Locus 1007

Sequence ID 2L_DroMel_CAF1
Location 2,892,840 – 2,892,995
Length 155
Max. P 0.976678
window1615 window1616 window1617

overview

Window 5

Location 2,892,840 – 2,892,955
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.53
Mean single sequence MFE -28.80
Consensus MFE -26.00
Energy contribution -26.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.90
SVM decision value 1.19
SVM RNA-class probability 0.927923
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2892840 115 + 22407834
AAC-----CACCACCCACUUGGCUGCCCGCAUUCUAUUGCAUUUCGGUCGCCCCCUCUUUGGCCGACUUUCUAUCAUUCGCCGCCUUUGGCAUUGGCCAAAAAGCGAAUUUGCUCCGUUG
...-----............(((.((..(((......)))...(((((((.........))))))).............)).)))((((((....)))))).((((....))))...... ( -26.40)
>DroSec_CAF1 11521 115 + 1
AAC-----CACCACCCACUUGGCUGCCCGCAUUCUAUUGCAUUUCGGUCGCCCCCUCUUUGGCCGACUUUCUAUCAUUCGCCGCCUUUGGCAUUGGCCAAAAAGCGAAUUUGCUCCGUUG
...-----............(((.((..(((......)))...(((((((.........))))))).............)).)))((((((....)))))).((((....))))...... ( -26.40)
>DroSim_CAF1 11843 115 + 1
AAC-----CGCCACCCACUUGGCUGCCCGCAUUCUAUUGCAUUUCGGUCGCCCCCUCUUUGGCCGACUUUCUAUCAUUCGCCGCCUUUGGCAUUGGCCAAAAAGCGAAUUUGCUCCGUUG
...-----.((((......)))).((..(((......)))...(((((((.........))))))).........((((((....((((((....))))))..))))))..))....... ( -29.00)
>DroEre_CAF1 11737 120 + 1
AACAUGCCAACCACCCACUUGGCUGCCCGCAUUCUAUUGCAUUUCGGUCGCCCCCUCGUUGGCCGACUUUCUAUCAUUCGCUGCCUUUGGCAUUGGCCAAAAAGCGAAUUUUCUCCGUUG
.....((((((.........(((.(((.(((......))).....))).))).....))))))((((........(((((((...((((((....)))))).))))))).......)))) ( -33.20)
>DroYak_CAF1 11848 109 + 1
-----------CACCCACUUGGCUGCCCGCAUUCUAUUGCAUUUCGGUCGCCCCCUCUUUGGCCGACUUUCUAUCAUUCGCUGCCUUUGGCAUUGGCCAAAAAGCGAAUUUGCUCCGUUG
-----------.........((..((..(((......)))...(((((((.........))))))).........(((((((...((((((....)))))).)))))))..)).)).... ( -29.00)
>consensus
AAC_____CACCACCCACUUGGCUGCCCGCAUUCUAUUGCAUUUCGGUCGCCCCCUCUUUGGCCGACUUUCUAUCAUUCGCCGCCUUUGGCAUUGGCCAAAAAGCGAAUUUGCUCCGUUG
....................(((.((..(((......)))...(((((((.........))))))).............)).)))((((((....)))))).((((.........)))). (-26.00 = -26.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,892,840 – 2,892,955
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.53
Mean single sequence MFE -36.48
Consensus MFE -32.58
Energy contribution -32.74
Covariance contribution 0.16
Combinations/Pair 1.03
Mean z-score -1.69
Structure conservation index 0.89
SVM decision value 1.78
SVM RNA-class probability 0.976678
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2892840 115 - 22407834
CAACGGAGCAAAUUCGCUUUUUGGCCAAUGCCAAAGGCGGCGAAUGAUAGAAAGUCGGCCAAAGAGGGGGCGACCGAAAUGCAAUAGAAUGCGGGCAGCCAAGUGGGUGGUG-----GUU
.......(((..(((.((((((((((..((((......))))...(((.....))))))))))))).((....))))).)))........((.(.((.((....)).)).).-----)). ( -36.40)
>DroSec_CAF1 11521 115 - 1
CAACGGAGCAAAUUCGCUUUUUGGCCAAUGCCAAAGGCGGCGAAUGAUAGAAAGUCGGCCAAAGAGGGGGCGACCGAAAUGCAAUAGAAUGCGGGCAGCCAAGUGGGUGGUG-----GUU
.......(((..(((.((((((((((..((((......))))...(((.....))))))))))))).((....))))).)))........((.(.((.((....)).)).).-----)). ( -36.40)
>DroSim_CAF1 11843 115 - 1
CAACGGAGCAAAUUCGCUUUUUGGCCAAUGCCAAAGGCGGCGAAUGAUAGAAAGUCGGCCAAAGAGGGGGCGACCGAAAUGCAAUAGAAUGCGGGCAGCCAAGUGGGUGGCG-----GUU
...(((.((....((.((((((((((..((((......))))...(((.....))))))))))))).))))..)))...((((......))))(.((.((....)).)).).-----... ( -37.90)
>DroEre_CAF1 11737 120 - 1
CAACGGAGAAAAUUCGCUUUUUGGCCAAUGCCAAAGGCAGCGAAUGAUAGAAAGUCGGCCAACGAGGGGGCGACCGAAAUGCAAUAGAAUGCGGGCAGCCAAGUGGGUGGUUGGCAUGUU
.((((......((((((((((((((....)))))))..)))))))........((((((((.((....(((..((....((((......))))))..)))...))..)))))))).)))) ( -38.50)
>DroYak_CAF1 11848 109 - 1
CAACGGAGCAAAUUCGCUUUUUGGCCAAUGCCAAAGGCAGCGAAUGAUAGAAAGUCGGCCAAAGAGGGGGCGACCGAAAUGCAAUAGAAUGCGGGCAGCCAAGUGGGUG-----------
...(((.((....((.((((((((((..((((...))))......(((.....))))))))))))).))))..)))...((((......))))..((.((....)).))----------- ( -33.20)
>consensus
CAACGGAGCAAAUUCGCUUUUUGGCCAAUGCCAAAGGCGGCGAAUGAUAGAAAGUCGGCCAAAGAGGGGGCGACCGAAAUGCAAUAGAAUGCGGGCAGCCAAGUGGGUGGUG_____GUU
...(((.((....((.((((((((((..((((...))))......(((.....))))))))))))).))))..)))...((((......))))..((.((....)).))........... (-32.58 = -32.74 +   0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,892,875 – 2,892,995
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.83
Mean single sequence MFE -31.04
Consensus MFE -29.94
Energy contribution -29.70
Covariance contribution -0.24
Combinations/Pair 1.03
Mean z-score -1.42
Structure conservation index 0.96
SVM decision value 0.78
SVM RNA-class probability 0.848629
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2892875 120 - 22407834
ACCAGACAAAUUUUAAUAAUUCAACUCUAUAAUGUGGACGCAACGGAGCAAAUUCGCUUUUUGGCCAAUGCCAAAGGCGGCGAAUGAUAGAAAGUCGGCCAAAGAGGGGGCGACCGAAAU
...................(((.((........))((.(((..((((.....))).((((((((((..((((......))))...(((.....))))))))))))))..))).))))).. ( -31.40)
>DroSec_CAF1 11556 120 - 1
ACCAGACAAAUUUUAAUAAUUCAACUCUAUAAUGUGGACGCAACGGAGCAAAUUCGCUUUUUGGCCAAUGCCAAAGGCGGCGAAUGAUAGAAAGUCGGCCAAAGAGGGGGCGACCGAAAU
...................(((.((........))((.(((..((((.....))).((((((((((..((((......))))...(((.....))))))))))))))..))).))))).. ( -31.40)
>DroSim_CAF1 11878 120 - 1
ACCAGACAAAUUUUAAUAAUUCAACUCUAUAAUGUGGACGCAACGGAGCAAAUUCGCUUUUUGGCCAAUGCCAAAGGCGGCGAAUGAUAGAAAGUCGGCCAAAGAGGGGGCGACCGAAAU
...................(((.((........))((.(((..((((.....))).((((((((((..((((......))))...(((.....))))))))))))))..))).))))).. ( -31.40)
>DroEre_CAF1 11777 120 - 1
ACCAGACAAAUUUUAAUAAUUCAACUCUAUAAUGUGGACGCAACGGAGAAAAUUCGCUUUUUGGCCAAUGCCAAAGGCAGCGAAUGAUAGAAAGUCGGCCAACGAGGGGGCGACCGAAAU
...................(((...(((((..(((....))).........((((((((((((((....)))))))..))))))).)))))..((((.((.......)).)))).))).. ( -29.70)
>DroYak_CAF1 11877 120 - 1
ACCAGACAAAUUUUAAUAAUUCAACUCUAUAAUGUGGACGCAACGGAGCAAAUUCGCUUUUUGGCCAAUGCCAAAGGCAGCGAAUGAUAGAAAGUCGGCCAAAGAGGGGGCGACCGAAAU
...................(((..((((.....((.(((((......))..((((((((((((((....)))))))..)))))))........))).))...)))).((....))))).. ( -31.30)
>consensus
ACCAGACAAAUUUUAAUAAUUCAACUCUAUAAUGUGGACGCAACGGAGCAAAUUCGCUUUUUGGCCAAUGCCAAAGGCGGCGAAUGAUAGAAAGUCGGCCAAAGAGGGGGCGACCGAAAU
...................(((...(((((..(((....))).........((((((((((((((....)))))))..))))))).)))))..((((.((.......)).)))).))).. (-29.94 = -29.70 +  -0.24)

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 09:50:54 2006