Locus 6284

Sequence ID	3R_DroMel_CAF1
Location	16,398,795 – 16,398,986
Length	191
Max. P	0.997383

overview

Window 9

Location	16,398,795 – 16,398,908
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	83.92
Mean single sequence MFE	-36.94
Consensus MFE	-25.95
Energy contribution	-26.67
Covariance contribution	0.72
Combinations/Pair	1.09
Mean z-score	-2.61
Structure conservation index	0.70
SVM decision value	1.52
SVM RNA-class probability	0.960841
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16398795 113 - 27905053
UUUCACUAUGUCUUCGGGUCCACCGCUCAGGUGGGCCCAAUUUCCAAGCACUAGCGCGGACUCCGAUUCUCCGAGUCGGACUCGGACUCGAACUCGGACCUCCCUCGAUGGCU
.........(((.(((((((((((.....)))))))))....(((..((....))..))).((((((((((((((.....))))))...))).)))))........)).))). ( -44.60)
>DroSec_CAF1 2556 101 - 1
UUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGGCCCAAUUUCCAAGCACUCGCGCGGACUCCGAUUCUCCG------------ACUCGAACUCGGACCUCCCUCGAUGACU
.........(((.(((((((((((.....)))))))))....(((..((....))..))).((((((((....------------....))).)))))........)).))). ( -35.80)
>DroSim_CAF1 7710 99 - 1
UUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGGCCCAAUUUCCAAGCACUCG--CGGACUCCGAUUCUCCG------------ACUCGAACUCGGACCUCCCUCGAUGGCU
...............(((((((((.....)))))))))........(((..(((--.((..((((((((....------------....))).)))))....)).)))..))) ( -35.00)
>DroEre_CAF1 3970 97 - 1
UUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGGCCCAAUUUCAAAGCACUCG--CGGACU------C--------GUAGUCGGACUCGAACUCGGACCUCCCUCGAUGGCU
.....(((((.....(((((((((.....))))))))).....)))))((.(((--.(((.(------(--------(.(((((....)).))))))...)))..)))))... ( -31.70)
>DroYak_CAF1 6363 102 - 1
UUUUACUUUGUCUUCGGGUCCACCACUCAGGUGGGCCCAAUUUUA-AGUACUCG--CGGACUUGGAGUC--------GGAGUCGGACUCGAACUCGGACCUCCCUCGAUGGCU
.........(((.(((((((((((.....)))))))))......(-(((.....--...))))((((((--------.((((((....)).)))).)).))))...)).))). ( -37.60)
>consensus
UUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGGCCCAAUUUCCAAGCACUCG__CGGACUCCGAUUCUCCG____G_A_UCGGACUCGAACUCGGACCUCCCUCGAUGGCU
.........(((.(((((((((((.....)))))))))...................(((.(((((...........................)))))..)))...)).))). (-25.95 = -26.67 +   0.72)

alignment

secondary structure

dotplot

Window 0

Location	16,398,873 – 16,398,986
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	97.96
Mean single sequence MFE	-39.00
Consensus MFE	-38.35
Energy contribution	-38.23
Covariance contribution	-0.12
Combinations/Pair	1.05
Mean z-score	-1.94
Structure conservation index	0.98
SVM decision value	2.85
SVM RNA-class probability	0.997383
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16398873 113 - 27905053
GGGCAGCGAAGUGGAACCAUUUAUUAAGUGGUACACGUAUCCGAGCGUGUAUUGUCUCUAGUAGCCGUCUAAUACUUGUUUCACUAUGUCUUCGGGUCCACCGCUCAGGUGGG
((((.(((.((((((((.(..(((((..((((((((((......))))))((((....)))).))))..)))))..))))))))).)))(....))))).((((....)))). ( -35.70)
>DroSec_CAF1 2622 113 - 1
GGGCAGCGAAGUGGAACCAUUUAUUAAGUGGUACACGUAUCCGAGCGUGUAUUGUCUCUAGGAGCCGUCUAAUACUUGUUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGG
((((.((((((((((((.(..(((((..((((((((((......))))))....((.....))))))..)))))..)))))))))))))(....))))).((((....)))). ( -40.60)
>DroSim_CAF1 7774 113 - 1
GGGCAGCGAAGUGGAACCAUUUAUUAAGUGGUACACGUAUCCGAGCGUGUAUUGUCUCUAGUAGCCGUCUAAUACUUGUUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGG
((((.((((((((((((.(..(((((..((((((((((......))))))((((....)))).))))..)))))..)))))))))))))(....))))).((((....)))). ( -39.60)
>DroEre_CAF1 4032 113 - 1
GGGCAGCGAAGUGGAACCAUUUAUUAAGUGGUACACGUAUCCGAGCGUGUAUUGUCUCUAGUAGCCGUCUAAUACUUGUUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGG
((((.((((((((((((.(..(((((..((((((((((......))))))((((....)))).))))..)))))..)))))))))))))(....))))).((((....)))). ( -39.60)
>DroYak_CAF1 6430 113 - 1
GGGCAGCGAAGUGGAACCAUUUAUUAAGUGGUACACGUAUCCAAGCGUGUAUUGUCUCUAGCAGCCGUCUAAUACUUGUUUUACUUUGUCUUCGGGUCCACCACUCAGGUGGG
((((.((((((((((((.(..(((((..((((((((((......))))))..(((.....)))))))..)))))..)))))))))))))(....))))).((((....)))). ( -39.50)
>consensus
GGGCAGCGAAGUGGAACCAUUUAUUAAGUGGUACACGUAUCCGAGCGUGUAUUGUCUCUAGUAGCCGUCUAAUACUUGUUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGG
((((.((((((((((((.(..(((((..((((((((((......)))))).............))))..)))))..)))))))))))))(....))))).((((....)))). (-38.35 = -38.23 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:39 2006