Locus 12235

Sequence ID dm3.chr3R
Location 26,668,508 – 26,668,615
Length 107
Max. P 0.831421
window16828 window16829

overview

Window 8

Location 26,668,508 – 26,668,615
Length 107
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 80.25
Shannon entropy 0.36170
G+C content 0.54956
Mean single sequence MFE -32.40
Consensus MFE -25.62
Energy contribution -26.82
Covariance contribution 1.20
Combinations/Pair 1.17
Mean z-score -1.31
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.77
SVM RNA-class probability 0.811163
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 26668508 107 + 27905053
AUGUGAAGGUCGCUGAACGACCUUGCUUGCGGUCGCCUUC-------UUUCCACCUUGGAUGCCUCCAUCCUCCGUCCUCGAAAGAAGCUGCUUCUUAGGCGUCUGCGUGUCGU
.....(((((((.....)))))))((.(((((.(((((((-------((((.((...(((((....)))))...))....))))))...........))))).))))).))... ( -34.40, z-score =  -1.86, R)
>droSim1.chr3R 26309313 107 + 27517382
AUGUGAAGGUCGCUGAACGACCUUGCUUGCGGUCGCCUUC-------UUUCCACCUUGGAUGCCUCCAUCCUCCGUCCUCGAAAGAAGCUGCUUCUUAGGCGUCUGCGUGUCGU
.....(((((((.....)))))))((.(((((.(((((((-------((((.((...(((((....)))))...))....))))))...........))))).))))).))... ( -34.40, z-score =  -1.86, R)
>droSec1.super_4 5493711 107 + 6179234
AUGUGAAGGUCGCUGAGCGACCUUGCUUGCGGUCGCCUUC-------UUUCCACCUUGGAUGCCUCCAUCCUCCGUCCUCGAACGAAGCUGCUUCUUAGGCGUUUGCGUGUCGU
.....((((((((...))))))))((.(((((.(((((..-------....((.((((((((....)))))..(((......)))))).))......))))).))))).))... ( -32.90, z-score =  -0.85, R)
>droYak2.chr3R 27590777 110 + 28832112
AUGUGAAGGUCGCUGAACGACCUUGCUUGCGGUCGGUUGGAAAGAAGUUUCCACCUUGGAUGCCACCAUCCUCUA----CAGAAGAAGCUGCUUCUUAGGCGUCUGCGUGUCGU
.....(((((((.....)))))))((.(((((.((((.(((((....))))))))..(((((....)))))((((----.(((((......))))))))).).))))).))... ( -34.70, z-score =  -0.56, R)
>droEre2.scaffold_4820 9142700 100 - 10470090
AUGUGAAGGUCGCUGAACGACCUUGCUUGCGGUCGCCUUC-------UUUCCACCUUGGAUGCCUCCGUCCUC-------GAAAGAAGCUGCUUCUUUGGCGUCUGCGUGUCGU
.....(((((((.....)))))))((.(((((.((((...-------..........(((((....)))))..-------.(((((((...))))))))))).))))).))... ( -34.30, z-score =  -2.28, R)
>droWil1.scaffold_181130 10244426 81 + 16660200
AUCUGAAGGUCGCUGAACGACCUUGCUUGCGGUCGACUUG-----------CACCGUAAAUG----------------------GGGAAUAUAUGUUUGGCGUCUGCGUGUCGU
....((.((.(((..((((.((((..(((((((.......-----------.)))))))..)----------------------)))......))))..))).)).....)).. ( -23.70, z-score =  -0.43, R)
>consensus
AUGUGAAGGUCGCUGAACGACCUUGCUUGCGGUCGCCUUC_______UUUCCACCUUGGAUGCCUCCAUCCUCCG____CGAAAGAAGCUGCUUCUUAGGCGUCUGCGUGUCGU
.....(((((((.....)))))))((.(((((.((((....................(((((....)))))...........((((((...)))))).)))).))))).))... (-25.62 = -26.82 +   1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 26,668,508 – 26,668,615
Length 107
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 80.25
Shannon entropy 0.36170
G+C content 0.54956
Mean single sequence MFE -31.11
Consensus MFE -24.47
Energy contribution -26.30
Covariance contribution 1.83
Combinations/Pair 1.18
Mean z-score -1.35
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.84
SVM RNA-class probability 0.831421
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 26668508 107 - 27905053
ACGACACGCAGACGCCUAAGAAGCAGCUUCUUUCGAGGACGGAGGAUGGAGGCAUCCAAGGUGGAAA-------GAAGGCGACCGCAAGCAAGGUCGUUCAGCGACCUUCACAU
.......((.(.(((((.....((..(((((((((....))))))).))..)).(((.....)))..-------..))))).).))..(.(((((((.....)))))))).... ( -34.90, z-score =  -1.49, R)
>droSim1.chr3R 26309313 107 - 27517382
ACGACACGCAGACGCCUAAGAAGCAGCUUCUUUCGAGGACGGAGGAUGGAGGCAUCCAAGGUGGAAA-------GAAGGCGACCGCAAGCAAGGUCGUUCAGCGACCUUCACAU
.......((.(.(((((.....((..(((((((((....))))))).))..)).(((.....)))..-------..))))).).))..(.(((((((.....)))))))).... ( -34.90, z-score =  -1.49, R)
>droSec1.super_4 5493711 107 - 6179234
ACGACACGCAAACGCCUAAGAAGCAGCUUCGUUCGAGGACGGAGGAUGGAGGCAUCCAAGGUGGAAA-------GAAGGCGACCGCAAGCAAGGUCGCUCAGCGACCUUCACAU
......(((...(((((.........(((((((....)))))))..((((....)))))))))....-------...(((((((........)))))))..))).......... ( -36.30, z-score =  -1.76, R)
>droYak2.chr3R 27590777 110 - 28832112
ACGACACGCAGACGCCUAAGAAGCAGCUUCUUCUG----UAGAGGAUGGUGGCAUCCAAGGUGGAAACUUCUUUCCAACCGACCGCAAGCAAGGUCGUUCAGCGACCUUCACAU
.......((....((((..((.((.((((((((..----..))))).))).)).))..))))(((((....)))))........))..(.(((((((.....)))))))).... ( -32.10, z-score =  -0.83, R)
>droEre2.scaffold_4820 9142700 100 + 10470090
ACGACACGCAGACGCCAAAGAAGCAGCUUCUUUC-------GAGGACGGAGGCAUCCAAGGUGGAAA-------GAAGGCGACCGCAAGCAAGGUCGUUCAGCGACCUUCACAU
.......((.(.((((.........((((((.((-------...)).)))))).(((.....)))..-------...)))).).))..(.(((((((.....)))))))).... ( -31.00, z-score =  -1.41, R)
>droWil1.scaffold_181130 10244426 81 - 16660200
ACGACACGCAGACGCCAAACAUAUAUUCCC----------------------CAUUUACGGUG-----------CAAGUCGACCGCAAGCAAGGUCGUUCAGCGACCUUCAGAU
.((((..(((..((................----------------------......)).))-----------)..)))).......(.(((((((.....)))))))).... ( -17.45, z-score =  -1.10, R)
>consensus
ACGACACGCAGACGCCUAAGAAGCAGCUUCUUUCG____CGGAGGAUGGAGGCAUCCAAGGUGGAAA_______GAAGGCGACCGCAAGCAAGGUCGUUCAGCGACCUUCACAU
......(((...(((((..((.((..(((((((((....))))))).))..)).))..)))))..............(((((((........)))))))..))).......... (-24.47 = -26.30 +   1.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:58:22 2011