Locus 1249

Sequence ID dm3.chr2L
Location 9,463,507 – 9,463,604
Length 97
Max. P 0.986987
window1702 window1703

overview

Window 2

Location 9,463,507 – 9,463,604
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 84.36
Shannon entropy 0.25743
G+C content 0.34724
Mean single sequence MFE -20.48
Consensus MFE -17.50
Energy contribution -17.94
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -2.46
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.26
SVM RNA-class probability 0.986987
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 9463507 97 + 23011544
AAGCGUAGCUACAUAUAUCAACAGAUCGACUUAACUCAAACCUAUGCAAAGGUUUUGUAUAUAUGUAUAAAAAGCGAGUCGCUCUGAAUGAUUUAUC
.(((...)))..(((.((((.((((.((((((.......((((......))))(((((((....)))))))....)))))).))))..)))).))). ( -20.20, z-score =  -1.64, R)
>droSim1.chr2L 9240064 97 + 22036055
AUGCGUAACUACAUAAAUCAACAGAUCGACUUCCCUCAAACCUAUGCAAAGGUUUUGUAUAUAUGUAUAUAAAGCGAGUCGCUCUGAAUGAUUUAUC
............((((((((.((((.((((((.........((......))((((((((((....)))))))))))))))).))))..)))))))). ( -24.20, z-score =  -3.61, R)
>droSec1.super_3 4917388 97 + 7220098
AAGCAUAACUACAUAAAUCAACAGAUCGACUUCCCUCAAACCUAUGCAAAGGUUUUGUAUAUAUGUAUAAAAAGCGAGUCGCUCUGAAUGAUUUAUC
............((((((((.((((.((((((.(.....((((......))))(((((((....)))))))..).)))))).))))..)))))))). ( -22.60, z-score =  -3.60, R)
>droEre2.scaffold_4929 10073057 81 + 26641161
---------UACAUAUAUCAACAGAUCGACUUCCCUGAAGCCUUUGCCAAGGUUUUGUAAAUAU-----AAAAGCAGGUCGC--UGAAUGAUUUAUA
---------...(((.((((.(((..((((((....((((((((....))))))))((......-----....)))))))))--))..)))).))). ( -14.90, z-score =  -1.00, R)
>consensus
AAGCGUAACUACAUAAAUCAACAGAUCGACUUCCCUCAAACCUAUGCAAAGGUUUUGUAUAUAUGUAUAAAAAGCGAGUCGCUCUGAAUGAUUUAUC
............((((((((.((((.((((((.....((((((......)))))).((...............)))))))).))))..)))))))). (-17.50 = -17.94 +   0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,463,507 – 9,463,604
Length 97
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 84.36
Shannon entropy 0.25743
G+C content 0.34724
Mean single sequence MFE -21.75
Consensus MFE -17.32
Energy contribution -19.19
Covariance contribution 1.87
Combinations/Pair 1.04
Mean z-score -1.93
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.905016
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 9463507 97 - 23011544
GAUAAAUCAUUCAGAGCGACUCGCUUUUUAUACAUAUAUACAAAACCUUUGCAUAGGUUUGAGUUAAGUCGAUCUGUUGAUAUAUGUAGCUACGCUU
.(((.((((..((((.(((((.((((..((((....))))..((((((......))))))))))..))))).)))).)))).)))............ ( -20.30, z-score =  -1.26, R)
>droSim1.chr2L 9240064 97 - 22036055
GAUAAAUCAUUCAGAGCGACUCGCUUUAUAUACAUAUAUACAAAACCUUUGCAUAGGUUUGAGGGAAGUCGAUCUGUUGAUUUAUGUAGUUACGCAU
.((((((((..((((.((((((.((((((((....)))))..((((((......))))))))).).))))).)))).))))))))............ ( -27.10, z-score =  -3.46, R)
>droSec1.super_3 4917388 97 - 7220098
GAUAAAUCAUUCAGAGCGACUCGCUUUUUAUACAUAUAUACAAAACCUUUGCAUAGGUUUGAGGGAAGUCGAUCUGUUGAUUUAUGUAGUUAUGCUU
.((((((((..((((.((((((.(((..((((....))))..((((((......))))))))).).))))).)))).))))))))(((....))).. ( -25.80, z-score =  -2.95, R)
>droEre2.scaffold_4929 10073057 81 - 26641161
UAUAAAUCAUUCA--GCGACCUGCUUUU-----AUAUUUACAAAACCUUGGCAAAGGCUUCAGGGAAGUCGAUCUGUUGAUAUAUGUA---------
((((.((((..((--(((((....((((-----........))))(((((((....))..)))))..))))..))).)))).))))..--------- ( -13.80, z-score =  -0.03, R)
>consensus
GAUAAAUCAUUCAGAGCGACUCGCUUUUUAUACAUAUAUACAAAACCUUUGCAUAGGUUUGAGGGAAGUCGAUCUGUUGAUAUAUGUAGUUACGCUU
.((((((((..((((.((((((.(((................((((((......))))))))).).))))).)))).))))))))............ (-17.32 = -19.19 +   1.87)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:28:20 2011