Locus 2575

Sequence ID 3L_DroMel_CAF1
Location 7,193,109 – 7,193,213
Length 104
Max. P 0.848800
window3998 window3999

overview

Window 8

Location 7,193,109 – 7,193,213
Length 104
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 97.63
Mean single sequence MFE -24.68
Consensus MFE -22.05
Energy contribution -22.30
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.35
Structure conservation index 0.89
SVM decision value 0.78
SVM RNA-class probability 0.848800
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7193109 104 + 23771897
CACACGCACACGCAUGCAGAGGUG---GCAAUGCAAAAUGUAUGCAUGCAACAACAUCCAGCCUGUGGAACAAUAAAUAAAAUGCAGCAAAAUGCAUUUCAAAGAAG
((((.((....(((((((...((.---.....))....)))))))(((......)))...)).))))............(((((((......)))))))........ ( -23.00)
>DroSec_CAF1 6598 107 + 1
CACACGCACACGCAUGCAGAGGUGGCGGCAAUGCAAAAUGUAUGCAUGCAACAACAUCCAGCCUGUGGAACAAUAAAUAAAAUGCAGCAAAAUGCAUUGCAAAGAAG
....(((.(((..........))))))((((((((...(((.(((((.........((((.....))))............))))))))...))))))))....... ( -27.30)
>DroEre_CAF1 6523 104 + 1
CACACGCACACGCAUGCAGAGGUG---GCAAUGCAAAAUGUAUGCAUGCAACAACAUCCAGCCUGUGGAACAAUAAAUAAAAUGCAGCAAAAUGCAUUGCAAAGAAG
(((..(((......)))....)))---((((((((...(((.(((((.........((((.....))))............))))))))...))))))))....... ( -24.70)
>DroYak_CAF1 3606 104 + 1
UACACGCACACGCAUGCAGAGGUG---GCAAUGCAAAAUGUAUGCAUGCAACAACAUCCAGCCUGUGGAACAAUAAAUAAAAUGCAGCAAAAUGCAUUGCAAAGAAG
.....((....(((((((.(.((.---((...))...)).).))))))).......((((.....))))...........((((((......))))))))....... ( -23.70)
>consensus
CACACGCACACGCAUGCAGAGGUG___GCAAUGCAAAAUGUAUGCAUGCAACAACAUCCAGCCUGUGGAACAAUAAAUAAAAUGCAGCAAAAUGCAUUGCAAAGAAG
.....((...((((.((.(.((((...(((.((((.......))))))).....))))).)).)))).............((((((......))))))))....... (-22.05 = -22.30 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 7,193,109 – 7,193,213
Length 104
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 97.63
Mean single sequence MFE -27.17
Consensus MFE -24.67
Energy contribution -24.92
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.91
SVM decision value 0.25
SVM RNA-class probability 0.653828
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7193109 104 - 23771897
CUUCUUUGAAAUGCAUUUUGCUGCAUUUUAUUUAUUGUUCCACAGGCUGGAUGUUGUUGCAUGCAUACAUUUUGCAUUGC---CACCUCUGCAUGCGUGUGCGUGUG
......(((((((((......)))))))))........((((.....)))).......((((((((((.....((((.((---.......)))))))))))))))). ( -27.80)
>DroSec_CAF1 6598 107 - 1
CUUCUUUGCAAUGCAUUUUGCUGCAUUUUAUUUAUUGUUCCACAGGCUGGAUGUUGUUGCAUGCAUACAUUUUGCAUUGCCGCCACCUCUGCAUGCGUGUGCGUGUG
.......((((((((...(((((((...(((((((((.....)))..))))))....)))).))).......))))))))..........((((((....)))))). ( -26.90)
>DroEre_CAF1 6523 104 - 1
CUUCUUUGCAAUGCAUUUUGCUGCAUUUUAUUUAUUGUUCCACAGGCUGGAUGUUGUUGCAUGCAUACAUUUUGCAUUGC---CACCUCUGCAUGCGUGUGCGUGUG
.......((((((((...(((((((...(((((((((.....)))..))))))....)))).))).......))))))))---.......((((((....)))))). ( -26.90)
>DroYak_CAF1 3606 104 - 1
CUUCUUUGCAAUGCAUUUUGCUGCAUUUUAUUUAUUGUUCCACAGGCUGGAUGUUGUUGCAUGCAUACAUUUUGCAUUGC---CACCUCUGCAUGCGUGUGCGUGUA
.......((((((((...(((((((...(((((((((.....)))..))))))....)))).))).......))))))))---......(((((((....))))))) ( -27.10)
>consensus
CUUCUUUGCAAUGCAUUUUGCUGCAUUUUAUUUAUUGUUCCACAGGCUGGAUGUUGUUGCAUGCAUACAUUUUGCAUUGC___CACCUCUGCAUGCGUGUGCGUGUG
.......((((((((...(((((((...(((((((((.....)))..))))))....)))).))).......))))))))..........((((((....)))))). (-24.67 = -24.92 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:04 2006