Locus 6764

Sequence ID	2L_DroMel_CAF1
Location	18,907,122 – 18,907,212
Length	90
Max. P	0.907519

overview

Window 1

Location	18,907,122 – 18,907,212
Length	90
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	79.72
Mean single sequence MFE	-36.83
Consensus MFE	-25.53
Energy contribution	-26.12
Covariance contribution	0.59
Combinations/Pair	1.37
Mean z-score	-1.24
Structure conservation index	0.69
SVM decision value	0.13
SVM RNA-class probability	0.596279
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18907122 90 + 22407834
CGAGGGCAGAGAGGCGGAAGUGGGCGGGGUUCUGCCGAAGGGGU--UGUGGUCUGCGCCCAGAAGUGUGGGCGUGGCAU----------GCCACUGCCACUG
..(((((((...(((((((.(......).))))))).....(((--....(((.(((((((......))))))))))..----------))).))))).)). ( -39.80)
>DroSec_CAF1 32264 90 + 1
CGAGGGCGGAGAGGCGGAAGUGGGUGGGGUUCUGCCGAAGGGGU--UGCGGUCUGCGCCCAGAAGUGUGGGCGUGGCAU----------GCCACUGCCACUG
..(((((((...(((((((.(......).))))))).....(((--....(((.(((((((......))))))))))..----------))).))))).)). ( -39.10)
>DroSim_CAF1 31818 90 + 1
CGAGGGCAGGGAGGCGGAAGUGGGUGGGGUUCUGCCGAAGGGGU--UGUGGUCUGCGCCCAGAAGUGUGGGCGUGGCAU----------GCCACUGCCACUG
..(((((((...(((((((.(......).))))))).....(((--....(((.(((((((......))))))))))..----------))).))))).)). ( -40.00)
>DroEre_CAF1 30473 82 + 1
CG-GCGCAGGGAGGCGGAAGUGG-AGGGGUUCAGCCGAAGGGGU--UGUGGUCUGCGCCCAGAAGUGUGGGCGUGGCAU----------GCCACUG------
((-((........((....))((-(....))).)))).......--.((((((..((((((......))))))..)...----------)))))..------ ( -30.60)
>DroYak_CAF1 31163 89 + 1
CG-GGGCAGAGGGGCGGAAGUGGGUGGGGCUCUGCCGAAAGGGU--UGUGGUCUGCGCCCAGAAGUGUGGGCGUGGCAU----------GCCACUGCCACUG
((-((((((((..((....))........))))))).....(((--.((((((..((((((......))))))..)...----------))))).))).))) ( -40.20)
>DroAna_CAF1 17770 99 + 1
AG-UGGCUCUGCUCUGGAGGUGGGUGGGUUAUUGGUGAAGGGGUUUUGUGGUUUAUACCGAGAAGUGUGGGCGUGCCACUACCUCCUGCUCCACUGUUCC--
((-(((....((...((((((((.(((.......(..(((...)))..).((((((((......))))))))...))))))))))).)).))))).....-- ( -31.30)
>consensus
CG_GGGCAGAGAGGCGGAAGUGGGUGGGGUUCUGCCGAAGGGGU__UGUGGUCUGCGCCCAGAAGUGUGGGCGUGGCAU__________GCCACUGCCACUG
....(((((...(((((((.(......).))))))).....(((......(((((((((((......))))))))).))..........))).))))).... (-25.53 = -26.12 +   0.59)

alignment

secondary structure

dotplot

Window 2

Location	18,907,122 – 18,907,212
Length	90
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	79.72
Mean single sequence MFE	-27.83
Consensus MFE	-17.30
Energy contribution	-19.22
Covariance contribution	1.92
Combinations/Pair	1.10
Mean z-score	-2.28
Structure conservation index	0.62
SVM decision value	1.05
SVM RNA-class probability	0.907519
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18907122 90 - 22407834
CAGUGGCAGUGGC----------AUGCCACGCCCACACUUCUGGGCGCAGACCACA--ACCCCUUCGGCAGAACCCCGCCCACUUCCGCCUCUCUGCCCUCG
..(((((.((((.----------...))))(((((......)))))...).)))).--........((((((.....((........))...)))))).... ( -30.70)
>DroSec_CAF1 32264 90 - 1
CAGUGGCAGUGGC----------AUGCCACGCCCACACUUCUGGGCGCAGACCGCA--ACCCCUUCGGCAGAACCCCACCCACUUCCGCCUCUCCGCCCUCG
..((((.((.(((----------.((((..(((((......)))))((.....)).--........))))(((..........))).))).))))))..... ( -28.30)
>DroSim_CAF1 31818 90 - 1
CAGUGGCAGUGGC----------AUGCCACGCCCACACUUCUGGGCGCAGACCACA--ACCCCUUCGGCAGAACCCCACCCACUUCCGCCUCCCUGCCCUCG
.((.((((((((.----------.(((...(((((......))))))))..)))).--........(((.(((..........))).)))....)))))).. ( -29.00)
>DroEre_CAF1 30473 82 - 1
------CAGUGGC----------AUGCCACGCCCACACUUCUGGGCGCAGACCACA--ACCCCUUCGGCUGAACCCCU-CCACUUCCGCCUCCCUGCGC-CG
------..((((.----------.(((...(((((......))))))))..)))).--.......((((.((.....)-).......((......))))-)) ( -23.10)
>DroYak_CAF1 31163 89 - 1
CAGUGGCAGUGGC----------AUGCCACGCCCACACUUCUGGGCGCAGACCACA--ACCCUUUCGGCAGAGCCCCACCCACUUCCGCCCCUCUGCCC-CG
..(((((.((((.----------...))))(((((......)))))...).)))).--........(((((((..................))))))).-.. ( -31.67)
>DroAna_CAF1 17770 99 - 1
--GGAACAGUGGAGCAGGAGGUAGUGGCACGCCCACACUUCUCGGUAUAAACCACAAAACCCCUUCACCAAUAACCCACCCACCUCCAGAGCAGAGCCA-CU
--.....(((((.((.((((((.((((.....)))).......(((....)))............................))))))...))....)))-)) ( -24.20)
>consensus
CAGUGGCAGUGGC__________AUGCCACGCCCACACUUCUGGGCGCAGACCACA__ACCCCUUCGGCAGAACCCCACCCACUUCCGCCUCUCUGCCC_CG
..((((.(((((............((((.((((((......))))))..((.............)))))).........))))).))))............. (-17.30 = -19.22 +   1.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:26 2006