Locus 6065

Sequence ID dm3.chr3L
Location 3,421,432 – 3,421,527
Length 95
Max. P 0.984557
window8350 window8351

overview

Window 0

Location 3,421,432 – 3,421,527
Length 95
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 87.23
Shannon entropy 0.24899
G+C content 0.39830
Mean single sequence MFE -26.85
Consensus MFE -19.68
Energy contribution -21.38
Covariance contribution 1.70
Combinations/Pair 1.17
Mean z-score -2.85
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.17
SVM RNA-class probability 0.984557
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3421432 95 + 24543557
UUAGUCACGGGGCUAACUCGUGACUUGACCAAAUGCAAAACAAUAAACAGUUUUGGCAUUGUCUUUGUUGUUUACCAAUAUAGAUAGUACCGGCG
..(((((((((.....))))))))).........(((((((........)))))((.(((((((.(((((.....))))).))))))).)).)). ( -29.20, z-score =  -3.42, R)
>droSim1.chr3L 2959076 95 + 22553184
UGAGUCACGGAGCUAACUCGUGACUUGACCAAAUGCAAAACAAUAAACAGUUUUGGCAUUGUCUUUGUUGUUUACCAAUAUUGAUAAUACCGGCG
.((((((((.((....))))))))))........(((((((........)))))((.((((((..(((((.....)))))..)))))).)).)). ( -26.20, z-score =  -2.86, R)
>droSec1.super_2 3413663 94 + 7591821
UGAGUCACGGGGCUAACUCGUGACUUGACCAAAUGCAAAACAAUAAACAGUUU-GGCAUUGUCUUUGUUGUUUACCAAUAUUGAUAAUACCGGCG
.((((((((((.....))))))))))........((.((((........))))-((.((((((..(((((.....)))))..)))))).)).)). ( -29.50, z-score =  -3.58, R)
>droYak2.chr3L 3969337 95 + 24197627
UGAGUCACGGGGCUAACUCGUGACUUGAUCAAAUGCAAAACAAUAAACAGUUGUGGCAUUGUCUUUGUUGUUUGCCAAUAUUGAUAAUACCGUCG
.((((((((((.....))))))))))(((..........(((((.....)))))((.((((((..(((((.....)))))..)))))).))))). ( -29.70, z-score =  -3.30, R)
>droEre2.scaffold_4784 6111425 95 + 25762168
UGAGUCACGGGGCUAACUCGUGACUUGACCAAAUGCAAAACAAUAAACAGUUUUGGCAUUGUCUUUGUUGUUUGCCAAUAUUGAUAAUACCGGCG
.((((((((((.....))))))))))........(((((((........)))))((.((((((..(((((.....)))))..)))))).)).)). ( -30.40, z-score =  -3.43, R)
>droAna3.scaffold_13337 13272206 83 - 23293914
CAAGUCACAUGGCUAACCCGUGACUUGGCCAAAUGCAAAAUAACAAACACUUUUAG----GU--------UUUGCCAAUAUUGAUAAUAAUGCGC
((((((((..((....)).)))))))).......(((((((...(((....)))..----))--------))))).................... ( -16.10, z-score =  -0.54, R)
>consensus
UGAGUCACGGGGCUAACUCGUGACUUGACCAAAUGCAAAACAAUAAACAGUUUUGGCAUUGUCUUUGUUGUUUACCAAUAUUGAUAAUACCGGCG
(((((((((((.....)))))))))))...........................((.((((((..(((((.....)))))..)))))).)).... (-19.68 = -21.38 +   1.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 3,421,432 – 3,421,527
Length 95
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 87.23
Shannon entropy 0.24899
G+C content 0.39830
Mean single sequence MFE -24.14
Consensus MFE -16.93
Energy contribution -18.98
Covariance contribution 2.06
Combinations/Pair 1.11
Mean z-score -2.10
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.73
SVM RNA-class probability 0.800715
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3421432 95 - 24543557
CGCCGGUACUAUCUAUAUUGGUAAACAACAAAGACAAUGCCAAAACUGUUUAUUGUUUUGCAUUUGGUCAAGUCACGAGUUAGCCCCGUGACUAA
.(((((((.......)))))))..........(((.((((.(((((........)))))))))...))).(((((((.........))))))).. ( -24.50, z-score =  -2.10, R)
>droSim1.chr3L 2959076 95 - 22553184
CGCCGGUAUUAUCAAUAUUGGUAAACAACAAAGACAAUGCCAAAACUGUUUAUUGUUUUGCAUUUGGUCAAGUCACGAGUUAGCUCCGUGACUCA
.((((((((.....))))))))..........(((.((((.(((((........)))))))))...))).(((((((((....)).))))))).. ( -27.70, z-score =  -3.31, R)
>droSec1.super_2 3413663 94 - 7591821
CGCCGGUAUUAUCAAUAUUGGUAAACAACAAAGACAAUGCC-AAACUGUUUAUUGUUUUGCAUUUGGUCAAGUCACGAGUUAGCCCCGUGACUCA
.((((((((.....))))))))..........(((.((((.-((((........)))).))))...))).(((((((.........))))))).. ( -25.20, z-score =  -2.41, R)
>droYak2.chr3L 3969337 95 - 24197627
CGACGGUAUUAUCAAUAUUGGCAAACAACAAAGACAAUGCCACAACUGUUUAUUGUUUUGCAUUUGAUCAAGUCACGAGUUAGCCCCGUGACUCA
.(((((((((.((....(((.....)))....)).)))))).(((.(((..(....)..))).))).....)))..((((((......)))))). ( -19.90, z-score =  -0.84, R)
>droEre2.scaffold_4784 6111425 95 - 25762168
CGCCGGUAUUAUCAAUAUUGGCAAACAACAAAGACAAUGCCAAAACUGUUUAUUGUUUUGCAUUUGGUCAAGUCACGAGUUAGCCCCGUGACUCA
.((((((((.....))))))))..........(((.((((.(((((........)))))))))...))).(((((((.........))))))).. ( -27.90, z-score =  -3.15, R)
>droAna3.scaffold_13337 13272206 83 + 23293914
GCGCAUUAUUAUCAAUAUUGGCAAA--------AC----CUAAAAGUGUUUGUUAUUUUGCAUUUGGCCAAGUCACGGGUUAGCCAUGUGACUUG
..((........(((...(((((((--------..----(.....)..)))))))..)))......))(((((((((((....)).))))))))) ( -19.64, z-score =  -0.81, R)
>consensus
CGCCGGUAUUAUCAAUAUUGGCAAACAACAAAGACAAUGCCAAAACUGUUUAUUGUUUUGCAUUUGGUCAAGUCACGAGUUAGCCCCGUGACUCA
.((((((((.....))))))))..........((((((((.(((((........))))))))))..))).(((((((.........))))))).. (-16.93 = -18.98 +   2.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:00:41 2011