Locus 5394

Sequence ID	2L_DroMel_CAF1
Location	15,384,165 – 15,384,265
Length	100
Max. P	0.791774

overview

Window 3

Location	15,384,165 – 15,384,265
Length	100
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	81.45
Mean single sequence MFE	-27.96
Consensus MFE	-17.80
Energy contribution	-18.48
Covariance contribution	0.68
Combinations/Pair	1.33
Mean z-score	-1.82
Structure conservation index	0.64
SVM decision value	0.26
SVM RNA-class probability	0.656797
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15384165 100 + 22407834
UGUUGGGUGUUUCCGCCGUACACCCGAUACUUGGAAAA--AACUCUUUAUCUGGGUGUUUCUGACUCAAGCUUAAUUUGGUUUUAAGCUUAUUAGCAAAAGC
((((((((((.........)))))))))).(..((((.--.((((.......)))).))))..)...((((((((.......))))))))............ ( -26.40)
>DroSec_CAF1 129997 100 + 1
UGUUGGGUGUUUCCGCCGUACACCCGAUACUUGGAAAA--AACUCUAGAUCUGGGUGUUUCUGACCCAAGAUUAUGUCGGUUCCAAGUUUAUUAGCAAAUGC
.(((((((((.........)))))))))((((((((..--.((....(((((((((.......)))).)))))..))...)))))))).............. ( -31.40)
>DroSim_CAF1 134915 100 + 1
UGUUGGGUGUUUCCGCCGUACACCCGAUACUUGGAAAA--AACUCUAGAUCUGGGUGUUUCUGACCCAAGCUUAUGUCGGUUCCAAGUUUAUUAGCAAAUGU
.(((((((((.........)))))))))((((((((..--.((...((...(((((.......)))))..))...))...)))))))).............. ( -30.20)
>DroEre_CAF1 136325 102 + 1
UGUUGGGUGUUUCCGCCGUACACCCGAUACUUGGAAAAAUAAUUGCUUAUCUGGGCAUUUGCGACCGAAGUCUAUGUUAGUUCCAAGUUUAUUUGCUAAUGU
.(((((((((.........)))))))))((((((((...(((((((((....))))).....(((....)))...)))).)))))))).............. ( -27.40)
>DroYak_CAF1 136891 95 + 1
UGUUGGGUGUUUCCGCCGUACACCCGAUACUUGGAAAA--AAUGGUUUAUCUCGGUAUGUCUG-----AGCUUUUGUAAGAUCCUGGCAUACUAGUUAAUGU
((((((((((.........)))))))))).........--......(((.((.((((((((.(-----(.(((....))).))..)))))))))).)))... ( -24.40)
>consensus
UGUUGGGUGUUUCCGCCGUACACCCGAUACUUGGAAAA__AACUCUUUAUCUGGGUGUUUCUGACCCAAGCUUAUGUCGGUUCCAAGUUUAUUAGCAAAUGU
((((((((((.........))))))))))(((((((.........(((((.(((((.............))))).))))))))))))............... (-17.80 = -18.48 +   0.68)

alignment

secondary structure

dotplot

Window 4

Location	15,384,165 – 15,384,265
Length	100
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	81.45
Mean single sequence MFE	-25.32
Consensus MFE	-13.49
Energy contribution	-15.53
Covariance contribution	2.04
Combinations/Pair	1.10
Mean z-score	-2.28
Structure conservation index	0.53
SVM decision value	0.59
SVM RNA-class probability	0.791774
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15384165 100 - 22407834
GCUUUUGCUAAUAAGCUUAAAACCAAAUUAAGCUUGAGUCAGAAACACCCAGAUAAAGAGUU--UUUUCCAAGUAUCGGGUGUACGGCGGAAACACCCAACA
..(((((((..(((((((((.......))))))))))).)))))((((((.((((..(((..--..)))....))))))))))..((.(....).))..... ( -27.70)
>DroSec_CAF1 129997 100 - 1
GCAUUUGCUAAUAAACUUGGAACCGACAUAAUCUUGGGUCAGAAACACCCAGAUCUAGAGUU--UUUUCCAAGUAUCGGGUGUACGGCGGAAACACCCAACA
((....))......((((((((..(((.((((((.((((.......)))))))).))..)))--..))))))))...((((((.........)))))).... ( -28.90)
>DroSim_CAF1 134915 100 - 1
ACAUUUGCUAAUAAACUUGGAACCGACAUAAGCUUGGGUCAGAAACACCCAGAUCUAGAGUU--UUUUCCAAGUAUCGGGUGUACGGCGGAAACACCCAACA
..............((((((((..(((...((.((((((.......))))))..))...)))--..))))))))...((((((.........)))))).... ( -26.70)
>DroEre_CAF1 136325 102 - 1
ACAUUAGCAAAUAAACUUGGAACUAACAUAGACUUCGGUCGCAAAUGCCCAGAUAAGCAAUUAUUUUUCCAAGUAUCGGGUGUACGGCGGAAACACCCAACA
..............((((((((........(((....)))((....))..((((((....))))))))))))))...((((((.........)))))).... ( -27.30)
>DroYak_CAF1 136891 95 - 1
ACAUUAACUAGUAUGCCAGGAUCUUACAAAAGCU-----CAGACAUACCGAGAUAAACCAUU--UUUUCCAAGUAUCGGGUGUACGGCGGAAACACCCAACA
..........(((((((..((((((..(((((((-----(.........))).........)--))))..))).))).)))))))((.(....).))..... ( -16.00)
>consensus
ACAUUUGCUAAUAAACUUGGAACCAACAUAAGCUUGGGUCAGAAACACCCAGAUAAAGAGUU__UUUUCCAAGUAUCGGGUGUACGGCGGAAACACCCAACA
..............((((((((...........((((((.......))))))..............))))))))...((((((.........)))))).... (-13.49 = -15.53 +   2.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:05 2006