Locus 3909

Sequence ID	X_DroMel_CAF1
Location	10,460,190 – 10,460,281
Length	91
Max. P	0.937665

overview

Window 2

Location	10,460,190 – 10,460,281
Length	91
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	77.35
Mean single sequence MFE	-34.53
Consensus MFE	-19.89
Energy contribution	-21.20
Covariance contribution	1.31
Combinations/Pair	1.06
Mean z-score	-2.29
Structure conservation index	0.58
SVM decision value	1.26
SVM RNA-class probability	0.937665
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10460190 91 + 22224390
GAAGCGGGGAAUGGCGGUGCCCAUAUUCAAAGCGCCAAAUGG------------CAAUGCAACAGCAGCAACAAAAAGUGUG--UGGCCCGCUGGCCA---UGGGCGA
...((..((...(((((.(((((((((....(((((....))------------)..(((....))))).......))))))--.))))))))..)).---...)).. ( -31.00)
>DroSec_CAF1 4660 101 + 1
GAAGAGGGGAGAAGCGGUGCCCAUAUUCAAAGCGCCAAAUGGCGCGCUCGACUGCAAUGCAACAGCAGCAACAAAAAGUGUG--UGGCA---UGGCCA--GCGGGCGG
(((...(((..........)))...)))...(((((....)))))(((((.((((.((((.(((...((........)).))--).)))---).).))--)))))).. ( -35.40)
>DroSim_CAF1 4428 101 + 1
NNNNNNNNNNNNNNNNNNGCCCAUAUUCAAAGCGCCAAAUGGCGCGCUCGACUGCAAUGCAACAGCAGCAACAAAAAGUGUG--UGGCA---UGGCCA--GCGGGCGG
....................((.........(((((....)))))(((((.((((.((((.(((...((........)).))--).)))---).).))--)))))))) ( -30.50)
>DroYak_CAF1 4598 105 + 1
GAAGGGGGGCGAAGCGGUGCCCAUAUUCAAAGCGCCAAAUGGCGCGCUCGACUGCAAUGCAACAGCAGCAACAAAAAGUGUGUGUGGCG---UGGCAAGAGCGAGCGG
(((...(((((......)))))...)))...(((((....)))))(((((..(((.((((.(((...(((........))).))).)))---).)))....))))).. ( -41.20)
>consensus
GAAG_GGGGAGAAGCGGUGCCCAUAUUCAAAGCGCCAAAUGGCGCGCUCGACUGCAAUGCAACAGCAGCAACAAAAAGUGUG__UGGCA___UGGCCA__GCGGGCGG
..................((((.........(((((....)))))............(((....)))............((...((((......))))..)))))).. (-19.89 = -21.20 +   1.31)

alignment

secondary structure

dotplot

Window 3

Location	10,460,190 – 10,460,281
Length	91
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	77.35
Mean single sequence MFE	-30.48
Consensus MFE	-19.98
Energy contribution	-22.60
Covariance contribution	2.62
Combinations/Pair	1.08
Mean z-score	-1.65
Structure conservation index	0.66
SVM decision value	0.18
SVM RNA-class probability	0.621585
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10460190 91 - 22224390
UCGCCCA---UGGCCAGCGGGCCA--CACACUUUUUGUUGCUGCUGUUGCAUUG------------CCAUUUGGCGCUUUGAAUAUGGGCACCGCCAUUCCCCGCUUC
..(((((---(((((....)))).--.......((((..(((((....)))..(------------((....)))))..)))).))))))...((........))... ( -27.80)
>DroSec_CAF1 4660 101 - 1
CCGCCCGC--UGGCCA---UGCCA--CACACUUUUUGUUGCUGCUGUUGCAUUGCAGUCGAGCGCGCCAUUUGGCGCUUUGAAUAUGGGCACCGCUUCUCCCCUCUUC
..(((((.--..((.(---(((.(--(((((........).)).))).)))).))..(((((.(((((....))))))))))...))))).................. ( -31.40)
>DroSim_CAF1 4428 101 - 1
CCGCCCGC--UGGCCA---UGCCA--CACACUUUUUGUUGCUGCUGUUGCAUUGCAGUCGAGCGCGCCAUUUGGCGCUUUGAAUAUGGGCNNNNNNNNNNNNNNNNNN
..(((((.--..((.(---(((.(--(((((........).)).))).)))).))..(((((.(((((....))))))))))...))))).................. ( -29.70)
>DroYak_CAF1 4598 105 - 1
CCGCUCGCUCUUGCCA---CGCCACACACACUUUUUGUUGCUGCUGUUGCAUUGCAGUCGAGCGCGCCAUUUGGCGCUUUGAAUAUGGGCACCGCUUCGCCCCCCUUC
..((((((((.(((.(---((.((((.(((.....))))).)).))).)))..).)).)))))(((((....))))).........((((........))))...... ( -33.00)
>consensus
CCGCCCGC__UGGCCA___UGCCA__CACACUUUUUGUUGCUGCUGUUGCAUUGCAGUCGAGCGCGCCAUUUGGCGCUUUGAAUAUGGGCACCGCUUCUCCCC_CUUC
..(((((...((((......)))).............(((((((....)))..))))(((((.(((((....))))))))))...))))).................. (-19.98 = -22.60 +   2.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:27 2006