Locus 1692

Sequence ID 3L_DroMel_CAF1
Location 4,949,317 – 4,949,425
Length 108
Max. P 0.984483
window2609 window2610

overview

Window 9

Location 4,949,317 – 4,949,425
Length 108
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 79.04
Mean single sequence MFE -22.34
Consensus MFE -17.78
Energy contribution -18.22
Covariance contribution 0.44
Combinations/Pair 1.06
Mean z-score -1.59
Structure conservation index 0.80
SVM decision value 0.68
SVM RNA-class probability 0.820587
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4949317 108 + 23771897
ACCGCCCACCAACCCGCCAACAUUUUCUCGCUCAAGCU-UUUUGCAUAUUUUUCCGCUGCUUUCUGCUGCAACCGUCCGAAAGUUGUUGUUGCGGACUGCUGAUCCUCU
......((.((..((((((((((((((..((....((.-....))..........((.((.....)).))....))..))))).)))))..))))..)).))....... ( -22.60)
>DroPse_CAF1 218947 84 + 1
GUCUCC--------------------GUUUAUCAUUC--UUUUGCAUAUUUUUCCGCUGCUUUCCGCUGCAGUCGUCCGAAAGAUG---UUUCGGACUGCUGAUCCUAU
......--------------------...........--....(((.........(((((........))))).((((((((....---)))))))))))......... ( -19.30)
>DroSec_CAF1 170308 88 + 1
ACCGCC--------------------CUCGCUCAAGCU-UUUUGCAUAUUUUUCCGCUGCUUUCUGCUGCAGCCGUCCGAAAGUUGUUGUUUCGGACUGCUGAUCCUCU
......--------------------...((....)).-....(((.........(((((........))))).((((((((.......)))))))))))......... ( -22.10)
>DroSim_CAF1 180350 88 + 1
ACCGCC--------------------CUCGCUCAAGCU-UUUUGCAUAUUUUUCCGCUGCUUUCUGCUGCAGCCGUCCGAAAGUUGUUGUUUCGGACUGCUGAUCCUCU
......--------------------...((....)).-....(((.........(((((........))))).((((((((.......)))))))))))......... ( -22.10)
>DroYak_CAF1 176147 108 + 1
UCAGCCCGCCAA-ACGCCCACGUUUUCUCGCUCAAGCCUUUUUGCAUAUUUUUCCGCUGCUUUCUGCUGCAGCCGUCCGAAAGUUGUUGUUGCGGACUGCUGAUCCUCU
(((((((((.((-(((....)))))..(((..(..((......))..........(((((........))))).)..)))...........))))...)))))...... ( -25.60)
>consensus
ACCGCC____________________CUCGCUCAAGCU_UUUUGCAUAUUUUUCCGCUGCUUUCUGCUGCAGCCGUCCGAAAGUUGUUGUUUCGGACUGCUGAUCCUCU
...........................................(((.........(((((........))))).((((((((.......)))))))))))......... (-17.78 = -18.22 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,949,317 – 4,949,425
Length 108
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 79.04
Mean single sequence MFE -27.88
Consensus MFE -19.34
Energy contribution -19.66
Covariance contribution 0.32
Combinations/Pair 1.11
Mean z-score -2.41
Structure conservation index 0.69
SVM decision value 1.98
SVM RNA-class probability 0.984483
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4949317 108 - 23771897
AGAGGAUCAGCAGUCCGCAACAACAACUUUCGGACGGUUGCAGCAGAAAGCAGCGGAAAAAUAUGCAAAA-AGCUUGAGCGAGAAAAUGUUGGCGGGUUGGUGGGCGGU
....(..((.((..((((..(((((..(((((..(.(((((........))))).)........((....-.)).....)))))...)))))))))..)).))..)... ( -31.40)
>DroPse_CAF1 218947 84 - 1
AUAGGAUCAGCAGUCCGAAA---CAUCUUUCGGACGACUGCAGCGGAAAGCAGCGGAAAAAUAUGCAAAA--GAAUGAUAAAC--------------------GGAGAC
.........(((((((((((---....))))))))..((((.((.....)).)))).......)))....--...........--------------------(....) ( -21.90)
>DroSec_CAF1 170308 88 - 1
AGAGGAUCAGCAGUCCGAAACAACAACUUUCGGACGGCUGCAGCAGAAAGCAGCGGAAAAAUAUGCAAAA-AGCUUGAGCGAG--------------------GGCGGU
.....(((.(((((((((((.......)))))))).(((((........))))).........)))....-.((((......)--------------------)))))) ( -26.20)
>DroSim_CAF1 180350 88 - 1
AGAGGAUCAGCAGUCCGAAACAACAACUUUCGGACGGCUGCAGCAGAAAGCAGCGGAAAAAUAUGCAAAA-AGCUUGAGCGAG--------------------GGCGGU
.....(((.(((((((((((.......)))))))).(((((........))))).........)))....-.((((......)--------------------)))))) ( -26.20)
>DroYak_CAF1 176147 108 - 1
AGAGGAUCAGCAGUCCGCAACAACAACUUUCGGACGGCUGCAGCAGAAAGCAGCGGAAAAAUAUGCAAAAAGGCUUGAGCGAGAAAACGUGGGCGU-UUGGCGGGCUGA
..........((((((((.........(((((..(.(((((........))))).)........((......)).....)))))(((((....)))-)).)))))))). ( -33.70)
>consensus
AGAGGAUCAGCAGUCCGAAACAACAACUUUCGGACGGCUGCAGCAGAAAGCAGCGGAAAAAUAUGCAAAA_AGCUUGAGCGAG____________________GGCGGU
.........(((((((((((.......)))))))).(((((........))))).........)))......((....))............................. (-19.34 = -19.66 +   0.32)

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 10:13:47 2006