Locus 2219

Sequence ID	X_DroMel_CAF1
Location	5,987,894 – 5,988,024
Length	130
Max. P	0.938275

overview

Window 8

Location	5,987,894 – 5,987,984
Length	90
Sequences	3
Columns	91
Reading direction	forward
Mean pairwise identity	79.12
Mean single sequence MFE	-28.33
Consensus MFE	-22.26
Energy contribution	-22.77
Covariance contribution	0.50
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.79
SVM decision value	1.21
SVM RNA-class probability	0.931270
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5987894 90 + 22224390
ACAGAAGCACGACGACCUGUUGUCCGUCCAUCAACGAGCUUCCUUUGGCUCCUC-GUCCCCUUGUCCAUUCGACCAUUUGACAGGACGAGG
..........(((((...((((.........))))(((((......))))).))-))).((((((((..((((....))))..)))))))) ( -28.20)
>DroSec_CAF1 3075 72 + 1
ACAGAAGCACGACGACCUGUUGUCCG----------A---------GGCUCCUCUGGCUCCUCGUCCCCUCGCUCAUUUGACAGGACGAGG
.(((((((..(((((....)))))..----------.---------.)))..))))...((((((((..(((......)))..)))))))) ( -26.60)
>DroSim_CAF1 4628 91 + 1
ACAGAAGCACGACGACCUGUUGUCCGUCCAUCAACGAGGCUCCUCUGGCUCCUCUGGCUCCUCGUCCCCUCGCUCAUUUGACAGGACGAGG
.(((((((..((((..(....)..)))).......(((....)))..)))..))))...((((((((..(((......)))..)))))))) ( -30.20)
>consensus
ACAGAAGCACGACGACCUGUUGUCCGUCCAUCAACGAG__UCCU_UGGCUCCUCUGGCUCCUCGUCCCCUCGCUCAUUUGACAGGACGAGG
.(((((((..(((((....)))))...........(((....)))..)))..))))...((((((((..(((......)))..)))))))) (-22.26 = -22.77 +   0.50)

alignment

secondary structure

dotplot

Window 9

Location	5,987,894 – 5,987,984
Length	90
Sequences	3
Columns	91
Reading direction	reverse
Mean pairwise identity	79.12
Mean single sequence MFE	-33.63
Consensus MFE	-24.90
Energy contribution	-27.07
Covariance contribution	2.17
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.74
SVM decision value	1.27
SVM RNA-class probability	0.938275
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5987894 90 - 22224390
CCUCGUCCUGUCAAAUGGUCGAAUGGACAAGGGGAC-GAGGAGCCAAAGGAAGCUCGUUGAUGGACGGACAACAGGUCGUCGUGCUUCUGU
(((((((((.(......(((.....))).).)))))-)))).......((((((....(((((..(........)..))))).)))))).. ( -31.50)
>DroSec_CAF1 3075 72 - 1
CCUCGUCCUGUCAAAUGAGCGAGGGGACGAGGAGCCAGAGGAGCC---------U----------CGGACAACAGGUCGUCGUGCUUCUGU
(((((((((.((........)).)))))))))...((((((.((.---------.----------((..(....)..))..)).)))))). ( -31.50)
>DroSim_CAF1 4628 91 - 1
CCUCGUCCUGUCAAAUGAGCGAGGGGACGAGGAGCCAGAGGAGCCAGAGGAGCCUCGUUGAUGGACGGACAACAGGUCGUCGUGCUUCUGU
(((((((((.((........)).)))))))))...((((((.((..(((....))).......((((..(....)..)))))).)))))). ( -37.90)
>consensus
CCUCGUCCUGUCAAAUGAGCGAGGGGACGAGGAGCCAGAGGAGCCA_AGGA__CUCGUUGAUGGACGGACAACAGGUCGUCGUGCUUCUGU
(((((((((.((........)).)))))))))......(((((((.(((....))).......((((..(....)..))))).)))))).. (-24.90 = -27.07 +   2.17)

alignment

secondary structure

dotplot

Window 0

Location	5,987,914 – 5,988,024
Length	110
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	71.66
Mean single sequence MFE	-36.40
Consensus MFE	-21.37
Energy contribution	-23.43
Covariance contribution	2.06
Combinations/Pair	1.08
Mean z-score	-1.79
Structure conservation index	0.59
SVM decision value	0.98
SVM RNA-class probability	0.893537
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5987914 110 - 22224390
GCCACGUGAAUACGUGCAUUGUAUUCAUUACACAAAUGCGCCUCGUCCUGUCAA-------AUGGUCGAAUGGACAAGGGGAC-GAGGAGCCAAAGGAAGCUCGUUGAUGGACGGACA
.((..(((((((((.....))))))))).........((.(((((((((.(...-------...(((.....))).).)))))-)))).))....))..(..((((....))))..). ( -35.30)
>DroSec_CAF1 3095 92 - 1
GCCACGUGAGUACGUGCAUUGUAUUCAUUACACAAAUGUGCCUCGUCCUGUCAA-------AUGAGCGAGGGGACGAGGAGCCAGAGGAGCC---------U----------CGGACA
.....(((((((((.....)))))))))..(((....)))(((((((((.((..-------......)).))))))))).(((.(((....)---------)----------))).). ( -35.00)
>DroSim_CAF1 4648 111 - 1
GCCACGUGAGUACGUGCAUUGUAUUCAUUACACAAAUGUGCCUCGUCCUGUCAA-------AUGAGCGAGGGGACGAGGAGCCAGAGGAGCCAGAGGAGCCUCGUUGAUGGACGGACA
.((..(((((((((.....)))))))))..(((((..((.(((((((((.((..-------......)).))))))))).))..((((..((...))..)))).))).))...))... ( -41.10)
>DroYak_CAF1 4999 98 - 1
GCCACU-GAGUACGUGCACUGUAUUCAUUACACAAAUGCGCCUCGUCCCGUCAGGAAGGAGAGC--------GAGGAGGGGCGAGAG-----------UCCUUGUUGUGGGACGGAUA
.((..(-(((((((.....))))))))...(((((.....(((((((((........)).)).)--------))))((((((....)-----------))))).)))))....))... ( -34.20)
>consensus
GCCACGUGAGUACGUGCAUUGUAUUCAUUACACAAAUGCGCCUCGUCCUGUCAA_______AUGAGCGAGGGGACGAGGAGCCAGAGGAGCC_______CCUCGUUGAUGGACGGACA
.((..(((((((((.....))))))))).........((.(((((((((.((...............)).))))))))).))...............................))... (-21.37 = -23.43 +   2.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:05 2006