Locus 11206

Sequence ID dm3.chr3R
Location 19,403,412 – 19,403,557
Length 145
Max. P 0.763511
window15400 window15401

overview

Window 0

Location 19,403,412 – 19,403,522
Length 110
Sequences 7
Columns 111
Reading direction forward
Mean pairwise identity 68.76
Shannon entropy 0.62499
G+C content 0.58342
Mean single sequence MFE -23.50
Consensus MFE -9.92
Energy contribution -10.51
Covariance contribution 0.60
Combinations/Pair 1.31
Mean z-score -1.29
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.714856
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19403412 110 + 27905053
CCAAGUUUAAGUGCAGCCCCCAUUCCCAUUUGUUCGACACCACGACCACCCCAACCUCC-AGCACCUACCAAUCCACUUCCGCCCCUCAUGGAGGCAGUGCACUCUGCUGA
...(((...((((((((.............((.(((......))).))...........-.))..................(((((....)).)))..))))))..))).. ( -19.91, z-score =  -1.02, R)
>droSim1.chr3R 19225463 95 + 27517382
CCAAGUUUAAGUGCAGCCCCC-UUCCCAUUUGUUCGACACCACGAGCACCCCACCG---------------AUCCACUUCCGCCCCUCGUGGAGGCAGUGCACUCUGCUGA
...(((...(((((((((...-........((((((......))))))........---------------.......(((((.....))))))))..))))))..))).. ( -25.10, z-score =  -2.03, R)
>droSec1.super_0 19762494 110 + 21120651
CCAAGUUUAAGUGCAGCCCCC-UUCCCAUUUGUUCGACACCACGAGCACCCCACCGCCCCACCGAGCACCGAUCCACUUCCGCCCCUCGUGGAGGCAGUGCACUCUGCUGA
...(((...((((((......-........((((((......)))))).......(((((((.(((...((.........))...))))))).)))..))))))..))).. ( -30.20, z-score =  -2.71, R)
>droEre2.scaffold_4820 1829433 91 - 10470090
CCAAGUUUAAGUGCAGCCCCC-UUUCUAUUUGUUCGACAACCC---CACCCAGGCC----------------CCCACUUCCGCCCCUCGUGAAGGCAGUGCACUUUGCUGA
...(((..((((((((((...-.......(((.....)))...---(((...(((.----------------.........)))....)))..)))..))))))).))).. ( -18.60, z-score =  -0.73, R)
>droYak2.chr3R 20289305 106 + 28832112
CCAAGUUUAAGUGCAGCCCCCCUAUCCAUUUGUUCAACAACCC--CCACCCCACUCC---AUCGCCUACCGCUCCACUUCCGCCCCUCGUGAAGGCAGUGCACUCUGCUGA
...(((...(((((...............(((.....)))...--.......(((((---.((((.....((.........)).....)))).)).))))))))..))).. ( -16.30, z-score =  -0.76, R)
>droAna3.scaffold_13340 3553328 111 - 23697760
CCAUGUAUAAGUAGGGGCCUACCGCCAACCCAUCCCCACUAAUGUACUCCCCUUCCCCGCAAAGCUUCCCGCUCCACUGCCGCCUCUUGUGAUGGCAGUGCACUUUGCUGA
....((((((((.((((................)))))))..)))))...........(((((((.....))..((((((((.(......).))))))))...)))))... ( -27.29, z-score =  -1.18, R)
>dp4.chr2 2890654 98 + 30794189
CAAAGCUUAAGUGUGGACCUAUAACCCCUACGUGGGGGAGCUCCACUUCCUCUUCCAC-------------CUCCACUUCCGCCUCUCAGAAAGGCAGUGCACUCUGCUGA
...(((...((((((((.((....((((.....)))).)).)))))............-------------...((((...((((.......)))))))).)))..))).. ( -27.10, z-score =  -0.57, R)
>consensus
CCAAGUUUAAGUGCAGCCCCC_UUCCCAUUUGUUCGACACCACGACCACCCCACCCCC__A_______CC_AUCCACUUCCGCCCCUCGUGAAGGCAGUGCACUCUGCUGA
...(((...((((((...................((......)).....................................(((((....)).)))..))))))..))).. ( -9.92 = -10.51 +   0.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,403,451 – 19,403,557
Length 106
Sequences 7
Columns 108
Reading direction forward
Mean pairwise identity 75.62
Shannon entropy 0.48621
G+C content 0.57532
Mean single sequence MFE -26.67
Consensus MFE -18.34
Energy contribution -18.67
Covariance contribution 0.33
Combinations/Pair 1.06
Mean z-score -0.95
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.763511
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19403451 106 + 27905053
-CCACGACCACCCCAACCUCCAGCACCU-ACCAAUCCACUUCCGCCCCUCAUGGAGGCAGUGCACUCUGCUGACAGCAGCAAACACAGAAAGGGAGGAAUUAUCAAGC
-...............(((((.......-..............(((((....)).))).(((....((((.....))))....)))......)))))........... ( -25.30, z-score =  -1.01, R)
>droSim1.chr3R 19225501 92 + 27517382
----------------CCACGAGCACCCCACCGAUCCACUUCCGCCCCUCGUGGAGGCAGUGCACUCUGCUGACAGCAGCAAACACAGAAAGGGAGGAAUUAUCAAGC
----------------................(((...((((((((((....)).))).(((....((((.....))))....))).....))))).....))).... ( -23.60, z-score =  -0.12, R)
>droSec1.super_0 19762532 107 + 21120651
-CCACGAGCACCCCACCGCCCCACCGAGCACCGAUCCACUUCCGCCCCUCGUGGAGGCAGUGCACUCUGCUGACAGCAGCAAACACAGAAAGGGAGGAAUUAUCCAGC
-......((.((((((.(((((((.(((...((.........))...))))))).))).))).....(((((....)))))..........))).(((....))).)) ( -30.60, z-score =  -1.15, R)
>droEre2.scaffold_4820 1829471 88 - 10470090
-----------------ACCCCACCCAGGCCC---CCACUUCCGCCCCUCGUGAAGGCAGUGCACUUUGCUGACAGCAGCAAACACAGAAAGGGAGGAAUUAUCCAGC
-----------------...((.(((..(((.---.(((...........)))..))).(((...(((((((....)))))))))).....))).))........... ( -24.40, z-score =  -0.79, R)
>droYak2.chr3R 20289344 102 + 28832112
-ACCCCCACCCCACUCCAUCGC-----CUACCGCUCCACUUCCGCCCCUCGUGAAGGCAGUGCACUCUGCUGACAGCAGCAAACACUGAAAGGGAGGAAUUAUCAAGC
-.(((((........((.((((-----.....((.........)).....)))).))(((((....((((.....))))....)))))...))).))........... ( -24.40, z-score =  -0.54, R)
>droAna3.scaffold_13340 3553366 108 - 23697760
CUAAUGUACUCCCCUUCCCCGCAAAGCUUCCCGCUCCACUGCCGCCUCUUGUGAUGGCAGUGCACUUUGCUGACAGCAGCAAACACUGAAAGGGAGGAAUUAUCAAGC
.((((...(((((.(((...((..(((.....)))..(((((((.(......).)))))))))..(((((((....)))))))....))).)))))..))))...... ( -33.70, z-score =  -2.03, R)
>dp4.chr2 2890693 94 + 30794189
-------GCUCCACUUCCUCUU-----CCACC--UCCACUUCCGCCUCUCAGAAAGGCAGUGCACUCUGCUGACAGCAGCAAACACUGAAAGGGAGGAAUUAUCAAGC
-------...............-----...((--(((..(((.((((.......))))((((....((((.....))))....)))))))..)))))........... ( -24.70, z-score =  -0.98, R)
>consensus
________C_CCCCU_CCCCCCACACCCCACCGAUCCACUUCCGCCCCUCGUGAAGGCAGUGCACUCUGCUGACAGCAGCAAACACAGAAAGGGAGGAAUUAUCAAGC
......................................((((((((((....)).))).(((.....(((((....)))))..))).....)))))............ (-18.34 = -18.67 +   0.33)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:38:27 2011