Locus 12182

Sequence ID dm3.chr3R
Location 26,293,846 – 26,293,944
Length 98
Max. P 0.935948
window16753 window16754

overview

Window 3

Location 26,293,846 – 26,293,944
Length 98
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 69.71
Shannon entropy 0.46158
G+C content 0.34229
Mean single sequence MFE -17.15
Consensus MFE -10.44
Energy contribution -11.12
Covariance contribution 0.69
Combinations/Pair 1.33
Mean z-score -1.29
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.736720
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26293846 98 + 27905053
AUAUGUACGUUAUCAAAAGUGCUUUCUGGAAUUUCCUGAAUAUUUCUGAUAGUAUGCAAA-GCUAAUAAUCAGCGUGCGUAGCAAUGAAUGCAAACGUG
.((((((((((.(((.(((((..(((.((.....)).)))))))).)))((((.......-))))......))))))))))(((.....)))....... ( -21.00, z-score =  -0.73, R)
>droSim1.chr3R 25939312 83 + 27517382
----AUACGUUAUCAAAAGUGCUUUCUAGAAUUUCCAGAAUAUUUCUGAUAGAAUGCAAA-GCUGAUAAUCAGCGUGUGUACGAAUGG-----------
----(((((((((((....(((.(((((.......((((.....)))).))))).)))..-..)))))....))))))..........----------- ( -16.90, z-score =  -1.04, R)
>droSec1.super_4 5118183 84 + 6179234
----AUACGUUAUCAAAAGUGCUUUCUAGAAUUUCCAAAAUAUUUCUGAUAGAAUGCAAAAGCUGAUAAUCAGCGUGUGUACGAAUGG-----------
----...(((...((....(((.((((((((............))))...)))).)))...((((.....)))).))...))).....----------- ( -14.80, z-score =  -0.71, R)
>droYak2.chr3R 27212581 82 + 28832112
----AUACGUUAUCAAUGCUGCUUUGUGGAAUUUCUACAA-AUUCCUGAUAAACAGCAAACUUUUCAUACCGAUGAAUGCAAACUUA------------
----....(((.....(((((.((((((((((((....))-)))))..)))))))))).....(((((....)))))....)))...------------ ( -15.90, z-score =  -2.67, R)
>consensus
____AUACGUUAUCAAAAGUGCUUUCUAGAAUUUCCAGAAUAUUUCUGAUAGAAUGCAAA_GCUGAUAAUCAGCGUGUGUACGAAUGG___________
....((((.((((((.((((...((((((.....)))))).)))).)))))).........((((.....))))))))..................... (-10.44 = -11.12 +   0.69)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 4

Location 26,293,846 – 26,293,944
Length 98
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 69.71
Shannon entropy 0.46158
G+C content 0.34229
Mean single sequence MFE -17.35
Consensus MFE -10.11
Energy contribution -10.55
Covariance contribution 0.44
Combinations/Pair 1.29
Mean z-score -1.84
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.40
SVM RNA-class probability 0.935948
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26293846 98 - 27905053
CACGUUUGCAUUCAUUGCUACGCACGCUGAUUAUUAGC-UUUGCAUACUAUCAGAAAUAUUCAGGAAAUUCCAGAAAGCACUUUUGAUAACGUACAUAU
.((((..(((.....)))...(((.(((((...)))))-..)))....((((((((...(((.((.....)).))).....))))))))))))...... ( -17.90, z-score =  -0.99, R)
>droSim1.chr3R 25939312 83 - 27517382
-----------CCAUUCGUACACACGCUGAUUAUCAGC-UUUGCAUUCUAUCAGAAAUAUUCUGGAAAUUCUAGAAAGCACUUUUGAUAACGUAU----
-----------......((((....((((.....))))-.........((((((((...((((((.....)))))).....))))))))..))))---- ( -18.10, z-score =  -2.72, R)
>droSec1.super_4 5118183 84 - 6179234
-----------CCAUUCGUACACACGCUGAUUAUCAGCUUUUGCAUUCUAUCAGAAAUAUUUUGGAAAUUCUAGAAAGCACUUUUGAUAACGUAU----
-----------......((((....((((.....))))..........((((((((...((((((.....)))))).....))))))))..))))---- ( -15.50, z-score =  -1.82, R)
>droYak2.chr3R 27212581 82 - 28832112
------------UAAGUUUGCAUUCAUCGGUAUGAAAAGUUUGCUGUUUAUCAGGAAU-UUGUAGAAAUUCCACAAAGCAGCAUUGAUAACGUAU----
------------......(((.(((((....))))).....((((((((....(((((-((....)))))))...))))))))........))).---- ( -17.90, z-score =  -1.83, R)
>consensus
___________CCAUUCGUACACACGCUGAUUAUCAGC_UUUGCAUUCUAUCAGAAAUAUUCUGGAAAUUCCAGAAAGCACUUUUGAUAACGUAU____
..................(((....((((.....))))..........((((((((...((((((.....)))))).....))))))))..)))..... (-10.11 = -10.55 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:57:20 2011