Locus 10921

Sequence ID dm3.chr3R
Location 17,481,216 – 17,481,270
Length 54
Max. P 0.940204
window15010 window15011

overview

Window 0

Location 17,481,216 – 17,481,270
Length 54
Sequences 8
Columns 57
Reading direction forward
Mean pairwise identity 72.22
Shannon entropy 0.54987
G+C content 0.43016
Mean single sequence MFE -8.84
Consensus MFE -5.69
Energy contribution -5.67
Covariance contribution -0.02
Combinations/Pair 1.29
Mean z-score -1.23
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.46
SVM RNA-class probability 0.940204
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17481216 54 + 27905053
GCUCUUACGCUUCACCGUCUAGGUGACACACAUA---AACUCAAAUUCAAGCAUGUG
((......)).(((((.....)))))..(((((.---..((........)).))))) (  -8.70, z-score =  -1.31, R)
>droSim1.chr3R 23528094 54 - 27517382
GCUCUUACGCUUCACCGUCUAGGUGACACACAUA---AACUCAAAUUUAAGCAUGUG
((......)).(((((.....)))))..(((((.---..((........)).))))) (  -8.70, z-score =  -1.27, R)
>droSec1.super_6 347212 54 - 4358794
GCUCUUACGCUUCACCGUUUAGGUGACACACAUA---AACUCAAAUUUAAGCAUGUG
((......)).(((((.....)))))..(((((.---..((........)).))))) (  -8.70, z-score =  -1.21, R)
>droYak2.chr3R 6319360 53 + 28832112
GCUUUUACGCGUCUCCGUCUAGGUGACACACACA----ACUCAAAAUAAAGCAUGUG
((......))(((.((.....)).)))...((((----.((........))..)))) (  -8.60, z-score =  -0.64, R)
>droEre2.scaffold_4770 13562088 55 - 17746568
GCUUGUACGCGUCGCCCUCUUGGUGACAUACACACAUAACUAAAAUUGAAGCCUG--
(((((....)((((((.....)))))).....................))))...-- ( -10.50, z-score =  -1.26, R)
>droAna3.scaffold_13340 18051938 52 - 23697760
GCUUCAGAGCGUCACCGUCUAGGUGACACACACA-----UCCACAAUGCAGCUUUUA
.....(((((((((((.....)))))).....((-----(.....)))..))))).. ( -14.10, z-score =  -2.79, R)
>dp4.chr2 23895687 51 + 30794189
GCUUUUACGCUUCACUGUUUAGGCGACACACAUA-GU-AUUCAUACAUAUUCA----
((((..(((......)))..))))..........-((-(....))).......---- (  -5.20, z-score =  -1.01, R)
>droPer1.super_3 6669703 52 + 7375914
GCUUUUACGCUUCACUGUUUAGGUGACACACAUA-GUCGUACAUAAAUAUUCA----
.....(((((((((((.....))))).......)-).))))............---- (  -6.21, z-score =  -0.37, R)
>consensus
GCUUUUACGCUUCACCGUCUAGGUGACACACAUA___AACUCAAAUUUAAGCAUGUG
((......)).(((((.....)))))............................... ( -5.69 =  -5.67 +  -0.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 17,481,216 – 17,481,270
Length 54
Sequences 8
Columns 57
Reading direction reverse
Mean pairwise identity 72.22
Shannon entropy 0.54987
G+C content 0.43016
Mean single sequence MFE -11.89
Consensus MFE -5.97
Energy contribution -6.30
Covariance contribution 0.33
Combinations/Pair 1.30
Mean z-score -1.05
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.533149
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17481216 54 - 27905053
CACAUGCUUGAAUUUGAGUU---UAUGUGUGUCACCUAGACGGUGAAGCGUAAGAGC
.....((((......))))(---(((((...(((((.....))))).)))))).... ( -12.90, z-score =  -1.18, R)
>droSim1.chr3R 23528094 54 + 27517382
CACAUGCUUAAAUUUGAGUU---UAUGUGUGUCACCUAGACGGUGAAGCGUAAGAGC
.....(((((....)))))(---(((((...(((((.....))))).)))))).... ( -13.30, z-score =  -1.56, R)
>droSec1.super_6 347212 54 + 4358794
CACAUGCUUAAAUUUGAGUU---UAUGUGUGUCACCUAAACGGUGAAGCGUAAGAGC
.....(((((....)))))(---(((((...(((((.....))))).)))))).... ( -13.30, z-score =  -1.77, R)
>droYak2.chr3R 6319360 53 - 28832112
CACAUGCUUUAUUUUGAGU----UGUGUGUGUCACCUAGACGGAGACGCGUAAAAGC
((((.((((......))))----)))).(((((.((.....)).)))))........ ( -14.00, z-score =  -1.43, R)
>droEre2.scaffold_4770 13562088 55 + 17746568
--CAGGCUUCAAUUUUAGUUAUGUGUGUAUGUCACCAAGAGGGCGACGCGUACAAGC
--..((((........))))...((((..((((.((.....)).))))..))))... ( -12.00, z-score =  -0.48, R)
>droAna3.scaffold_13340 18051938 52 + 23697760
UAAAAGCUGCAUUGUGGA-----UGUGUGUGUCACCUAGACGGUGACGCUCUGAAGC
.....((((((((...))-----)))(.((((((((.....)))))))).)...))) ( -16.20, z-score =  -2.09, R)
>dp4.chr2 23895687 51 - 30794189
----UGAAUAUGUAUGAAU-AC-UAUGUGUGUCGCCUAAACAGUGAAGCGUAAAAGC
----...............-..-(((((...((((.......)))).)))))..... (  -6.50, z-score =  -0.04, R)
>droPer1.super_3 6669703 52 - 7375914
----UGAAUAUUUAUGUACGAC-UAUGUGUGUCACCUAAACAGUGAAGCGUAAAAGC
----..................-(((((...((((.......)))).)))))..... (  -6.90, z-score =   0.16, R)
>consensus
CACAUGCUUAAAUUUGAGUU___UAUGUGUGUCACCUAGACGGUGAAGCGUAAAAGC
.......................(((((...(((((.....))))).)))))..... ( -5.97 =  -6.30 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:33:03 2011