Locus 8524

Sequence ID dm3.chr3L
Location 24,436,923 – 24,437,013
Length 90
Max. P 0.998098
window11711 window11712

overview

Window 1

Location 24,436,923 – 24,437,013
Length 90
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 58.05
Shannon entropy 0.54641
G+C content 0.57932
Mean single sequence MFE -41.17
Consensus MFE -23.29
Energy contribution -22.97
Covariance contribution -0.32
Combinations/Pair 1.30
Mean z-score -2.54
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.26
SVM RNA-class probability 0.998098
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24436923 90 + 24543557
--------------------------UGCUAACACUCAGCGUUUUG---CCCUCUAGACUUCUGGCUGCCGAGGGGGUUUCGACGGGGGAUCGCCGAGGAUGAAUGGCCAGGCGGUAAC
--------------------------........(((..((((..(---((((((.(.(........).).)))))))...)))).)))((((((..((........)).))))))... ( -27.60, z-score =   1.05, R)
>droSec1.super_85 23031 84 + 117257
---------------------------------AUAUUCUGUCUCAG--CUCUCUAUGGCUCUGGUUGUCGAGGCGGCUUUGGCGGGGGACCGCCGAGGGUAAAUGCUGAGGCGGUAAC
---------------------------------.....(((((((((--(((((.(..((....))..).))))...(((((((((....)))))))))......)))))))))).... ( -42.20, z-score =  -4.82, R)
>droSim1.chr2h_random 1168459 119 - 3178526
AUACUAUGUCUCAGCGUUUAAGUGGGCCGCAACAAAGUACUUCUGGGUGCCCUCUAUAGCUCUGGUUGUCAAGGCGUCUUUGGCGGGGGACCGCCGAGGGUGAAUGCUGAGGCGGUAAC
.((((..(((((((((((((((.(((((.((............)).).)))).))...((..((.....))..)).((((((((((....))))))))))))))))))))))))))).. ( -53.70, z-score =  -3.84, R)
>consensus
______________________________AACAAACUACGUCUCGG__CCCUCUAUAGCUCUGGUUGUCGAGGCGGCUUUGGCGGGGGACCGCCGAGGGUGAAUGCUGAGGCGGUAAC
.................................................(((((....(((..((((((....))))))..))))))))((((((...(((....)))..))))))... (-23.29 = -22.97 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 24,436,923 – 24,437,013
Length 90
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 58.05
Shannon entropy 0.54641
G+C content 0.57932
Mean single sequence MFE -28.03
Consensus MFE -13.09
Energy contribution -13.10
Covariance contribution 0.01
Combinations/Pair 1.25
Mean z-score -1.83
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.34
SVM RNA-class probability 0.928693
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24436923 90 - 24543557
GUUACCGCCUGGCCAUUCAUCCUCGGCGAUCCCCCGUCGAAACCCCCUCGGCAGCCAGAAGUCUAGAGGG---CAAAACGCUGAGUGUUAGCA--------------------------
((((.(((..(((.........((((((......))))))....((((((((........)))..)))))---......)))..))).)))).-------------------------- ( -27.10, z-score =  -0.90, R)
>droSec1.super_85 23031 84 - 117257
GUUACCGCCUCAGCAUUUACCCUCGGCGGUCCCCCGCCAAAGCCGCCUCGACAACCAGAGCCAUAGAGAG--CUGAGACAGAAUAU---------------------------------
......(.((((((..........(((((....)))))......(.(((........))).).......)--))))).).......--------------------------------- ( -23.50, z-score =  -3.03, R)
>droSim1.chr2h_random 1168459 119 + 3178526
GUUACCGCCUCAGCAUUCACCCUCGGCGGUCCCCCGCCAAAGACGCCUUGACAACCAGAGCUAUAGAGGGCACCCAGAAGUACUUUGUUGCGGCCCACUUAAACGCUGAGACAUAGUAU
......((....)).....((((((((((....)))))......((.(((.....))).))....))))).........(((((.(((..((((..........))))..))).))))) ( -33.50, z-score =  -1.57, R)
>consensus
GUUACCGCCUCAGCAUUCACCCUCGGCGGUCCCCCGCCAAAGCCGCCUCGACAACCAGAGCUAUAGAGGG__CCAAGACGCAAUAUGUU______________________________
...................(((((((((......))))........(((........))).....)))))................................................. (-13.09 = -13.10 +   0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:47:15 2011