Locus 8048

Sequence ID 3L_DroMel_CAF1
Location 21,221,897 – 21,222,137
Length 240
Max. P 0.723327
window13150 window13151

overview

Window 0

Location 21,221,897 – 21,222,017
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.97
Mean single sequence MFE -46.95
Consensus MFE -40.12
Energy contribution -40.38
Covariance contribution 0.25
Combinations/Pair 1.12
Mean z-score -1.59
Structure conservation index 0.85
SVM decision value 0.41
SVM RNA-class probability 0.723327
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21221897 120 + 23771897
GCAACUUCGGCCGGAGCCACUGCCCUAAAUUCGGCAGCUACGGCUUUACUAAGCGAUGAGCCCGGAGAGGCAACUGGUAAGGCCGGUGACGAGAGCGGCGAGCAAAACGCAGAGGCCGAC
......((((((...(((..((((........))))(((..(((((((((..((.....))......((....)))))))))))(....)...))))))..((.....))...)))))). ( -45.90)
>DroSim_CAF1 88938 120 + 1
GGAACAUCGGCCGGAGCCACUGCCCUCAAUUCGGCAGCUACGGCUUUACUGAGCGAUGAGCCCGGAGAGGCAUCUGGUAAGGCCGGUGACGAAAGCGGCGAGCAAAACGCAGAGGCCGAC
....((((((((...((((.(((((((...((((.(((....)))...))))((.....))...))).))))..))))..)))))))).(....)((((..((.....))....)))).. ( -46.90)
>DroEre_CAF1 41321 120 + 1
GGAACUUCGGCCGGAGCCGCUGCCCUUAAUUCGGCAGCUACGGCUUUACUAAGCGAUGAGCCCGGAGAGGCAUCGGGUAAAGCCGGAGACGAGAGUGGCGAGCAAAAUGCAGAGGCUGAC
......((((((...(((((((((........))))))..((((((((((...((((..(((......)))))))))))))))))...((....)))))..((.....))...)))))). ( -51.00)
>DroYak_CAF1 146476 120 + 1
GGAACUACGGCCGGAGCCACUGCCCUUAAUUCGGCAGCUACGGCUUUACUAAGCGAUGAACCCGGGGACGCAUCUGGUAAAACCGUAGACGAGAGCGGUGAGCAAAAUGCAGAGGCCGAC
.......(((((...(((.(((((........)))))((((((.(((((((...((((....((....))))))))))))).))))))........)))..((.....))...))))).. ( -44.00)
>consensus
GGAACUUCGGCCGGAGCCACUGCCCUUAAUUCGGCAGCUACGGCUUUACUAAGCGAUGAGCCCGGAGAGGCAUCUGGUAAAGCCGGAGACGAGAGCGGCGAGCAAAACGCAGAGGCCGAC
......((((((...(((.(((((........)))))...(((((((((((...((((..(.....)...)))))))))))))))...........)))..((.....))...)))))). (-40.12 = -40.38 +   0.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,222,017 – 21,222,137
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.47
Mean single sequence MFE -36.10
Consensus MFE -29.15
Energy contribution -30.77
Covariance contribution 1.63
Combinations/Pair 1.09
Mean z-score -1.61
Structure conservation index 0.81
SVM decision value -0.03
SVM RNA-class probability 0.516215
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21222017 120 - 23771897
GGUUAUGCCUCCACUGCCCUCCUGCGAGGUAAUAACCAUCUCGCCGCCUUUGCUUCCCGGUUUGGGCGCCUCACCGCUCUCGUUCUUGUCGGAGUGGAGCUUUUCAAACAGGCUCUCAAU
(((((((((((((.........)).))))).)))))).....(((((((..(((....)))..))))......((((((.((.......)))))))).............)))....... ( -38.50)
>DroSim_CAF1 89058 120 - 1
GGUUAUGCCUCCACUGCCCUCCUGCGAGGUAAUAACCAUCUCGCCGCCUUUGCUUCCAGCUUUGGGCGCCUCACCGCUCUCGUUCUUGUCGGAGUGGAGCUUUUCAAACAGGCUCUCAAU
(((((((((((((.........)).))))).)))))).....(((((((..((.....))...))))......((((((.((.......)))))))).............)))....... ( -38.40)
>DroEre_CAF1 41441 120 - 1
GGUUAUGCCGCCACUGCCCUCCUGCGAGGUAAUAACCAUUUCGCCGCCUUUGCUUCCAGGCUUGGUCGCCUCUCCGCUCUCGUUCUUGUCGGAGUGGAGCUUUUCAAACAAACUCUCGAU
((((((...(((..(((......))).))).))))))...((((.(((...(((....)))..))).))..((((((((.((.......))))))))))..................)). ( -33.60)
>DroYak_CAF1 146596 120 - 1
GGUUAUGCCUCCACUGCCCUCCUGCGAUGUAAUAACCAUCUCGCCGCCCUUGCUUCCCGACUUGGGCGCCUCUCCGCUCUCGUUCUUGUCAGAGUGGAGCUUUUCAAAAAGGCUCUCAAU
((((((.....((.(((......))).))..)))))).....(((((((..(........)..))))....(((((((((.(.......))))))))))...........)))....... ( -33.90)
>consensus
GGUUAUGCCUCCACUGCCCUCCUGCGAGGUAAUAACCAUCUCGCCGCCUUUGCUUCCAGGCUUGGGCGCCUCACCGCUCUCGUUCUUGUCGGAGUGGAGCUUUUCAAACAGGCUCUCAAU
(((((((((((((.........)).))))).)))))).....(((((((..(((....)))..))))....(((((((((..(....)..)))))))))...........)))....... (-29.15 = -30.77 +   1.63)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:50 2006