Locus 2870

Sequence ID	3R_DroMel_CAF1
Location	7,692,428 – 7,692,531
Length	103
Max. P	0.874032

overview

Window 4

Location	7,692,428 – 7,692,531
Length	103
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	92.06
Mean single sequence MFE	-25.50
Consensus MFE	-20.42
Energy contribution	-20.05
Covariance contribution	-0.37
Combinations/Pair	1.05
Mean z-score	-2.24
Structure conservation index	0.80
SVM decision value	0.88
SVM RNA-class probability	0.874032
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7692428 103 + 27905053
AGGGCAAUAAAACAUAACAAGUUGUCACAAGUGUGACACUGAUUGAAAUUAUAAACUGUCACCAGCAGGGACAUCCCUCGGAUGC--GUA----GAUACACCCAUCCAC--
((((..........(((..(((.(((((....))))))))..)))...........((((.((....)))))).)))).(((((.--((.----.....)).)))))..-- ( -26.00)
>DroSec_CAF1 42362 103 + 1
AGGGCAAUAAAACAUAACAAGUUGUCACAAGUGUGACACUGAUUGAAAUUAUAAACUAUCACCAGCAGGGACAUCCCUCGGAUGC--GUA----GAUACACCCACACAC--
.(((..........(((..(((.(((((....))))))))..)))..........((((((((.(.((((....))))))).)).--)))----).....)))......-- ( -23.80)
>DroSim_CAF1 42345 103 + 1
AGGGCAAUAAAACAUAACAAGUUGUCACAAGUGUGACACUGAUUGAAAUUAUAAACUGUCACCAGCAGGGACAUCCCUCGGAUGC--GUA----GAUACACCCACACAC--
.(((..........(((..(((.(((((....))))))))..)))...........((((((((.(((((....)))).)..)).--)).----))))..)))......-- ( -22.40)
>DroAna_CAF1 45041 111 + 1
AGUGCAAUAAAACAUAACAAGUUGUCACAAGAGUGACACUGAUUGAAAUUAUAAACUGUCACCAGCAGGGACAUCCCUCGGAUCCUCGUAUCUGGAGACACGCACACAUCC
.((((.........(((..(((.(((((....))))))))..)))...........((((.((((.((((....))))(((....)))...)))).)))).))))...... ( -29.80)
>consensus
AGGGCAAUAAAACAUAACAAGUUGUCACAAGUGUGACACUGAUUGAAAUUAUAAACUGUCACCAGCAGGGACAUCCCUCGGAUGC__GUA____GAUACACCCACACAC__
.(((..........(((..(((.(((((....))))))))..)))................((.(.((((....)))))))...................)))........ (-20.42 = -20.05 +  -0.37)

alignment

secondary structure

dotplot

Window 5

Location	7,692,428 – 7,692,531
Length	103
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	92.06
Mean single sequence MFE	-32.00
Consensus MFE	-23.54
Energy contribution	-23.60
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-2.16
Structure conservation index	0.74
SVM decision value	0.22
SVM RNA-class probability	0.641371
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7692428 103 - 27905053
--GUGGAUGGGUGUAUC----UAC--GCAUCCGAGGGAUGUCCCUGCUGGUGACAGUUUAUAAUUUCAAUCAGUGUCACACUUGUGACAACUUGUUAUGUUUUAUUGCCCU
--.((((((.(((....----)))--.))))))((((....))))((((....))))..........(((.((((((((....))))).))).)))............... ( -31.30)
>DroSec_CAF1 42362 103 - 1
--GUGUGUGGGUGUAUC----UAC--GCAUCCGAGGGAUGUCCCUGCUGGUGAUAGUUUAUAAUUUCAAUCAGUGUCACACUUGUGACAACUUGUUAUGUUUUAUUGCCCU
--(((((((((....))----)))--))))...((((....))))...((..((((..((((((.........((((((....))))))....))))))..))))..)).. ( -32.72)
>DroSim_CAF1 42345 103 - 1
--GUGUGUGGGUGUAUC----UAC--GCAUCCGAGGGAUGUCCCUGCUGGUGACAGUUUAUAAUUUCAAUCAGUGUCACACUUGUGACAACUUGUUAUGUUUUAUUGCCCU
--(((((((((....))----)))--))))...((((....))))((((....))))..........(((.((((((((....))))).))).)))............... ( -29.40)
>DroAna_CAF1 45041 111 - 1
GGAUGUGUGCGUGUCUCCAGAUACGAGGAUCCGAGGGAUGUCCCUGCUGGUGACAGUUUAUAAUUUCAAUCAGUGUCACUCUUGUGACAACUUGUUAUGUUUUAUUGCACU
((((.(...((((((....)))))).).)))).((((....))))((((....))))..........(((.((((((((....))))).))).))).(((......))).. ( -34.60)
>consensus
__GUGUGUGGGUGUAUC____UAC__GCAUCCGAGGGAUGUCCCUGCUGGUGACAGUUUAUAAUUUCAAUCAGUGUCACACUUGUGACAACUUGUUAUGUUUUAUUGCCCU
........((((.....................((((....))))((((....))))..........(((.((((((((....))))).))).)))..........)))). (-23.54 = -23.60 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:42 2006