Locus 9960

Sequence ID dm3.chr3R
Location 10,163,838 – 10,163,937
Length 99
Max. P 0.995569
window13686 window13687

overview

Window 6

Location 10,163,838 – 10,163,937
Length 99
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 55.28
Shannon entropy 0.70082
G+C content 0.54827
Mean single sequence MFE -28.98
Consensus MFE -15.43
Energy contribution -15.30
Covariance contribution -0.13
Combinations/Pair 1.44
Mean z-score -1.67
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.82
SVM RNA-class probability 0.995569
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10163838 99 + 27905053
GAGUGCUCCCUGGAUGAGGCACACAACGUGGAGCGAGCUGCACCGCUGU-GGCGGUGCCAAUGGCAGCCACCUCAAUUCAACUCAUCU-CAUCCACAUCAU---
(((((......(((((((.........((((.((.(...(((((((...-.)))))))...).))..))))..........)))))))-....))).))..--- ( -33.41, z-score =  -0.68, R)
>droYak2.chr3R 12549190 103 - 28832112
GAGUGCUCCCUGGAUGAGGCACACAACGCGAAGAGAGAUGCACCACUGU-GGUGGUGCCAAUGGCAGCCACCUCAACUCAUCUCAUCCACAUCCACAUACACAU
..(((.....((((((..((.......)).....((((((......((.-(((((((((...)))).))))).))...)))))).....))))))....))).. ( -33.50, z-score =  -1.58, R)
>droEre2.scaffold_4770 9697027 77 + 17746568
------------GAUGAGGCAUGCAACGUGGAGAGA--UGCACCACCAUUGGUGGUGCCAAUGGCAGCCACCUCAACUCAACUCAUCU-CAU------------
------------((((((.((((...))))..(((.--.((((((((...))))))))....((......))....)))..)))))).-...------------ ( -26.50, z-score =  -1.53, R)
>droMoj3.scaffold_6540 15928299 85 - 34148556
-------------GUGGGCGCAGCAGCCCACGAACCCGUUCGUAGCAGC--UCUCCACGAUUGAGAGCCACCACCUUUCCCCUUAUCC-AAUGUUUAUAAU---
-------------((((((......))))))(((....)))((.(..((--((((.......))))))..).))..............-............--- ( -22.50, z-score =  -2.89, R)
>consensus
____________GAUGAGGCACACAACGCGGAGAGAG_UGCACCACUGU_GGCGGUGCCAAUGGCAGCCACCUCAACUCAACUCAUCC_CAUCCACAUAAU___
...........(((((((.....................(((((((.....)))))))...((.....))...........)))))))................ (-15.43 = -15.30 +  -0.13)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 10,163,838 – 10,163,937
Length 99
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 55.28
Shannon entropy 0.70082
G+C content 0.54827
Mean single sequence MFE -36.33
Consensus MFE -15.20
Energy contribution -15.83
Covariance contribution 0.63
Combinations/Pair 1.36
Mean z-score -2.04
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.55
SVM RNA-class probability 0.992633
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10163838 99 - 27905053
---AUGAUGUGGAUG-AGAUGAGUUGAAUUGAGGUGGCUGCCAUUGGCACCGCC-ACAGCGGUGCAGCUCGCUCCACGUUGUGUGCCUCAUCCAGGGAGCACUC
---(..(((((((..-.(.(((((((.((((..(((((((((...))))..)))-))..)))).)))))))))))))))..)(((((((.....))).)))).. ( -43.20, z-score =  -2.32, R)
>droYak2.chr3R 12549190 103 + 28832112
AUGUGUAUGUGGAUGUGGAUGAGAUGAGUUGAGGUGGCUGCCAUUGGCACCACC-ACAGUGGUGCAUCUCUCUUCGCGUUGUGUGCCUCAUCCAGGGAGCACUC
..((((.(.((((((.((..((((((.((((.(((((.((((...)))))))))-.))))....))))))....(((.....))))).)))))).)..)))).. ( -40.00, z-score =  -1.14, R)
>droEre2.scaffold_4770 9697027 77 - 17746568
------------AUG-AGAUGAGUUGAGUUGAGGUGGCUGCCAUUGGCACCACCAAUGGUGGUGCA--UCUCUCCACGUUGCAUGCCUCAUC------------
------------...-.((((((.((.((.((((((((..(((((((.....)))))))..)).))--))))...))....))...))))))------------ ( -30.50, z-score =  -1.99, R)
>droMoj3.scaffold_6540 15928299 85 + 34148556
---AUUAUAAACAUU-GGAUAAGGGGAAAGGUGGUGGCUCUCAAUCGUGGAGA--GCUGCUACGAACGGGUUCGUGGGCUGCUGCGCCCAC-------------
---............-.......(((...((..(((((((((.......))))--))).(((((((....)))))))))..))...)))..------------- ( -31.60, z-score =  -2.71, R)
>consensus
___AUUAUGUGGAUG_AGAUGAGUUGAAUUGAGGUGGCUGCCAUUGGCACCACC_ACAGCGGUGCA_CUCUCUCCACGUUGCGUGCCUCAUC____________
.................((((((.((...(((.((((.........(((((((.....)))))))........)))).)))..)).))))))............ (-15.20 = -15.83 +   0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:14:42 2011