Locus 11527

Sequence ID dm3.chr3R
Location 21,854,697 – 21,854,835
Length 138
Max. P 0.990961
window15839 window15840

overview

Window 9

Location 21,854,697 – 21,854,803
Length 106
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 82.12
Shannon entropy 0.34076
G+C content 0.43008
Mean single sequence MFE -24.73
Consensus MFE -17.36
Energy contribution -18.78
Covariance contribution 1.42
Combinations/Pair 1.16
Mean z-score -2.70
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.45
SVM RNA-class probability 0.990961
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21854697 106 - 27905053
GUCUUCCAGCUGAAGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCAC--CAGCAACUUCUGCUGCAACGAAUCAUGUCUUCCAAUUGAAUCGUUA-ACAAUGU
........((((((((....))))))))....((((((...............--(((((.....))))).(((((.(((...........))).))))).-.)))))) ( -28.30, z-score =  -3.98, R)
>droSim1.chr3R 21706196 106 - 27517382
GUCUUCCAGCUGAGGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCAC--CAGCAGCUUCUGCUGCAACGAAUCAUGUCUUCCAAUUGAAUCGUUA-ACCAUGU
........((((((((....))))))))...((((........))))......--..(((((....)))))(((((.(((...........))).))))).-....... ( -29.60, z-score =  -3.29, R)
>droSec1.super_13 649299 106 - 2104621
GUCUUCCAGCUGAGGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCAC--CAGCAACUUCUGCUGCAACGAAUCAUGUCUUCCAAUUGAAUCGUUA-ACCAUGU
........((((((((....))))))))...((((........))))......--(((((.....))))).(((((.(((...........))).))))).-....... ( -25.60, z-score =  -2.45, R)
>droYak2.chr3R 4211363 106 + 28832112
GUCUUCCAGCUGAGGAAUCUUCUUCAGCACCGACAUUGAAUCCUGUCUUCCAC--CAGCAACUUCUGUUGCAACGAAUCAAGUCUUCCAAUUGAAUCGUUA-ACCAUGU
........((((((((....))))))))...((((........))))......--..(((((....)))))(((((.((((.........)))).))))).-....... ( -28.30, z-score =  -3.55, R)
>droEre2.scaffold_4820 4278576 106 + 10470090
GUCUUCCAGCUGAGGAAUACUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCAC--CAGCAACUUCUGCUGCAACGAAUCAUGUCUUCCAAUUGAAUCGUUU-ACAAUGU
........((((((((....))))))))....((((((...............--(((((.....))))).(((((.(((...........))).))))).-.)))))) ( -27.60, z-score =  -3.12, R)
>droMoj3.scaffold_6540 15810023 102 - 34148556
------CAACUACAACCACAACCAUAGCAACGA-AUCAUGUCUUCCAAUUGACUACAACUACAACCAUAACAACGAAUCAUGUCUUCCAAUUGACUCGAUGUAAACUGU
------....................(((.(((-.....(((........)))............................(((........)))))).)))....... (  -9.00, z-score =   0.20, R)
>consensus
GUCUUCCAGCUGAGGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCAC__CAGCAACUUCUGCUGCAACGAAUCAUGUCUUCCAAUUGAAUCGUUA_ACAAUGU
........((((((((....))))))))...((((........))))........(((((.....))))).(((((.(((...........))).)))))......... (-17.36 = -18.78 +   1.42)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,854,743 – 21,854,835
Length 92
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 69.37
Shannon entropy 0.42259
G+C content 0.47276
Mean single sequence MFE -14.20
Consensus MFE -9.03
Energy contribution -10.83
Covariance contribution 1.81
Combinations/Pair 1.06
Mean z-score -1.83
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.39
SVM RNA-class probability 0.934600
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21854743 92 - 27905053
---CACCAUCACCAUCAUCAUCGACAUCGAAUCCAGUCUUCCAGCUGAAGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCC-ACCAGCAAC
---...................((((..((.((..(((.....((((((((....))))))))...)))...)).)).))))....-......... ( -17.70, z-score =  -2.67, R)
>droYak2.chr3R 4211409 95 + 28832112
CAUCACCACCAACAUCAUCAACGACAUCGAAUCCAGUCUUCCAGCUGAGGAAUCUUCUUCAGCACCGACAUUGAAUCCUGUCUUCC-ACCAGCAAC
......................((((..((.((..(((.....((((((((....))))))))...)))...)).)).))))....-......... ( -17.40, z-score =  -2.14, R)
>dp4.chr2 11602840 75 + 30794189
---CAUUAGCGACUUCGACUACGACUACGAAUCCUGUCUUCCAACCAA-----------------CGACUACGAAUCCUGUCUUCCAACCAACAA-
---...(((((....)).))).(((...((.((..(((..........-----------------.)))...)).))..))).............- (  -7.50, z-score =  -0.69, R)
>consensus
___CACCACCAACAUCAUCAACGACAUCGAAUCCAGUCUUCCAGCUGA_GAAUCUUCUUCAGCA_CGACAUUGAAUCCUGUCUUCC_ACCAGCAAC
......................(((...((.((..(((.....((((((((....))))))))...)))...)).))..))).............. ( -9.03 = -10.83 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:44:37 2011