Locus 5652

Sequence ID 3L_DroMel_CAF1
Location 15,509,222 – 15,509,312
Length 90
Max. P 0.777006
window8939 window8940

overview

Window 9

Location 15,509,222 – 15,509,312
Length 90
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 82.43
Mean single sequence MFE -27.87
Consensus MFE -16.40
Energy contribution -18.56
Covariance contribution 2.17
Combinations/Pair 1.00
Mean z-score -2.80
Structure conservation index 0.59
SVM decision value 0.55
SVM RNA-class probability 0.777006
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15509222 90 + 23771897
UUAGCCGCAUUCAAGCGGUUUUUGUGGCCCAAGAGCCACUCCAGCUCCAUCUUCAGCGCC------------AACUUGAGCUCCAAACUCGAGCAUCGCACC
..((((((......))))))...(((((......)))))................(((..------------..((((((.......))))))...)))... ( -25.40)
>DroSec_CAF1 11984 89 + 1
UUAGCCGCAUUCAAGCGGUUUUUGUGGCCCAAGAGCCACUCCAGCUCCAUCUUCAGCUCC------------AACUUGAGCUCCAA-GUCGAGCAUCGCACC
..((((((......))))))...(((((......)))))....((((...(((.(((((.------------.....)))))..))-)..))))........ ( -28.50)
>DroSim_CAF1 7563 89 + 1
UUAGCCGCAUUCAAGCGGUUUUUGUGGCCCAAGAGCCACUCCAGCUCCAUCUUCAGCUCC------------AACUUGAGCUCCAA-GUCGAGCAUCGCACC
..((((((......))))))...(((((......)))))....((((...(((.(((((.------------.....)))))..))-)..))))........ ( -28.50)
>DroEre_CAF1 20215 89 + 1
UUAGCCGCAUUCAAGCGGUUUUUGUGGCCCAAGAGCCACUCCAGCUCCAUCUUCAGCUCC------------AACUCGAGCUCCGA-GUCGAGCAUCGCACC
..((((((......))))))...(((((......)))))....((((...(((.(((((.------------.....)))))..))-)..))))........ ( -29.00)
>DroYak_CAF1 20267 101 + 1
UUAGCCGCAUUCAAGCGGUUUUUGUGGCCCAAGAGCCACUCCAGCUCCAUCUUCAGCUCCAACUUGAGCUCCAACUCGAGCUCCAA-GUCGAGCAUCGCACC
..((((((......))))))...(((((......)))))................((((..((((((((((......))))).)))-)).))))........ ( -34.10)
>DroAna_CAF1 21029 68 + 1
UUAGCCGC--UCAAGCGGUUUUUGCGGCUUAAGAGGCA-----------ACUUCAGC----------------ACUCGAAGCC-----UGAAGCACCGCACC
........--....((((((((((.(((((..(((((.-----------......))----------------.))).)))))-----))))).)))))... ( -21.70)
>consensus
UUAGCCGCAUUCAAGCGGUUUUUGUGGCCCAAGAGCCACUCCAGCUCCAUCUUCAGCUCC____________AACUCGAGCUCCAA_GUCGAGCAUCGCACC
..((((((......))))))...(((((......)))))....((((.......(((((..................)))))........))))........ (-16.40 = -18.56 +   2.17)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,509,222 – 15,509,312
Length 90
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 82.43
Mean single sequence MFE -31.80
Consensus MFE -22.37
Energy contribution -22.63
Covariance contribution 0.27
Combinations/Pair 1.25
Mean z-score -1.74
Structure conservation index 0.70
SVM decision value 0.24
SVM RNA-class probability 0.647078
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15509222 90 - 23771897
GGUGCGAUGCUCGAGUUUGGAGCUCAAGUU------------GGCGCUGAAGAUGGAGCUGGAGUGGCUCUUGGGCCACAAAAACCGCUUGAAUGCGGCUAA
(((((.(.(((.((((.....)))).))))------------.))))).....(((.......((((((....)))))).....((((......))))))). ( -31.00)
>DroSec_CAF1 11984 89 - 1
GGUGCGAUGCUCGAC-UUGGAGCUCAAGUU------------GGAGCUGAAGAUGGAGCUGGAGUGGCUCUUGGGCCACAAAAACCGCUUGAAUGCGGCUAA
(.((((..((((...-...))))((((((.------------((((((........))))...((((((....)))))).....)))))))).)))).)... ( -32.40)
>DroSim_CAF1 7563 89 - 1
GGUGCGAUGCUCGAC-UUGGAGCUCAAGUU------------GGAGCUGAAGAUGGAGCUGGAGUGGCUCUUGGGCCACAAAAACCGCUUGAAUGCGGCUAA
(.((((..((((...-...))))((((((.------------((((((........))))...((((((....)))))).....)))))))).)))).)... ( -32.40)
>DroEre_CAF1 20215 89 - 1
GGUGCGAUGCUCGAC-UCGGAGCUCGAGUU------------GGAGCUGAAGAUGGAGCUGGAGUGGCUCUUGGGCCACAAAAACCGCUUGAAUGCGGCUAA
(((.(((.(((((((-(((.....))))))------------.))))........(((((.....)))))))).))).......((((......)))).... ( -32.40)
>DroYak_CAF1 20267 101 - 1
GGUGCGAUGCUCGAC-UUGGAGCUCGAGUUGGAGCUCAAGUUGGAGCUGAAGAUGGAGCUGGAGUGGCUCUUGGGCCACAAAAACCGCUUGAAUGCGGCUAA
(((.(((.(((((((-(((.(((((......))))))))))).))))........(((((.....)))))))).))).......((((......)))).... ( -39.80)
>DroAna_CAF1 21029 68 - 1
GGUGCGGUGCUUCA-----GGCUUCGAGU----------------GCUGAAGU-----------UGCCUCUUAAGCCGCAAAAACCGCUUGA--GCGGCUAA
..((((((((((((-----(((.....))----------------.)))))))-----------..........))))))....((((....--)))).... ( -22.80)
>consensus
GGUGCGAUGCUCGAC_UUGGAGCUCAAGUU____________GGAGCUGAAGAUGGAGCUGGAGUGGCUCUUGGGCCACAAAAACCGCUUGAAUGCGGCUAA
(.(((...((((.......))))((((((...............((((........))))...((((((....)))))).......))))))..))).)... (-22.37 = -22.63 +   0.27)

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 11:55:45 2006