Locus 1000

Sequence ID 3R_DroMel_CAF1
Location 3,190,131 – 3,190,236
Length 105
Max. P 0.633130
window1620

overview

Window 0

Location 3,190,131 – 3,190,236
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.55
Mean single sequence MFE -37.82
Consensus MFE -25.05
Energy contribution -26.17
Covariance contribution 1.12
Combinations/Pair 1.12
Mean z-score -1.83
Structure conservation index 0.66
SVM decision value 0.21
SVM RNA-class probability 0.633130
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3190131 105 + 27905053
UCCACAGGGUCCACAGGGUCCACAGCAGGAUCCGCACGGCCCACAUCGGGGUCCACAAGGUCCACAGCAGGGACCACA------GCAGUAAUAUCC---------GCAGCACGAUCCACA
......(((((....((((((......))))))((..(((((......))))).....(((((.......)))))...------((.(......).---------)).))..)))))... ( -36.50)
>DroSec_CAF1 9586 105 + 1
UCCACAGGGUCCACAGGGUCCACAGCAGGAUCCGCACGGACCACAUCGGGGUCCACAAGGUCCACAGCAGGGACCACA------GCAGUAACAUCC---------GCAGCACGAUCCACA
......(((((....((((((......))))))((..(((((.......)))))....(((((.......)))))...------((.(......).---------)).))..)))))... ( -37.50)
>DroSim_CAF1 16201 105 + 1
UCCACAGGGUCCACAGGGUCCACAGCAGGAUCCGCACGGACCACAUCGGGGUCCACAAGGUCCACAGCAGGGACCACA------GCAGUAACAUCC---------GCAGCACGAUCCACA
......(((((....((((((......))))))((..(((((.......)))))....(((((.......)))))...------((.(......).---------)).))..)))))... ( -37.50)
>DroEre_CAF1 10938 120 + 1
UCCACAGGGUCCACAGGGUCCACAGCAGGGUCCACACGGACCGCAACAUGGUCCACAAGGUCGACAGCAGGGUCCACAGGGGGAGCAGCAAUAGCCGCAGGGUCCGCAGCACGAUCCACA
(((...((..((...((..((......))..))....((((((.....))))))...............))..))....)))..((.((....)).)).(((((........)))))... ( -39.30)
>DroYak_CAF1 15024 111 + 1
UCCACAG---------GGUCCACAGCAGGAUCCACACGGACCACAACGUGGUCCACAAGGUCCACAGCAGGGUCCACAGGGAGAGCAGUAAUAUCCGCAAGGUCCACAGCACGAUCCACA
(((...(---------(((((......))))))....(((((.....((((.((....)).)))).....)))))....)))..((.((.....((....))...)).)).......... ( -38.30)
>consensus
UCCACAGGGUCCACAGGGUCCACAGCAGGAUCCGCACGGACCACAUCGGGGUCCACAAGGUCCACAGCAGGGACCACA______GCAGUAAUAUCC_________GCAGCACGAUCCACA
......(((((.....(((((...((.(((.((....(((((.......)))))....)))))...))..))))).........((.((................)).))..)))))... (-25.05 = -26.17 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:02 2006