG--------------------
------..((((((((.(((.(((.((((((((((((((.----((....))...)))))....))))).----))))...))).)))))))..))))..-------------------- ( -33.20, z-score =  -2.60, R)
>droSec1.super_2 525709 86 + 7591821
------CCAAUCUCGAUCGCCAUCUUCCCCGGCUGCCACU----CCAUUUGGUCUGUGGCCAGUAGCUUU----GGGGCUUGAUUGCGUCGAUCGGUUUG--------------------
------..((((((((.(((.(((..(((((((((((((.----((....))...)))))....))))..----))))...))).)))))))..))))..-------------------- ( -31.90, z-score =  -2.54, R)
>droYak2.chr3L 482806 120 + 24197627
CCAAUCUCGAUCUCGAUCGCCAUCUUCCCCGGCUGCCAUUUGGACCACUUGGUCUUUGGCCAGUGGCUGUCUGUGCGGCUUGAUUGCGUCGAUCGGUUUGUGGAGUUGGAGUUGCAAUUG
((((.(((.((.((((((((((...((...((((((((..(((.(((((.(((.....)))))))))))..)).)))))).)).)).).)))))))...)).)))))))........... ( -42.20, z-score =  -1.32, R)
>consensus
______CCAAUCUCGAUCGCCAUCUUCCCCGGCUGCCACU____CCAUUUGGUCUGUGGCCAGUAGCUGU____GGGGCUUGAUUGCGUCGAUCGGUUUG____________________
........((((((((.(((.(((..(((((((((((((.....((....))...)))))....))))......))))...))).)))))))..))))...................... (-25.52 = -25.90 +   0.38)

alignment

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secondary structure

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dotplot

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Window 2

Location 504,201 – 504,291
Length 90
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.59
Shannon entropy 0.30431
G+C content 0.56696
Mean single sequence MFE -31.40
Consensus MFE -24.61
Energy contribution -25.68
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -2.31
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.98
SVM RNA-class probability 0.977579
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 504201 90 - 24543557
----------------CACACAAACCGAUCGACGCAAUCAAGCCCC----ACAGCUACUGGCCACAGACCAAAUGG----AUUGGCAGCCGGGGAAGAUGGCGAUCGAGAUUGG------
----------------........(((((((((((.(((...((((----.(((...)))((((....((....))----..))))....))))..))).))).))))..))))------ ( -29.20, z-score =  -2.52, R)
>droSim1.chr2R 8723128 86 - 19596830
--------------------CAAACCGAUCGACGCAAUCAAGCCCC----ACAGCUACUGGCCACAGACCAAAUGG----AGUGGCAGCCGGGGAAGAUGGCGAUCGAGAUUGG------
--------------------....(((((((((((.(((...((((----.(((...)))(((((...((....))----.)))))....))))..))).))).))))..))))------ ( -32.40, z-score =  -3.20, R)
>droSec1.super_2 525709 86 - 7591821
--------------------CAAACCGAUCGACGCAAUCAAGCCCC----AAAGCUACUGGCCACAGACCAAAUGG----AGUGGCAGCCGGGGAAGAUGGCGAUCGAGAUUGG------
--------------------....(((((((((((.(((...((((----...(((....(((((...((....))----.)))))))).))))..))).))).))))..))))------ ( -31.70, z-score =  -3.07, R)
>droYak2.chr3L 482806 120 - 24197627
CAAUUGCAACUCCAACUCCACAAACCGAUCGACGCAAUCAAGCCGCACAGACAGCCACUGGCCAAAGACCAAGUGGUCCAAAUGGCAGCCGGGGAAGAUGGCGAUCGAGAUCGAGAUUGG
........................((((((..(((.(((...((.(.(((.......)))((((..((((....))))....))))....).))..))).))).(((....))))))))) ( -32.30, z-score =  -0.45, R)
>consensus
____________________CAAACCGAUCGACGCAAUCAAGCCCC____ACAGCUACUGGCCACAGACCAAAUGG____AGUGGCAGCCGGGGAAGAUGGCGAUCGAGAUUGG______
........................(((((((((((.(((...((((.....(((...)))(((((...((....)).....)))))....))))..))).))).))))..))))...... (-24.61 = -25.68 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:53:10 2011