Locus 1635

Sequence ID dm3.chr2L
Location 12,752,670 – 12,752,739
Length 69
Max. P 0.987199
window2238 window2239

overview

Window 8

Location 12,752,670 – 12,752,739
Length 69
Sequences 8
Columns 69
Reading direction forward
Mean pairwise identity 81.62
Shannon entropy 0.36882
G+C content 0.50074
Mean single sequence MFE -26.55
Consensus MFE -14.32
Energy contribution -14.90
Covariance contribution 0.58
Combinations/Pair 1.27
Mean z-score -2.97
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.27
SVM RNA-class probability 0.987199
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12752670 69 + 23011544
GGAAAUUCAGCGGAGUGAGGAAGCGGAAGUGGGAGUGCGCUUUUAUAGCAUUUAGCUUCCGCUUCUGCA
....((((....))))(.((((((((((((..((((((.........)))))).)))))))))))).). ( -28.50, z-score =  -3.26, R)
>droSim1.chr2L 12551176 69 + 22036055
GGAAAUUCAGCGGAGUGAGGAAGCGGAAGUGGGAGUGCGCUUUUAUAGCAUUUAGCUUCCGCUUCUGCA
....((((....))))(.((((((((((((..((((((.........)))))).)))))))))))).). ( -28.50, z-score =  -3.26, R)
>droSec1.super_16 927417 69 + 1878335
GGAAAUUCAGCGAAGUGAGGAAGCGGAAGUGGGAGUGUGCUUUUAUAGCAUUUAGCUUCCGCUUGUGCA
.....((((......))))...(((.(((((((((((((((.....)))))...)))))))))).))). ( -25.20, z-score =  -3.03, R)
>droYak2.chr2L 9182398 69 + 22324452
GGAAAUUCAGCGGAGUGAGGAAGCGGAAGUGGGAGUGCGCUUUUAUAGCAUUUAGCUUCCGCUUUCUCG
....((((....))))((((((((((((((..((((((.........)))))).)))))))))))))). ( -32.40, z-score =  -4.81, R)
>droEre2.scaffold_4929 13963464 69 - 26641161
GGAAAUUCAGCGGAGUGAGGAAGCGGAAGUGGGAGUGCGCUUUUAUAGCAUUUAGCUUCCGCUUCUACA
....((((....))))(.((((((((((((..((((((.........)))))).)))))))))))).). ( -28.50, z-score =  -3.88, R)
>droAna3.scaffold_12916 3520641 69 - 16180835
GGGUCUAGGGCCGAGCGAGGAACAGGAAGUGGCAGUGCGCUUUUAUAGCAUUUAGCUUCCGCUUCUGCC
.(((.....)))..((((((....((((((...(((((.........)))))..)))))).)))).)). ( -22.50, z-score =  -0.14, R)
>dp4.chr4_group4 376976 67 + 6586962
GGGAAAGCAGGGGG-CAAAAAAGAAGUGCAGGGAAU-CGCUUUUAUAGCAUUUAGCUUCCGCUUUUCCA
((((((((.(((((-(.......((((((...(((.-....)))...)))))).)))))))))))))). ( -24.10, z-score =  -3.03, R)
>droPer1.super_68 276793 68 - 338515
GGGAAAGCAGGGGGGCAAAAACGAAGUGCAGGGAAU-CGCUUUUAUAGCAUUUAGCUUCCGCUUUUCCA
((((((((..((((((.......((((((...(((.-....)))...)))))).)))))))))))))). ( -22.70, z-score =  -2.35, R)
>consensus
GGAAAUUCAGCGGAGUGAGGAAGCGGAAGUGGGAGUGCGCUUUUAUAGCAUUUAGCUUCCGCUUCUGCA
........................((((((((((((..(((.....))).....))))))))))))... (-14.32 = -14.90 +   0.58)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,752,670 – 12,752,739
Length 69
Sequences 8
Columns 69
Reading direction reverse
Mean pairwise identity 81.62
Shannon entropy 0.36882
G+C content 0.50074
Mean single sequence MFE -17.70
Consensus MFE -8.76
Energy contribution -8.40
Covariance contribution -0.36
Combinations/Pair 1.33
Mean z-score -2.44
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.860975
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12752670 69 - 23011544
UGCAGAAGCGGAAGCUAAAUGCUAUAAAAGCGCACUCCCACUUCCGCUUCCUCACUCCGCUGAAUUUCC
....((((((((((.....((((.....))))........))))))))))................... ( -17.72, z-score =  -2.51, R)
>droSim1.chr2L 12551176 69 - 22036055
UGCAGAAGCGGAAGCUAAAUGCUAUAAAAGCGCACUCCCACUUCCGCUUCCUCACUCCGCUGAAUUUCC
....((((((((((.....((((.....))))........))))))))))................... ( -17.72, z-score =  -2.51, R)
>droSec1.super_16 927417 69 - 1878335
UGCACAAGCGGAAGCUAAAUGCUAUAAAAGCACACUCCCACUUCCGCUUCCUCACUUCGCUGAAUUUCC
.....(((((((((.....((((.....))))........))))))))).................... ( -14.92, z-score =  -2.76, R)
>droYak2.chr2L 9182398 69 - 22324452
CGAGAAAGCGGAAGCUAAAUGCUAUAAAAGCGCACUCCCACUUCCGCUUCCUCACUCCGCUGAAUUUCC
.(((.(((((((((.....((((.....))))........))))))))).)))................ ( -19.72, z-score =  -3.41, R)
>droEre2.scaffold_4929 13963464 69 + 26641161
UGUAGAAGCGGAAGCUAAAUGCUAUAAAAGCGCACUCCCACUUCCGCUUCCUCACUCCGCUGAAUUUCC
((..((((((((((.....((((.....))))........))))))))))..))............... ( -19.02, z-score =  -3.30, R)
>droAna3.scaffold_12916 3520641 69 + 16180835
GGCAGAAGCGGAAGCUAAAUGCUAUAAAAGCGCACUGCCACUUCCUGUUCCUCGCUCGGCCCUAGACCC
(((((.(((....)))....(((.....)))...)))))...((..(..((......))..)..))... ( -18.90, z-score =  -0.76, R)
>dp4.chr4_group4 376976 67 - 6586962
UGGAAAAGCGGAAGCUAAAUGCUAUAAAAGCG-AUUCCCUGCACUUCUUUUUUG-CCCCCUGCUUUCCC
.(((((.((((.(((.....)))......(((-......)))............-....))))))))). ( -14.50, z-score =  -1.26, R)
>droPer1.super_68 276793 68 + 338515
UGGAAAAGCGGAAGCUAAAUGCUAUAAAAGCG-AUUCCCUGCACUUCGUUUUUGCCCCCCUGCUUUCCC
.(((((.((((.(((.....))).((((((((-(...........))))))))).....))))))))). ( -19.10, z-score =  -3.02, R)
>consensus
UGCAGAAGCGGAAGCUAAAUGCUAUAAAAGCGCACUCCCACUUCCGCUUCCUCACUCCGCUGAAUUUCC
.((...(((....)))...((((.....))))..........................))......... ( -8.76 =  -8.40 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:35:46 2011