Locus 9383

Sequence ID dm3.chr3R
Location 6,333,017 – 6,333,112
Length 95
Max. P 0.804739
window12864 window12865

overview

Window 4

Location 6,333,017 – 6,333,112
Length 95
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 76.69
Shannon entropy 0.45050
G+C content 0.58410
Mean single sequence MFE -33.10
Consensus MFE -23.26
Energy contribution -24.50
Covariance contribution 1.24
Combinations/Pair 1.20
Mean z-score -1.13
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.68
SVM RNA-class probability 0.786001
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6333017 95 + 27905053
AGAGCGGGUCGAAAGCAGGGUCAGUUGGCGCUGGUCUAAGGGUUCCGCAGUGUGUUAAAGUUGGGCUUGAGUUCGAGGGCCAGCCAACUGACAGC
...((..(.(....))...((((((((((..((((((..(..(((...(((.((.......)).))).)))..)..)))))))))))))))).)) ( -34.00, z-score =  -1.24, R)
>droSim1.chr3R 12469990 95 - 27517382
AGAGCGGGUCGAAUGGAGGGUCAGUUGGCGCUGGUCUAAGGGUUCCGCAGUGAGUUAAAGUUGGGCUUGAGUUCGAGGGCCAGCCAACUGACAGC
...................((((((((((..((((((..(..(((......(((((.......))))))))..)..))))))))))))))))... ( -31.90, z-score =  -0.77, R)
>droSec1.super_0 5512126 95 - 21120651
AGAGCGGGUCGAAAGCAGGGUCAGUUGGCGCUGGUCUAAGGGUUCCGCAGUGAGUUAAAGUUGGGCUUGAGUUCGAGGGCCAGCCAACUGACAGC
...((..(.(....))...((((((((((..((((((..(..(((......(((((.......))))))))..)..)))))))))))))))).)) ( -33.70, z-score =  -1.21, R)
>droYak2.chr3R 10361192 95 + 28832112
AGAGCGGGUCGAAAGCAGGGUCAGUUGGCGCUGGUCUAAGGGUUCCACCUUCAGUUGAAGUUGGGCUUGAGUUCGAGGGCCAGCCAACUGACAGC
...((..(.(....))...((((((((((..(((((.......((((.((((....)))).))))((((....))))))))))))))))))).)) ( -37.30, z-score =  -1.69, R)
>droEre2.scaffold_4770 2470239 94 - 17746568
AGAGCGG-UCGAAAGCAGGGUCAGUUGGCGCUGCUCUAAGGGUUCCACAUUCAGUUAAAGUUGGGCUCGAGUUCGAGGGCCAGCCAACUGACAGC
...((..-......))...((((((((((...(((((..((((((.((...........)).)))))).......)))))..))))))))))... ( -32.90, z-score =  -1.25, R)
>droMoj3.scaffold_6540 5369310 80 + 34148556
---------CCGGCCCGGGGUCAGCUGUGAUCCAGAUCAGAAU-CGGCAGCGAGAUCGCGGCACGGUCA--UCC---AGUUGUCCAGCUGACAGU
---------(((...))).((((((((((((....))))....-.(((((((((((((.....))))).--)).---.))))))))))))))... ( -28.80, z-score =  -0.61, R)
>consensus
AGAGCGGGUCGAAAGCAGGGUCAGUUGGCGCUGGUCUAAGGGUUCCGCAGUGAGUUAAAGUUGGGCUUGAGUUCGAGGGCCAGCCAACUGACAGC
...................((((((((((..((((((..(..(((......(((((.......))))))))..)..))))))))))))))))... (-23.26 = -24.50 +   1.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 6,333,017 – 6,333,112
Length 95
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 76.69
Shannon entropy 0.45050
G+C content 0.58410
Mean single sequence MFE -25.42
Consensus MFE -15.90
Energy contribution -16.10
Covariance contribution 0.20
Combinations/Pair 1.29
Mean z-score -1.38
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.74
SVM RNA-class probability 0.804739
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6333017 95 - 27905053
GCUGUCAGUUGGCUGGCCCUCGAACUCAAGCCCAACUUUAACACACUGCGGAACCCUUAGACCAGCGCCAACUGACCCUGCUUUCGACCCGCUCU
((.((((((((((.(((............)))...............((((..........)).))))))))))))...)).............. ( -23.60, z-score =  -1.33, R)
>droSim1.chr3R 12469990 95 + 27517382
GCUGUCAGUUGGCUGGCCCUCGAACUCAAGCCCAACUUUAACUCACUGCGGAACCCUUAGACCAGCGCCAACUGACCCUCCAUUCGACCCGCUCU
...((((((((((.(((............)))...............((((..........)).))))))))))))................... ( -21.80, z-score =  -1.19, R)
>droSec1.super_0 5512126 95 + 21120651
GCUGUCAGUUGGCUGGCCCUCGAACUCAAGCCCAACUUUAACUCACUGCGGAACCCUUAGACCAGCGCCAACUGACCCUGCUUUCGACCCGCUCU
((.((((((((((.(((............)))...............((((..........)).))))))))))))...)).............. ( -23.60, z-score =  -1.30, R)
>droYak2.chr3R 10361192 95 - 28832112
GCUGUCAGUUGGCUGGCCCUCGAACUCAAGCCCAACUUCAACUGAAGGUGGAACCCUUAGACCAGCGCCAACUGACCCUGCUUUCGACCCGCUCU
((.(((((((((((((.....(....)....(((.((((....)))).)))..........)))..))))))))))...)).............. ( -27.50, z-score =  -1.40, R)
>droEre2.scaffold_4770 2470239 94 + 17746568
GCUGUCAGUUGGCUGGCCCUCGAACUCGAGCCCAACUUUAACUGAAUGUGGAACCCUUAGAGCAGCGCCAACUGACCCUGCUUUCGA-CCGCUCU
((.(((((((((((((..((((....)))).))).......(((..((.((...)).))...))).))))))))))...))......-....... ( -28.70, z-score =  -2.13, R)
>droMoj3.scaffold_6540 5369310 80 - 34148556
ACUGUCAGCUGGACAACU---GGA--UGACCGUGCCGCGAUCUCGCUGCCG-AUUCUGAUCUGGAUCACAGCUGACCCCGGGCCGG---------
...((((((((((...(.---.((--(.(.((.((.(((....))).))))-....).)))..).)).)))))))).(((...)))--------- ( -27.30, z-score =  -0.92, R)
>consensus
GCUGUCAGUUGGCUGGCCCUCGAACUCAAGCCCAACUUUAACUCACUGCGGAACCCUUAGACCAGCGCCAACUGACCCUGCUUUCGACCCGCUCU
...((((((((((.(((............)))...............((((..........)).))))))))))))................... (-15.90 = -16.10 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:03:20 2011