Locus 5786

Sequence ID	3R_DroMel_CAF1
Location	15,087,811 – 15,087,915
Length	104
Max. P	0.891535

overview

Window 3

Location	15,087,811 – 15,087,915
Length	104
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	76.17
Mean single sequence MFE	-24.43
Consensus MFE	-11.22
Energy contribution	-11.83
Covariance contribution	0.61
Combinations/Pair	1.06
Mean z-score	-2.05
Structure conservation index	0.46
SVM decision value	0.44
SVM RNA-class probability	0.735536
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15087811 104 + 27905053
GAACAGAUCAAUGCUCCCUCCCAGGAGUGGGAC-----------ACCGCGAAGAUUGGUAGAUUGAGGCAAGCAGAAAUAUUGGCAAAAAUGCCAAUAAAUUUUUGACAAGACAU
.......((((((((.((((((((..((((...-----------.)))).....))))......))))..))))....((((((((....)))))))).....))))........ ( -27.30)
>DroPse_CAF1 11917 94 + 1
GAACAGAUCAAUGC-------AAGGGGCAGCAA-----------GCGGGCAGCAA--UCAGAUUGAAAUGGACA-AAAUAUUGGCAAAAAUGCCAAUAAAUUUUUGACAAGACAU
...((..(((((.(-------..(..((.((..-----------....)).))..--)..))))))..))..((-(((((((((((....))))))))...)))))......... ( -18.90)
>DroSec_CAF1 12641 98 + 1
GAACAGAUCAAUGC------CCAGGAGUGGGAC-----------ACCGCGAAGAUUGGUAGAUUGAGGCAAGCAGAAAUAUUGGCAAAAAUGCCAAUAAAUUUUUGACAAGACAU
.....(.(((((..------((((..((((...-----------.)))).....))))...)))))..)..(((((((((((((((....))))))))..)))))).)....... ( -24.40)
>DroEre_CAF1 12407 100 + 1
GAACAGAUCAAUGCUC----CCAGGAGUGGGAC-----------ACCGCGAAGAUUGGUGGAUCGCGGCAAACAGAAAUACUGGCAAAAAUGCCAAUAAAUUUUUGACAAGACAU
.....((((.....((----(((....)))))(-----------((((.......)))))))))........(((((((..(((((....)))))....)))))))......... ( -25.50)
>DroAna_CAF1 10365 109 + 1
GAACAGAUCACAGAUG----CGGAGAGUGGGUCUGGACGGUCUUACCGCGAAGAUUGCCAGAUUGAACCGAC--AAAAUAUUGGCAAAAAUGCCAAUAAAUUUUUGACAAGACAU
..........((((((----(((....(.(((((((.(((((((......)))))))))))))).).))).)--)...((((((((....))))))))....))))......... ( -31.60)
>DroPer_CAF1 7153 94 + 1
GAACAGAUCAAUGC-------AAGGGGCAGCAA-----------GCGGGCAGCAA--UCAGAUUGAAAUGGACA-AAAUAUUGGCAAAAAUGCCAAUAAAUUUUUGACAAGACAU
...((..(((((.(-------..(..((.((..-----------....)).))..--)..))))))..))..((-(((((((((((....))))))))...)))))......... ( -18.90)
>consensus
GAACAGAUCAAUGC______CCAGGAGUGGGAC___________ACCGCGAAGAUUGGCAGAUUGAAGCAAACAGAAAUAUUGGCAAAAAUGCCAAUAAAUUUUUGACAAGACAU
...((((...................((((...............)))).............................((((((((....))))))))....))))......... (-11.22 = -11.83 +   0.61)

alignment

secondary structure

dotplot

Window 4

Location	15,087,811 – 15,087,915
Length	104
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	76.17
Mean single sequence MFE	-24.03
Consensus MFE	-10.38
Energy contribution	-9.55
Covariance contribution	-0.83
Combinations/Pair	1.27
Mean z-score	-2.36
Structure conservation index	0.43
SVM decision value	0.97
SVM RNA-class probability	0.891535
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15087811 104 - 27905053
AUGUCUUGUCAAAAAUUUAUUGGCAUUUUUGCCAAUAUUUCUGCUUGCCUCAAUCUACCAAUCUUCGCGGU-----------GUCCCACUCCUGGGAGGGAGCAUUGAUCUGUUC
.......(((((.....((((((((....))))))))....(((((.((((....((((.........)))-----------)..(((....)))))))))))))))))...... ( -27.70)
>DroPse_CAF1 11917 94 - 1
AUGUCUUGUCAAAAAUUUAUUGGCAUUUUUGCCAAUAUUU-UGUCCAUUUCAAUCUGA--UUGCUGCCCGC-----------UUGCUGCCCCUU-------GCAUUGAUCUGUUC
.......(.(((((...((((((((....)))))))))))-)).)((..((((((...--..((.((....-----------..)).)).....-------).)))))..))... ( -18.50)
>DroSec_CAF1 12641 98 - 1
AUGUCUUGUCAAAAAUUUAUUGGCAUUUUUGCCAAUAUUUCUGCUUGCCUCAAUCUACCAAUCUUCGCGGU-----------GUCCCACUCCUGG------GCAUUGAUCUGUUC
.................((((((((....))))))))..............................((((-----------(.((((....)))------))))))........ ( -19.60)
>DroEre_CAF1 12407 100 - 1
AUGUCUUGUCAAAAAUUUAUUGGCAUUUUUGCCAGUAUUUCUGUUUGCCGCGAUCCACCAAUCUUCGCGGU-----------GUCCCACUCCUGG----GAGCAUUGAUCUGUUC
.......(((((.....((((((((....))))))))....(((..(((((((...........)))))))-----------.(((((....)))----))))))))))...... ( -30.20)
>DroAna_CAF1 10365 109 - 1
AUGUCUUGUCAAAAAUUUAUUGGCAUUUUUGCCAAUAUUUU--GUCGGUUCAAUCUGGCAAUCUUCGCGGUAAGACCGUCCAGACCCACUCUCCG----CAUCUGUGAUCUGUUC
..(((((..(.......((((((((....))))))))..((--(((((......))))))).......)..))))).(..((((..(((......----.....))).))))..) ( -29.70)
>DroPer_CAF1 7153 94 - 1
AUGUCUUGUCAAAAAUUUAUUGGCAUUUUUGCCAAUAUUU-UGUCCAUUUCAAUCUGA--UUGCUGCCCGC-----------UUGCUGCCCCUU-------GCAUUGAUCUGUUC
.......(.(((((...((((((((....)))))))))))-)).)((..((((((...--..((.((....-----------..)).)).....-------).)))))..))... ( -18.50)
>consensus
AUGUCUUGUCAAAAAUUUAUUGGCAUUUUUGCCAAUAUUUCUGUUCGCCUCAAUCUACCAAUCUUCGCGGU___________GUCCCACUCCUGG______GCAUUGAUCUGUUC
.......(((((.....((((((((....))))))))........((........))...............................................)))))...... (-10.38 =  -9.55 +  -0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:47 2006