Locus 17

Sequence ID	3R_DroMel_CAF1
Location	186,734 – 186,826
Length	92
Max. P	0.694417

overview

Window 1

Location	186,734 – 186,826
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	84.67
Mean single sequence MFE	-32.73
Consensus MFE	-24.32
Energy contribution	-25.08
Covariance contribution	0.76
Combinations/Pair	1.12
Mean z-score	-1.76
Structure conservation index	0.74
SVM decision value	0.34
SVM RNA-class probability	0.694417
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 186734 92 + 27905053
CCCUCGCGCUCUCGCUCUCUCUUAAGAGAGAGGGAGAGGAGAGUCCCGACGCUCGGGAAUUUGCUUUAAGUGUGCGCUGUUAUCACACCAGC
..(((.(.(((((.(((((((....))))))).)))))).)))(((((.....)))))....(((....(((((.........))))).))) ( -37.90)
>DroSec_CAF1 21023 92 + 1
CCCUCGCGCUCUCGCUCUCUCCUAAGAGAGUGGGAGAGGAGAGUCCCGUCGCUUGGGCAUUUGAUUUAAGUGUGCGCUGUUAUCACACCAGC
(((..(((((((((((((((....)))))))))))).((......))..)))..)))....((((...(((....)))...))))....... ( -32.90)
>DroSim_CAF1 20947 92 + 1
CCCUCGCGCUCUCGCUCUCUCCUAAGAGAGUGGGAGAGGAGAGUCCCGUCGCUCGGGCAUUUGCUUUAAGUGUGCGCUGUUAUCACACCAGC
.....(((((((((((((((....)))))))))))((((..(((((((.....)))).)))..))))....))))((((.........)))) ( -34.70)
>DroEre_CAF1 21721 92 + 1
CCCUCGCGCUCUCGUUCUCUCUUCAGAGAGAGGGAGAGGAGAGACACGGUCCUCGGGCAUUUGCUUAAAAUGUGCGCUGUUAUCACACCAGC
........(((((.(((((((....))))))).)))))(((.(((...))))))(.((((((.....)))))).)((((.........)))) ( -33.00)
>DroYak_CAF1 22602 81 + 1
-----------UCGUUCUCUCUUCAGAGAGAGGGAGAGGCGAGACCCGUUGCUCGAGAAUUUGAGUUAAAUGUGCGCUGUUAUUACAGCAGC
-----------((.(((((((....))))))).))...(((.........((((((....))))))......)))(((((....)))))... ( -25.16)
>consensus
CCCUCGCGCUCUCGCUCUCUCUUAAGAGAGAGGGAGAGGAGAGUCCCGUCGCUCGGGCAUUUGCUUUAAGUGUGCGCUGUUAUCACACCAGC
........(((((.(((((((....))))))).)))))..(((........)))(.((((((.....)))))).)((((.........)))) (-24.32 = -25.08 +   0.76)

alignment

secondary structure

dotplot

Window 2

Location	186,734 – 186,826
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	84.67
Mean single sequence MFE	-30.88
Consensus MFE	-23.08
Energy contribution	-25.56
Covariance contribution	2.48
Combinations/Pair	1.04
Mean z-score	-1.74
Structure conservation index	0.75
SVM decision value	0.31
SVM RNA-class probability	0.683220
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 186734 92 - 27905053
GCUGGUGUGAUAACAGCGCACACUUAAAGCAAAUUCCCGAGCGUCGGGACUCUCCUCUCCCUCUCUCUUAAGAGAGAGCGAGAGCGCGAGGG
(((((((((.........))))))...)))....(((((.....)))))(((.((((((.(((((((....))))))).))))).).))).. ( -40.60)
>DroSec_CAF1 21023 92 - 1
GCUGGUGUGAUAACAGCGCACACUUAAAUCAAAUGCCCAAGCGACGGGACUCUCCUCUCCCACUCUCUUAGGAGAGAGCGAGAGCGCGAGGG
...((((((.........))))))...........(((..(((......((((((((((((.........)).))))).))))))))..))) ( -28.70)
>DroSim_CAF1 20947 92 - 1
GCUGGUGUGAUAACAGCGCACACUUAAAGCAAAUGCCCGAGCGACGGGACUCUCCUCUCCCACUCUCUUAGGAGAGAGCGAGAGCGCGAGGG
(((((((((.........))))))...))).....((((.....)))).(((.((((((.(.(((((....))))).).))))).).))).. ( -33.50)
>DroEre_CAF1 21721 92 - 1
GCUGGUGUGAUAACAGCGCACAUUUUAAGCAAAUGCCCGAGGACCGUGUCUCUCCUCUCCCUCUCUCUGAAGAGAGAACGAGAGCGCGAGGG
(((.(((((.......)))))......))).....(((((((((...))).)))(((((..((((((....))))))..))))).....))) ( -30.80)
>DroYak_CAF1 22602 81 - 1
GCUGCUGUAAUAACAGCGCACAUUUAACUCAAAUUCUCGAGCAACGGGUCUCGCCUCUCCCUCUCUCUGAAGAGAGAACGA-----------
((.(((((....))))))).................(((......(((..........)))((((((....)))))).)))----------- ( -20.80)
>consensus
GCUGGUGUGAUAACAGCGCACACUUAAAGCAAAUGCCCGAGCGACGGGACUCUCCUCUCCCUCUCUCUUAAGAGAGAGCGAGAGCGCGAGGG
((((.........))))..................((((.....)))).(((.((((((.(((((((....))))))).))))).).))).. (-23.08 = -25.56 +   2.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:20 2006