Locus 10305

Sequence ID dm3.chr3R
Location 12,882,521 – 12,882,639
Length 118
Max. P 0.998001
window14170 window14171

overview

Window 0

Location 12,882,521 – 12,882,639
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.67
Shannon entropy 0.12741
G+C content 0.61257
Mean single sequence MFE -54.92
Consensus MFE -50.98
Energy contribution -51.78
Covariance contribution 0.80
Combinations/Pair 1.10
Mean z-score -3.56
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.23
SVM RNA-class probability 0.998001
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12882521 118 + 27905053
GUUCCCCCCCACCAUCGUCCGUCUCUUUCUCGCUGACAGCUGAUGCUGCCGCACAGAUCUUU-GCAUAUGCACUGGCGUCGGCUGUCCGUUGGUGAAAGAGGGCGGGGAGGGGG-UAUUA
.....(((((.((.((((((...((((((((((.(((((((((((((((.(((........)-))....))...))))))))))))).).))).)))))))))))))).)))))-..... ( -53.90, z-score =  -3.10, R)
>droSim1.chr3R 18928206 113 - 27517382
-----CCCCCACCAUCGUCCGUCUCUUUCCCGCCGACAGCUGAUGCUGCCGCACAGAUCUUU-GCAUAUGCACUGGCGUCGGCUCUCCGUCGGUGAAAGAGGGCGGGGAGGGGA-CAUUA
-----.((((.((.((((((...((((((..((((((.(..((.((((.(((.(((.....(-((....))))))))).))))))..))))))))))))))))))))).)))).-..... ( -50.40, z-score =  -2.59, R)
>droSec1.super_12 850055 115 - 2123299
---ACCCCCCACCAUCGUCCGUCUCUUUCCCGCCGACAGCUGAUGCUGCCGCACAGAUCUUU-GCAUAUGCACUGGCGUCGGCUCUCCGUCGGUGAAAGAGGGCGGGGAGGGGA-CAUUA
---...((((.((.((((((...((((((..((((((.(..((.((((.(((.(((.....(-((....))))))))).))))))..))))))))))))))))))))).)))).-..... ( -50.40, z-score =  -2.46, R)
>droYak2.chr3R 17331134 116 - 28832112
----CCCCCCACCAUCGUCCGUCUCUUUCCCGCCGACAGCUGAUGCUGCCGCACAGAUCUUUUGCAUAUGCACUGGCGUCGGCUGUCCGUCGGCGAAAGAGGGCGUGGAGGGGGGCAUUA
----((((((.(((.(((((...((((((((((.((((((((((((((..(((((((...))))....)))..)))))))))))))).).))).)))))))))))))).))))))..... ( -62.60, z-score =  -5.10, R)
>droEre2.scaffold_4770 8998613 116 - 17746568
----CCCCCCACCAUCGUGCGUCUCUUUCCCGCCGACAGCUGAUGCUGCCGCACAGAUCUUUUGCAUAUGCACUGGCGUCGGCUGUCCGUCGGUGAAAGAGGACGAGAAGGGGGGCAUUA
----((((((....((((...((((((((((((.((((((((((((((..(((((((...))))....)))..)))))))))))))).).))).))))))))))))...))))))..... ( -57.30, z-score =  -4.57, R)
>consensus
____CCCCCCACCAUCGUCCGUCUCUUUCCCGCCGACAGCUGAUGCUGCCGCACAGAUCUUU_GCAUAUGCACUGGCGUCGGCUGUCCGUCGGUGAAAGAGGGCGGGGAGGGGG_CAUUA
.....(((((.((.((((((...((((((((((.((((((((((((((..(((...............)))..)))))))))))))).).))).)))))))))))))).)))))...... (-50.98 = -51.78 +   0.80)

alignment

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secondary structure

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dotplot

Postscript

Window 1

Location 12,882,521 – 12,882,639
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.67
Shannon entropy 0.12741
G+C content 0.61257
Mean single sequence MFE -51.54
Consensus MFE -45.38
Energy contribution -45.38
Covariance contribution -0.00
Combinations/Pair 1.06
Mean z-score -2.92
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.41
SVM RNA-class probability 0.990337
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12882521 118 - 27905053
UAAUA-CCCCCUCCCCGCCCUCUUUCACCAACGGACAGCCGACGCCAGUGCAUAUGC-AAAGAUCUGUGCGGCAGCAUCAGCUGUCAGCGAGAAAGAGACGGACGAUGGUGGGGGGGAAC
.....-...(((((((((((((((((.....(((....))).(((..(..((.((..-....)).))..)((((((....)))))).))).))))))).(....)..))))))))))... ( -49.00, z-score =  -3.25, R)
>droSim1.chr3R 18928206 113 + 27517382
UAAUG-UCCCCUCCCCGCCCUCUUUCACCGACGGAGAGCCGACGCCAGUGCAUAUGC-AAAGAUCUGUGCGGCAGCAUCAGCUGUCGGCGGGAAAGAGACGGACGAUGGUGGGGG-----
.....-.((((.((.(((((((((((.((..(((....)))..(((.(..((.((..-....)).))..)((((((....))))))))))))))))))..)).))..)).)))).----- ( -48.40, z-score =  -2.11, R)
>droSec1.super_12 850055 115 + 2123299
UAAUG-UCCCCUCCCCGCCCUCUUUCACCGACGGAGAGCCGACGCCAGUGCAUAUGC-AAAGAUCUGUGCGGCAGCAUCAGCUGUCGGCGGGAAAGAGACGGACGAUGGUGGGGGGU---
.....-....((((((((((((((((.((..(((....)))..(((.(..((.((..-....)).))..)((((((....)))))))))))))))))).(....)..))))))))).--- ( -50.40, z-score =  -2.09, R)
>droYak2.chr3R 17331134 116 + 28832112
UAAUGCCCCCCUCCACGCCCUCUUUCGCCGACGGACAGCCGACGCCAGUGCAUAUGCAAAAGAUCUGUGCGGCAGCAUCAGCUGUCGGCGGGAAAGAGACGGACGAUGGUGGGGGG----
.....((((((.((((((((((((((.(((.(.((((((.((.((...((((((..(....)...))))))...)).)).)))))).)))))))))))..)).)).))).))))))---- ( -57.40, z-score =  -3.93, R)
>droEre2.scaffold_4770 8998613 116 + 17746568
UAAUGCCCCCCUUCUCGUCCUCUUUCACCGACGGACAGCCGACGCCAGUGCAUAUGCAAAAGAUCUGUGCGGCAGCAUCAGCUGUCGGCGGGAAAGAGACGCACGAUGGUGGGGGG----
.....((((((.((((((.(((((((.(((.(.((((((.((.((...((((((..(....)...))))))...)).)).)))))).)))))))))))....)))).)).))))))---- ( -52.50, z-score =  -3.24, R)
>consensus
UAAUG_CCCCCUCCCCGCCCUCUUUCACCGACGGACAGCCGACGCCAGUGCAUAUGC_AAAGAUCUGUGCGGCAGCAUCAGCUGUCGGCGGGAAAGAGACGGACGAUGGUGGGGGG____
......(((((.((.(((((((((((.....(((....))).((((...(((((...........)))))((((((....)))))))))).)))))))..)).))..)).)))))..... (-45.38 = -45.38 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:21:25 2011