Locus 4716

Sequence ID	3R_DroMel_CAF1
Location	12,385,848 – 12,385,941
Length	93
Max. P	0.758862

overview

Window 7

Location	12,385,848 – 12,385,941
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	84.78
Mean single sequence MFE	-24.78
Consensus MFE	-17.16
Energy contribution	-18.04
Covariance contribution	0.88
Combinations/Pair	1.07
Mean z-score	-1.61
Structure conservation index	0.69
SVM decision value	-0.05
SVM RNA-class probability	0.510515
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12385848 93 + 27905053
UUAUAUUGAAUGCGAGAGAAGGCCCGAUUGUGUCCGGGCCUGAAAAGCCGGCAAAAAAAAAAAAAAAAACCCGGUCAAGCGUGGGACACGCCG
.....((((..........(((((((........)))))))......((((...................))))))))(((((...))))).. ( -24.81)
>DroSec_CAF1 54286 82 + 1
UUAUAUUGAAUGCGAGAGAAGGCCCGAUUGUGUACGGGUCUGAAAAGCCGG-----------AAAAAAACCCGGUCAAGCGUGGGACACGCCG
.....((((..........(((((((........)))))))......((((-----------........))))))))(((((...))))).. ( -24.10)
>DroSim_CAF1 53634 82 + 1
UUAUAUUGAAUGCGAGAGAAGGCCCGAUUGUGUACGGGCCUGAAAAGCCGG-----------AAAAAAACCCGGUCAAGCGUGGGACACGCCG
.....((((..........(((((((........)))))))......((((-----------........))))))))(((((...))))).. ( -26.80)
>DroEre_CAF1 54966 71 + 1
UUAUAUUGAAUGCGAGAGAAAGCCCGCUUGUGACCGG-------------GCC---------AAAAAAACCCGGUCAAGCGUGGGACACGCCG
...........(((.(......(((((...(((((((-------------(..---------.......))))))))...))))).).))).. ( -25.20)
>DroYak_CAF1 51729 84 + 1
UUAUAUUGAAUGCGAGAGAAGGCCCGUUUGUGUCAGGGCCUGAAAACCCGGCA---------AAAAAAACCCGGUCAAGCGUGGGACACGCCG
.....((((..........((((((..........))))))......((((..---------........))))))))(((((...))))).. ( -23.00)
>consensus
UUAUAUUGAAUGCGAGAGAAGGCCCGAUUGUGUCCGGGCCUGAAAAGCCGGC__________AAAAAAACCCGGUCAAGCGUGGGACACGCCG
...........(((.....(((((((........)))))))............................(((((.....).))))...))).. (-17.16 = -18.04 +   0.88)

alignment

secondary structure

dotplot

Window 8

Location	12,385,848 – 12,385,941
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	84.78
Mean single sequence MFE	-25.72
Consensus MFE	-16.03
Energy contribution	-17.83
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-2.36
Structure conservation index	0.62
SVM decision value	0.50
SVM RNA-class probability	0.758862
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12385848 93 - 27905053
CGGCGUGUCCCACGCUUGACCGGGUUUUUUUUUUUUUUUUUGCCGGCUUUUCAGGCCCGGACACAAUCGGGCCUUCUCUCGCAUUCAAUAUAA
..((((((((...((((((((((...................))))....))))))..))))))....(((......)))))........... ( -24.81)
>DroSec_CAF1 54286 82 - 1
CGGCGUGUCCCACGCUUGACCGGGUUUUUUU-----------CCGGCUUUUCAGACCCGUACACAAUCGGGCCUUCUCUCGCAUUCAAUAUAA
.((((((...))))))((((((((......)-----------))))......((.((((........)))).))..........)))...... ( -20.60)
>DroSim_CAF1 53634 82 - 1
CGGCGUGUCCCACGCUUGACCGGGUUUUUUU-----------CCGGCUUUUCAGGCCCGUACACAAUCGGGCCUUCUCUCGCAUUCAAUAUAA
.((((((...))))))((((((((......)-----------))))......(((((((........)))))))..........)))...... ( -27.70)
>DroEre_CAF1 54966 71 - 1
CGGCGUGUCCCACGCUUGACCGGGUUUUUUU---------GGC-------------CCGGUCACAAGCGGGCUUUCUCUCGCAUUCAAUAUAA
.((((((...))))))((((((((((.....---------)))-------------)))))))...(((((......)))))........... ( -30.20)
>DroYak_CAF1 51729 84 - 1
CGGCGUGUCCCACGCUUGACCGGGUUUUUUU---------UGCCGGGUUUUCAGGCCCUGACACAAACGGGCCUUCUCUCGCAUUCAAUAUAA
.((((((...)))))).((((.(((......---------.))).))))...((((((..........))))))................... ( -25.30)
>consensus
CGGCGUGUCCCACGCUUGACCGGGUUUUUUU__________GCCGGCUUUUCAGGCCCGGACACAAUCGGGCCUUCUCUCGCAUUCAAUAUAA
.((((((...))))))(((((((...................))))......(((((((........)))))))..........)))...... (-16.03 = -17.83 +   1.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:15 2006