Locus 489

Sequence ID	X_DroMel_CAF1
Location	1,417,163 – 1,417,263
Length	100
Max. P	0.881617

overview

Window 2

Location	1,417,163 – 1,417,263
Length	100
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	81.69
Mean single sequence MFE	-30.84
Consensus MFE	-18.12
Energy contribution	-18.60
Covariance contribution	0.48
Combinations/Pair	1.14
Mean z-score	-1.94
Structure conservation index	0.59
SVM decision value	0.20
SVM RNA-class probability	0.630469
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1417163 100 + 22224390
GAUGUGGAGGUUGGGUGGUUGUGGGUGGUGGGUGGUGGGUGGUGGGCCCACCAAGAAGUGCCACCAAGCA-AGCGCUAGAAAAAAGCAUGCGAAAGUGCGC
.((((.....((.((((.((((.((((((...((((((((.....))))))))......))))))..)))-).)))).)).....))))((....)).... ( -39.40)
>DroSec_CAF1 23631 94 + 1
GAUGUGGGGGUUGGGUGAUUG--GG---UGG-CUGUGAGUGGUGGGCCCACCAAGAAGUGCCACCAGGCA-AGCGCUAGAAAAAAGCAUGCGAAAGUGCGC
.((((.....((.((((.(((--((---(((-(......(((((....)))))......))))))...))-).)))).)).....))))((....)).... ( -31.10)
>DroSim_CAF1 14252 95 + 1
GAUGUGGGGGUUGGGUGAUUG--GG---UGG-CUGUGGGUGGUGGGCCCACCAAGAAGUGCCACCAAGCAAAGCGCUAGAAAAAAGCAUGCGAAAGUGCGC
......((.(((..((.....--((---(((-(......(((((....)))))......))))))..))..))).))........((..((....))..)) ( -32.40)
>DroEre_CAF1 18940 89 + 1
G-CGU-----AUGGGUGGUCGUGGG---UGU-UCGUGGGUGGUGGACCCAGCAAGAAGUGCCACC-AGCA-AGCGCUAGAAAAAAGCAUGCGAAAGUGCGC
(-(((-----((.((((((......---(((-...(((((.....))))))))......))))))-.(((-.((...........)).)))....)))))) ( -30.40)
>DroYak_CAF1 15164 83 + 1
-------------GGUGGUGAUGGG---UGG-AAUUGGGCGGUGGACCCAGCAAGAAGUGCCAUCAAGCA-AGCGCUAGAAAAAAGCAUGCGAAAGUGCGC
-------------.((..((((((.---...-...(((((....).))))((.....)).)))))).)).-.(((((.......)))..((....)))).. ( -20.90)
>consensus
GAUGUGG_GGUUGGGUGGUUGUGGG___UGG_CUGUGGGUGGUGGGCCCACCAAGAAGUGCCACCAAGCA_AGCGCUAGAAAAAAGCAUGCGAAAGUGCGC
.............((((((.........(((....(((((.....))))))))......)))))).......(((((.......)))..((....)))).. (-18.12 = -18.60 +   0.48)

alignment

secondary structure

dotplot

Window 3

Location	1,417,163 – 1,417,263
Length	100
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	81.69
Mean single sequence MFE	-22.28
Consensus MFE	-16.38
Energy contribution	-16.66
Covariance contribution	0.28
Combinations/Pair	1.11
Mean z-score	-2.00
Structure conservation index	0.74
SVM decision value	0.92
SVM RNA-class probability	0.881617
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1417163 100 - 22224390
GCGCACUUUCGCAUGCUUUUUUCUAGCGCU-UGCUUGGUGGCACUUCUUGGUGGGCCCACCACCCACCACCCACCACCCACAACCACCCAACCUCCACAUC
((((......))..(((.......))))).-((..((((((.......(((((((.......))))))).))))))..))..................... ( -24.80)
>DroSec_CAF1 23631 94 - 1
GCGCACUUUCGCAUGCUUUUUUCUAGCGCU-UGCCUGGUGGCACUUCUUGGUGGGCCCACCACUCACAG-CCA---CC--CAAUCACCCAACCCCCACAUC
((((......))..(((.......))))).-.....((((((......(((((....)))))......)-)))---))--..................... ( -24.30)
>DroSim_CAF1 14252 95 - 1
GCGCACUUUCGCAUGCUUUUUUCUAGCGCUUUGCUUGGUGGCACUUCUUGGUGGGCCCACCACCCACAG-CCA---CC--CAAUCACCCAACCCCCACAUC
((((......))..(((.......))))).......((((((......(((((....)))))......)-)))---))--..................... ( -24.30)
>DroEre_CAF1 18940 89 - 1
GCGCACUUUCGCAUGCUUUUUUCUAGCGCU-UGCU-GGUGGCACUUCUUGCUGGGUCCACCACCCACGA-ACA---CCCACGACCACCCAU-----ACG-C
(((.......(((((((.......))))..-))).-(((((..........(((((.....)))))((.-...---....)).)))))...-----.))-) ( -20.10)
>DroYak_CAF1 15164 83 - 1
GCGCACUUUCGCAUGCUUUUUUCUAGCGCU-UGCUUGAUGGCACUUCUUGCUGGGUCCACCGCCCAAUU-CCA---CCCAUCACCACC-------------
((((......))..(((.......))))).-....((((((((.....)))(((((.....)))))...-...---..))))).....------------- ( -17.90)
>consensus
GCGCACUUUCGCAUGCUUUUUUCUAGCGCU_UGCUUGGUGGCACUUCUUGGUGGGCCCACCACCCACAA_CCA___CCCACAACCACCCAACC_CCACAUC
((.((((...(((((((.......))))...)))..)))))).......(((((.....)))))..................................... (-16.38 = -16.66 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:49 2006