Locus 9064

Sequence ID dm3.chr3R
Location 3,892,231 – 3,892,326
Length 95
Max. P 0.999252
window12436 window12437

overview

Window 6

Location 3,892,231 – 3,892,326
Length 95
Sequences 7
Columns 95
Reading direction forward
Mean pairwise identity 69.28
Shannon entropy 0.54235
G+C content 0.63195
Mean single sequence MFE -29.87
Consensus MFE -19.55
Energy contribution -19.61
Covariance contribution 0.06
Combinations/Pair 1.18
Mean z-score -2.70
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.71
SVM RNA-class probability 0.999213
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3892231 95 + 27905053
AGCACACCCAGCAGUUGGACCUGCACCGCCCCAACCGCACUCCGCUUUUCCAACCCACAGACCACCUCCAACCACGGAUAUCCUUGGGUGUGCCC
.((((((((((..((((((...((...((.......)).....))...))))))............(((......))).....)))))))))).. ( -28.20, z-score =  -3.23, R)
>droSim1.chr3R 10159869 95 - 27517382
AGCACACCCAGCAGUUGGACCUGCACUGCCCCAACCGCGCUCCGCUUUUCCAGCCCACAGCCCAGCUCCAACCACGGAUAUCCUUGGGUGUGCCC
.((((((((((..((((((.(((....((.......))(((..(((.....)))....))).))).))))))...((....)))))))))))).. ( -33.20, z-score =  -3.02, R)
>droSec1.super_0 3195923 95 - 21120651
AGCACACCCAGCAGUUGGACCUGCACUGCCCCAACCGCGCUCCGCUUUUCCAACCCACAGCCCAACUCCAACCACGGAUAUCCUUGGGUGUGCCC
.((((((((((..((((((...((...(((......).))...))...))))))............(((......))).....)))))))))).. ( -30.20, z-score =  -3.07, R)
>droYak2.chr3R 7971983 76 + 28832112
AGCACACCCAGCAGUUGGACCUGCUCUGCCCCAUCCGCGUGCC-------------------CACCUCCAACCACGGAUAUCCUUGGGUGUGCCC
.((((((((((..((((((..((..((((.......))).)..-------------------))..))))))...((....)))))))))))).. ( -28.00, z-score =  -2.76, R)
>droEre2.scaffold_4770 66370 76 - 17746568
AGCACGCCCAGCAGUUGGAGCUGCACAGCCCCAUCCGCGUUUC-------------------CACCGCCAACCACGGAUAUCCUUGGGUGUGCCC
.(((((((((((.(.(((.(((....))).))).).)).....-------------------..(((.......))).......))))))))).. ( -29.80, z-score =  -2.96, R)
>dp4.chr2 24396963 80 - 30794189
AGCACACCCAGCAGCAGUCUGUCCUCUGUUCUGCACCUCCUGCC---------------GCCUAGAACCAUCCUUGGCUGCCCUUGGGUGUGGCC
..(((((((((..((((((........((((((((.....))).---------------....))))).......))))))..)))))))))... ( -29.86, z-score =  -1.93, R)
>droPer1.super_0 11602153 80 - 11822988
AGCACACCCAGCAGCAGUCUGUCCUCUGUUCUGCACCUCCUGCC---------------GCCUAGAACCAUCCUUGGCUGCCCUUGGGUGUGGCC
..(((((((((..((((((........((((((((.....))).---------------....))))).......))))))..)))))))))... ( -29.86, z-score =  -1.93, R)
>consensus
AGCACACCCAGCAGUUGGACCUGCACUGCCCCAACCGCGCUCCG_______________GCCCACCUCCAACCACGGAUAUCCUUGGGUGUGCCC
.(((((((((((((.((......))))))..............................................((....)).))))))))).. (-19.55 = -19.61 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 3,892,231 – 3,892,326
Length 95
Sequences 7
Columns 95
Reading direction reverse
Mean pairwise identity 69.28
Shannon entropy 0.54235
G+C content 0.63195
Mean single sequence MFE -40.56
Consensus MFE -21.79
Energy contribution -21.77
Covariance contribution -0.02
Combinations/Pair 1.25
Mean z-score -3.02
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.74
SVM RNA-class probability 0.999252
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3892231 95 - 27905053
GGGCACACCCAAGGAUAUCCGUGGUUGGAGGUGGUCUGUGGGUUGGAAAAGCGGAGUGCGGUUGGGGCGGUGCAGGUCCAACUGCUGGGUGUGCU
.((((((((((.((....))(..((((((.....(((((...........)))))(..(.((....)).)..)...))))))..))))))))))) ( -41.70, z-score =  -2.93, R)
>droSim1.chr3R 10159869 95 + 27517382
GGGCACACCCAAGGAUAUCCGUGGUUGGAGCUGGGCUGUGGGCUGGAAAAGCGGAGCGCGGUUGGGGCAGUGCAGGUCCAACUGCUGGGUGUGCU
.((((((((((.((....))(..((((((.(((.(((((...((.((...(((...)))..)).))))))).))).))))))..))))))))))) ( -51.80, z-score =  -4.70, R)
>droSec1.super_0 3195923 95 + 21120651
GGGCACACCCAAGGAUAUCCGUGGUUGGAGUUGGGCUGUGGGUUGGAAAAGCGGAGCGCGGUUGGGGCAGUGCAGGUCCAACUGCUGGGUGUGCU
.((((((((((.((....))(..((((((.(((.(((((...(..(....(((...)))..)..).))))).))).))))))..))))))))))) ( -47.70, z-score =  -4.40, R)
>droYak2.chr3R 7971983 76 - 28832112
GGGCACACCCAAGGAUAUCCGUGGUUGGAGGUG-------------------GGCACGCGGAUGGGGCAGAGCAGGUCCAACUGCUGGGUGUGCU
.(((((((((.....(((((((((((.......-------------------))).))))))))......(((((......)))))))))))))) ( -36.60, z-score =  -2.91, R)
>droEre2.scaffold_4770 66370 76 + 17746568
GGGCACACCCAAGGAUAUCCGUGGUUGGCGGUG-------------------GAAACGCGGAUGGGGCUGUGCAGCUCCAACUGCUGGGCGUGCU
.(((((.((((.((....))(..(((..(.(((-------------------....))).)..((((((....)))))))))..))))).))))) ( -37.30, z-score =  -2.61, R)
>dp4.chr2 24396963 80 + 30794189
GGCCACACCCAAGGGCAGCCAAGGAUGGUUCUAGGC---------------GGCAGGAGGUGCAGAACAGAGGACAGACUGCUGCUGGGUGUGCU
(((.((((((...((.(((((....))))))).(((---------------(((((...((.(........).))...))))))))))))))))) ( -34.40, z-score =  -1.81, R)
>droPer1.super_0 11602153 80 + 11822988
GGCCACACCCAAGGGCAGCCAAGGAUGGUUCUAGGC---------------GGCAGGAGGUGCAGAACAGAGGACAGACUGCUGCUGGGUGUGCU
(((.((((((...((.(((((....))))))).(((---------------(((((...((.(........).))...))))))))))))))))) ( -34.40, z-score =  -1.81, R)
>consensus
GGGCACACCCAAGGAUAUCCGUGGUUGGAGCUGGGC_______________CGGAGCGCGGUUGGGGCAGUGCAGGUCCAACUGCUGGGUGUGCU
.(((((((((.......((((....))))....................................(((((((......)).)))))))))))))) (-21.79 = -21.77 +  -0.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:57:22 2011