Locus 1462

Sequence ID	3R_DroMel_CAF1
Location	4,210,798 – 4,210,889
Length	91
Max. P	0.998488

overview

Window 3

Location	4,210,798 – 4,210,889
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	94.93
Mean single sequence MFE	-42.20
Consensus MFE	-39.44
Energy contribution	-39.24
Covariance contribution	-0.20
Combinations/Pair	1.06
Mean z-score	-1.98
Structure conservation index	0.93
SVM decision value	3.12
SVM RNA-class probability	0.998488
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4210798 91 + 27905053
CUUGGACGUCGACCUCGAAUGUUGCUGAUGCGGCAGCAGCAGUGGCACGGUUGUUGCUGCCGCAACGCUGGACGUCGCUGCUGCUGUCGGC
....(((((((....)).))))).......((((((((((((((((.((((.(((((....)))))))))...)))))))))))))))).. ( -46.00)
>DroSec_CAF1 22016 91 + 1
CUUGGACGUGGACCUCGAAUGUUGCUGAUGCGGCAGCAGCAGUGGCACGGUUGUUGCUGCCGCAACGCUGGACGUCGCUGCUGCUGUCGGC
....(((((.........))))).......((((((((((((((((.((((.(((((....)))))))))...)))))))))))))))).. ( -43.50)
>DroSim_CAF1 22886 91 + 1
CUUGGACGUGGACCUCGAAUGUUGCUGAUGCGGCAGCAGCAGUGGCACGGUUGUUGCUGCCGCAACGCUGGACGUCGCUGCUGCUGUCGGC
....(((((.........))))).......((((((((((((((((.((((.(((((....)))))))))...)))))))))))))))).. ( -43.50)
>DroEre_CAF1 22699 89 + 1
CUUGGACGUGGACCUCGAAUGUUGCUGAUGCGGCAGCAGCAGUGGUGCGGUGGUUGCUGCCGCAACGCUGGACGUCGCUGCUGCUGUCG--
....(((((.........)))))((....))(((((((((((((((.(((((.((((....))))))))).))..))))))))))))).-- ( -41.10)
>DroYak_CAF1 22432 89 + 1
CUUGGACGUGGACCUCGGAUGUUGCUGAUGCGGCAGCAGCAGUGGUGCGGUGGUUGUUGCCGCAACGCUGGACGUCGCUGCUGCUGGCG--
......(((.....((((......))))..((((((((((((((.(((((..(...)..))))).)))).(....))))))))))))))-- ( -36.90)
>consensus
CUUGGACGUGGACCUCGAAUGUUGCUGAUGCGGCAGCAGCAGUGGCACGGUUGUUGCUGCCGCAACGCUGGACGUCGCUGCUGCUGUCGGC
....(((((.........)))))((....))(((((((((((((((.((((.(((((....)))))))))...)))))))))))))))... (-39.44 = -39.24 +  -0.20)

alignment

secondary structure

dotplot

Window 4

Location	4,210,798 – 4,210,889
Length	91
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	94.93
Mean single sequence MFE	-31.60
Consensus MFE	-27.80
Energy contribution	-28.48
Covariance contribution	0.68
Combinations/Pair	1.04
Mean z-score	-1.31
Structure conservation index	0.88
SVM decision value	0.40
SVM RNA-class probability	0.719687
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4210798 91 - 27905053
GCCGACAGCAGCAGCGACGUCCAGCGUUGCGGCAGCAACAACCGUGCCACUGCUGCUGCCGCAUCAGCAACAUUCGAGGUCGACGUCCAAG
((.(.((((((((((((((.....))))))((((.(.......)))))..))))))))).))...........(((....)))........ ( -32.90)
>DroSec_CAF1 22016 91 - 1
GCCGACAGCAGCAGCGACGUCCAGCGUUGCGGCAGCAACAACCGUGCCACUGCUGCUGCCGCAUCAGCAACAUUCGAGGUCCACGUCCAAG
((((.((((((((((((((.....))))))((((.(.......)))))..)))))))).)((....)).........)))........... ( -32.70)
>DroSim_CAF1 22886 91 - 1
GCCGACAGCAGCAGCGACGUCCAGCGUUGCGGCAGCAACAACCGUGCCACUGCUGCUGCCGCAUCAGCAACAUUCGAGGUCCACGUCCAAG
((((.((((((((((((((.....))))))((((.(.......)))))..)))))))).)((....)).........)))........... ( -32.70)
>DroEre_CAF1 22699 89 - 1
--CGACAGCAGCAGCGACGUCCAGCGUUGCGGCAGCAACCACCGCACCACUGCUGCUGCCGCAUCAGCAACAUUCGAGGUCCACGUCCAAG
--.(((.((....))(((.((..((..((((((((((......(((....)))))))))))))...)).......)).)))...))).... ( -30.20)
>DroYak_CAF1 22432 89 - 1
--CGCCAGCAGCAGCGACGUCCAGCGUUGCGGCAACAACCACCGCACCACUGCUGCUGCCGCAUCAGCAACAUCCGAGGUCCACGUCCAAG
--.(((.((((((((((((.....))))((((.........))))......)))))))).((....)).........)))........... ( -29.50)
>consensus
GCCGACAGCAGCAGCGACGUCCAGCGUUGCGGCAGCAACAACCGUGCCACUGCUGCUGCCGCAUCAGCAACAUUCGAGGUCCACGUCCAAG
..(((((((((((((((((.....))))))(((.((.......)))))..))))))))..((....)).....))).((.......))... (-27.80 = -28.48 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:12 2006