Locus 1542

Sequence ID	3L_DroMel_CAF1
Location	4,463,354 – 4,463,454
Length	100
Max. P	0.752315

overview

Window 8

Location	4,463,354 – 4,463,454
Length	100
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	91.30
Mean single sequence MFE	-30.70
Consensus MFE	-22.26
Energy contribution	-21.83
Covariance contribution	-0.44
Combinations/Pair	1.14
Mean z-score	-2.37
Structure conservation index	0.73
SVM decision value	0.40
SVM RNA-class probability	0.721900
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4463354 100 + 23771897
GCCACUAAGUAUUAACGAAAUAUACUUAAAAUAUUAAGUGGCCGUUUGGAUGAUUUGGCGGUUAGGCCGGGGGUGAAAGGGGGACUCCCAAAUC---GUGGCU
(((((..........((((...(((((((....)))))))....))))...((((((((......)))((((((.........)))))))))))---))))). ( -31.90)
>DroSec_CAF1 40899 100 + 1
GCCACUAAGUAUUAACGAAAUAUAUUAAAAAUAUUAAGUGGCCGUUUGGAUGAUUUGGAGGUUAGGCCGGGGGAGAAAGGGGGACCCCCAAAUC---GUGGCU
((((((.((((((................)))))).)))))).......(((((((((.((((...((..........))..)))).)))))))---)).... ( -28.69)
>DroEre_CAF1 44584 100 + 1
GCCACUAAGAAUUAAUGAAAUAUACUAAAAAUAUUAAGUGGCCGUUUGGCUGCUUUGGAGGUUAGGACGGGGGAGAAAGGGGGACUCCCAAAUC---GUGGCU
(((((...................((((.......(((..(((....)))..)))......))))((...(((((.........)))))...))---))))). ( -30.22)
>DroYak_CAF1 42773 103 + 1
GCCACUAAGUAUUAAUGAAAUAUAUUAAAAGUAUUAAGUGGCCGUUUGGCUGUUUAGGUGGUUAGGCCGGGGGAGAAAGGGGGACCCCCAAAUCGUCGUGGCU
((((((..(((((.....)))))...........((((..(((....)))..))))))))))..(((((.((..((...(((....)))...)).)).))))) ( -32.00)
>consensus
GCCACUAAGUAUUAACGAAAUAUACUAAAAAUAUUAAGUGGCCGUUUGGAUGAUUUGGAGGUUAGGCCGGGGGAGAAAGGGGGACCCCCAAAUC___GUGGCU
(((((.........((..(((((.......)))))..))((((.....................))))(((((...........)))))........))))). (-22.26 = -21.83 +  -0.44)

alignment

secondary structure

dotplot

Window 9

Location	4,463,354 – 4,463,454
Length	100
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	91.30
Mean single sequence MFE	-24.68
Consensus MFE	-17.50
Energy contribution	-18.25
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-3.24
Structure conservation index	0.71
SVM decision value	0.48
SVM RNA-class probability	0.752315
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4463354 100 - 23771897
AGCCAC---GAUUUGGGAGUCCCCCUUUCACCCCCGGCCUAACCGCCAAAUCAUCCAAACGGCCACUUAAUAUUUUAAGUAUAUUUCGUUAAUACUUAGUGGC
.(((((---((((((((((.......))).....(((.....)))))))))).....(((((..((((((....)))))).....)))))........))))) ( -25.20)
>DroSec_CAF1 40899 100 - 1
AGCCAC---GAUUUGGGGGUCCCCCUUUCUCCCCCGGCCUAACCUCCAAAUCAUCCAAACGGCCACUUAAUAUUUUUAAUAUAUUUCGUUAAUACUUAGUGGC
.(((((---(((((((((((...((..........))....))))))))))).....(((((......(((((.......))))))))))........))))) ( -26.50)
>DroEre_CAF1 44584 100 - 1
AGCCAC---GAUUUGGGAGUCCCCCUUUCUCCCCCGUCCUAACCUCCAAAGCAGCCAAACGGCCACUUAAUAUUUUUAGUAUAUUUCAUUAAUUCUUAGUGGC
.(((((---(((..(((((.........)))))..)))((((......(((..(((....)))..))).......))))...................))))) ( -22.62)
>DroYak_CAF1 42773 103 - 1
AGCCACGACGAUUUGGGGGUCCCCCUUUCUCCCCCGGCCUAACCACCUAAACAGCCAAACGGCCACUUAAUACUUUUAAUAUAUUUCAUUAAUACUUAGUGGC
.(((((........(((((...........)))))((((.....................))))..................................))))) ( -24.40)
>consensus
AGCCAC___GAUUUGGGAGUCCCCCUUUCUCCCCCGGCCUAACCUCCAAAUCAGCCAAACGGCCACUUAAUAUUUUUAAUAUAUUUCAUUAAUACUUAGUGGC
.(((((........(((((...........)))))((((.....................))))..................................))))) (-17.50 = -18.25 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:16 2006