Locus 2970

Sequence ID	X_DroMel_CAF1
Location	7,905,524 – 7,905,724
Length	200
Max. P	0.926690

overview

Window 7

Location	7,905,524 – 7,905,644
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.42
Mean single sequence MFE	-26.30
Consensus MFE	-22.15
Energy contribution	-24.21
Covariance contribution	2.06
Combinations/Pair	1.04
Mean z-score	-1.78
Structure conservation index	0.84
SVM decision value	0.56
SVM RNA-class probability	0.781651
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7905524 120 + 22224390
AAAUGUAACGUAACCCACAACGUAAGCGUCUUCUGUACGUCACCACGCUACGUAGGCCACGUAACGGUAUGCUAACGUUACCGACGGCGCCGCAAAACCGCAAAAUCAAAAAAUACAAUA
...((((((((........))))..(((((.....(((((..(((((...))).))..))))).(((((.((....)))))))..))))).((......))............))))... ( -28.30)
>DroSec_CAF1 6165 112 + 1
AAAUGUAACGUAACCCACAACGUAAGCGUCUUCUGCACGUCACCACGCUACGUAGGCCACGUAACGGUAUGCUAACGUUACCGACGGCGCCGC--------AAAAUCAAAAAAUACAAUA
...((((((((........))))..(((((......((((..(((((...))).))..))))..(((((.((....)))))))..)))))...--------............))))... ( -25.90)
>DroSim_CAF1 9299 112 + 1
AAAUGUAACGUAACCCACAACGUAAGCGUCUUCUGCACGUCACCACGCUACGUAGGCCACGUAACGGUAUGCUAACGUUACCGACGGCGCCGC--------AAAAUCAAAAAAUACAAUA
...((((((((........))))..(((((......((((..(((((...))).))..))))..(((((.((....)))))))..)))))...--------............))))... ( -25.90)
>DroYak_CAF1 9432 119 + 1
AAAUGUAACGUAACCCACAACGUA-GCCUCUUCUGUACGUCACCACGCUACGUAGGCAACGUAACGGUAUGCUAACGUUAUCGACGGAGCCGCAAAACCGCAAAAUUAAAAAAUACAAUA
...((((............(((((-((......((.....))....))))))).(((..(((..(((((.((....))))))))))..)))((......))............))))... ( -25.10)
>consensus
AAAUGUAACGUAACCCACAACGUAAGCGUCUUCUGCACGUCACCACGCUACGUAGGCCACGUAACGGUAUGCUAACGUUACCGACGGCGCCGC________AAAAUCAAAAAAUACAAUA
...((((............(((((.((((...............))))))))).(((..(((..(((((.((....))))))))))..)))......................))))... (-22.15 = -24.21 +   2.06)

alignment

secondary structure

dotplot

Window 8

Location	7,905,604 – 7,905,724
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.61
Mean single sequence MFE	-25.11
Consensus MFE	-19.25
Energy contribution	-20.88
Covariance contribution	1.62
Combinations/Pair	1.08
Mean z-score	-2.54
Structure conservation index	0.77
SVM decision value	1.18
SVM RNA-class probability	0.926690
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7905604 120 + 22224390
CCGACGGCGCCGCAAAACCGCAAAAUCAAAAAAUACAAUAACAAAAUCGACAAAAUUAUAGAUUUUCAAUGUGCACGUCGGUUUCUUUUUGCUAGCGAAAAUCAACUAGCGCUAGUAUAU
((((((((((.((......)).....................((((((............))))))....)))).))))))........((((((((............))))))))... ( -29.10)
>DroSec_CAF1 6245 112 + 1
CCGACGGCGCCGC--------AAAAUCAAAAAAUACAAUAACAAAAUCGACAAAACUAUAGAUUUUCAAUGUGCACGUCGGUUUCUUUUUGCUAGCGAACAGCAACUAGUGCUAGUAUAU
((((((((((...--------((((((.................................))))))....)))).))))))........((((((((...((...))..))))))))... ( -24.51)
>DroSim_CAF1 9379 112 + 1
CCGACGGCGCCGC--------AAAAUCAAAAAAUACAAUAACAAAAUCGACAAAAUUAUAGAUUUUCAAUGUGCACGUCGGUUUCUUUUUGCUAGCGAACAGCAACUAGCGCUAGUAAAU
((((((((((...--------((((((.................................))))))....)))).))))))......((((((((((............)))))))))). ( -28.11)
>DroYak_CAF1 9511 120 + 1
UCGACGGAGCCGCAAAACCGCAAAAUUAAAAAAUACAAUAACAAAAUCGACAAAAUUAUAGAUUUUCUAUGUGCACGUCGGUUUCUUUUUGCUAACGAAAAACAACUAGCACAAGUAUAC
...((((((((((......))...........................(((.....(((((.....))))).....)))))))))....(((((............)))))...)).... ( -18.70)
>consensus
CCGACGGCGCCGC________AAAAUCAAAAAAUACAAUAACAAAAUCGACAAAAUUAUAGAUUUUCAAUGUGCACGUCGGUUUCUUUUUGCUAGCGAAAAGCAACUAGCGCUAGUAUAU
((((((((((.((......)).....................((((((............))))))....)))).))))))........((((((((............))))))))... (-19.25 = -20.88 +   1.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:04 2006