Locus 3880

Sequence ID	3L_DroMel_CAF1
Location	11,236,120 – 11,236,216
Length	96
Max. P	0.721644

overview

Window 6

Location	11,236,120 – 11,236,216
Length	96
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	89.39
Mean single sequence MFE	-23.00
Consensus MFE	-19.58
Energy contribution	-19.98
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.35
Structure conservation index	0.85
SVM decision value	0.13
SVM RNA-class probability	0.595788
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11236120 96 + 23771897
AAUUUUUUCGAGAACAAGUAUCCGGCAGAUACAUCUGAAUUGCCACGAAGUGGCCACAAUGCUGC---GGCAUUGGAUCGUUUUUUUUUUUUUUUUU-UU
.........((((((..(((((.....)))))....((...(((((...)))))..((((((...---.))))))..))))))))............-.. ( -21.70)
>DroSec_CAF1 44658 88 + 1
AAUU-UUUCGAGAACAAGUAUCCGGCAGAUACAUCUGAAUUGCCACGAAGUGGCCACAAUGCUGCGGCGGCAUUGGAUCGUUUUU----------GU-UU
....-...(((((((..(((((.....)))))....((...(((((...)))))..((((((((...))))))))..))))))))----------).-.. ( -25.50)
>DroSim_CAF1 44891 88 + 1
AAUU-UUUCGAGAACAAGUAUCCGGCAGAUACAUCUGAAUUGCCACGAAGUGGCCACAAUGCUGCGGCGGCAUUGGAUCGUUUUU----------GU-UU
....-...(((((((..(((((.....)))))....((...(((((...)))))..((((((((...))))))))..))))))))----------).-.. ( -25.50)
>DroEre_CAF1 46543 86 + 1
AAUUUUUUCGAGAACAAGUAUCCGGCAGAUACAUCUGAAUUGCCACGAAGUGGCCACAAUGCUGC---GGCAUUGAAUAUUUUUU----------GU-UU
...........(((((((((((.....))))).........(((((...)))))..((((((...---.))))))........))----------))-)) ( -20.50)
>DroYak_CAF1 47809 86 + 1
AAUUU-CCCGAGAACAAGUAUCCGGCAGAUACAUCUGAAUUGCCACGAAGUGGCCACAAUGCUGC---GGCAUUGGAUCUUUUUU----------GUUUU
.....-....((((((((((((.....)))))(((......(((((...)))))..((((((...---.))))))))).....))----------))))) ( -21.80)
>consensus
AAUUUUUUCGAGAACAAGUAUCCGGCAGAUACAUCUGAAUUGCCACGAAGUGGCCACAAUGCUGC___GGCAUUGGAUCGUUUUU__________GU_UU
.........((((((..(((((.....))))).........(((((...)))))..(((((((.....)))))))....))))))............... (-19.58 = -19.98 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	11,236,120 – 11,236,216
Length	96
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	89.39
Mean single sequence MFE	-19.92
Consensus MFE	-19.76
Energy contribution	-19.44
Covariance contribution	-0.32
Combinations/Pair	1.09
Mean z-score	-1.21
Structure conservation index	0.99
SVM decision value	0.40
SVM RNA-class probability	0.721644
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11236120 96 - 23771897
AA-AAAAAAAAAAAAAAAAACGAUCCAAUGCC---GCAGCAUUGUGGCCACUUCGUGGCAAUUCAGAUGUAUCUGCCGGAUACUUGUUCUCGAAAAAAUU
..-......................((((((.---...))))))..(((((...)))))..((((((.(((((.....)))))....))).)))...... ( -20.20)
>DroSec_CAF1 44658 88 - 1
AA-AC----------AAAAACGAUCCAAUGCCGCCGCAGCAUUGUGGCCACUUCGUGGCAAUUCAGAUGUAUCUGCCGGAUACUUGUUCUCGAAA-AAUU
..-..----------..........((((((.......))))))..(((((...)))))..((((((.(((((.....)))))....))).))).-.... ( -19.90)
>DroSim_CAF1 44891 88 - 1
AA-AC----------AAAAACGAUCCAAUGCCGCCGCAGCAUUGUGGCCACUUCGUGGCAAUUCAGAUGUAUCUGCCGGAUACUUGUUCUCGAAA-AAUU
..-..----------..........((((((.......))))))..(((((...)))))..((((((.(((((.....)))))....))).))).-.... ( -19.90)
>DroEre_CAF1 46543 86 - 1
AA-AC----------AAAAAAUAUUCAAUGCC---GCAGCAUUGUGGCCACUUCGUGGCAAUUCAGAUGUAUCUGCCGGAUACUUGUUCUCGAAAAAAUU
..-..----------..........((((((.---...))))))..(((((...)))))..((((((.(((((.....)))))....))).)))...... ( -20.00)
>DroYak_CAF1 47809 86 - 1
AAAAC----------AAAAAAGAUCCAAUGCC---GCAGCAUUGUGGCCACUUCGUGGCAAUUCAGAUGUAUCUGCCGGAUACUUGUUCUCGGG-AAAUU
..(((----------((.....(((((((((.---...))))))..(((((...)))))......)))(((((.....))))))))))......-..... ( -19.60)
>consensus
AA_AC__________AAAAACGAUCCAAUGCC___GCAGCAUUGUGGCCACUUCGUGGCAAUUCAGAUGUAUCUGCCGGAUACUUGUUCUCGAAAAAAUU
.........................((((((.......))))))..(((((...)))))..((((((.(((((.....)))))....))).)))...... (-19.76 = -19.44 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:59 2006