Locus 4098

Sequence ID 2R_DroMel_CAF1
Location 13,490,714 – 13,490,807
Length 93
Max. P 0.930277
window6602 window6603

overview

Window 2

Location 13,490,714 – 13,490,807
Length 93
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 89.45
Mean single sequence MFE -21.66
Consensus MFE -16.62
Energy contribution -16.50
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -1.54
Structure conservation index 0.77
SVM decision value 0.10
SVM RNA-class probability 0.581978
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13490714 93 + 20766785
GUCAGUUCUUAAUAUUGAGCUCGUUAGCACUACCAGGACCCGAAAA--UACACGUUUUCGUUGAUUAUUUUCGAGAUCCUUGAAGUGACAUAAAU
((((.(((..........(((....)))......((((.(((((((--((.(((....)))....)))))))).).)))).))).))))...... ( -22.30)
>DroSec_CAF1 39297 93 + 1
GUCAGUUCUUAAUAUUGAGCUCGUUAGCACUCCCAGGACUCAAAAA--UACGCAAAUUCGUUUAUGAUUUUCGAGAUCCUUGAAGUGGCUUAAAU
...(((((........)))))......((((.(.(((((((.((((--(.((.(((....))).))))))).))).)))).).))))........ ( -18.10)
>DroSim_CAF1 39524 93 + 1
GUCAGUUCUUAAUAUUGAGCUCGUUAGCACUCCCAGGACCCGAAAA--UACGCAUUUUCGUUUAUGAUUUUCGAGAUCCUUGAAGUGACAUAAAU
((((.(((..........(((....)))......((((.(((((((--((((......))).....))))))).).)))).))).))))...... ( -19.90)
>DroEre_CAF1 39649 93 + 1
GUCAGUUCUUAAUAUUGAGCUCGAUAGCACUGCCAGGACCCGAAAA--UACACGUUUUCGUUACAUAUUUUCGAGGUCCUUGAAGUGACAUGAAU
((((((((........))))).))).(((((.(.((((((((((((--((.(((....)))....)))))))).)))))).).)))).)...... ( -30.50)
>DroYak_CAF1 41201 95 + 1
GUCAGUUCUUAAUAUUGAGCUCGUUAGUACUGCCAGGACCCGAAAACUUACUCCUUUUUGUUUAUUAUUUUCGAGAUCCUUGAAGUGACAUGAAU
((((((((........))))).......(((.(.((((.(((((((...((........))......)))))).).)))).).))))))...... ( -17.50)
>consensus
GUCAGUUCUUAAUAUUGAGCUCGUUAGCACUCCCAGGACCCGAAAA__UACACAUUUUCGUUUAUUAUUUUCGAGAUCCUUGAAGUGACAUAAAU
((((.(((..........(((....)))......(((((.((((((...((........))......)))))).).)))).))).))))...... (-16.62 = -16.50 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,490,714 – 13,490,807
Length 93
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 89.45
Mean single sequence MFE -24.90
Consensus MFE -18.12
Energy contribution -18.24
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -2.69
Structure conservation index 0.73
SVM decision value 1.20
SVM RNA-class probability 0.930277
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13490714 93 - 20766785
AUUUAUGUCACUUCAAGGAUCUCGAAAAUAAUCAACGAAAACGUGUA--UUUUCGGGUCCUGGUAGUGCUAACGAGCUCAAUAUUAAGAACUGAC
......((((.(((.((((((.((((((((....(((....))).))--))))))))))))....(.(((....))).)........))).)))) ( -26.50)
>DroSec_CAF1 39297 93 - 1
AUUUAAGCCACUUCAAGGAUCUCGAAAAUCAUAAACGAAUUUGCGUA--UUUUUGAGUCCUGGGAGUGCUAACGAGCUCAAUAUUAAGAACUGAC
.....(((.(((((.((((.(((((((((.....(((......))))--)))))))))))).))))))))......................... ( -23.00)
>DroSim_CAF1 39524 93 - 1
AUUUAUGUCACUUCAAGGAUCUCGAAAAUCAUAAACGAAAAUGCGUA--UUUUCGGGUCCUGGGAGUGCUAACGAGCUCAAUAUUAAGAACUGAC
......((((.(((.((((((.(((((((.....(((......))))--))))))))))))..((((.(....).))))........))).)))) ( -25.80)
>DroEre_CAF1 39649 93 - 1
AUUCAUGUCACUUCAAGGACCUCGAAAAUAUGUAACGAAAACGUGUA--UUUUCGGGUCCUGGCAGUGCUAUCGAGCUCAAUAUUAAGAACUGAC
......((((.(((.((((((.(((((((((...(((....))))))--))))))))))))....(.(((....))).)........))).)))) ( -28.80)
>DroYak_CAF1 41201 95 - 1
AUUCAUGUCACUUCAAGGAUCUCGAAAAUAAUAAACAAAAAGGAGUAAGUUUUCGGGUCCUGGCAGUACUAACGAGCUCAAUAUUAAGAACUGAC
......((((.(((.((((((.(((((((......(.....)......))))))))))))).(.(((.(....).))))........))).)))) ( -20.40)
>consensus
AUUUAUGUCACUUCAAGGAUCUCGAAAAUAAUAAACGAAAACGCGUA__UUUUCGGGUCCUGGCAGUGCUAACGAGCUCAAUAUUAAGAACUGAC
......((((.(((.((((.((((((((......(((......)))...))))))))))))....(.(((....))).)........))).)))) (-18.12 = -18.24 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:47 2006