Locus 3876

Sequence ID	3R_DroMel_CAF1
Location	10,540,906 – 10,541,040
Length	134
Max. P	0.999953

overview

Window 0

Location	10,540,906 – 10,541,002
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	93.08
Mean single sequence MFE	-24.78
Consensus MFE	-21.86
Energy contribution	-21.90
Covariance contribution	0.04
Combinations/Pair	1.11
Mean z-score	-2.01
Structure conservation index	0.88
SVM decision value	2.52
SVM RNA-class probability	0.994918
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10540906 96 + 27905053
UGUGUUGAGUGUGCAUGCAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUACGAAUGUAUGUAUCAAAAAAGCAUUGCACGCG
........((((((((((.....((((.((((((....)))))).))))........(.((((((....))).))).)......))).))))))). ( -26.30)
>DroSec_CAF1 15853 95 + 1
UGU-UUGAGUGUGCAUGCAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUACGAAUGAAUGUAUCAAAAAAGCAUUGCACGGG
.((-(((((((.((..(((((((.....((((((....))))))..)))))))....)))))).))))).(((((.........)))))....... ( -21.70)
>DroEre_CAF1 15966 95 + 1
UGU-UUGAGUGUGCAUGCAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUACGAAUGUAUGUAUCAAAAAAGCAUUGCAUGCG
.((-(((((((.((..(((((((.....((((((....))))))..)))))))....)))))).)))))(((((((............))))))). ( -26.70)
>DroYak_CAF1 15980 95 + 1
UGU-UUGAGUGUGCAUGCAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUAUGAAUGUAUGUAUCAGAAAAGCAUUGCAUGCG
..(-((((...((((((((((((((((.((((((....)))))).))))..((....)).....)))))))))))))))))...((((...)))). ( -26.40)
>DroAna_CAF1 15742 95 + 1
UAU-CUGUGUGUGAAUGCAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUACGAAUGUAUGUAUCAAGUAUGCAAUGCAUACA
...-..((((((..((((((((.((((.((((((....)))))).))))..((....))......))))))))((((.....))))...)))))). ( -22.80)
>consensus
UGU_UUGAGUGUGCAUGCAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUACGAAUGUAUGUAUCAAAAAAGCAUUGCAUGCG
........((((((((((.....((((.((((((....)))))).))))........(.((((((....))).))).)......))).))))))). (-21.86 = -21.90 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	10,540,906 – 10,541,002
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	93.08
Mean single sequence MFE	-28.48
Consensus MFE	-25.50
Energy contribution	-26.46
Covariance contribution	0.96
Combinations/Pair	1.03
Mean z-score	-3.89
Structure conservation index	0.90
SVM decision value	4.82
SVM RNA-class probability	0.999953
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10540906 96 - 27905053
CGCGUGCAAUGCUUUUUUGAUACAUACAUUCGUAGUAGCUUUGGCAUUUAAGGCAAUGCGCGCAUUGCUUUAAUAAAUGCAUGCACACUCAACACA
.((((((((((((.......(((.(((....)))))).....)))))(((((((((((....)))))))))))....)))))))............ ( -30.80)
>DroSec_CAF1 15853 95 - 1
CCCGUGCAAUGCUUUUUUGAUACAUUCAUUCGUAGUAGCUUUGGCAUUUAAGGCAAUGCGCGCAUUGCUUUAAUAAAUGCAUGCACACUCAA-ACA
...(((((.((((....(((.....))).....))))......(((((((((((((((....))))))))...))))))).)))))......-... ( -27.40)
>DroEre_CAF1 15966 95 - 1
CGCAUGCAAUGCUUUUUUGAUACAUACAUUCGUAGUAGCUUUGGCAUUUAAGGCAAUGCGCGCAUUGCUUUAAUAAAUGCAUGCACACUCAA-ACA
.((((((((((((.......(((.(((....)))))).....)))))(((((((((((....)))))))))))....)))))))........-... ( -31.20)
>DroYak_CAF1 15980 95 - 1
CGCAUGCAAUGCUUUUCUGAUACAUACAUUCAUAGUAGCUUUGGCAUUUAAGGCAAUGCGCGCAUUGCUUUAAUAAAUGCAUGCACACUCAA-ACA
.((((((((((((.......(((...........))).....)))))(((((((((((....)))))))))))....)))))))........-... ( -28.40)
>DroAna_CAF1 15742 95 - 1
UGUAUGCAUUGCAUACUUGAUACAUACAUUCGUAGUAGCUUUGGCAUUUAAGGCAAUGCGCGCAUUGCUUUAAUAAAUGCAUUCACACACAG-AUA
((.(((((((((.(((((((.........))).))))))........(((((((((((....)))))))))))..))))))).)).......-... ( -24.60)
>consensus
CGCAUGCAAUGCUUUUUUGAUACAUACAUUCGUAGUAGCUUUGGCAUUUAAGGCAAUGCGCGCAUUGCUUUAAUAAAUGCAUGCACACUCAA_ACA
.((((((((((((.......(((.(((....)))))).....)))))(((((((((((....)))))))))))....)))))))............ (-25.50 = -26.46 +   0.96)

alignment

secondary structure

dotplot

Window 2

Location	10,540,923 – 10,541,040
Length	117
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	82.34
Mean single sequence MFE	-23.90
Consensus MFE	-17.78
Energy contribution	-18.22
Covariance contribution	0.44
Combinations/Pair	1.05
Mean z-score	-1.95
Structure conservation index	0.74
SVM decision value	0.80
SVM RNA-class probability	0.853029
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10540923 117 + 27905053
CAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUACGAAUGUAUGUAUCAAAAAAGCAUUGCACGCGUACACUGGAAACAA-AAUGUAAAGGACUCAAGGCAUU-GU
.......(((.((((((....)))))).)))((((((..((((..((((..((((((..((((.......))).)..)))))).((....)).-..))))..)).))...))))))-.. ( -26.70)
>DroSec_CAF1 15869 118 + 1
CAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUACGAAUGAAUGUAUCAAAAAAGCAUUGCACGGGUACACUGGAAACAA-AAUGUAAAGGAAUCAAGACAUACGG
...........((((((((.(((((......))))))..............(((.....))).....))))))).(...((((.((....)).-..))))..)................ ( -21.40)
>DroEre_CAF1 15982 113 + 1
CAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUACGAAUGUAUGUAUCAAAAAAGCAUUGCAUGCGUACACUGGAAACAAGAAAGUC-----CACAAGCCAUU-AA
((((((.....((((((....))))))..)))))).....(((........((((((((((((.......))).))))))))).((....))........-----....)))....-.. ( -23.40)
>DroYak_CAF1 15996 106 + 1
CAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUAUGAAUGUAUGUAUCAGAAAAGCAUUGCAUGCGUACACUGGAAACAAUAAUGUA--------AAGCUA-----
((((((.....((((((....))))))..))))))....((((....((.(((((((((............))))))))).)).((....))........--------.)))).----- ( -24.40)
>DroAna_CAF1 15758 99 + 1
CAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUACGAAUGUAUGUAUCAAGUAUGCAAUGCAUACAUGCACUGAAAAAAA--AGGCAG------------------
......((((.((((((....)))))).)))).((((...(.((((((....))).))).)..((((((...))))))...............--.)))).------------------ ( -23.60)
>consensus
CAUUUAUUAAAGCAAUGCGCGCAUUGCCUUAAAUGCCAAAGCUACUACGAAUGUAUGUAUCAAAAAAGCAUUGCAUGCGUACACUGGAAACAA_AAUGUA_______CAAGCCAU____
...........((((((((.(((((......))))))...(.((((((....))).))).)......)))))))..........((....))........................... (-17.78 = -18.22 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:18 2006