Locus 4508

Sequence ID dm3.chr2R
Location 13,568,022 – 13,568,114
Length 92
Max. P 0.964808
window6168 window6169

overview

Window 8

Location 13,568,022 – 13,568,114
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 95.06
Shannon entropy 0.08388
G+C content 0.49553
Mean single sequence MFE -23.98
Consensus MFE -22.68
Energy contribution -22.68
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.73
SVM RNA-class probability 0.964061
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13568022 92 + 21146708
UUCGUCUUUCAUUUACCUAAGCGAAGGUUUUUUCACGGCUCAGCCGCCAGAGUUUUAAGUCACAGGUCAGGUUAAGUGACCUGCGGCCCAUC
((((.(((..........)))))))((.........(((......)))..........(((.(((((((.......))))))).)))))... ( -23.00, z-score =  -1.25, R)
>droSim1.chr2R 12304538 87 + 19596830
UUCGUCUUUCAUUUACCUAAGCGAAGGUUUUUUCACGGCUCAGCCGCCAGAGUUUUAAGUCACAGGUCA-----AGUGACCUGCGGCCCAAC
((((.(((..........)))))))((.........(((......)))..........(((.((((((.-----...)))))).)))))... ( -22.80, z-score =  -1.64, R)
>droSec1.super_1 11067043 87 + 14215200
UUCGUCUUUCAUUUACCUAAGCGAAGGUUUUUUCACGGCUCAGCCGCCAGAGUUACAAGUCACAGGUCA-----AGUGACCUGCGGCCCAUC
...((..(((....((((......))))........(((......))).)))..))..(((.((((((.-----...)))))).)))..... ( -24.00, z-score =  -2.21, R)
>droYak2.chr2R 5523507 87 - 21139217
UUCGUCUUUCAUUUUCCUAAGCGAAGGUUUUUUCACGGCUCAGCCGCCAGAGUUUCAAGUCACAGGUCA-----AGUGACCUGCGGCCCAUC
((((.(((..........)))))))((..((((..((((...))))..))))..))..(((.((((((.-----...)))))).)))..... ( -23.40, z-score =  -2.04, R)
>droEre2.scaffold_4845 7797316 87 + 22589142
UUCGUCUUUCAUUUUCCUAAGCGAAGGUUUUUUCACGGCUCAGCCGCCAGAGUUUUAAGUCACAGGUCA-----AGUGACCUGUGGCCCAUC
((((.(((..........)))))))((.........(((......)))..........((((((((((.-----...))))))))))))... ( -26.70, z-score =  -3.36, R)
>consensus
UUCGUCUUUCAUUUACCUAAGCGAAGGUUUUUUCACGGCUCAGCCGCCAGAGUUUUAAGUCACAGGUCA_____AGUGACCUGCGGCCCAUC
((((.(((..........)))))))((.........(((......)))..........(((.(((((((.......))))))).)))))... (-22.68 = -22.68 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 13,568,022 – 13,568,114
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 95.06
Shannon entropy 0.08388
G+C content 0.49553
Mean single sequence MFE -26.54
Consensus MFE -25.44
Energy contribution -25.04
Covariance contribution -0.40
Combinations/Pair 1.08
Mean z-score -2.04
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.74
SVM RNA-class probability 0.964808
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13568022 92 - 21146708
GAUGGGCCGCAGGUCACUUAACCUGACCUGUGACUUAAAACUCUGGCGGCUGAGCCGUGAAAAAACCUUCGCUUAGGUAAAUGAAAGACGAA
..((((.(((((((((.......))))))))).))))....(((.(((((...)))))......((((......)))).......))).... ( -26.70, z-score =  -2.04, R)
>droSim1.chr2R 12304538 87 - 19596830
GUUGGGCCGCAGGUCACU-----UGACCUGUGACUUAAAACUCUGGCGGCUGAGCCGUGAAAAAACCUUCGCUUAGGUAAAUGAAAGACGAA
.(((((.((((((((...-----.)))))))).)))))...(((.(((((...)))))......((((......)))).......))).... ( -27.30, z-score =  -2.03, R)
>droSec1.super_1 11067043 87 - 14215200
GAUGGGCCGCAGGUCACU-----UGACCUGUGACUUGUAACUCUGGCGGCUGAGCCGUGAAAAAACCUUCGCUUAGGUAAAUGAAAGACGAA
.(..((.((((((((...-----.)))))))).))..)...(((.(((((...)))))......((((......)))).......))).... ( -27.50, z-score =  -2.04, R)
>droYak2.chr2R 5523507 87 + 21139217
GAUGGGCCGCAGGUCACU-----UGACCUGUGACUUGAAACUCUGGCGGCUGAGCCGUGAAAAAACCUUCGCUUAGGAAAAUGAAAGACGAA
.......((((((((...-----.)))))))).(((((......(((......)))(((((......))))))))))............... ( -25.00, z-score =  -1.59, R)
>droEre2.scaffold_4845 7797316 87 - 22589142
GAUGGGCCACAGGUCACU-----UGACCUGUGACUUAAAACUCUGGCGGCUGAGCCGUGAAAAAACCUUCGCUUAGGAAAAUGAAAGACGAA
..((((.((((((((...-----.)))))))).))))....((((((......)))(((((......)))))...))).............. ( -26.20, z-score =  -2.51, R)
>consensus
GAUGGGCCGCAGGUCACU_____UGACCUGUGACUUAAAACUCUGGCGGCUGAGCCGUGAAAAAACCUUCGCUUAGGUAAAUGAAAGACGAA
..((((.(((((((((.......))))))))).))))....((((((......)))(((((......))))).............))).... (-25.44 = -25.04 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:30:24 2011