Locus 3914

Sequence ID 3R_DroMel_CAF1
Location 10,658,965 – 10,659,065
Length 100
Max. P 0.837741
window6268 window6269

overview

Window 8

Location 10,658,965 – 10,659,065
Length 100
Sequences 3
Columns 100
Reading direction forward
Mean pairwise identity 98.67
Mean single sequence MFE -29.43
Consensus MFE -26.89
Energy contribution -29.00
Covariance contribution 2.11
Combinations/Pair 1.04
Mean z-score -1.93
Structure conservation index 0.91
SVM decision value 0.33
SVM RNA-class probability 0.690000
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10658965 100 + 27905053
GGAGCGGCAGAAACGGGCUGCCAAAAAGUGCUAACUCUAAUGGCCAUAAAUUCACAGUGACCAUGAAAGUGGUGCAAAGACCUGGAUUAGCCGACAGCCU
((..((((.((..((((((((((...(((....)))....))))............((.(((((....)))))))..)).))))..)).))))....)). ( -30.70)
>DroSec_CAF1 633 100 + 1
GGAGCGGCAGAAACGGGCUGCCAAAAAGUGCUAACUCUAAUGGCCAUAAAUUCACAGUGACCAUGAAAGUGGUGCAAAGACCUGGAUUAGCCGACAGCCU
((..((((.((..((((((((((...(((....)))....))))............((.(((((....)))))))..)).))))..)).))))....)). ( -30.70)
>DroSim_CAF1 646 100 + 1
GGAGCGGCAAAAAAGGGCUGCCAAAAAGUGCUAACUCUAAUGGCCAUAAAUUCACAGUGACCAUGAAAGUGGUGCAAAGACCUGGAUUAGCCGACAGCCU
((..((((......(((((((((...(((....)))....))))............((.(((((....)))))))..)).)))......))))....)). ( -26.90)
>consensus
GGAGCGGCAGAAACGGGCUGCCAAAAAGUGCUAACUCUAAUGGCCAUAAAUUCACAGUGACCAUGAAAGUGGUGCAAAGACCUGGAUUAGCCGACAGCCU
((..((((.((..((((((((((...(((....)))....))))............((.(((((....)))))))..)).))))..)).))))....)). (-26.89 = -29.00 +   2.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 10,658,965 – 10,659,065
Length 100
Sequences 3
Columns 100
Reading direction reverse
Mean pairwise identity 98.67
Mean single sequence MFE -29.50
Consensus MFE -29.50
Energy contribution -29.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 1.00
SVM decision value 0.74
SVM RNA-class probability 0.837741
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10658965 100 - 27905053
AGGCUGUCGGCUAAUCCAGGUCUUUGCACCACUUUCAUGGUCACUGUGAAUUUAUGGCCAUUAGAGUUAGCACUUUUUGGCAGCCCGUUUCUGCCGCUCC
.(((((((((((......))))..(((...(((((.(((((((.((......))))))))).)))))..)))......)))))))............... ( -29.50)
>DroSec_CAF1 633 100 - 1
AGGCUGUCGGCUAAUCCAGGUCUUUGCACCACUUUCAUGGUCACUGUGAAUUUAUGGCCAUUAGAGUUAGCACUUUUUGGCAGCCCGUUUCUGCCGCUCC
.(((((((((((......))))..(((...(((((.(((((((.((......))))))))).)))))..)))......)))))))............... ( -29.50)
>DroSim_CAF1 646 100 - 1
AGGCUGUCGGCUAAUCCAGGUCUUUGCACCACUUUCAUGGUCACUGUGAAUUUAUGGCCAUUAGAGUUAGCACUUUUUGGCAGCCCUUUUUUGCCGCUCC
.(((((((((((......))))..(((...(((((.(((((((.((......))))))))).)))))..)))......)))))))............... ( -29.50)
>consensus
AGGCUGUCGGCUAAUCCAGGUCUUUGCACCACUUUCAUGGUCACUGUGAAUUUAUGGCCAUUAGAGUUAGCACUUUUUGGCAGCCCGUUUCUGCCGCUCC
.(((((((((((......))))..(((...(((((.(((((((.((......))))))))).)))))..)))......)))))))............... (-29.50 = -29.50 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:15 2006