Locus 54

Sequence ID dm3.chr2L
Location 433,965 – 434,076
Length 111
Max. P 0.965623
window80 window81 window82 window83

overview

Window 0

Location 433,965 – 434,055
Length 90
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 93.31
Shannon entropy 0.12594
G+C content 0.47424
Mean single sequence MFE -29.28
Consensus MFE -27.28
Energy contribution -27.25
Covariance contribution -0.03
Combinations/Pair 1.09
Mean z-score -1.93
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.48
SVM RNA-class probability 0.942183
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 433965 90 + 23011544
UGUUUGGCCAUAACUGGCACAACAAGUGGAAUUCCGCAGCUCGGAAUUCGGCAUUUGCCGCUUUGCUGUUUUAUUUCU--CAGUCGCUUGUU
......((((....))))..((((((((((((((((.....))))))))(((....))).....((((..........--)))))))))))) ( -29.90, z-score =  -2.54, R)
>droSim1.chr2L 440426 90 + 22036055
UGUUUGGCCAUAACUGGCACAACAAGUGGAAUUCCGCAGCUCGGAAUUCGGCAUUUGCCGCUUUGCUGUUUUGUUUCU--CAGUCGCUUGUU
......((((....))))..((((((((((((((((.....))))))))(((....))).....((((..........--)))))))))))) ( -29.90, z-score =  -2.13, R)
>droSec1.super_14 417752 90 + 2068291
UGUUUGGCCAUAACUGGCACAACAAGUGGAAUUCCGCAGCUCGGAAUUCGGCAUUUGCCGCUUUGCUGUUUUGUUUUU--CAGUCGCUUGUU
......((((....))))..((((((((((((((((.....))))))))(((....))).....((((..........--)))))))))))) ( -29.90, z-score =  -2.18, R)
>droYak2.chr2L 418815 90 + 22324452
UGUUUAGCCAUAACUGGCACAGCAAGUGGAAUUCCGCAGCUCGGAAUUCGGCAUUUGCCGCUUUGCUGUUUUGUUUCU--CAGUCGCUUGUU
......((((....))))..((((((((((((((((.....))))))))(((....))).....((((..........--)))))))))))) ( -30.10, z-score =  -2.13, R)
>droEre2.scaffold_4929 486362 90 + 26641161
UGUUUGGCCAUAACUGGCACAGCAAGUGGAAUUCCGCAGCUCGGAAUUCGGCAUUUGCCGCUGUGCUGUUUUGUUUCU--CAGUCGCUUGUU
((...(((...(((.((((((((.....((((((((.....))))))))(((....))))))))))))))..)))...--)).......... ( -32.20, z-score =  -2.11, R)
>droAna3.scaffold_12943 224282 92 - 5039921
UGUUUGGCCAUAACUGGCACAACAAGUGGAAUUUCGGAAUUCGGAAUUCGGCAUUUGCCGCUGUUUGGUUUUGUUUCUGUCUGUCGCCUCUU
.....(((.(((((.((((.(((.(((.((((((((.....))))))))(((....)))))).....))).))))...)).))).))).... ( -23.70, z-score =  -0.51, R)
>consensus
UGUUUGGCCAUAACUGGCACAACAAGUGGAAUUCCGCAGCUCGGAAUUCGGCAUUUGCCGCUUUGCUGUUUUGUUUCU__CAGUCGCUUGUU
......((((....))))..((((((((((((((((.....))))))))(((....))).........................)))))))) (-27.28 = -27.25 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 1

Location 433,965 – 434,055
Length 90
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 93.31
Shannon entropy 0.12594
G+C content 0.47424
Mean single sequence MFE -26.93
Consensus MFE -24.59
Energy contribution -24.73
Covariance contribution 0.14
Combinations/Pair 1.10
Mean z-score -2.24
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.75
SVM RNA-class probability 0.965623
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 433965 90 - 23011544
AACAAGCGACUG--AGAAAUAAAACAGCAAAGCGGCAAAUGCCGAAUUCCGAGCUGCGGAAUUCCACUUGUUGUGCCAGUUAUGGCCAAACA
............--.........(((((((...(((....)))((((((((.....))))))))...)))))))((((....))))...... ( -26.90, z-score =  -2.14, R)
>droSim1.chr2L 440426 90 - 22036055
AACAAGCGACUG--AGAAACAAAACAGCAAAGCGGCAAAUGCCGAAUUCCGAGCUGCGGAAUUCCACUUGUUGUGCCAGUUAUGGCCAAACA
............--.........(((((((...(((....)))((((((((.....))))))))...)))))))((((....))))...... ( -26.90, z-score =  -1.95, R)
>droSec1.super_14 417752 90 - 2068291
AACAAGCGACUG--AAAAACAAAACAGCAAAGCGGCAAAUGCCGAAUUCCGAGCUGCGGAAUUCCACUUGUUGUGCCAGUUAUGGCCAAACA
............--.........(((((((...(((....)))((((((((.....))))))))...)))))))((((....))))...... ( -26.90, z-score =  -2.12, R)
>droYak2.chr2L 418815 90 - 22324452
AACAAGCGACUG--AGAAACAAAACAGCAAAGCGGCAAAUGCCGAAUUCCGAGCUGCGGAAUUCCACUUGCUGUGCCAGUUAUGGCUAAACA
............--.........(((((((...(((....)))((((((((.....))))))))...)))))))((((....))))...... ( -29.70, z-score =  -2.91, R)
>droEre2.scaffold_4929 486362 90 - 26641161
AACAAGCGACUG--AGAAACAAAACAGCACAGCGGCAAAUGCCGAAUUCCGAGCUGCGGAAUUCCACUUGCUGUGCCAGUUAUGGCCAAACA
.....(((((((--.(........).((((((((((....)))((((((((.....)))))))).....))))))))))))...))...... ( -31.10, z-score =  -3.24, R)
>droAna3.scaffold_12943 224282 92 + 5039921
AAGAGGCGACAGACAGAAACAAAACCAAACAGCGGCAAAUGCCGAAUUCCGAAUUCCGAAAUUCCACUUGUUGUGCCAGUUAUGGCCAAACA
.....(((((((.....................(((....)))(((((.((.....)).)))))...)))))))((((....))))...... ( -20.10, z-score =  -1.07, R)
>consensus
AACAAGCGACUG__AGAAACAAAACAGCAAAGCGGCAAAUGCCGAAUUCCGAGCUGCGGAAUUCCACUUGUUGUGCCAGUUAUGGCCAAACA
.......................((((((....(((....)))((((((((.....))))))))....))))))((((....))))...... (-24.59 = -24.73 +   0.14)

alignment

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secondary structure

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dotplot

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Window 2

Location 433,981 – 434,076
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 97.89
Shannon entropy 0.03416
G+C content 0.47368
Mean single sequence MFE -26.10
Consensus MFE -24.99
Energy contribution -24.80
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.07
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.58
SVM RNA-class probability 0.952107
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 433981 95 + 23011544
GCACAACAAGUGGAAUUCCGCAGCUCGGAAUUCGGCAUUUGCCGCUUUGCUGUUUUAUUUCUCAGUCGCUUGUUCCCUGAUUUCUGUUUUCUCCU
....((((((((((((((((.....))))))))(((....))).....((((..........))))))))))))..................... ( -24.80, z-score =  -2.09, R)
>droSim1.chr2L 440442 95 + 22036055
GCACAACAAGUGGAAUUCCGCAGCUCGGAAUUCGGCAUUUGCCGCUUUGCUGUUUUGUUUCUCAGUCGCUUGUUCCCUGAUUUCUGUUUUCUCCU
....((((((((((((((((.....))))))))(((....))).....((((..........))))))))))))..................... ( -24.80, z-score =  -1.73, R)
>droSec1.super_14 417768 95 + 2068291
GCACAACAAGUGGAAUUCCGCAGCUCGGAAUUCGGCAUUUGCCGCUUUGCUGUUUUGUUUUUCAGUCGCUUGUUCCCUGAUUUCUGUUUUCUCCU
....((((((((((((((((.....))))))))(((....))).....((((..........))))))))))))..................... ( -24.80, z-score =  -1.78, R)
>droEre2.scaffold_4929 486378 95 + 26641161
GCACAGCAAGUGGAAUUCCGCAGCUCGGAAUUCGGCAUUUGCCGCUGUGCUGUUUUGUUUCUCAGUCGCUUGUUCCCUGAUUUCUGUUUUCUCCU
(((((((.....((((((((.....))))))))(((....))))))))))...........((((...........))))............... ( -30.00, z-score =  -2.69, R)
>consensus
GCACAACAAGUGGAAUUCCGCAGCUCGGAAUUCGGCAUUUGCCGCUUUGCUGUUUUGUUUCUCAGUCGCUUGUUCCCUGAUUUCUGUUUUCUCCU
....((((((((((((((((.....))))))))(((....))).....((((..........))))))))))))..................... (-24.99 = -24.80 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 433,981 – 434,076
Length 95
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 97.89
Shannon entropy 0.03416
G+C content 0.47368
Mean single sequence MFE -26.28
Consensus MFE -24.89
Energy contribution -24.95
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -2.04
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.43
SVM RNA-class probability 0.939856
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 433981 95 - 23011544
AGGAGAAAACAGAAAUCAGGGAACAAGCGACUGAGAAAUAAAACAGCAAAGCGGCAAAUGCCGAAUUCCGAGCUGCGGAAUUCCACUUGUUGUGC
...............((((...........))))........(((((((...(((....)))((((((((.....))))))))...))))))).. ( -24.80, z-score =  -1.70, R)
>droSim1.chr2L 440442 95 - 22036055
AGGAGAAAACAGAAAUCAGGGAACAAGCGACUGAGAAACAAAACAGCAAAGCGGCAAAUGCCGAAUUCCGAGCUGCGGAAUUCCACUUGUUGUGC
...............((((...........))))........(((((((...(((....)))((((((((.....))))))))...))))))).. ( -24.80, z-score =  -1.53, R)
>droSec1.super_14 417768 95 - 2068291
AGGAGAAAACAGAAAUCAGGGAACAAGCGACUGAAAAACAAAACAGCAAAGCGGCAAAUGCCGAAUUCCGAGCUGCGGAAUUCCACUUGUUGUGC
...............((((...........))))........(((((((...(((....)))((((((((.....))))))))...))))))).. ( -24.80, z-score =  -1.71, R)
>droEre2.scaffold_4929 486378 95 - 26641161
AGGAGAAAACAGAAAUCAGGGAACAAGCGACUGAGAAACAAAACAGCACAGCGGCAAAUGCCGAAUUCCGAGCUGCGGAAUUCCACUUGCUGUGC
...............((((...........))))...........((((((((((....)))((((((((.....)))))))).....))))))) ( -30.70, z-score =  -3.20, R)
>consensus
AGGAGAAAACAGAAAUCAGGGAACAAGCGACUGAGAAACAAAACAGCAAAGCGGCAAAUGCCGAAUUCCGAGCUGCGGAAUUCCACUUGUUGUGC
...............((((...........))))........(((((((...(((....)))((((((((.....))))))))...))))))).. (-24.89 = -24.95 +   0.06)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:05:48 2011