Locus 4627

Sequence ID X_DroMel_CAF1
Location 12,098,184 – 12,098,318
Length 134
Max. P 0.987662
window7603 window7604

overview

Window 3

Location 12,098,184 – 12,098,287
Length 103
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.93
Mean single sequence MFE -29.76
Consensus MFE -15.38
Energy contribution -15.75
Covariance contribution 0.38
Combinations/Pair 1.05
Mean z-score -3.24
Structure conservation index 0.52
SVM decision value 2.09
SVM RNA-class probability 0.987662
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12098184 103 - 22224390
CGAGCAUCAAAAAAGAAGGAAAA-------------UGUAUGUGUGUGUGUGCGCGGCACACAUAUCAGCAUAAGUCA----GGAUGCGGAUAUACAUACAUGUGUACAUGUGAGUAUCA
...(((((..........((...-------------..(((((((((((((((...))))))))))..)))))..)).----.))))).(((((...((((((....)))))).))))). ( -30.90)
>DroSec_CAF1 10550 99 - 1
GGAGCAUCAAAAAGGAAGAAAAA-------------UGUAUGUGUGUGU----GCGGCACACAUAUCAGCAUAAGUCAGGCAGGAUGCGGAUAUA----CAUGUGUACAUGUGAGUAUCA
...(((((......((.......-------------((.(((((((((.----....))))))))))).......))......))))).((((((----((((....)))))..))))). ( -30.14)
>DroEre_CAF1 22165 91 - 1
GGAGCAUCAAAAAAGAAGGAAAA-------------UGUGU--GUGUGUGUGGGCGGCACACAUAUCAGCAUAAGUCA----GGA------UGUA----CAUGUGUACAUGUGAGUAUCA
.((...(((.........((..(-------------(((((--((((((((.....))))))))))..))))...)).----..(------((((----(....)))))).)))...)). ( -24.10)
>DroYak_CAF1 22639 110 - 1
GGAGCAUCAAAAAAGAGGGAAUACAUACAUUUUCCUUGUGG--GUGUGUGUGUGUGACACACAUAUCAGCAUAAGUCA----GGAUGUGGAUGUA----CAUGUGUACAUGUGAGUAUCA
...(((((......(((((((.........)))))))((.(--(((((((((.....)))))))))).))........----.))))).((((((----((((....))))))..)))). ( -33.90)
>consensus
GGAGCAUCAAAAAAGAAGGAAAA_____________UGUAU__GUGUGUGUG_GCGGCACACAUAUCAGCAUAAGUCA____GGAUGCGGAUAUA____CAUGUGUACAUGUGAGUAUCA
.((...(((...........................(((....((((((((.....))))))))....)))............................((((....)))))))...)). (-15.38 = -15.75 +   0.38)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,098,222 – 12,098,318
Length 96
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 83.04
Mean single sequence MFE -25.72
Consensus MFE -17.48
Energy contribution -18.35
Covariance contribution 0.87
Combinations/Pair 1.05
Mean z-score -2.38
Structure conservation index 0.68
SVM decision value 1.31
SVM RNA-class probability 0.940438
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12098222 96 - 22224390
CGCUUAUCAAUGAGCAACAAAAACGAGCUCACGAGCAUCAAAAAAGAAGGAAAA-------------UGUAUGUGUGUGUGUGCGCGGCACACAUAUCAGCAUAAGUCA--
.((((.....(((((...........))))).)))).............((...-------------..(((((((((((((((...))))))))))..)))))..)).-- ( -24.90)
>DroSec_CAF1 10586 94 - 1
CGCUUAUCAAUGAGCAACAAAAACGAGCUCAGGAGCAUCAAAAAGGAAGAAAAA-------------UGUAUGUGUGUGU----GCGGCACACAUAUCAGCAUAAGUCAGG
.((((.....(((((...........))))).))))............((...(-------------((((((((((((.----....)))))))))..))))...))... ( -25.20)
>DroEre_CAF1 22193 94 - 1
CGCUUAUCAAUGAGCAACAAAAACGAGCCGAGGAGCAUCAAAAAAGAAGGAAAA-------------UGUGU--GUGUGUGUGGGCGGCACACAUAUCAGCAUAAGUCA--
.(((((....))))).........((((......)).))..........((..(-------------(((((--((((((((.....))))))))))..))))...)).-- ( -21.30)
>DroYak_CAF1 22673 107 - 1
CGCUUAUCAAUGAGCAACAGAAACGAGCUCAGGAGCAUCAAAAAAGAGGGAAUACAUACAUUUUCCUUGUGG--GUGUGUGUGUGUGACACACAUAUCAGCAUAAGUCA--
.((((.....(((((...........))))).)))).........(((((((.........)))))))((.(--(((((((((.....)))))))))).))........-- ( -31.50)
>consensus
CGCUUAUCAAUGAGCAACAAAAACGAGCUCAGGAGCAUCAAAAAAGAAGGAAAA_____________UGUAU__GUGUGUGUG_GCGGCACACAUAUCAGCAUAAGUCA__
.((((.....(((((...........))))).))))...............................(((....((((((((.....))))))))....)))......... (-17.48 = -18.35 +   0.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:42 2006