Locus 6542

Sequence ID	3L_DroMel_CAF1
Location	17,291,209 – 17,291,329
Length	120
Max. P	0.930517

overview

Window 9

Location	17,291,209 – 17,291,329
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-29.51
Consensus MFE	-26.99
Energy contribution	-28.24
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.91
SVM decision value	0.36
SVM RNA-class probability	0.704254
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17291209 120 + 23771897
GUUUUUUAUCUUGUUGCUCUGGCCGACGGUAUUGGUAUUGGCAUUGGCAUUGGCACUUUCUUCACACAAUACUCAGAGCCAAUAUCAAUUGCGCCUUUGCAAUUUGCCAACAUUUUGCAG
............(((((....).))))(((((((((((((((.((((.((((..............)))).).))).))))))))))))...)))..(((((..((....))..))))). ( -30.24)
>DroSec_CAF1 174972 120 + 1
GUUUUUUAUCUUGUUGCUCUAGCCGACGGUAUUGGUAUUGGCAUUGGCAUUGGCACUUUCUUCACACAAUACUCAGAGCCAAUAUCAAUUGCGCCUUUGCAAUUUGCCAACAUUUUGCAG
............(((((....).))))(((((((((((((((.((((.((((..............)))).).))).))))))))))))...)))..(((((..((....))..))))). ( -30.14)
>DroSim_CAF1 171185 120 + 1
GUUUUUUAUCUUGUUGCUCUAGCCGACGGUAUUGGUAUUGGCAUUGGCAUUGGCACUUUCUUCACACAAUACUCAGAGCCAAUAUCAAUUGCGCCUUUGCAAUUUGCCAACAUUUUGCAG
............(((((....).))))(((((((((((((((.((((.((((..............)))).).))).))))))))))))...)))..(((((..((....))..))))). ( -30.14)
>DroYak_CAF1 183696 114 + 1
GUUUUUUAUCUGGUUGCUCCAGCUGACGGUAUUGGUAUUGGC------AUUGGCACUUUCCUCACACAAUACUCAGAGCCAAUAUCAACUGCGCCUUUGCAAUUUGCCAACAUUUUGCAG
.....(((.((((.....)))).))).(((.(((((((((((------.((((...................)))).)))))))))))....)))..(((((..((....))..))))). ( -27.51)
>consensus
GUUUUUUAUCUUGUUGCUCUAGCCGACGGUAUUGGUAUUGGCAUUGGCAUUGGCACUUUCUUCACACAAUACUCAGAGCCAAUAUCAAUUGCGCCUUUGCAAUUUGCCAACAUUUUGCAG
............(((((....)).)))(((((((((((((((.((((.((((..............)))).).))).))))))))))))...)))..(((((..((....))..))))). (-26.99 = -28.24 +   1.25)

alignment

secondary structure

dotplot

Window 0

Location	17,291,209 – 17,291,329
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-31.55
Consensus MFE	-28.35
Energy contribution	-28.98
Covariance contribution	0.62
Combinations/Pair	1.06
Mean z-score	-2.15
Structure conservation index	0.90
SVM decision value	1.21
SVM RNA-class probability	0.930517
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17291209 120 - 23771897
CUGCAAAAUGUUGGCAAAUUGCAAAGGCGCAAUUGAUAUUGGCUCUGAGUAUUGUGUGAAGAAAGUGCCAAUGCCAAUGCCAAUACCAAUACCGUCGGCCAGAGCAACAAGAUAAAAAAC
........(((((((.....))...((((..((((.(((((((..((.((((((.((.........))))))))))..))))))).))))..))))........)))))........... ( -31.50)
>DroSec_CAF1 174972 120 - 1
CUGCAAAAUGUUGGCAAAUUGCAAAGGCGCAAUUGAUAUUGGCUCUGAGUAUUGUGUGAAGAAAGUGCCAAUGCCAAUGCCAAUACCAAUACCGUCGGCUAGAGCAACAAGAUAAAAAAC
.(((.....((((((....(((......)))((((.(((((((..((.((((((.((.........))))))))))..))))))).))))...))))))....))).............. ( -31.70)
>DroSim_CAF1 171185 120 - 1
CUGCAAAAUGUUGGCAAAUUGCAAAGGCGCAAUUGAUAUUGGCUCUGAGUAUUGUGUGAAGAAAGUGCCAAUGCCAAUGCCAAUACCAAUACCGUCGGCUAGAGCAACAAGAUAAAAAAC
.(((.....((((((....(((......)))((((.(((((((..((.((((((.((.........))))))))))..))))))).))))...))))))....))).............. ( -31.70)
>DroYak_CAF1 183696 114 - 1
CUGCAAAAUGUUGGCAAAUUGCAAAGGCGCAGUUGAUAUUGGCUCUGAGUAUUGUGUGAGGAAAGUGCCAAU------GCCAAUACCAAUACCGUCAGCUGGAGCAACCAGAUAAAAAAC
.(((((..((....))..)))))..((((..((((.(((((((..((.(((((..........)))))))..------))))))).))))..))))..((((.....))))......... ( -31.30)
>consensus
CUGCAAAAUGUUGGCAAAUUGCAAAGGCGCAAUUGAUAUUGGCUCUGAGUAUUGUGUGAAGAAAGUGCCAAUGCCAAUGCCAAUACCAAUACCGUCGGCUAGAGCAACAAGAUAAAAAAC
.(((.....((((((....(((......)))((((.(((((((..((.((((((.((.........))))))))))..))))))).))))...))))))....))).............. (-28.35 = -28.98 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:44 2006