Locus 8421

Sequence ID	3L_DroMel_CAF1
Location	22,128,355 – 22,128,469
Length	114
Max. P	0.720242

overview

Window 2

Location	22,128,355 – 22,128,469
Length	114
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	81.30
Mean single sequence MFE	-34.70
Consensus MFE	-22.10
Energy contribution	-23.94
Covariance contribution	1.84
Combinations/Pair	1.04
Mean z-score	-1.89
Structure conservation index	0.64
SVM decision value	0.40
SVM RNA-class probability	0.720242
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22128355 114 + 23771897
GCAUUUGGGCA-ACUGGGCAACUGGGUGGCUGGGUGGCUGGGUGGUUGGCACCAGAAAGUGGAAAAAUAAUCAGAGAAGUUAAAUCUGUGGGCGCCAUAUGCCCACCGCCAGGUC
.((((..(.((-.(..(....)..).)).)..))))(((.((((((.(((((((.....)))........(((.(((.......))).)))........)))).)))))).))). ( -40.30)
>DroSec_CAF1 114171 98 + 1
GCAGUUGGGCA-ACUG----------------GGUGGCUGGGUGGAUGGCACCAGGAAGUGGAAAAAUAAUCAGAGAAGUUAAAUCUGUGGGCGCCAUAUGCCCACCGCCAGGUC
.(((((....)-))))----------------(((((.((((((.(((((.(((.....)))........(((.(((.......))).)))..))))).)))))))))))..... ( -36.60)
>DroSim_CAF1 122277 98 + 1
GCAGUUGGGCA-ACUG----------------GGUGGCUGGGUGGCUGGCACCAGGAAGUGGAAAAAUAAUCAGAGAAGUUAAAUCUGUGGGCGCCAUAUGCCCACCGCCAGGUC
.(((((....)-))))----------------(((((.((((((..((((.(((.....)))........(((.(((.......))).)))..))))..)))))))))))..... ( -35.00)
>DroYak_CAF1 157229 94 + 1
GCAUUUAGGGAG---------------------GUUGCUGGGUGGUUGGCACCAGAAAGUGGAAAAAUAAUCAGAGAAGUUAAAUCUGUGGGCGCCAUAUGCCCAGCGCCAGGAC
...........(---------------------((.((((((((..((((.(((.....)))........(((.(((.......))).)))..))))..)))))))))))..... ( -30.80)
>DroAna_CAF1 131518 93 + 1
---GUUGGGCG-GUGG----------------GGCGGAUGGGCGGCGAGCAGCCGGAAGUGGAAAAAUAAUCAGAGAAGUUAAAUCUGUGGGCGCCAUAUGCCCACCA--AGGGC
---.......(-((((----------------(.((.(((((((((.....)))................(((.(((.......))).))))).)))).)))))))).--..... ( -30.80)
>consensus
GCAGUUGGGCA_ACUG________________GGUGGCUGGGUGGCUGGCACCAGGAAGUGGAAAAAUAAUCAGAGAAGUUAAAUCUGUGGGCGCCAUAUGCCCACCGCCAGGUC
................................(((((.((((((..((((.(((.....)))........(((.(((.......))).)))..))))..)))))))))))..... (-22.10 = -23.94 +   1.84)

alignment

secondary structure

dotplot

Window 3

Location	22,128,355 – 22,128,469
Length	114
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	81.30
Mean single sequence MFE	-26.79
Consensus MFE	-16.84
Energy contribution	-17.76
Covariance contribution	0.92
Combinations/Pair	1.14
Mean z-score	-1.81
Structure conservation index	0.63
SVM decision value	0.21
SVM RNA-class probability	0.635794
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22128355 114 - 23771897
GACCUGGCGGUGGGCAUAUGGCGCCCACAGAUUUAACUUCUCUGAUUAUUUUUCCACUUUCUGGUGCCAACCACCCAGCCACCCAGCCACCCAGUUGCCCAGU-UGCCCAAAUGC
.....(((((((((((..(((((((((.(((.......))).))..................)))))))........((......))........)))))).)-))))....... ( -28.06)
>DroSec_CAF1 114171 98 - 1
GACCUGGCGGUGGGCAUAUGGCGCCCACAGAUUUAACUUCUCUGAUUAUUUUUCCACUUCCUGGUGCCAUCCACCCAGCCACC----------------CAGU-UGCCCAACUGC
....(((((((((....((((((((((.(((.......))).))..................)))))))))))))..))))..----------------((((-(....))))). ( -28.16)
>DroSim_CAF1 122277 98 - 1
GACCUGGCGGUGGGCAUAUGGCGCCCACAGAUUUAACUUCUCUGAUUAUUUUUCCACUUCCUGGUGCCAGCCACCCAGCCACC----------------CAGU-UGCCCAACUGC
....((((((..(((...(((((((((.(((.......))).))..................))))))))))..)).))))..----------------((((-(....))))). ( -27.76)
>DroYak_CAF1 157229 94 - 1
GUCCUGGCGCUGGGCAUAUGGCGCCCACAGAUUUAACUUCUCUGAUUAUUUUUCCACUUUCUGGUGCCAACCACCCAGCAAC---------------------CUCCCUAAAUGC
((....))((((((....(((((((((.(((.......))).))..................)))))))....))))))...---------------------............ ( -24.06)
>DroAna_CAF1 131518 93 - 1
GCCCU--UGGUGGGCAUAUGGCGCCCACAGAUUUAACUUCUCUGAUUAUUUUUCCACUUCCGGCUGCUCGCCGCCCAUCCGCC----------------CCAC-CGCCCAAC---
.....--.(((((((..((((.((...((((.........)))).................(((.....)))))))))..).)----------------))))-).......--- ( -25.90)
>consensus
GACCUGGCGGUGGGCAUAUGGCGCCCACAGAUUUAACUUCUCUGAUUAUUUUUCCACUUCCUGGUGCCAACCACCCAGCCACC________________CAGU_UGCCCAACUGC
....(((((((((.....(((((((((.(((.......))).))..................))))))).)))))..)))).................................. (-16.84 = -17.76 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:57 2006