Locus 955

Sequence ID 3R_DroMel_CAF1
Location 3,137,098 – 3,137,251
Length 153
Max. P 0.971063
window1531 window1532

overview

Window 1

Location 3,137,098 – 3,137,211
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.75
Mean single sequence MFE -22.03
Consensus MFE -13.69
Energy contribution -13.17
Covariance contribution -0.52
Combinations/Pair 1.26
Mean z-score -1.48
Structure conservation index 0.62
SVM decision value 0.50
SVM RNA-class probability 0.759889
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3137098 113 - 27905053
CGAAAUGCGAUAAGGAAAU-UUGUGCUGCACUCAAAUAAAUGAAAAGCGGCACGGAAAGCGCAUAAAAU--GGCAGCCGA----CAAAUGGAAGACCAUAAAAAAUAUGCAAUUGCGGCG
((...((((((.......(-(((((((((..(((......)))...))))))))))....(((((..((--(((..(((.----....)))..).))))......))))).)))))).)) ( -29.30)
>DroPse_CAF1 11571 106 - 1
--------------GAAAUUUUGUAUGGCACUCAAGUAAAUGAAAGCCCGCACGAAGAGCUCAUAAAAAAUACGAAUAUACUUCUAAAUGACAAGUCAUAAAAAAUAGUUAAUUGCAGUG
--------------.....((((((((((..(((......)))..))).((.......)).........)))))))...........((((....))))..................... ( -11.90)
>DroSec_CAF1 13022 113 - 1
CGAAAUGCGAUAAGGAAAU-UUGUGCUGCACUCAAAUAAAUGAAAAGCGGCACGGAAAGCGCAUAAAAU--GGCAGUCGA----CAAAUGGAAGACCAUAAAAAAUAUGUAAUUGCGGCA
.....(((..........(-(((((((((..(((......)))...))))))))))...((((......--.(((.....----...((((....))))........)))...))))))) ( -25.79)
>DroSim_CAF1 13533 113 - 1
CGAAAUGCGAUAAGGAAAU-UUGUGCUGCACUCAAAUAAAUGAAAAGCGGCACGGAAAGCGCAUUAAAU--GGCAGCCGA----CAAAUGGAAGACCAUAAAAAAUAUGUAAUUGCGGCA
...((((((.........(-(((((((((..(((......)))...))))))))))...))))))....--....((((.----(((((((....)))).............))))))). ( -28.71)
>DroPer_CAF1 11544 106 - 1
--------------GAAAUUUUGUAUGGCACUCAAGUAAAUGAAAGCCCGCACGAAGAGCUCAUAAAAAAUACGAAUAUACUUCUAAAUGACAAGUCAUAAAAAAUAGUUAAUUGCAGUG
--------------.....((((((((((..(((......)))..))).((.......)).........)))))))...........((((....))))..................... ( -11.90)
>DroEre_CAF1 13499 111 - 1
CCAAAUGCGAUAAGGAAAU-UU-UGCUGCACUCAAAUAAAUGAAAAGCGGCACGGAAAGCGCAUAAAAU--GGCAGCCGA----CAAAUGGAAGGCCAUAAAAAAUAUGUAAUUGCGGC-
.....((((((........-..-((((((..(((......)))...))))))........(((((..((--(((..(((.----....)))...)))))......))))).))))))..- ( -24.60)
>consensus
CGAAAUGCGAUAAGGAAAU_UUGUGCUGCACUCAAAUAAAUGAAAAGCGGCACGGAAAGCGCAUAAAAU__GGCAGCCGA____CAAAUGGAAGACCAUAAAAAAUAUGUAAUUGCGGCG
....................(((((((((..(((......)))...)))))))))....................((((........((((....))))....(((.....))).)))). (-13.69 = -13.17 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,137,134 – 3,137,251
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.05
Mean single sequence MFE -27.40
Consensus MFE -16.56
Energy contribution -16.45
Covariance contribution -0.11
Combinations/Pair 1.19
Mean z-score -2.33
Structure conservation index 0.60
SVM decision value 1.67
SVM RNA-class probability 0.971063
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3137134 117 - 27905053
AAGUGGCAUUGAUGACAGUGCAAACAAGAGCGGCGACAGUCGAAAUGCGAUAAGGAAAU-UUGUGCUGCACUCAAAUAAAUGAAAAGCGGCACGGAAAGCGCAUAAAAU--GGCAGCCGA
.....((((((....)))))).........((((....((((..(((((.........(-(((((((((..(((......)))...))))))))))...)))))....)--))).)))). ( -33.90)
>DroPse_CAF1 11611 94 - 1
AAAUGGCAUUGAUGACAGUGCAAACAAG--------------------------GAAAUUUUGUAUGGCACUCAAGUAAAUGAAAGCCCGCACGAAGAGCUCAUAAAAAAUACGAAUAUA
.....((((((....)))))).......--------------------------.....((((((((((..(((......)))..))).((.......)).........))))))).... ( -16.70)
>DroSec_CAF1 13058 117 - 1
AAGUGGCAUUGAUGACAGUGCAAACAAGAGCGGCGACAGUCGAAAUGCGAUAAGGAAAU-UUGUGCUGCACUCAAAUAAAUGAAAAGCGGCACGGAAAGCGCAUAAAAU--GGCAGUCGA
.....((((((....))))))............((((.((((..(((((.........(-(((((((((..(((......)))...))))))))))...)))))....)--))).)))). ( -32.90)
>DroSim_CAF1 13569 117 - 1
AAGUGGCAUUGAUGACAGUGCAAACAAGAGCGGCGACAGUCGAAAUGCGAUAAGGAAAU-UUGUGCUGCACUCAAAUAAAUGAAAAGCGGCACGGAAAGCGCAUUAAAU--GGCAGCCGA
.....((((((....)))))).........((((....((((.((((((.........(-(((((((((..(((......)))...))))))))))...))))))...)--))).)))). ( -35.10)
>DroPer_CAF1 11584 94 - 1
AAAUGGCAUUGAUGACAGUGCAAACAAG--------------------------GAAAUUUUGUAUGGCACUCAAGUAAAUGAAAGCCCGCACGAAGAGCUCAUAAAAAAUACGAAUAUA
.....((((((....)))))).......--------------------------.....((((((((((..(((......)))..))).((.......)).........))))))).... ( -16.70)
>DroEre_CAF1 13534 116 - 1
AAGUGCCAUUGAUGACAGUGCAAACAAGAGCGGCGACAGUCCAAAUGCGAUAAGGAAAU-UU-UGCUGCACUCAAAUAAAUGAAAAGCGGCACGGAAAGCGCAUAAAAU--GGCAGCCGA
..(((((((((....))))((........(((((((...(((...........)))...-.)-))))))..(((......)))...)))))))((...((.(((...))--)))..)).. ( -29.10)
>consensus
AAGUGGCAUUGAUGACAGUGCAAACAAGAGCGGCGACAGUCGAAAUGCGAUAAGGAAAU_UUGUGCUGCACUCAAAUAAAUGAAAAGCGGCACGGAAAGCGCAUAAAAU__GGCAGCCGA
..(((((((((....)))))).......................................(((((((((..(((......)))...)))))))))......)))................ (-16.56 = -16.45 +  -0.11)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:35 2006