Locus 1132

Sequence ID	3L_DroMel_CAF1
Location	3,301,149 – 3,301,265
Length	116
Max. P	0.863545

overview

Window 3

Location	3,301,149 – 3,301,265
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.38
Mean single sequence MFE	-23.70
Consensus MFE	-20.33
Energy contribution	-21.32
Covariance contribution	1.00
Combinations/Pair	1.04
Mean z-score	-1.44
Structure conservation index	0.86
SVM decision value	0.11
SVM RNA-class probability	0.587212
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3301149 116 + 23771897
ACUAAAAUAAUUAAAUCUCUGGUUAGACUAGGAACUUCUGGGAAACCCAAGGGCG----UGCACUUAAUACAGAUGUCACUCAUCCAUAUUCCAUAGUCUAUUAUUAAAGCAAUUGCUUC
.......................((((((((((((((..((....))..)))(.(----((((((......)).)).))).).......)))).)))))))......((((....)))). ( -23.70)
>DroSec_CAF1 6777 120 + 1
ACUAAAAUAAUGAAAUCUCUGCUUAAACUAGGAGCUUCUGGGAAACCCUAGAGCGUGCGUGCACUUGAUACAGAUGUCACUCAUCCAUAUUCCAUAGUCUAUUAUUAAAGCAAUUGCUUC
.....((((((((....)).......((((((((((.(((((....))))))))(((.(((((.(((...))).)).))).)))......))).))))..)))))).((((....)))). ( -23.10)
>DroSim_CAF1 7158 116 + 1
ACUAAAAUAAUUAAAUCUCUGCUUAAACUAGGAGCUUCUGGGAAACCCAAGAGCG----UGCACUUGAUACAGAUGUCACUCAUCCAUAUUCCAUAGUCUAUUAUUAAAGCAAUUGCUUC
..........................((((((((((..((((...))))..)))(----((((.(((...))).)).)))..........))).)))).........((((....)))). ( -21.30)
>DroEre_CAF1 12158 116 + 1
AUAACAAUAAUUCCACUUCUGGUUAGACUAGGAGCUUCUGGGAAACCCAAGGGCG----UGCACUUAAUACAGAUGUCACUCAUCCAUAUUCCAUAGUCUAUUAUUAAAGCAAUUGCCUC
.....(((((..(((....))).(((((((((((((..((((...))))..)))(----((((((......)).)).)))..........))).))))))))))))...((....))... ( -26.70)
>consensus
ACUAAAAUAAUUAAAUCUCUGCUUAAACUAGGAGCUUCUGGGAAACCCAAGAGCG____UGCACUUAAUACAGAUGUCACUCAUCCAUAUUCCAUAGUCUAUUAUUAAAGCAAUUGCUUC
.......................(((((((((((((..((((...))))..)))..................((((.....)))).....))).)))))))......((((....)))). (-20.33 = -21.32 +   1.00)

alignment

secondary structure

dotplot

Window 4

Location	3,301,149 – 3,301,265
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.38
Mean single sequence MFE	-30.08
Consensus MFE	-27.58
Energy contribution	-27.70
Covariance contribution	0.12
Combinations/Pair	1.09
Mean z-score	-1.68
Structure conservation index	0.92
SVM decision value	0.84
SVM RNA-class probability	0.863545
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3301149 116 - 23771897
GAAGCAAUUGCUUUAAUAAUAGACUAUGGAAUAUGGAUGAGUGACAUCUGUAUUAAGUGCA----CGCCCUUGGGUUUCCCAGAAGUUCCUAGUCUAACCAGAGAUUUAAUUAUUUUAGU
(((((....))))).....(((((((.(((((.(((....(((.((.((......))))))----)(((....)))...)))...))))))))))))....(((((......)))))... ( -29.20)
>DroSec_CAF1 6777 120 - 1
GAAGCAAUUGCUUUAAUAAUAGACUAUGGAAUAUGGAUGAGUGACAUCUGUAUCAAGUGCACGCACGCUCUAGGGUUUCCCAGAAGCUCCUAGUUUAAGCAGAGAUUUCAUUAUUUUAGU
(((((....))))).....(((((((.((((((((((((.....)))))))))...(((....)))(((((.(((...))))).))))))))))))).((.(((((......))))).)) ( -30.30)
>DroSim_CAF1 7158 116 - 1
GAAGCAAUUGCUUUAAUAAUAGACUAUGGAAUAUGGAUGAGUGACAUCUGUAUCAAGUGCA----CGCUCUUGGGUUUCCCAGAAGCUCCUAGUUUAAGCAGAGAUUUAAUUAUUUUAGU
(((((....))))).....(((((((.((((((((((((.....)))))))))........----.(((..((((...))))..))))))))))))).((.(((((......))))).)) ( -29.90)
>DroEre_CAF1 12158 116 - 1
GAGGCAAUUGCUUUAAUAAUAGACUAUGGAAUAUGGAUGAGUGACAUCUGUAUUAAGUGCA----CGCCCUUGGGUUUCCCAGAAGCUCCUAGUCUAACCAGAAGUGGAAUUAUUGUUAU
(((((....)))))((((((((((((.((((((((((((.....)))))))))........----.((..(((((...)))))..)))))))))))).(((....)))..)))))..... ( -30.90)
>consensus
GAAGCAAUUGCUUUAAUAAUAGACUAUGGAAUAUGGAUGAGUGACAUCUGUAUCAAGUGCA____CGCCCUUGGGUUUCCCAGAAGCUCCUAGUCUAACCAGAGAUUUAAUUAUUUUAGU
(((((....))))).....(((((((.((((((((((((.....))))))))).............(((.(((((...))))).)))))))))))))....................... (-27.58 = -27.70 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:59 2006