Locus 8906

Sequence ID	3R_DroMel_CAF1
Location	23,893,303 – 23,893,407
Length	104
Max. P	0.878315

overview

Window 7

Location	23,893,303 – 23,893,407
Length	104
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	84.50
Mean single sequence MFE	-33.36
Consensus MFE	-20.68
Energy contribution	-21.12
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-2.66
Structure conservation index	0.62
SVM decision value	0.90
SVM RNA-class probability	0.878315
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23893303 104 + 27905053
AUAGGUGAAGCAAGGCAGGAAGCCAGGAGGCCGGGAGGCCAGGUGAACGGAAAGGGACAGGUGCGUCCUCGGCAAAUAUACAAAACACUUGUAACUGCCGUGCA
.........(((.(((((...(((....((((....)))).............(((((......))))).))).....(((((.....))))).))))).))). ( -38.40)
>DroSec_CAF1 99143 96 + 1
AUAGGUGAAGCAAGGCAGGAAGCCAGGA--------GGCCAGGUGAACGGAAAGGGACAGGUGCGUCCUCGGCAAAUAUACAAAACACUUGUAACUGCCGUGCA
.........(((.(((((...(((((((--------.(((..((...(.....)..))..).)).)))).))).....(((((.....))))).))))).))). ( -32.60)
>DroSim_CAF1 101809 104 + 1
AUAGGUGAAGCAAGGCAGGAAGCCAGGAGGCCAGGAGGCCAGGUGAACGGAAAGGGACAGGUGCGUCCUCGGCAAAUAUACAAAACACUUGUAACUGCCGUGCA
.........(((.(((((...(((....((((....)))).............(((((......))))).))).....(((((.....))))).))))).))). ( -36.20)
>DroEre_CAF1 103101 96 + 1
GUGGGUGAAGUAAGUCAGGA--------GGCCAGGAGACCAGGUGAACGGAAAGGGCCGGGUGCCUCCAUGGCAAAUAUACAAAACACUUGUAACUGCCGUGCA
((((((..(((..(((((((--------((((.(....)........(((......))).).)))))).)))).....(((((.....))))))))))).))). ( -28.00)
>DroYak_CAF1 106182 89 + 1
AUAGGUGAAGUGAGGCAGG---------------GCAGUCAGGUGAACGGAAGGGGACAGGUGCGUCCUCGGCAAAUAUACAAAACACUUGUAACUGCCGUGCA
..............(((.(---------------(((((((((((..(....)(((((......)))))................))))))..)))))).))). ( -31.60)
>consensus
AUAGGUGAAGCAAGGCAGGAAGCCAGGAGGCC_GGAGGCCAGGUGAACGGAAAGGGACAGGUGCGUCCUCGGCAAAUAUACAAAACACUUGUAACUGCCGUGCA
.........(((.(((((...................(((.(.....).....(((((......))))).))).....(((((.....))))).))))).))). (-20.68 = -21.12 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	23,893,303 – 23,893,407
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	84.50
Mean single sequence MFE	-27.67
Consensus MFE	-15.48
Energy contribution	-16.52
Covariance contribution	1.04
Combinations/Pair	1.05
Mean z-score	-2.27
Structure conservation index	0.56
SVM decision value	0.00
SVM RNA-class probability	0.534104
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23893303 104 - 27905053
UGCACGGCAGUUACAAGUGUUUUGUAUAUUUGCCGAGGACGCACCUGUCCCUUUCCGUUCACCUGGCCUCCCGGCCUCCUGGCUUCCUGCCUUGCUUCACCUAU
.(((.(((((.((((((...)))))).....((((.(((((....)))))..............((((....))))...))))...))))).)))......... ( -31.00)
>DroSec_CAF1 99143 96 - 1
UGCACGGCAGUUACAAGUGUUUUGUAUAUUUGCCGAGGACGCACCUGUCCCUUUCCGUUCACCUGGCC--------UCCUGGCUUCCUGCCUUGCUUCACCUAU
.(((.(((((.((((((...)))))).....(((.((((.((...((..(......)..))....)).--------)))))))...))))).)))......... ( -26.30)
>DroSim_CAF1 101809 104 - 1
UGCACGGCAGUUACAAGUGUUUUGUAUAUUUGCCGAGGACGCACCUGUCCCUUUCCGUUCACCUGGCCUCCUGGCCUCCUGGCUUCCUGCCUUGCUUCACCUAU
.(((.(((((.((((((...)))))).....((((.(((((....)))))..............((((....))))...))))...))))).)))......... ( -31.60)
>DroEre_CAF1 103101 96 - 1
UGCACGGCAGUUACAAGUGUUUUGUAUAUUUGCCAUGGAGGCACCCGGCCCUUUCCGUUCACCUGGUCUCCUGGCC--------UCCUGACUUACUUCACCCAC
.....(((((.((((((...))))))...)))))..((((((....((((..............)))).....)))--------)))................. ( -24.74)
>DroYak_CAF1 106182 89 - 1
UGCACGGCAGUUACAAGUGUUUUGUAUAUUUGCCGAGGACGCACCUGUCCCCUUCCGUUCACCUGACUGC---------------CCUGCCUCACUUCACCUAU
.(((.(((((((((((((((.....)))))))..(.(((((....))))).)...........)))))))---------------).))).............. ( -24.70)
>consensus
UGCACGGCAGUUACAAGUGUUUUGUAUAUUUGCCGAGGACGCACCUGUCCCUUUCCGUUCACCUGGCCUCC_GGCCUCCUGGCUUCCUGCCUUGCUUCACCUAU
.(((.(((((...(((((((.....)))))))....(((((....)))))....................................))))).)))......... (-15.48 = -16.52 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:28 2006