Locus 1030

Sequence ID	3R_DroMel_CAF1
Location	3,219,473 – 3,219,573
Length	100
Max. P	0.980760

overview

Window 8

Location	3,219,473 – 3,219,573
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	97.70
Mean single sequence MFE	-30.43
Consensus MFE	-29.03
Energy contribution	-29.27
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.26
Structure conservation index	0.95
SVM decision value	0.48
SVM RNA-class probability	0.752892
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3219473 100 + 27905053
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGGAGCUUUGGGCCCCCACCCGCAUUU
.........((((((.(((((.((....))......(((((((((....))).......)))))).))))).((((.((.....)))))).))))))... ( -32.11)
>DroSec_CAF1 44194 100 + 1
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGGAGCUUUGGGCCCCCACCCGCAUUU
.........((((((.(((((.((....))......(((((((((....))).......)))))).))))).((((.((.....)))))).))))))... ( -32.11)
>DroSim_CAF1 45556 100 + 1
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGGAGCUUUGGGCCCCCACCCGCAUUU
.........((((((.(((((.((....))......(((((((((....))).......)))))).))))).((((.((.....)))))).))))))... ( -32.11)
>DroEre_CAF1 38521 98 + 1
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGCAGCUUUGGGCCCCCACUCGCAU--
.......((.((((..(((((.((....))......(((((((((....))).......)))))).))))).((((........))))))))..))..-- ( -26.21)
>DroYak_CAF1 28846 100 + 1
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGGAGCUUUGGGCCCCCACCCGGAUUG
.(((((((..(((((..((((((...((................))...))))))......(((((((((.....)))))))))...)))))))))))). ( -29.59)
>consensus
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGGAGCUUUGGGCCCCCACCCGCAUUU
.........((((((.(((((.((....))......(((((((((....))).......)))))).))))).((((.((.....)))))).))))))... (-29.03 = -29.27 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	3,219,473 – 3,219,573
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	97.70
Mean single sequence MFE	-28.55
Consensus MFE	-28.31
Energy contribution	-28.35
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	0.99
SVM decision value	1.87
SVM RNA-class probability	0.980760
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3219473 100 - 27905053
AAAUGCGGGUGGGGGCCCAAAGCUCCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
.....((((.((((((.....))))))))))(((.(((((.......((((....)))))))))...)))..((((((((.........))).))))).. ( -29.11)
>DroSec_CAF1 44194 100 - 1
AAAUGCGGGUGGGGGCCCAAAGCUCCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
.....((((.((((((.....))))))))))(((.(((((.......((((....)))))))))...)))..((((((((.........))).))))).. ( -29.11)
>DroSim_CAF1 45556 100 - 1
AAAUGCGGGUGGGGGCCCAAAGCUCCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
.....((((.((((((.....))))))))))(((.(((((.......((((....)))))))))...)))..((((((((.........))).))))).. ( -29.11)
>DroEre_CAF1 38521 98 - 1
--AUGCGAGUGGGGGCCCAAAGCUGCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
--..(((((..(((((........)))).(((((..(((((......((((....)))).......))))).))))))..)))))............... ( -26.22)
>DroYak_CAF1 28846 100 - 1
CAAUCCGGGUGGGGGCCCAAAGCUCCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
.....((((.((((((.....))))))))))(((.(((((.......((((....)))))))))...)))..((((((((.........))).))))).. ( -29.21)
>consensus
AAAUGCGGGUGGGGGCCCAAAGCUCCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
.....((((.((((((.....))))))))))(((.(((((.......((((....)))))))))...)))..((((((((.........))).))))).. (-28.31 = -28.35 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:48 2006