Locus 404

Sequence ID 2R_DroMel_CAF1
Location 2,411,718 – 2,411,847
Length 129
Max. P 0.998030
window792 window793 window794

overview

Window 2

Location 2,411,718 – 2,411,808
Length 90
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 85.49
Mean single sequence MFE -23.51
Consensus MFE -21.08
Energy contribution -21.09
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.90
SVM decision value 0.78
SVM RNA-class probability 0.849266
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2411718 90 + 20766785
GCUGCCAGCGAGUGCCUGACCUUUUUGCCAGCCAUGCAGUAGCUCC----CACCGCCUUCAGCUUUCAGCUUUCAGCUUUCGCCUUGCUGGCUU
...(((((((((.((..((.((..((((.......)))).)).)).----....((....(((.....)))....))....))))))))))).. ( -25.70)
>DroSec_CAF1 68114 76 + 1
GCUGCCAGCGAGUGCCUGACCUUUUUGCCAGCCAUGCAGUAGCUCC----CACCAC--------------UCUCAGCUUUCGCCUUGCUGGCUU
...(((((((((((...((.((..((((.......)))).)).)).----...)))--------------))...((....))...)))))).. ( -22.10)
>DroSim_CAF1 25222 76 + 1
GCUGCCAGCGAGUGCCUGACCUUUUUGCCAGCCAUGCAGUAGCUCC----CACCAC--------------UCUCAGCUUUCGCCUUGCUGGCUU
...(((((((((((...((.((..((((.......)))).)).)).----...)))--------------))...((....))...)))))).. ( -22.10)
>DroYak_CAF1 24520 80 + 1
GCUGCCAGCGAGUGCCUAACCUUUUUGCCAGCCAUGCAGUAGCUGCCUUUCACUGC--------------CUUCAGCUUUCGCCUUGCUGGCUU
...(((((((((.((.........((((.......)))).(((((...........--------------...)))))...))))))))))).. ( -24.14)
>consensus
GCUGCCAGCGAGUGCCUGACCUUUUUGCCAGCCAUGCAGUAGCUCC____CACCAC______________UCUCAGCUUUCGCCUUGCUGGCUU
...(((((((((.((.........((((.......)))).((((..............................))))...))))))))))).. (-21.08 = -21.09 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,411,718 – 2,411,808
Length 90
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 85.49
Mean single sequence MFE -36.00
Consensus MFE -33.00
Energy contribution -32.88
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -4.57
Structure conservation index 0.92
SVM decision value 2.99
SVM RNA-class probability 0.998030
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2411718 90 - 20766785
AAGCCAGCAAGGCGAAAGCUGAAAGCUGAAAGCUGAAGGCGGUG----GGAGCUACUGCAUGGCUGGCAAAAAGGUCAGGCACUCGCUGGCAGC
..((((((..(((....)))...(((.....)))((..((((((----(...))))))).((.(((((......))))).)).))))))))... ( -37.70)
>DroSec_CAF1 68114 76 - 1
AAGCCAGCAAGGCGAAAGCUGAGA--------------GUGGUG----GGAGCUACUGCAUGGCUGGCAAAAAGGUCAGGCACUCGCUGGCAGC
..((((((..(((....)))(((.--------------(..(((----(...))))..).((.(((((......))))).)))))))))))... ( -37.00)
>DroSim_CAF1 25222 76 - 1
AAGCCAGCAAGGCGAAAGCUGAGA--------------GUGGUG----GGAGCUACUGCAUGGCUGGCAAAAAGGUCAGGCACUCGCUGGCAGC
..((((((..(((....)))(((.--------------(..(((----(...))))..).((.(((((......))))).)))))))))))... ( -37.00)
>DroYak_CAF1 24520 80 - 1
AAGCCAGCAAGGCGAAAGCUGAAG--------------GCAGUGAAAGGCAGCUACUGCAUGGCUGGCAAAAAGGUUAGGCACUCGCUGGCAGC
..((((((..(((....)))((..--------------((((((.........)))))).((.(((((......))))).)).))))))))... ( -32.30)
>consensus
AAGCCAGCAAGGCGAAAGCUGAAA______________GCGGUG____GGAGCUACUGCAUGGCUGGCAAAAAGGUCAGGCACUCGCUGGCAGC
..((((((..(((....)))(((...............((((((.........)))))).((.(((((......))))).)))))))))))... (-33.00 = -32.88 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,411,751 – 2,411,847
Length 96
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 85.90
Mean single sequence MFE -21.15
Consensus MFE -16.09
Energy contribution -16.40
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -1.53
Structure conservation index 0.76
SVM decision value 0.16
SVM RNA-class probability 0.612072
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2411751 96 - 20766785
AAGGGGAUCCAAUAAAUUCGAUUGCAACCGAAGCAUGAAAAGCCAGCAAGGCGAAAGCUGAAAGCUGAAAGCUGAAGGCGGUG----GGAGCUACUGCAU
..((....))......((((..(((.......))))))).(((((((..(((....)))....))))...)))....((((((----(...))))))).. ( -24.50)
>DroSec_CAF1 68147 82 - 1
AAGGGGAUUCAAUAAAUUCGAUUGCAAUCGAAGCAUGAAAAGCCAGCAAGGCGAAAGCUGAGA--------------GUGGUG----GGAGCUACUGCAU
....((.((((.....((((((....))))))...))))...)).((..(((....)))...(--------------(((((.----...)))))))).. ( -22.10)
>DroSim_CAF1 25255 82 - 1
AAGGGGAUCCAAUAAAUUCGAUUGCAACCGAAGCAUGAAAAGCCAGCAAGGCGAAAGCUGAGA--------------GUGGUG----GGAGCUACUGCAU
.((..(.(((......((((..(((.......)))))))..((((.(..(((....)))..).--------------.)))).----))).)..)).... ( -19.40)
>DroYak_CAF1 24553 86 - 1
AAGGGGAUCCAAUAAAUUCGAUUGCAACCGAAGCAUGAAAAGCCAGCAAGGCGAAAGCUGAAG--------------GCAGUGAAAGGCAGCUACUGCAU
..((....))......(((.(((((.......((.((......))))..(((....)))....--------------))))))))..((((...)))).. ( -18.60)
>consensus
AAGGGGAUCCAAUAAAUUCGAUUGCAACCGAAGCAUGAAAAGCCAGCAAGGCGAAAGCUGAAA______________GCGGUG____GGAGCUACUGCAU
....((..........((((........))))..........)).(((.(((....)))..................(((((........)))))))).. (-16.09 = -16.40 +   0.31)

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 09:37:46 2006