Locus 6202

Sequence ID	3L_DroMel_CAF1
Location	16,460,619 – 16,460,712
Length	93
Max. P	0.964348

overview

Window 5

Location	16,460,619 – 16,460,712
Length	93
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	81.85
Mean single sequence MFE	-28.35
Consensus MFE	-16.40
Energy contribution	-18.15
Covariance contribution	1.75
Combinations/Pair	1.05
Mean z-score	-2.60
Structure conservation index	0.58
SVM decision value	1.05
SVM RNA-class probability	0.906529
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16460619 93 + 23771897
GGUCUGUUAGGUUUGGUGGUG-----------AAAGCUUUUAUGCUGUAGAUGUUUUUUUUUUUUACCGCUUAGCUUUUGCAAUUCAAAAUGUCACCGCCAAAC
..........(((((((((((-----------(..(((.....((.(((((...........))))).))..)))(((((.....)))))..)))))))))))) ( -25.90)
>DroSec_CAF1 72119 97 + 1
GGUCUGUUAGGUUUGGUGGUGAGUGUAAGCUGAAAGCUUUUAUGCUCUAGCUGUUU-------UUACCGCUUAGCUUUUGCAAUUCAAAAUGUAACCGCCAAAC
(((..((((.(((((((((((((....(((((..(((......))).)))))...)-------))))))))..((....))......)))).)))).))).... ( -28.90)
>DroSim_CAF1 74334 98 + 1
GUUCUGUUAGGUUUGGUGGUGAGUGUAAGCUGAAAGCUUUUAUGCUCUAGCUGUUU------UUUAGCGCUUAGCUUUUGCAAUUCAAAAAGUAACCGCCAAAC
..........((((((((((((((((((((.....)))..)))))))..((((...------..)))).....((((((........)))))).)))))))))) ( -30.20)
>DroYak_CAF1 75918 98 + 1
GGUCCGUUAUGUUUGGGGGAGAGUAUCCGCUCAAAGCUCUUAUGCUCUCGCGGUUU------UUUACCGCUUAGCUUUCGCAAUUCAAAAUUUAACCGCCAAAA
(((..((((..((((((.((((((((..((.....))....))))))))(((((..------...)))))...((....))..))))))...)))).))).... ( -28.40)
>consensus
GGUCUGUUAGGUUUGGUGGUGAGUGUAAGCUGAAAGCUUUUAUGCUCUAGCUGUUU______UUUACCGCUUAGCUUUUGCAAUUCAAAAUGUAACCGCCAAAC
..........((((((((((.......((((...(((......)))..)))).....................((....)).............)))))))))) (-16.40 = -18.15 +   1.75)

alignment

secondary structure

dotplot

Window 6

Location	16,460,619 – 16,460,712
Length	93
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	81.85
Mean single sequence MFE	-23.05
Consensus MFE	-15.15
Energy contribution	-17.15
Covariance contribution	2.00
Combinations/Pair	1.04
Mean z-score	-2.50
Structure conservation index	0.66
SVM decision value	1.57
SVM RNA-class probability	0.964348
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16460619 93 - 23771897
GUUUGGCGGUGACAUUUUGAAUUGCAAAAGCUAAGCGGUAAAAAAAAAAAACAUCUACAGCAUAAAAGCUUU-----------CACCACCAAACCUAACAGACC
((((((.(((((..((((..(((((.........)))))..)))).............(((......))).)-----------)))).)))))).......... ( -21.10)
>DroSec_CAF1 72119 97 - 1
GUUUGGCGGUUACAUUUUGAAUUGCAAAAGCUAAGCGGUAA-------AAACAGCUAGAGCAUAAAAGCUUUCAGCUUACACUCACCACCAAACCUAACAGACC
((((((.(((..........(((((.........)))))..-------....(((((((((......))))).)))).......))).)))))).......... ( -22.20)
>DroSim_CAF1 74334 98 - 1
GUUUGGCGGUUACUUUUUGAAUUGCAAAAGCUAAGCGCUAAA------AAACAGCUAGAGCAUAAAAGCUUUCAGCUUACACUCACCACCAAACCUAACAGAAC
((((((.(((....(((((.....)))))(.((((((((...------....))).(((((......)))))..))))))....))).)))))).......... ( -22.40)
>DroYak_CAF1 75918 98 - 1
UUUUGGCGGUUAAAUUUUGAAUUGCGAAAGCUAAGCGGUAAA------AAACCGCGAGAGCAUAAGAGCUUUGAGCGGAUACUCUCCCCCAAACAUAACGGACC
.(((((.((..............((....))...(((((...------..)))))(((((.((....((.....))..)).))))))))))))........... ( -26.50)
>consensus
GUUUGGCGGUUACAUUUUGAAUUGCAAAAGCUAAGCGGUAAA______AAACAGCUAGAGCAUAAAAGCUUUCAGCUUACACUCACCACCAAACCUAACAGACC
((((((.(((..........(((((.........))))).............(((((((((......))))).)))).......))).)))))).......... (-15.15 = -17.15 +   2.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:38 2006