Locus 812

Sequence ID X_DroMel_CAF1
Location 2,253,714 – 2,253,812
Length 98
Max. P 0.704252
window1312 window1313

overview

Window 2

Location 2,253,714 – 2,253,812
Length 98
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 87.04
Mean single sequence MFE -32.65
Consensus MFE -23.82
Energy contribution -24.48
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.73
SVM decision value -0.05
SVM RNA-class probability 0.507760
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2253714 98 + 22224390
CAAUGUGCCACCAGCAACAGUGCAACGUUGCA--------ACAUCGCAACAUCGCAGAUGCACUGCAGCCAUU-ACUCAGCCUUACAUGGACAU------GGGGUGGCUAGCU
......((((((.((..((((((...(((((.--------.....)))))(((...)))))))))..))....-..(((.((......))...)------))))))))..... ( -32.60)
>DroSec_CAF1 16544 98 + 1
CAAUGUGCCACCAGCAACAGUGCAACAUUGCA--------ACAUCGCAACAUCGCAGAUGCACUGCAGCCAUU-ACUCAGCCUUACAUGGACAU------GGGGUGGCUAGCU
......((((((.((..(((((((...((((.--------.............)))).)))))))..))....-..(((.((......))...)------))))))))..... ( -29.24)
>DroYak_CAF1 17601 113 + 1
CAAUGUGCCACCAGCAACAGUGCAACAUUUCAGCCAUUCCACAUUGCAACAUCGCAGAUGCAGUGCAGCCAUUGACUCGGCCUUACAUGGACAUGGAAAUGGGGUGGCUGGCU
......((((((.(((....)))..(((((...(((((((((((((((.(......).)))))))..(((........)))......)))).))))))))).))))))..... ( -36.10)
>consensus
CAAUGUGCCACCAGCAACAGUGCAACAUUGCA________ACAUCGCAACAUCGCAGAUGCACUGCAGCCAUU_ACUCAGCCUUACAUGGACAU______GGGGUGGCUAGCU
......((((((.((..(((((((...((((......................)))).)))))))..))..........(((......)).)..........))))))..... (-23.82 = -24.48 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 2,253,714 – 2,253,812
Length 98
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 87.04
Mean single sequence MFE -36.60
Consensus MFE -32.23
Energy contribution -31.57
Covariance contribution -0.66
Combinations/Pair 1.11
Mean z-score -1.69
Structure conservation index 0.88
SVM decision value 0.36
SVM RNA-class probability 0.704252
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2253714 98 - 22224390
AGCUAGCCACCCC------AUGUCCAUGUAAGGCUGAGU-AAUGGCUGCAGUGCAUCUGCGAUGUUGCGAUGU--------UGCAACGUUGCACUGUUGCUGGUGGCACAUUG
.....((((((.(------(.(((.......)))))...-...(((.((((((((......((((((((....--------)))))))))))))))).)))))))))...... ( -36.70)
>DroSec_CAF1 16544 98 - 1
AGCUAGCCACCCC------AUGUCCAUGUAAGGCUGAGU-AAUGGCUGCAGUGCAUCUGCGAUGUUGCGAUGU--------UGCAAUGUUGCACUGUUGCUGGUGGCACAUUG
.....((((((.(------(.(((.......)))))...-...(((.((((((((..((((((((....))))--------))))....)))))))).)))))))))...... ( -36.50)
>DroYak_CAF1 17601 113 - 1
AGCCAGCCACCCCAUUUCCAUGUCCAUGUAAGGCCGAGUCAAUGGCUGCACUGCAUCUGCGAUGUUGCAAUGUGGAAUGGCUGAAAUGUUGCACUGUUGCUGGUGGCACAUUG
.....((((((.(((((((((.(((((((..(((((......)))))(((..(((((...)))))))).)))))))))))...)))))..(((....))).))))))...... ( -36.60)
>consensus
AGCUAGCCACCCC______AUGUCCAUGUAAGGCUGAGU_AAUGGCUGCAGUGCAUCUGCGAUGUUGCGAUGU________UGCAAUGUUGCACUGUUGCUGGUGGCACAUUG
.....((((((..............(((((.((((........))))....)))))..(((((..((((((((............))))))))..))))).))))))...... (-32.23 = -31.57 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:22 2006