Locus 4261

Sequence ID dm3.chr2R
Location 11,738,178 – 11,738,255
Length 77
Max. P 0.669576
window5839 window5840

overview

Window 9

Location 11,738,178 – 11,738,255
Length 77
Sequences 4
Columns 80
Reading direction forward
Mean pairwise identity 74.84
Shannon entropy 0.41201
G+C content 0.62370
Mean single sequence MFE -19.86
Consensus MFE -10.16
Energy contribution -11.29
Covariance contribution 1.13
Combinations/Pair 1.29
Mean z-score -1.76
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.587923
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11738178 77 + 21146708
CAUCCUUGCGCCGCCUC---CCUUCCACCACUGGCUUCCCGAAUUCGAAUUCUGCUUCUGAGAAUCCUGAUGCGGCGCCG
.......(((((((.((---........((..(((....((....))......)))..))........)).))))))).. ( -19.49, z-score =  -2.05, R)
>droAna3.scaffold_13266 7426891 65 - 19884421
-------------CCCUGGUCGCUCCACUAC--GCCCUCCCUCUUGGAGUCCUGUUCCGGAGAAUCCUGAUGCGGCGCCG
-------------....((.((((.((....--(..((((.....))))..)...((.((.....)).)))).)))))). ( -15.80, z-score =   0.44, R)
>droSec1.super_1 9232401 77 + 14215200
CAUCCGUGCGCCGCCUC---CCUUCCACCUCUGGCUUCCCGAAUUCGAAUCCUGCUUCUGAGAAUCCUGAUGCGGCGCCG
....((.(((((((.((---........(((.(((....((....))......)))...)))......)).))))))))) ( -22.04, z-score =  -2.56, R)
>droSim1.chr2R 10477680 80 + 19596830
CAUCCGUGCGCCGCCUCCUCCCUUCUACCUCUGGCUUCCCGAAUUCGAAUCCUGCUUCUGAGAAUCCUGAUGCGGCGCCG
....((.(((((((.((.....((((......(((....((....))......)))....))))....)).))))))))) ( -22.10, z-score =  -2.86, R)
>consensus
CAUCCGUGCGCCGCCUC___CCUUCCACCACUGGCUUCCCGAAUUCGAAUCCUGCUUCUGAGAAUCCUGAUGCGGCGCCG
.......(((((((.((.....(((.......((.(((........))).)).......)))......)).))))))).. (-10.16 = -11.29 +   1.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 11,738,178 – 11,738,255
Length 77
Sequences 4
Columns 80
Reading direction reverse
Mean pairwise identity 74.84
Shannon entropy 0.41201
G+C content 0.62370
Mean single sequence MFE -25.30
Consensus MFE -15.20
Energy contribution -17.07
Covariance contribution 1.88
Combinations/Pair 1.11
Mean z-score -1.50
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.38
SVM RNA-class probability 0.669576
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11738178 77 - 21146708
CGGCGCCGCAUCAGGAUUCUCAGAAGCAGAAUUCGAAUUCGGGAAGCCAGUGGUGGAAGG---GAGGCGGCGCAAGGAUG
..(((((((.((.((((((((....).)))))))......((....))............---)).)))))))....... ( -26.70, z-score =  -1.99, R)
>droAna3.scaffold_13266 7426891 65 + 19884421
CGGCGCCGCAUCAGGAUUCUCCGGAACAGGACUCCAAGAGGGAGGGC--GUAGUGGAGCGACCAGGG-------------
..(((((............(((......)))((((.....)))))))--))..(((.....)))...------------- ( -18.70, z-score =   0.61, R)
>droSec1.super_1 9232401 77 - 14215200
CGGCGCCGCAUCAGGAUUCUCAGAAGCAGGAUUCGAAUUCGGGAAGCCAGAGGUGGAAGG---GAGGCGGCGCACGGAUG
(((((((((.((.((((((((....).)))))))...(((((....)).)))........---)).))))))).)).... ( -27.90, z-score =  -2.21, R)
>droSim1.chr2R 10477680 80 - 19596830
CGGCGCCGCAUCAGGAUUCUCAGAAGCAGGAUUCGAAUUCGGGAAGCCAGAGGUAGAAGGGAGGAGGCGGCGCACGGAUG
(((((((((.((.((((((((....).)))))))...(((((....)).)))...........)).))))))).)).... ( -27.90, z-score =  -2.43, R)
>consensus
CGGCGCCGCAUCAGGAUUCUCAGAAGCAGGAUUCGAAUUCGGGAAGCCAGAGGUGGAAGG___GAGGCGGCGCACGGAUG
..(((((((.((.(((((((.......)))))))......((....))...............)).)))))))....... (-15.20 = -17.07 +   1.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:25:46 2011