Locus 12254

Sequence ID dm3.chr3R
Location 26,812,875 – 26,812,974
Length 99
Max. P 0.892657
window16853 window16854

overview

Window 3

Location 26,812,875 – 26,812,974
Length 99
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 83.70
Shannon entropy 0.31884
G+C content 0.55193
Mean single sequence MFE -31.84
Consensus MFE -21.32
Energy contribution -23.77
Covariance contribution 2.45
Combinations/Pair 1.10
Mean z-score -1.53
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.03
SVM RNA-class probability 0.507347
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26812875 99 + 27905053
CCUUGUGUGGCCAGUGGAACAGUGAACCAGGUGGACCAGCCAUUUCUCAUUGUUUGCCCGCAGCCGGUUUUCCUCGCUUUUCCUUUUUCCUGUGGCCAC
......(((((((((((((((((((...((((((.....)))))).))))))))...))))(((.((....))..)))..............))))))) ( -31.60, z-score =  -1.47, R)
>droAna3.scaffold_12911 1237325 78 - 5364042
UUUUCUGUGGCCGGGAGAGCAG--------GUGGACCAACCAUUUCUCAUUGUUUGCUCGCAGCAGGUGGCCCUCGCCUUUCUCAG-------------
....(((.(((.(((.(((.((--------((((.....))))))))).(..(((((.....)))))..))))..))).....)))------------- ( -23.70, z-score =   0.06, R)
>droEre2.scaffold_4820 9296796 99 - 10470090
CUUUGUGUGGCCAGUGGAACAGCGAGCCAGGUGGACCGGCCAUUUCUCAUUGUUUGCCCGCAGCCGGUUUUCCUCGCUUUUGCUUCUUCCUGUGGCCAC
......(((((((..((((.(((((((.(((..(((((((.......((.....))......)))))))..))).))))..)))..))))..))))))) ( -41.52, z-score =  -3.27, R)
>droYak2.chr3R 27748295 99 + 28832112
CUUUGUGUGGCCAGUGGAACAGUGAAGCAGGUGGACCAGCCAUUUCUCAUUGUUUGCCCGCAGCCGGUUUUCCUCGCUUUUCCUUUUUCCUGUGGCCAC
......(((((((..((((.((.((((((((..((((.((.......((.....))......)).))))..))).)))))..))..))))..))))))) ( -32.82, z-score =  -1.63, R)
>droSec1.super_4 5637852 99 + 6179234
CCUAGUGUGGCCAGUGGAACAGUGAACCAGGUGGACCAGCCAUUUCUCAUUGUUUGCCCACAGCCGGUUUUCCUCGCUUUUCCUUCUUCCUGUGGCCAC
......(((((((((((((((((((...((((((.....)))))).))))))))...))))(((.((....))..)))..............))))))) ( -32.00, z-score =  -1.62, R)
>droSim1.chr3R 26457362 99 + 27517382
CCUUGUGUGGCCAGUGGAACAGUGAACCAGGUAGACCAGCCAUUUCUCAUUGUUUGCCCGCAGCCGGUUUUCCUCGCUUUUCCUUCUUCCUGUGGCCAC
......(((((((((((((((((((....(((......))).....))))))))...))))(((.((....))..)))..............))))))) ( -29.40, z-score =  -1.28, R)
>consensus
CCUUGUGUGGCCAGUGGAACAGUGAACCAGGUGGACCAGCCAUUUCUCAUUGUUUGCCCGCAGCCGGUUUUCCUCGCUUUUCCUUCUUCCUGUGGCCAC
......(((((((((((((((((((...((((((.....)))))).))))))))...))))(((.((....))..)))..............))))))) (-21.32 = -23.77 +   2.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 26,812,875 – 26,812,974
Length 99
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 83.70
Shannon entropy 0.31884
G+C content 0.55193
Mean single sequence MFE -34.55
Consensus MFE -23.95
Energy contribution -26.62
Covariance contribution 2.67
Combinations/Pair 1.14
Mean z-score -2.02
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.11
SVM RNA-class probability 0.892657
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26812875 99 - 27905053
GUGGCCACAGGAAAAAGGAAAAGCGAGGAAAACCGGCUGCGGGCAAACAAUGAGAAAUGGCUGGUCCACCUGGUUCACUGUUCCACUGGCCACACAAGG
(((((((..((((...((...(((.(((...(((((((.....((.....))......)))))))...))).)))..)).))))..)))))))...... ( -35.00, z-score =  -1.83, R)
>droAna3.scaffold_12911 1237325 78 + 5364042
-------------CUGAGAAAGGCGAGGGCCACCUGCUGCGAGCAAACAAUGAGAAAUGGUUGGUCCAC--------CUGCUCUCCCGGCCACAGAAAA
-------------(((.(...((.((((((....(((.....)))..((((.(....).))))......--------..))))))))...).))).... ( -20.60, z-score =   0.46, R)
>droEre2.scaffold_4820 9296796 99 + 10470090
GUGGCCACAGGAAGAAGCAAAAGCGAGGAAAACCGGCUGCGGGCAAACAAUGAGAAAUGGCCGGUCCACCUGGCUCGCUGUUCCACUGGCCACACAAAG
(((((((..((((..(((...(((.(((...(((((((.....((.....))......)))))))...))).))).))).))))..)))))))...... ( -42.20, z-score =  -3.56, R)
>droYak2.chr3R 27748295 99 - 28832112
GUGGCCACAGGAAAAAGGAAAAGCGAGGAAAACCGGCUGCGGGCAAACAAUGAGAAAUGGCUGGUCCACCUGCUUCACUGUUCCACUGGCCACACAAAG
(((((((..((((...((..((((.(((...(((((((.....((.....))......)))))))...)))))))..)).))))..)))))))...... ( -36.90, z-score =  -2.84, R)
>droSec1.super_4 5637852 99 - 6179234
GUGGCCACAGGAAGAAGGAAAAGCGAGGAAAACCGGCUGUGGGCAAACAAUGAGAAAUGGCUGGUCCACCUGGUUCACUGUUCCACUGGCCACACUAGG
(((((((..((((..((....(((.(((...(((((((((...((.....))....)))))))))...))).)))..)).))))..)))))))...... ( -37.60, z-score =  -2.38, R)
>droSim1.chr3R 26457362 99 - 27517382
GUGGCCACAGGAAGAAGGAAAAGCGAGGAAAACCGGCUGCGGGCAAACAAUGAGAAAUGGCUGGUCUACCUGGUUCACUGUUCCACUGGCCACACAAGG
(((((((..((((..((....(((.(((...(((((((.....((.....))......)))))))...))).)))..)).))))..)))))))...... ( -35.00, z-score =  -1.99, R)
>consensus
GUGGCCACAGGAAGAAGGAAAAGCGAGGAAAACCGGCUGCGGGCAAACAAUGAGAAAUGGCUGGUCCACCUGGUUCACUGUUCCACUGGCCACACAAAG
(((((((..((((...((...(((.(((...(((((((.....((.....))......)))))))...))).)))..)).))))..)))))))...... (-23.95 = -26.62 +   2.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:58:44 2011