Locus 12002

Sequence ID dm3.chr3R
Location 25,019,761 – 25,019,899
Length 138
Max. P 0.563153
window16494 window16495

overview

Window 4

Location 25,019,761 – 25,019,871
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.17
Shannon entropy 0.46683
G+C content 0.36316
Mean single sequence MFE -15.98
Consensus MFE -8.98
Energy contribution -9.02
Covariance contribution 0.04
Combinations/Pair 1.08
Mean z-score -1.25
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.563153
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25019761 110 + 27905053
AAUCAUACUUAUAUACAUA----------CGCAGCAAGUCACAUUUCACGAAUGACAAAUUCCAUUGCCUACUUUUAGGCACUACCACAACUUUAGGCACCACAUUGCUUUUAAAUAGCC
...................----------.((...((((..........((((.....))))...((((((....))))))........))))...))........(((.......))). ( -13.80, z-score =  -1.18, R)
>droEre2.scaffold_4820 7459347 107 - 10470090
AAUCGUCCAUACUAAUAUGGUUUUUAUACAGCUCCCAGUUGCAUUUCCCGAUUGAAAUAUUCCGUUGCCUACUUUUAGGCAGUACUAC---------CAC----UUGCCUUCAAAUAUCU
(((((.(((((....)))))........((((.....)))).......)))))...........(((((((....)))))))......---------...----................ ( -16.20, z-score =  -1.05, R)
>droYak2.chr3R 7352969 116 - 28832112
AUUCAUCAAUUUUAAGAUGGCUUA-ACACCGCUCCAUGUCACAUUUCCCGAAUGAAAUAUUUCAUUGCCUACUUUUAGGCACUACUACU---UAAAGCACAAGAUUGCUUUCAAAUACCU
...((((........))))((...-.....))..................((((((....))))))(((((....))))).........---.((((((......))))))......... ( -16.40, z-score =  -1.27, R)
>droSec1.super_4 3882916 109 + 6179234
AAUCAUCCAUAUUAAUAU-----------CGCAGCAAGUCACAUUUCCCAAAUGAAAAAUUCCAUUGCCUACUUUUAGGCACUAAUACAACUUUGGGCUCCAAAUUGCUUUCAAAUACAG
..................-----------...(((((.........((((((((........)).((((((....))))))..........)))))).......)))))........... ( -16.29, z-score =  -1.76, R)
>droSim1.chr3R 24690759 109 + 27517382
AAUCAUAAAUAUUAAUAU-----------CGCAGCAAGUCACAUUUCCCGAAUGAAAAAUUCCAUUGCCUACUUUUAGGCACCAAUACAACUUUGGGCACCAAAUUGCUUUCAAAUGCAG
..................-----------.(((((((.........(((((((.....))))...((((((....)))))).............))).......)))).......))).. ( -17.20, z-score =  -0.97, R)
>consensus
AAUCAUCCAUAUUAAUAU___________CGCAGCAAGUCACAUUUCCCGAAUGAAAAAUUCCAUUGCCUACUUUUAGGCACUACUACAACUUUAGGCACCAAAUUGCUUUCAAAUACCG
..............................((.........(((((...)))))...........((((((....)))))).........................))............ ( -8.98 =  -9.02 +   0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 25,019,791 – 25,019,899
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.02
Shannon entropy 0.45041
G+C content 0.34028
Mean single sequence MFE -15.91
Consensus MFE -8.06
Energy contribution -9.18
Covariance contribution 1.12
Combinations/Pair 1.11
Mean z-score -1.49
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.04
SVM RNA-class probability 0.515316
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25019791 108 + 27905053
ACAUUUCACGAAUGACAAAUUCCAUUGCCUACUUUUAGGCACUACCACAACUUUAGGCACCACAUUGCUUUUAAAUAGC------------CAUAACUUUAAGAUCUUUUAUAGAUUUCU
.........((((.....))))...((((((....))))))..............(((...................))------------).........((((((.....)))))).. ( -13.81, z-score =  -1.85, R)
>droEre2.scaffold_4820 7459387 86 - 10470090
GCAUUUCCCGAUUGAAAUAUUCCGUUGCCUACUUUUAGGCAGUACUACCACUU-------------GCCUUCAAAUA---------------------UCUAUAUCUUGUGUAGAUUUGG
.......(((((((((.........((((((....))))))(((........)-------------)).)))))..(---------------------(((((((...)))))))))))) ( -15.40, z-score =  -1.52, R)
>droYak2.chr3R 7353008 117 - 28832112
ACAUUUCCCGAAUGAAAUAUUUCAUUGCCUACUUUUAGGCACUACUA---CUUAAAGCACAAGAUUGCUUUCAAAUACCUACAUACAUAUACAUAUCUACAAGUUCUUGUAUAAAUUUCU
..........((((((....))))))(((((....))))).......---...((((((......))))))................((((((..............))))))....... ( -15.94, z-score =  -2.36, R)
>droSec1.super_4 3882945 108 + 6179234
ACAUUUCCCAAAUGAAAAAUUCCAUUGCCUACUUUUAGGCACUAAUACAACUUUGGGCUCCAAAUUGCUUUCAAAUACA------------GAGAACUUCAAGAUCUUGUAUAGAUUUCU
............(((((........((((((....))))))......(((.(((((...)))))))).))))).(((((------------.(((.(.....).))))))))........ ( -16.20, z-score =  -0.60, R)
>droSim1.chr3R 24690788 108 + 27517382
ACAUUUCCCGAAUGAAAAAUUCCAUUGCCUACUUUUAGGCACCAAUACAACUUUGGGCACCAAAUUGCUUUCAAAUGCA------------GAUAACUUCAAGAUCUUGUAUAGAUUUCU
......(((((((.....))))...((((((....)))))).............))).......((((........)))------------).........((((((.....)))))).. ( -18.20, z-score =  -1.12, R)
>consensus
ACAUUUCCCGAAUGAAAAAUUCCAUUGCCUACUUUUAGGCACUACUACAACUUUAGGCACCAAAUUGCUUUCAAAUACA____________CAUAACUUCAAGAUCUUGUAUAGAUUUCU
............((((.........((((((....))))))..............(((........)))))))............................((((((.....)))))).. ( -8.06 =  -9.18 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:53:46 2011