Locus 2878

Sequence ID 2R_DroMel_CAF1
Location 9,952,707 – 9,952,867
Length 160
Max. P 0.967609
window4755 window4756

overview

Window 5

Location 9,952,707 – 9,952,805
Length 98
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 81.55
Mean single sequence MFE -28.72
Consensus MFE -20.88
Energy contribution -20.92
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.68
Structure conservation index 0.73
SVM decision value 0.32
SVM RNA-class probability 0.686281
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9952707 98 - 20766785
UAUAAAUCGGG-GAAUAUACCUAGAGAUAUGU------------AGUGGUAAACUGGCUGGCAACGCCGUCAACAAAUGAAAACUCCCCAGGGAGUUGGCGCAUGUUUGUU
........(((-.......)))..((((((((------------....((..((.(((.(....))))))..))....(..((((((....))))))..)))))))))... ( -26.10)
>DroSec_CAF1 9941 98 - 1
UAUAAAUCGGG-GGAUAUUCCUAGAGAUAUGU------------ACUGGCAAACUGGCUGGCAACGCCGUCAACAAAUGAAAACUCCCCAGGGAGUUGGCGCAUGUUUGUU
((((.(((..(-((.....)))...))).)))------------)..(((((((..((.(....)(((.(((.....))).((((((....)))))))))))..))))))) ( -29.60)
>DroSim_CAF1 10670 98 - 1
UAUAAAUCGGG-GGAUAUACCUAGAGAUAUGU------------ACUGGCAAACUGGCUGGCAACGCCGUCAACAAAUGAAAACUCCCCAGGGAGUUGGCGCAUGUUUGUU
((((.(((.((-(......)))...))).)))------------)..(((((((..((.(....)(((.(((.....))).((((((....)))))))))))..))))))) ( -29.70)
>DroEre_CAF1 10072 110 - 1
CAUAAAUCGGG-GGAUAUACCUAGAGAUGUGUACAUACAUACAUACAGGCAAACUGGCUGGCAACGCCGUCAACAAAUGAAAACUCCCCAGGGAGUUGGCGCAUGUUUGUU
((((..((.((-(......))).))..)))).....(((.((((.(((.....)))((.(....)(((.(((.....))).((((((....))))))))))))))).))). ( -31.20)
>DroAna_CAF1 8812 101 - 1
CAGAGCUUGUGCAGACAAACAA----------AAAUACAUAUAUACAUGCAAACUGGCUGGCAACGCCGUCAACAAAUGAAAAAUCCCCAGGGAGUUGGCGCAUGUUUGUU
....((....))..........----------........(((.((((((.....(((.(....))))((((((...(....).(((....))))))))))))))).))). ( -27.00)
>consensus
UAUAAAUCGGG_GGAUAUACCUAGAGAUAUGU____________ACUGGCAAACUGGCUGGCAACGCCGUCAACAAAUGAAAACUCCCCAGGGAGUUGGCGCAUGUUUGUU
................................................((((((..((.(....)(((.(((.....))).((((((....)))))))))))..)))))). (-20.88 = -20.92 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,952,774 – 9,952,867
Length 93
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 85.08
Mean single sequence MFE -29.90
Consensus MFE -20.49
Energy contribution -23.27
Covariance contribution 2.78
Combinations/Pair 1.03
Mean z-score -3.77
Structure conservation index 0.69
SVM decision value 1.61
SVM RNA-class probability 0.967609
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9952774 93 - 20766785
GCUGAGCUUGUGAGCCACCUACAUAUAUGUAUGUUCGGCAUAUACAUACAUACAUAUGUAU--------AUAUAAAUCGGGGAAUAUACCUAGAGAUAUGU
(((((((..(((...))).((((....)))).)))))))(((((((((......)))))))--------))....(((.(((......)))...))).... ( -21.20)
>DroSec_CAF1 10008 93 - 1
GCUGAGCUUGGGAGCCACCUA--------UAUGUUUGGCAUAUACAUGCAUACAUAUGUAUGUAUGUACAUAUAAAUCGGGGGAUAUUCCUAGAGAUAUGU
((..(((.((((.....))))--------...)))..))...(((((((((((....)))))))))))(((((...((..(((.....))).)).))))). ( -32.90)
>DroSim_CAF1 10737 93 - 1
GCUGAGCUUGGGAGCCACCUA--------UAUGUUCGGCAUACACAUGCAUACAUAUGUAUGUAUGUACAUAUAAAUCGGGGGAUAUACCUAGAGAUAUGU
(((((((.((((.....))))--------...)))))))....((((((((((....))))))))))((((((...((.(((......))).)).)))))) ( -35.60)
>consensus
GCUGAGCUUGGGAGCCACCUA________UAUGUUCGGCAUAUACAUGCAUACAUAUGUAUGUAUGUACAUAUAAAUCGGGGGAUAUACCUAGAGAUAUGU
(((((((.((((.....))))...........)))))))....((((((((((....))))))))))((((((...((.(((......))).)).)))))) (-20.49 = -23.27 +   2.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:47 2006