Locus 6028

Sequence ID dm3.chr3L
Location 3,141,726 – 3,141,830
Length 104
Max. P 0.656545
window8295 window8296

overview

Window 5

Location 3,141,726 – 3,141,830
Length 104
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 94.92
Shannon entropy 0.08893
G+C content 0.47412
Mean single sequence MFE -30.50
Consensus MFE -28.40
Energy contribution -28.64
Covariance contribution 0.24
Combinations/Pair 1.13
Mean z-score -1.33
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.35
SVM RNA-class probability 0.656545
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3141726 104 + 24543557
AGUGGAGCACUGGCAAGUGAGGAGUCAUCGUGGGAGU-ACCCACUUAUCAAUCACGUUUUAUGCUUUUACUGCACUUCGUAUCCGAAUCCAGUGCAGAGCUUUAA
..((((((...((((.((((.((....))(((((...-.))))).......))))......))))....((((((((((....)))....))))))).)))))). ( -30.60, z-score =  -1.47, R)
>droEre2.scaffold_4784 3150777 104 + 25762168
AACGGAGCACUGGCAAAUGAGGAGUCACCGUGGGAGU-GCCCACUUAUCAAUCACGUUUUAUGCGUUUACUGCACUUCGUAUCCGAAUCCAGUGCAGAGCUUUAA
...(((((....(((((((.((.....))(((((...-.)))))..........))))...))).....((((((((((....)))....))))))).))))).. ( -28.80, z-score =  -0.77, R)
>droYak2.chr3L 15396531 105 - 24197627
AGUGGAGCACUGGCAAAUGAGGAGUCACCGUGGGAGUUACCCACUUAUCAAUCACGUUUUAUGCCUUUACUGCACUUCAUAUCCGAAUCCAGUGCAGAGCUUUAA
..((((((...((((((((.((.....))(((((.....)))))..........))))...))))....(((((((((......))....))))))).)))))). ( -30.70, z-score =  -1.86, R)
>droSec1.super_2 3135348 104 + 7591821
AGUGGAGCACUGGCAAGUGAGGAGUCACCGUGGGAGU-ACCCACUCAUCAAUCGCGUUUUAUGUCUUUACUGCACUUCGUAUCCGAAUCCAGUGCAGAGCUUUAA
..((((((...((((.((((((.....))(((((...-.))))).......))))......))))....((((((((((....)))....))))))).)))))). ( -31.20, z-score =  -1.20, R)
>droSim1.chr3L 2669323 104 + 22553184
AGUGGAGCACUGGCAAGUGAGGAGUCACCGUGGGAGU-ACCCACUUAUCAAUCGCGUUUUAUGUCUUUACUGCACUUCGUAUCCGAAUCCAGUGCAGAGCUUUAA
..((((((...((((.((((((.....))(((((...-.))))).......))))......))))....((((((((((....)))....))))))).)))))). ( -31.20, z-score =  -1.34, R)
>consensus
AGUGGAGCACUGGCAAGUGAGGAGUCACCGUGGGAGU_ACCCACUUAUCAAUCACGUUUUAUGCCUUUACUGCACUUCGUAUCCGAAUCCAGUGCAGAGCUUUAA
..((((((...((((.((((((.....))(((((.....))))).......))))......))))....((((((((((....)))....))))))).)))))). (-28.40 = -28.64 +   0.24)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 6

Location 3,141,726 – 3,141,830
Length 104
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 94.92
Shannon entropy 0.08893
G+C content 0.47412
Mean single sequence MFE -29.76
Consensus MFE -26.82
Energy contribution -26.42
Covariance contribution -0.40
Combinations/Pair 1.09
Mean z-score -1.46
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.24
SVM RNA-class probability 0.607761
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3141726 104 - 24543557
UUAAAGCUCUGCACUGGAUUCGGAUACGAAGUGCAGUAAAAGCAUAAAACGUGAUUGAUAAGUGGGU-ACUCCCACGAUGACUCCUCACUUGCCAGUGCUCCACU
..........(((((((.((((....))))((((.......)))).....((((.......(((((.-...))))).........))))...)))))))...... ( -30.19, z-score =  -2.21, R)
>droEre2.scaffold_4784 3150777 104 - 25762168
UUAAAGCUCUGCACUGGAUUCGGAUACGAAGUGCAGUAAACGCAUAAAACGUGAUUGAUAAGUGGGC-ACUCCCACGGUGACUCCUCAUUUGCCAGUGCUCCGUU
....(((...(((((((.((((....))))((((.......)))).....((((.......(((((.-...)))))(....)...))))...)))))))...))) ( -29.60, z-score =  -1.11, R)
>droYak2.chr3L 15396531 105 + 24197627
UUAAAGCUCUGCACUGGAUUCGGAUAUGAAGUGCAGUAAAGGCAUAAAACGUGAUUGAUAAGUGGGUAACUCCCACGGUGACUCCUCAUUUGCCAGUGCUCCACU
....(((.(((((((..((......))..)))))))....((((......((((.......(((((.....)))))(....)...)))).))))...)))..... ( -28.90, z-score =  -0.99, R)
>droSec1.super_2 3135348 104 - 7591821
UUAAAGCUCUGCACUGGAUUCGGAUACGAAGUGCAGUAAAGACAUAAAACGCGAUUGAUGAGUGGGU-ACUCCCACGGUGACUCCUCACUUGCCAGUGCUCCACU
....(((.(((.((((.(((((....)).))).)))).............((((.(((.(((((((.-...)))))(....))).))).))))))).)))..... ( -30.80, z-score =  -1.59, R)
>droSim1.chr3L 2669323 104 - 22553184
UUAAAGCUCUGCACUGGAUUCGGAUACGAAGUGCAGUAAAGACAUAAAACGCGAUUGAUAAGUGGGU-ACUCCCACGGUGACUCCUCACUUGCCAGUGCUCCACU
....(((.(((.((((.(((((....)).))).)))).............((((.(((...(((((.-...)))))(....)...))).))))))).)))..... ( -29.30, z-score =  -1.41, R)
>consensus
UUAAAGCUCUGCACUGGAUUCGGAUACGAAGUGCAGUAAAGGCAUAAAACGUGAUUGAUAAGUGGGU_ACUCCCACGGUGACUCCUCACUUGCCAGUGCUCCACU
..........(((((((.((((....))))(((.((.........................(((((.....)))))(....)..)))))...)))))))...... (-26.82 = -26.42 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:59:55 2011