Locus 4590

Sequence ID 3L_DroMel_CAF1
Location 13,132,749 – 13,132,869
Length 120
Max. P 0.955429
window7192 window7193

overview

Window 2

Location 13,132,749 – 13,132,869
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.42
Mean single sequence MFE -21.78
Consensus MFE -18.39
Energy contribution -18.54
Covariance contribution 0.15
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.84
SVM decision value 1.45
SVM RNA-class probability 0.955429
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13132749 120 + 23771897
AGACUCUAGUCCACCGGCCACCCGAACAACCAAAUCACAAAGAGCCCAAUUGAAAUGGGCCGCACACGGAUCCCAAUUCCAUUCCAUUCUCACAUGUCACCAUGUGCCUCAACAGCUUUC
.(((....)))...(((....)))................(((((......(((.(((((((....)))..)))).)))...........((((((....))))))........))))). ( -22.60)
>DroSec_CAF1 120581 120 + 1
AGGCUCUAGUCCACCGGCCACCCGAACAACCAAAUCACAAAGAGCCCAAUUGAAAUGGGCCGCACACGGAUCCCAAUUCCAUUCCAUUCUCACAUGUCACCAUGUGCCUCAACAGCUUUC
.((((((.(....)(((....)))................)))))).....(((.(((((((....)))..)))).)))...........((((((....)))))).............. ( -24.70)
>DroSim_CAF1 118817 120 + 1
AGACUCUACUCCGCCGGCCACCCGAACAACCAAAUCACAAAGAGCCCAAUUGAAAUGGGCCGCACACGGAUCCCAAUUCCAUUCCAUUCUCACAUGUCACCAUGUGCCUCAACAGCUUUC
............(((((....))).................(((.......(((.(((((((....)))..)))).)))...........((((((....)))))).)))....)).... ( -21.00)
>DroEre_CAF1 117616 96 + 1
------------------------AACUACCAAAUCACAAAGAGCCCAAUUGAAAUGGGCCGCACACGGAUCCCAAUGCCAUUCCAUUCUCACAUGUCACCAUGUGCCUCAACAGCUUUC
------------------------................(((((....((((..(((((((....)))..))))...............((((((....))))))..))))..))))). ( -18.00)
>DroYak_CAF1 121595 120 + 1
AGACUCUAGUCCACCGGCCACCCGAACUACCAAAUCACAAAGAGCCCAAUUGAAAUGGGCCGCACACGGAUCCCAAUUCCAUUCCAUUCUCACAUGUCACCAUGUGCCUCAACAGCUUUC
.(((....)))...(((....)))................(((((......(((.(((((((....)))..)))).)))...........((((((....))))))........))))). ( -22.60)
>consensus
AGACUCUAGUCCACCGGCCACCCGAACAACCAAAUCACAAAGAGCCCAAUUGAAAUGGGCCGCACACGGAUCCCAAUUCCAUUCCAUUCUCACAUGUCACCAUGUGCCUCAACAGCUUUC
..............(((....)))................(((((....((((..(((((((....)))..))))...............((((((....))))))..))))..))))). (-18.39 = -18.54 +   0.15)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,132,749 – 13,132,869
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.42
Mean single sequence MFE -37.54
Consensus MFE -29.20
Energy contribution -31.88
Covariance contribution 2.68
Combinations/Pair 1.03
Mean z-score -1.64
Structure conservation index 0.78
SVM decision value 0.36
SVM RNA-class probability 0.703157
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13132749 120 - 23771897
GAAAGCUGUUGAGGCACAUGGUGACAUGUGAGAAUGGAAUGGAAUUGGGAUCCGUGUGCGGCCCAUUUCAAUUGGGCUCUUUGUGAUUUGGUUGUUCGGGUGGCCGGUGGACUAGAGUCU
.....(((((....((((((....))))))..)))))....(((.((((..(((....))))))).)))....(((((((..((...(((((..(....)..)))))...)).))))))) ( -39.30)
>DroSec_CAF1 120581 120 - 1
GAAAGCUGUUGAGGCACAUGGUGACAUGUGAGAAUGGAAUGGAAUUGGGAUCCGUGUGCGGCCCAUUUCAAUUGGGCUCUUUGUGAUUUGGUUGUUCGGGUGGCCGGUGGACUAGAGCCU
.....(((((....((((((....))))))..)))))....(((.((((..(((....))))))).)))....(((((((..((...(((((..(....)..)))))...)).))))))) ( -42.00)
>DroSim_CAF1 118817 120 - 1
GAAAGCUGUUGAGGCACAUGGUGACAUGUGAGAAUGGAAUGGAAUUGGGAUCCGUGUGCGGCCCAUUUCAAUUGGGCUCUUUGUGAUUUGGUUGUUCGGGUGGCCGGCGGAGUAGAGUCU
.....(((((....((((((....))))))..)))))....(((.((((..(((....))))))).)))....(((((((((.((...((((..(....)..)))).)).)).))))))) ( -38.90)
>DroEre_CAF1 117616 96 - 1
GAAAGCUGUUGAGGCACAUGGUGACAUGUGAGAAUGGAAUGGCAUUGGGAUCCGUGUGCGGCCCAUUUCAAUUGGGCUCUUUGUGAUUUGGUAGUU------------------------
...(((((..(((((((((((...(((((.(........).))).))....))))))))((((((.......))))))........)))..)))))------------------------ ( -31.00)
>DroYak_CAF1 121595 120 - 1
GAAAGCUGUUGAGGCACAUGGUGACAUGUGAGAAUGGAAUGGAAUUGGGAUCCGUGUGCGGCCCAUUUCAAUUGGGCUCUUUGUGAUUUGGUAGUUCGGGUGGCCGGUGGACUAGAGUCU
.....(((((....((((((....))))))..)))))....(((.((((..(((....))))))).)))....(((((((.........(((...((((....))))...)))))))))) ( -36.50)
>consensus
GAAAGCUGUUGAGGCACAUGGUGACAUGUGAGAAUGGAAUGGAAUUGGGAUCCGUGUGCGGCCCAUUUCAAUUGGGCUCUUUGUGAUUUGGUUGUUCGGGUGGCCGGUGGACUAGAGUCU
.....(((((....((((((....))))))..)))))..((((((.(((..(((....))))))))))))...(((((((.......(((((..(....)..)))))......))))))) (-29.20 = -31.88 +   2.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:44 2006