Locus 4013

Sequence ID 3L_DroMel_CAF1
Location 11,715,378 – 11,715,481
Length 103
Max. P 0.991448
window6252 window6253

overview

Window 2

Location 11,715,378 – 11,715,481
Length 103
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 93.31
Mean single sequence MFE -25.95
Consensus MFE -21.46
Energy contribution -22.53
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -2.19
Structure conservation index 0.83
SVM decision value 0.88
SVM RNA-class probability 0.874152
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11715378 103 + 23771897
GCAAAUAAAGGAUUUGGCUUAUGCGCGCUCUAUUUGUGGCCACUUUCCUUGGCUCACAUUGCACACAAGCCAACAGCAGUGCAUUUUCCAUUGCACCCA--ACCC
.........((..(((((((.((.(((.......((((((((.......)))).)))).))).)).)))))))..((((((.......))))))..)).--.... ( -29.80)
>DroSim_CAF1 24412 103 + 1
GCAAAUAAAGGAUUUGGCUUAUGCGCGCUCUAUUUGUGGCCACUUUCCUUGGCUCACAUUGCACACAAGCCAACAGCAGUGCAUUUGCCAUUGCACCCA--AUCC
.........(((((((((((.((.(((.......((((((((.......)))).)))).))).)).))))))...(((((((....).))))))....)--)))) ( -31.40)
>DroEre_CAF1 24615 105 + 1
GCAAAUAAAGGAUUUGGCUUAUGCGCGCUCUAUUUGUGGCCACUUUCCUUGGCUCACAUUGCACACAAACCACCAGCACUGCAUUUUCCCUUGCACCCACCACCC
((((.....((.((((((....))(.((......((((((((.......)))).))))..)).).))))))....((...))........))))........... ( -20.90)
>DroYak_CAF1 24647 103 + 1
GCAAAUAAAGGAUUUGGCUUAUGCGCGCUCUAUUUGUGGCCACUUUCCUUGGCUCACAUUGCACACAAACCACCAGCACUGCAUUUUCCCUUGC--CAGCCACCC
.........((...((((..(((((.(((.....((((((((.......)))).))))(((....)))......))).).))))........))--)).)).... ( -21.70)
>consensus
GCAAAUAAAGGAUUUGGCUUAUGCGCGCUCUAUUUGUGGCCACUUUCCUUGGCUCACAUUGCACACAAACCAACAGCACUGCAUUUUCCAUUGCACCCA__ACCC
.........((...((((((.((.(((.......((((((((.......)))).)))).))).)).))))))......(((((........)))))......)). (-21.46 = -22.53 +   1.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,715,378 – 11,715,481
Length 103
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 93.31
Mean single sequence MFE -36.48
Consensus MFE -33.06
Energy contribution -33.38
Covariance contribution 0.31
Combinations/Pair 1.07
Mean z-score -2.89
Structure conservation index 0.91
SVM decision value 2.27
SVM RNA-class probability 0.991448
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11715378 103 - 23771897
GGGU--UGGGUGCAAUGGAAAAUGCACUGCUGUUGGCUUGUGUGCAAUGUGAGCCAAGGAAAGUGGCCACAAAUAGAGCGCGCAUAAGCCAAAUCCUUUAUUUGC
((((--(.((((((.(....).)))))).....((((((((((((..((((.((((.......))))))))........)))))))))))))))))......... ( -39.30)
>DroSim_CAF1 24412 103 - 1
GGAU--UGGGUGCAAUGGCAAAUGCACUGCUGUUGGCUUGUGUGCAAUGUGAGCCAAGGAAAGUGGCCACAAAUAGAGCGCGCAUAAGCCAAAUCCUUUAUUUGC
((((--(.((((((........)))))).....((((((((((((..((((.((((.......))))))))........)))))))))))))))))......... ( -39.00)
>DroEre_CAF1 24615 105 - 1
GGGUGGUGGGUGCAAGGGAAAAUGCAGUGCUGGUGGUUUGUGUGCAAUGUGAGCCAAGGAAAGUGGCCACAAAUAGAGCGCGCAUAAGCCAAAUCCUUUAUUUGC
((((((.(((((((..(.......)..)))...((((((((((((..((((.((((.......))))))))........)))))))))))).)))).)))))).. ( -32.10)
>DroYak_CAF1 24647 103 - 1
GGGUGGCUG--GCAAGGGAAAAUGCAGUGCUGGUGGUUUGUGUGCAAUGUGAGCCAAGGAAAGUGGCCACAAAUAGAGCGCGCAUAAGCCAAAUCCUUUAUUUGC
((((.((..--(((..(.......)..)))..))(((((((((((..((((.((((.......))))))))........)))))))))))..))))......... ( -35.50)
>consensus
GGGU__UGGGUGCAAGGGAAAAUGCACUGCUGGUGGCUUGUGUGCAAUGUGAGCCAAGGAAAGUGGCCACAAAUAGAGCGCGCAUAAGCCAAAUCCUUUAUUUGC
((((....((((((........)))))).....((((((((((((..((((.((((.......))))))))........)))))))))))).))))......... (-33.06 = -33.38 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:25 2006