Locus 8929

Sequence ID dm3.chr3R
Location 2,736,041 – 2,736,138
Length 97
Max. P 0.958148
window12260 window12261

overview

Window 0

Location 2,736,041 – 2,736,138
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 88.87
Shannon entropy 0.19971
G+C content 0.44178
Mean single sequence MFE -18.28
Consensus MFE -13.51
Energy contribution -15.20
Covariance contribution 1.69
Combinations/Pair 1.05
Mean z-score -2.47
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.29
SVM RNA-class probability 0.921541
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 2736041 97 + 27905053
CUGUUCCUCUAUUUGCUGUCUUGGCCAAAAAUGACGAAAUUAACCUGCCCCUCGUCUCUCGAUUUGGUAGAAAAUCUCGUCUCCUUGGUGUUUUUUG
.......................(((((....(((((.(((...(((((..(((.....)))...)))))..))).)))))...)))))........ ( -20.00, z-score =  -3.01, R)
>droEre2.scaffold_4770 2987270 87 + 17746568
CUGUUCCUCUAUUUGCUGUCUUG----------ACGAAAUUAUCCUGCCCCUCGUCCCUCGAUUUGGUAGAAAAUCUCGUCUCCUUGGUGUUCUUUG
..............((((....(----------((((.(((...(((((..(((.....)))...)))))..))).)))))....))))........ ( -16.40, z-score =  -3.29, R)
>droYak2.chr3R 21156809 92 - 28832112
CUGUUCCUCUAUUUGCUGUCUUGGCCAAAAAUGACGAAAUUA----GCCCCUCGUCUCUCGAUUUGGUA-AAAACCUCGUCUCCUUGGUGUUCUUUG
.......................(((((....(((((.....----(((..(((.....)))...))).-......)))))...)))))........ ( -14.50, z-score =  -1.22, R)
>droSec1.super_6 2827571 96 + 4358794
CUGUUCCUCUAUUUGCUGUCUUGGCCAAAUAUGACGGAAUUAACCUGCCACUCCUCCCUCGAUUUGGUAGAAAAUCUCGUCUACUUGGUGUUUUUG-
.......................(((((.((.((((..(((...((((((.((.......))..))))))..)))..)))))).))))).......- ( -19.10, z-score =  -1.74, R)
>droSim1.chr3R 2772759 97 + 27517382
CUGUUCCUCUAUUUGCUGUCUUGGCCAAAAAUGACGAAAUUAACCUGCCACUCGUCCCUCGAUUUGGUAGAAAAUCUCGUCUCCUUGGUGUUUUUUG
.......................(((((....(((((.(((...((((((.(((.....)))..))))))..))).)))))...)))))........ ( -21.40, z-score =  -3.10, R)
>consensus
CUGUUCCUCUAUUUGCUGUCUUGGCCAAAAAUGACGAAAUUAACCUGCCCCUCGUCCCUCGAUUUGGUAGAAAAUCUCGUCUCCUUGGUGUUUUUUG
.......................(((((....(((((.(((...(((((..(((.....)))...)))))..))).)))))...)))))........ (-13.51 = -15.20 +   1.69)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,736,041 – 2,736,138
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 88.87
Shannon entropy 0.19971
G+C content 0.44178
Mean single sequence MFE -21.70
Consensus MFE -15.67
Energy contribution -17.52
Covariance contribution 1.85
Combinations/Pair 1.09
Mean z-score -2.77
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.65
SVM RNA-class probability 0.958148
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 2736041 97 - 27905053
CAAAAAACACCAAGGAGACGAGAUUUUCUACCAAAUCGAGAGACGAGGGGCAGGUUAAUUUCGUCAUUUUUGGCCAAGACAGCAAAUAGAGGAACAG
.........((((((((((((((((.(((.((...(((.....)))..)).)))..))))))))).)))))))........................ ( -23.80, z-score =  -3.40, R)
>droEre2.scaffold_4770 2987270 87 - 17746568
CAAAGAACACCAAGGAGACGAGAUUUUCUACCAAAUCGAGGGACGAGGGGCAGGAUAAUUUCGU----------CAAGACAGCAAAUAGAGGAACAG
................(((((((((((((.((...(((.....)))..)).)))).))))))))----------)...................... ( -18.90, z-score =  -3.13, R)
>droYak2.chr3R 21156809 92 + 28832112
CAAAGAACACCAAGGAGACGAGGUUUU-UACCAAAUCGAGAGACGAGGGGC----UAAUUUCGUCAUUUUUGGCCAAGACAGCAAAUAGAGGAACAG
.........((((((((((((((((..-..((...(((.....))).))..----.))))))))).)))))))........................ ( -21.50, z-score =  -2.76, R)
>droSec1.super_6 2827571 96 - 4358794
-CAAAAACACCAAGUAGACGAGAUUUUCUACCAAAUCGAGGGAGGAGUGGCAGGUUAAUUCCGUCAUAUUUGGCCAAGACAGCAAAUAGAGGAACAG
-........(((((((((((..(((.(((.(((..((......))..))).)))..)))..)))).)))))))........................ ( -20.80, z-score =  -1.81, R)
>droSim1.chr3R 2772759 97 - 27517382
CAAAAAACACCAAGGAGACGAGAUUUUCUACCAAAUCGAGGGACGAGUGGCAGGUUAAUUUCGUCAUUUUUGGCCAAGACAGCAAAUAGAGGAACAG
.........((((((((((((((((.(((.(((..(((.....))).))).)))..))))))))).)))))))........................ ( -23.50, z-score =  -2.75, R)
>consensus
CAAAAAACACCAAGGAGACGAGAUUUUCUACCAAAUCGAGGGACGAGGGGCAGGUUAAUUUCGUCAUUUUUGGCCAAGACAGCAAAUAGAGGAACAG
.........((((((((((((((((..((.((...(((.....)))..)).))...))))))))).)))))))........................ (-15.67 = -17.52 +   1.85)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:54:55 2011