Locus 10204

Sequence ID	3R_DroMel_CAF1
Location	27,376,041 – 27,376,132
Length	91
Max. P	0.999103

overview

Window 6

Location	27,376,041 – 27,376,132
Length	91
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	94.81
Mean single sequence MFE	-33.00
Consensus MFE	-28.02
Energy contribution	-28.66
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-3.01
Structure conservation index	0.85
SVM decision value	3.37
SVM RNA-class probability	0.999103
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27376041 91 + 27905053
UGCCAGCAUUUUCGCGUUGCUGCCUAUCGGCAGAUACAAUUCCACGGC------CACGGCAGCGCGAAUAAGCUGAAUAAAGUGAAUAAACUGCACG
(((((((...((((((((((((((....))))............((..------..))))))))))))...)))).....(((......)))))).. ( -32.20)
>DroSec_CAF1 121407 97 + 1
UGCCAGCAUUUUCGCGUUGCUGCCUAUCGGCAGAUACAAUUCCACGGCCACGGCCACGGCAGCGCGAAUAAACUGAAUAAAGUGAAUAAACUGCACG
((((((....((((((((((((((....)))..............(((....)))..)))))))))))....))).....(((......)))))).. ( -34.10)
>DroSim_CAF1 85629 97 + 1
UGCCAGCAUUUUCGCGUUGCUGCCUAUCGGCAGAUACAAUUCCACGGCCACGGCCACGGCAGCGCGAAUAAACUGAAUAAAGUGAAUAAAAUGCACG
.....(((((((((((((((((((....)))..............(((....)))..))))))))))....(((......))).....))))))... ( -34.30)
>DroEre_CAF1 89197 91 + 1
UGGCAGCAUUUUCGCGUUGCUGCCUAUCGGCAGAUACAAUUCCACGGC------CACGGCAGCGCGAAUAAACUGAAUAAAGUGAAUAAACUGCACG
..((((....((((((((((((((....))))............((..------..))))))))))))...(((......))).......))))... ( -29.40)
>DroYak_CAF1 79237 97 + 1
UGGCAGCAUUUUCGCGUUGCUGCCUAUCGGCAGAUACAAUUCCACGGCCACGGCCACGGCAGCGCGAAUAAACUGAAUAAAGUGAAUAAACUGCACG
..((((....((((((((((((((....)))..............(((....)))..)))))))))))...(((......))).......))))... ( -35.00)
>consensus
UGCCAGCAUUUUCGCGUUGCUGCCUAUCGGCAGAUACAAUUCCACGGCCACGGCCACGGCAGCGCGAAUAAACUGAAUAAAGUGAAUAAACUGCACG
.....(((..((((((((((((((....)))..............(((....)))..)))))))))))...(((......)))........)))... (-28.02 = -28.66 +   0.64)

alignment

secondary structure

dotplot

Window 7

Location	27,376,041 – 27,376,132
Length	91
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	94.81
Mean single sequence MFE	-31.72
Consensus MFE	-27.52
Energy contribution	-28.16
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.75
Structure conservation index	0.87
SVM decision value	1.55
SVM RNA-class probability	0.963039
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27376041 91 - 27905053
CGUGCAGUUUAUUCACUUUAUUCAGCUUAUUCGCGCUGCCGUG------GCCGUGGAAUUGUAUCUGCCGAUAGGCAGCAACGCGAAAAUGCUGGCA
..((((((......))).....((((...(((((((((((.((------((...(((......)))))))...))))))...)))))...))))))) ( -31.00)
>DroSec_CAF1 121407 97 - 1
CGUGCAGUUUAUUCACUUUAUUCAGUUUAUUCGCGCUGCCGUGGCCGUGGCCGUGGAAUUGUAUCUGCCGAUAGGCAGCAACGCGAAAAUGCUGGCA
..((((((......))).....((((...((((((.(((((((((....)))))))........(((((....))))))).))))))...))))))) ( -33.20)
>DroSim_CAF1 85629 97 - 1
CGUGCAUUUUAUUCACUUUAUUCAGUUUAUUCGCGCUGCCGUGGCCGUGGCCGUGGAAUUGUAUCUGCCGAUAGGCAGCAACGCGAAAAUGCUGGCA
.(((.(......)))).....(((((...((((((.(((((((((....)))))))........(((((....))))))).))))))...))))).. ( -32.40)
>DroEre_CAF1 89197 91 - 1
CGUGCAGUUUAUUCACUUUAUUCAGUUUAUUCGCGCUGCCGUG------GCCGUGGAAUUGUAUCUGCCGAUAGGCAGCAACGCGAAAAUGCUGCCA
.(.(((((......(((......)))...(((((((((((.((------((...(((......)))))))...))))))...)))))...)))))). ( -29.10)
>DroYak_CAF1 79237 97 - 1
CGUGCAGUUUAUUCACUUUAUUCAGUUUAUUCGCGCUGCCGUGGCCGUGGCCGUGGAAUUGUAUCUGCCGAUAGGCAGCAACGCGAAAAUGCUGCCA
.(.(((((......(((......)))...((((((.(((((((((....)))))))........(((((....))))))).))))))...)))))). ( -32.90)
>consensus
CGUGCAGUUUAUUCACUUUAUUCAGUUUAUUCGCGCUGCCGUGGCCGUGGCCGUGGAAUUGUAUCUGCCGAUAGGCAGCAACGCGAAAAUGCUGGCA
.(((.(.....).)))......((((...((((((.(((((((((....)))))))........(((((....))))))).))))))...))))... (-27.52 = -28.16 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:19 2006