Locus 4114

Sequence ID dm3.chr2R
Location 10,555,457 – 10,555,512
Length 55
Max. P 0.960201
window5642 window5643

overview

Window 2

Location 10,555,457 – 10,555,512
Length 55
Sequences 11
Columns 55
Reading direction forward
Mean pairwise identity 95.17
Shannon entropy 0.10870
G+C content 0.29970
Mean single sequence MFE -12.07
Consensus MFE -10.98
Energy contribution -11.35
Covariance contribution 0.37
Combinations/Pair 1.06
Mean z-score -2.24
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.68
SVM RNA-class probability 0.960201
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10555457 55 + 21146708
GGAAUGAUUUCAUUUACUUACAAUCAAUGAAAUUGCACUGAUGCAAUUUUGUUUC
.(((((....)))))..........((..((((((((....))))))))..)).. ( -11.70, z-score =  -2.40, R)
>droSim1.chr2R 9318399 55 + 19596830
GGAAUGAUUUCAUUUACUUACAAUCAAUGAAAUUGCACUGAUGCAAUUUUGUUUC
.(((((....)))))..........((..((((((((....))))))))..)).. ( -11.70, z-score =  -2.40, R)
>droSec1.super_1 8074983 55 + 14215200
GGAAUGAUUUCAUUUACUUACAAUCAAUGAAAUUGCACUGAUGCAAUUUUGUUUC
.(((((....)))))..........((..((((((((....))))))))..)).. ( -11.70, z-score =  -2.40, R)
>droYak2.chr2R 10487406 55 + 21139217
GGAAUGAUUUCAUUUACUUACAAUCAAUGAAAUUGCACUGAUGCAAUUUUGUUUC
.(((((....)))))..........((..((((((((....))))))))..)).. ( -11.70, z-score =  -2.40, R)
>droEre2.scaffold_4845 7296359 55 - 22589142
GGAAUGAUUUCAUUUACUUACAAUCAAUGAAAUUGCACUGAUGCAAUUUUGUUUC
.(((((....)))))..........((..((((((((....))))))))..)).. ( -11.70, z-score =  -2.40, R)
>droAna3.scaffold_13266 5032697 55 - 19884421
GGAAUGAUUUCAUUUACUUGCAAUCAAUGAAAUUGCACUGAUGCAAUUUUCCCUU
(((.(((((.((......)).)))))...((((((((....)))))))))))... ( -12.10, z-score =  -2.43, R)
>dp4.chr3 5205772 55 + 19779522
GGAAUGAUUUCAUUUACUUGCAAUCAAUGAAAUUGCACUGAUGCAAUUUUGUUUU
....(((((.((......)).)))))(..((((((((....))))))))..)... ( -12.10, z-score =  -1.79, R)
>droPer1.super_2 5413353 55 + 9036312
GGAAUGAUUUCAUUUACUUGCAAUCAAUGAAAUUGCACUGAUGCAAUUUUGUUUU
....(((((.((......)).)))))(..((((((((....))))))))..)... ( -12.10, z-score =  -1.79, R)
>droWil1.scaffold_180699 1267646 54 + 2593675
-GAAUGAUUUCAUUUACUUGCAAUCAAUGAAAUUGCACUGAUGCAAUUUUGUUUU
-...(((((.((......)).)))))(..((((((((....))))))))..)... ( -12.10, z-score =  -1.98, R)
>droMoj3.scaffold_6496 24421249 52 + 26866924
GGAAUGAUUUCAUUUACUUGCAAUCAAUGAAAUUGCACUGAUGCAAUUUCGC---
....(((((.((......)).)))))..(((((((((....)))))))))..--- ( -13.80, z-score =  -2.74, R)
>droGri2.scaffold_15112 4569521 55 - 5172618
GGAAUGAUUUCAUUUACUUGCAAUCAAUGAAAUUGCACUGAUGCAAUUUUGUUUG
....(((((.((......)).)))))(..((((((((....))))))))..)... ( -12.10, z-score =  -1.90, R)
>consensus
GGAAUGAUUUCAUUUACUUGCAAUCAAUGAAAUUGCACUGAUGCAAUUUUGUUUC
.(((((....)))))..........((((((((((((....)))))))))))).. (-10.98 = -11.35 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 10,555,457 – 10,555,512
Length 55
Sequences 11
Columns 55
Reading direction reverse
Mean pairwise identity 95.17
Shannon entropy 0.10870
G+C content 0.29970
Mean single sequence MFE -10.05
Consensus MFE -9.94
Energy contribution -9.69
Covariance contribution -0.25
Combinations/Pair 1.07
Mean z-score -1.44
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.26
SVM RNA-class probability 0.918443
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10555457 55 - 21146708
GAAACAAAAUUGCAUCAGUGCAAUUUCAUUGAUUGUAAGUAAAUGAAAUCAUUCC
.........(((((((((((......)))))).)))))...((((....)))).. (  -8.60, z-score =  -1.06, R)
>droSim1.chr2R 9318399 55 - 19596830
GAAACAAAAUUGCAUCAGUGCAAUUUCAUUGAUUGUAAGUAAAUGAAAUCAUUCC
.........(((((((((((......)))))).)))))...((((....)))).. (  -8.60, z-score =  -1.06, R)
>droSec1.super_1 8074983 55 - 14215200
GAAACAAAAUUGCAUCAGUGCAAUUUCAUUGAUUGUAAGUAAAUGAAAUCAUUCC
.........(((((((((((......)))))).)))))...((((....)))).. (  -8.60, z-score =  -1.06, R)
>droYak2.chr2R 10487406 55 - 21139217
GAAACAAAAUUGCAUCAGUGCAAUUUCAUUGAUUGUAAGUAAAUGAAAUCAUUCC
.........(((((((((((......)))))).)))))...((((....)))).. (  -8.60, z-score =  -1.06, R)
>droEre2.scaffold_4845 7296359 55 + 22589142
GAAACAAAAUUGCAUCAGUGCAAUUUCAUUGAUUGUAAGUAAAUGAAAUCAUUCC
.........(((((((((((......)))))).)))))...((((....)))).. (  -8.60, z-score =  -1.06, R)
>droAna3.scaffold_13266 5032697 55 + 19884421
AAGGGAAAAUUGCAUCAGUGCAAUUUCAUUGAUUGCAAGUAAAUGAAAUCAUUCC
...((((..(((((((((((......)))))).))))).....((....)))))) ( -11.70, z-score =  -1.54, R)
>dp4.chr3 5205772 55 - 19779522
AAAACAAAAUUGCAUCAGUGCAAUUUCAUUGAUUGCAAGUAAAUGAAAUCAUUCC
.........(((((((((((......)))))).)))))...((((....)))).. ( -10.60, z-score =  -1.66, R)
>droPer1.super_2 5413353 55 - 9036312
AAAACAAAAUUGCAUCAGUGCAAUUUCAUUGAUUGCAAGUAAAUGAAAUCAUUCC
.........(((((((((((......)))))).)))))...((((....)))).. ( -10.60, z-score =  -1.66, R)
>droWil1.scaffold_180699 1267646 54 - 2593675
AAAACAAAAUUGCAUCAGUGCAAUUUCAUUGAUUGCAAGUAAAUGAAAUCAUUC-
.........(((((((((((......)))))).)))))...((((....)))).- ( -10.60, z-score =  -1.48, R)
>droMoj3.scaffold_6496 24421249 52 - 26866924
---GCGAAAUUGCAUCAGUGCAAUUUCAUUGAUUGCAAGUAAAUGAAAUCAUUCC
---..(((((((((....)))))))))..(((((.((......)).))))).... ( -13.50, z-score =  -2.46, R)
>droGri2.scaffold_15112 4569521 55 + 5172618
CAAACAAAAUUGCAUCAGUGCAAUUUCAUUGAUUGCAAGUAAAUGAAAUCAUUCC
.........(((((((((((......)))))).)))))...((((....)))).. ( -10.60, z-score =  -1.73, R)
>consensus
GAAACAAAAUUGCAUCAGUGCAAUUUCAUUGAUUGCAAGUAAAUGAAAUCAUUCC
.........(((((((((((......)))))).)))))...((((....)))).. ( -9.94 =  -9.69 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:23:04 2011