Locus 8385

Sequence ID dm3.chr3L
Location 22,392,599 – 22,392,715
Length 116
Max. P 0.875359
window11518 window11519 window11520

overview

Window 8

Location 22,392,599 – 22,392,690
Length 91
Sequences 3
Columns 109
Reading direction forward
Mean pairwise identity 77.36
Shannon entropy 0.30329
G+C content 0.49484
Mean single sequence MFE -26.63
Consensus MFE -23.03
Energy contribution -23.03
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.13
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.713477
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22392599 91 + 24543557
------------------UAACUCAUAUACCCAGCCUUGGCACACAUCAAAUGAGUUGUGUGCCCUGCAAUAAGGCAAUAAGGCAGAAUGGCAGCCGCUCGGCACAAUG
------------------............((((((((((((((((.(......).)))))))).(((......)))..)))))....)))..(((....)))...... ( -27.70, z-score =  -1.28, R)
>droSim1.chr3L 21703779 100 + 22553184
UGACUCCUAUUCCCAGCCUGAUUCAUAUACCCAGCCUUGGCACACAUCAAAUGAAUUGUGUGCCGUGCAAUAAGGCAGAAAGGCAG---------CCCUCAGCACAAUG
.................................(((((((((((((((....))..)))))))).(((......)))..))))).(---------(.....))...... ( -24.10, z-score =  -0.73, R)
>droSec1.super_11 2329130 100 + 2888827
UGACUCCUAUUCCCAGCCUGGUUCAUAUACCCAGCCUUGGCACACAUCAAAUGAAUUGUGUGCCGUGCAAUAAGGCAGAAAGGCAG---------CCCUCAGCACAAUG
((((((((.(((...(((((((......)))..((..(((((((((((....))..))))))))).))....)))).)))))).))---------...)))........ ( -28.10, z-score =  -1.38, R)
>consensus
UGACUCCUAUUCCCAGCCUGAUUCAUAUACCCAGCCUUGGCACACAUCAAAUGAAUUGUGUGCCGUGCAAUAAGGCAGAAAGGCAG_________CCCUCAGCACAAUG
.................................(((((((((((((((....))..)))))))).(((......)))..)))))......................... (-23.03 = -23.03 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,392,618 – 22,392,715
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 84.83
Shannon entropy 0.25849
G+C content 0.45218
Mean single sequence MFE -26.32
Consensus MFE -17.41
Energy contribution -18.74
Covariance contribution 1.33
Combinations/Pair 1.04
Mean z-score -2.03
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.38
SVM RNA-class probability 0.669871
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22392618 97 + 24543557
UGGCACACAUCAAAUGAGUUGUGUGCCCUGCAAUAAGGCAAUAAGGCAGAAUGGCAGCCGCUCGGCACAAUGAGGAUUUUCACUUUUCUAGCUCACA
.((((((((.(......).)))))))).(((......)))....(((((((.((..(((....)))....((((....)))))).)))).))).... ( -25.80, z-score =  -0.02, R)
>droSim1.chr3L 21703816 88 + 22553184
UGGCACACAUCAAAUGAAUUGUGUGCCGUGCAAUAAGGCAGAAAGGCAGCC---------CUCAGCACAAUGAGGAUUUUCACUUUUCUAGCUCACA
.((((((((((....))..))))))))(((......((((((((((....(---------((((......))))).......))))))).)))))). ( -29.60, z-score =  -2.91, R)
>droSec1.super_11 2329167 88 + 2888827
UGGCACACAUCAAAUGAAUUGUGUGCCGUGCAAUAAGGCAGAAAGGCAGCC---------CUCAGCACAAUGAGGAUUUUCACUUUUCUAGCUCACA
.((((((((((....))..))))))))(((......((((((((((....(---------((((......))))).......))))))).)))))). ( -29.60, z-score =  -2.91, R)
>droYak2.chr3L 22821559 86 + 24197627
UGGCACACAUCAAAUGAAUUGUGUGCCGUACAAUAAGGAAGAAAG-CAGCC---------CUCAGCACAUUGAGGAUUU-CACUUUUCUAGCUCACA
.((((((((((....))..)))))))).........((((((..(-.(..(---------(((((....))))))..).-)..))))))........ ( -23.30, z-score =  -2.06, R)
>droEre2.scaffold_4784 22062827 76 + 25762168
UGGCACACAUCAAAUGAGUUGUGUGCCGUACAAUAAGGCAGAAAGGCAGA---------------------GAGGCUUUUCACUUUUCUAGCUCACA
.((((((((.(......).)))))))).........((((((((((..((---------------------((....)))).))))))).))).... ( -23.30, z-score =  -2.24, R)
>consensus
UGGCACACAUCAAAUGAAUUGUGUGCCGUGCAAUAAGGCAGAAAGGCAGCC_________CUCAGCACAAUGAGGAUUUUCACUUUUCUAGCUCACA
.((((((((((....))..)))))))).........((((((((((..............((((......))))(.....).))))))).))).... (-17.41 = -18.74 +   1.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,392,618 – 22,392,715
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 84.83
Shannon entropy 0.25849
G+C content 0.45218
Mean single sequence MFE -27.86
Consensus MFE -18.00
Energy contribution -18.44
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.40
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.875359
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22392618 97 - 24543557
UGUGAGCUAGAAAAGUGAAAAUCCUCAUUGUGCCGAGCGGCUGCCAUUCUGCCUUAUUGCCUUAUUGCAGGGCACACAACUCAUUUGAUGUGUGCCA
.(((((.(((((.(((((......)))))..(((....))).....))))).)))))(((......))).((((((((.(......).)))))))). ( -29.30, z-score =  -1.26, R)
>droSim1.chr3L 21703816 88 - 22553184
UGUGAGCUAGAAAAGUGAAAAUCCUCAUUGUGCUGAG---------GGCUGCCUUUCUGCCUUAUUGCACGGCACACAAUUCAUUUGAUGUGUGCCA
.............(((((......)))))((((..((---------(((.........)))))...))))((((((((..((....)))))))))). ( -29.50, z-score =  -2.51, R)
>droSec1.super_11 2329167 88 - 2888827
UGUGAGCUAGAAAAGUGAAAAUCCUCAUUGUGCUGAG---------GGCUGCCUUUCUGCCUUAUUGCACGGCACACAAUUCAUUUGAUGUGUGCCA
.............(((((......)))))((((..((---------(((.........)))))...))))((((((((..((....)))))))))). ( -29.50, z-score =  -2.51, R)
>droYak2.chr3L 22821559 86 - 24197627
UGUGAGCUAGAAAAGUG-AAAUCCUCAAUGUGCUGAG---------GGCUG-CUUUCUUCCUUAUUGUACGGCACACAAUUCAUUUGAUGUGUGCCA
.(((((..(((((.(((-...((((((......))))---------)).))-))))))..))))).....((((((((..((....)))))))))). ( -28.00, z-score =  -2.81, R)
>droEre2.scaffold_4784 22062827 76 - 25762168
UGUGAGCUAGAAAAGUGAAAAGCCUC---------------------UCUGCCUUUCUGCCUUAUUGUACGGCACACAACUCAUUUGAUGUGUGCCA
.(((((.((((((.((((........---------------------)).)).)))))).))))).....((((((((.(......).)))))))). ( -23.00, z-score =  -2.89, R)
>consensus
UGUGAGCUAGAAAAGUGAAAAUCCUCAUUGUGCUGAG_________GGCUGCCUUUCUGCCUUAUUGCACGGCACACAAUUCAUUUGAUGUGUGCCA
.(((((.((((((.((..................................)).)))))).))))).....((((((((..((....)))))))))). (-18.00 = -18.44 +   0.44)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:44:40 2011