Locus 2401

Sequence ID	3R_DroMel_CAF1
Location	6,751,364 – 6,751,483
Length	119
Max. P	0.756952

overview

Window 1

Location	6,751,364 – 6,751,483
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.14
Mean single sequence MFE	-38.67
Consensus MFE	-34.62
Energy contribution	-34.88
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.90
SVM decision value	0.49
SVM RNA-class probability	0.756952
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6751364 119 + 27905053
ACAGUUUUUAUUUUUU-UUGUUUCGCUUCCUUUUUGGCCACAAGUUGCGCGCUUGUUUGGCCAAGUUGAGAUCCCGGGAGGGCGGCAGUGGAUGCUCGGCCGAAGUUGUGCACAAUUUUC
................-((((((((((.((..(((((((((((((.....))))))..))))))).......(((....))).)).)))))).((.((((....)))).))))))..... ( -34.30)
>DroSec_CAF1 15553 120 + 1
AAAGUUUUUUUUUUUUUGUGUUUCGCUUCCUUUUUGGCCACAAGUUGCGCGCUUGUUUGGCCAAGUUGAGAUCCCGGGAGGGCGGCAGUGGAUGCUCCGCCGAAGUUGUGCACAAUUUUC
...............((((((...((((((..(((((((((((((.....))))))..)))))))..)............(((((.(((....)))))))))))))...))))))..... ( -40.10)
>DroSim_CAF1 19931 120 + 1
AAAGUUUUUUUUUUUUUGUGUUUCGCUUCCUUUUUGGCCACAAGUUGCGCGCUUGUUUGGCCAAGUUGAGAUCCCGGGAGGGCGGCAGUGGAUGCUCCGCCGAAGUUGUGCACAAUUUUC
...............((((((...((((((..(((((((((((((.....))))))..)))))))..)............(((((.(((....)))))))))))))...))))))..... ( -40.10)
>DroYak_CAF1 11878 118 + 1
AAAGUUUUUUUUU--GUAUUUUUCGCUUCCUUUUUGGCCACAAGUUGCGCGCUUGUUUGGCCAAGUUGGGAUCUCGGGAGGGCGGCAGUGGAUGCUCCGCCGAAGUUGUGCACAAUUUUC
.............--....((..((..((((.(((((((((((((.....))))))..)))))))..))))...))..))(((((.(((....))))))))(((((((....))))))). ( -40.20)
>consensus
AAAGUUUUUUUUUUUUUGUGUUUCGCUUCCUUUUUGGCCACAAGUUGCGCGCUUGUUUGGCCAAGUUGAGAUCCCGGGAGGGCGGCAGUGGAUGCUCCGCCGAAGUUGUGCACAAUUUUC
....................(..((..(((..(((((((((((((.....))))))..)))))))..).))...))..).(((((.(((....))))))))(((((((....))))))). (-34.62 = -34.88 +   0.25)

alignment

secondary structure

dotplot

Window 2

Location	6,751,364 – 6,751,483
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.14
Mean single sequence MFE	-29.65
Consensus MFE	-25.34
Energy contribution	-25.65
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.87
Structure conservation index	0.85
SVM decision value	0.42
SVM RNA-class probability	0.729830
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6751364 119 - 27905053
GAAAAUUGUGCACAACUUCGGCCGAGCAUCCACUGCCGCCCUCCCGGGAUCUCAACUUGGCCAAACAAGCGCGCAACUUGUGGCCAAAAAGGAAGCGAAACAA-AAAAAAUAAAAACUGU
.....((((((.(......(((((((((.....)))..(((....)))........))))))......).)))))).((((..((.....))..)))).....-................ ( -26.80)
>DroSec_CAF1 15553 120 - 1
GAAAAUUGUGCACAACUUCGGCGGAGCAUCCACUGCCGCCCUCCCGGGAUCUCAACUUGGCCAAACAAGCGCGCAACUUGUGGCCAAAAAGGAAGCGAAACACAAAAAAAAAAAAACUUU
.....(((((.....(((((((((........))))).(((....)))........((((((..(((((.......)))))))))))....)))).....)))))............... ( -31.50)
>DroSim_CAF1 19931 120 - 1
GAAAAUUGUGCACAACUUCGGCGGAGCAUCCACUGCCGCCCUCCCGGGAUCUCAACUUGGCCAAACAAGCGCGCAACUUGUGGCCAAAAAGGAAGCGAAACACAAAAAAAAAAAAACUUU
.....(((((.....(((((((((........))))).(((....)))........((((((..(((((.......)))))))))))....)))).....)))))............... ( -31.50)
>DroYak_CAF1 11878 118 - 1
GAAAAUUGUGCACAACUUCGGCGGAGCAUCCACUGCCGCCCUCCCGAGAUCCCAACUUGGCCAAACAAGCGCGCAACUUGUGGCCAAAAAGGAAGCGAAAAAUAC--AAAAAAAAACUUU
.....(((((.........(((((((......)).)))))....((...(((....((((((..(((((.......)))))))))))...)))..)).....)))--))........... ( -28.80)
>consensus
GAAAAUUGUGCACAACUUCGGCGGAGCAUCCACUGCCGCCCUCCCGGGAUCUCAACUUGGCCAAACAAGCGCGCAACUUGUGGCCAAAAAGGAAGCGAAACACAAAAAAAAAAAAACUUU
........(((.......((((((........))))))(((....))).(((....((((((..(((((.......)))))))))))...))).)))....................... (-25.34 = -25.65 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:42 2006