Locus 1977

Sequence ID X_DroMel_CAF1
Location 5,411,786 – 5,411,893
Length 107
Max. P 0.825109
window3221 window3222

overview

Window 1

Location 5,411,786 – 5,411,893
Length 107
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 91.93
Mean single sequence MFE -32.38
Consensus MFE -26.48
Energy contribution -26.35
Covariance contribution -0.13
Combinations/Pair 1.12
Mean z-score -1.95
Structure conservation index 0.82
SVM decision value 0.69
SVM RNA-class probability 0.825109
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5411786 107 + 22224390
GGCUUACAUUAAUUAUAAUUUGCAGGCGGUGGGUGAAUCGCAGCUUAUAAUUAUGCAAAAGUCUGCAAUGACACGCCCACCUAUGCAUGCCCGCCCCUC-----GGUAGCUG
(((.................((((...((((((((....(((...........)))....(((......))).))))))))..))))((((........-----))))))). ( -31.40)
>DroSec_CAF1 19829 107 + 1
GGCUUACAUUAAUUAUAAUUUGCAGGCUGUGGGUGAAUCGCAGCUUAUAAUUAUGCAAAAGUCUGCAAUGACACGCCCACCUAUGCAUCGCCGCCCCUC-----GGUAGCUA
((((................((((....(((((((....(((...........)))....(((......))).)))))))...))))..((((.....)-----))))))). ( -29.10)
>DroEre_CAF1 27913 107 + 1
GGCUUACAUUAAUUAUAAUUUGCAGGCUGCGGGUGAAUCGCAGCUUAUAAUUAUGCAAAAGUCUGCAAUGACACGCCCACCUAUGCAUGCCCGCCCCUC-----GGCAGCCA
((((..........((((((...(((((((((.....)))))))))..))))))(((...(((......)))..((........)).)))..(((....-----))))))). ( -31.00)
>DroYak_CAF1 20046 112 + 1
AGCUUGCAUUAAUUAUAAUUUGCAAGCUGCGGGUGAAUCGCAGCUUAUAAUUAUGCAAAAGUCUGCAAUGACACGCCCACCUAUGCAAGCCCGCCCCCCAGCUGGGCAGCUA
.((((((((....(((((((...(((((((((.....)))))))))..))))))).....(((......)))..........))))))))..((((.......))))..... ( -38.00)
>consensus
GGCUUACAUUAAUUAUAAUUUGCAGGCUGCGGGUGAAUCGCAGCUUAUAAUUAUGCAAAAGUCUGCAAUGACACGCCCACCUAUGCAUGCCCGCCCCUC_____GGCAGCUA
((((................((((....(((((((....(((...........)))....(((......))).)))))))...)))).....(((.........))))))). (-26.48 = -26.35 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,411,786 – 5,411,893
Length 107
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 91.93
Mean single sequence MFE -35.40
Consensus MFE -26.85
Energy contribution -26.48
Covariance contribution -0.38
Combinations/Pair 1.12
Mean z-score -1.80
Structure conservation index 0.76
SVM decision value 0.11
SVM RNA-class probability 0.589858
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5411786 107 - 22224390
CAGCUACC-----GAGGGGCGGGCAUGCAUAGGUGGGCGUGUCAUUGCAGACUUUUGCAUAAUUAUAAGCUGCGAUUCACCCACCGCCUGCAAAUUAUAAUUAAUGUAAGCC
..(((.(.-----...)))).(((.((((..((((((.(....(((((((.(((.((......)).)))))))))).).))))))...))))..(((((.....)))))))) ( -32.20)
>DroSec_CAF1 19829 107 - 1
UAGCUACC-----GAGGGGCGGCGAUGCAUAGGUGGGCGUGUCAUUGCAGACUUUUGCAUAAUUAUAAGCUGCGAUUCACCCACAGCCUGCAAAUUAUAAUUAAUGUAAGCC
..(((.(.-----...))))(((..((((..(((.((.(((..(((((((.(((.((......)).)))))))))).)))))...)))))))..(((((.....)))))))) ( -29.00)
>DroEre_CAF1 27913 107 - 1
UGGCUGCC-----GAGGGGCGGGCAUGCAUAGGUGGGCGUGUCAUUGCAGACUUUUGCAUAAUUAUAAGCUGCGAUUCACCCGCAGCCUGCAAAUUAUAAUUAAUGUAAGCC
.((((((.-----((((.((.(((((((........)))))))...))...)))).)).(((((((((((((((.......)))))).......))))))))).....)))) ( -35.41)
>DroYak_CAF1 20046 112 - 1
UAGCUGCCCAGCUGGGGGGCGGGCUUGCAUAGGUGGGCGUGUCAUUGCAGACUUUUGCAUAAUUAUAAGCUGCGAUUCACCCGCAGCUUGCAAAUUAUAAUUAAUGCAAGCU
..(((.(((....))).))).(((((((((..((..(((.(((......)))...)))((((((.(((((((((.......)))))))))..)))))).))..))))))))) ( -45.00)
>consensus
UAGCUACC_____GAGGGGCGGGCAUGCAUAGGUGGGCGUGUCAUUGCAGACUUUUGCAUAAUUAUAAGCUGCGAUUCACCCACAGCCUGCAAAUUAUAAUUAAUGUAAGCC
..(((((...........((((((........(((((.(....(((((((.(((.((......)).)))))))))).).))))).))))))..((((....)))))).))). (-26.85 = -26.48 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:22 2006