Locus 6594

Sequence ID	2R_DroMel_CAF1
Location	20,629,964 – 20,630,065
Length	101
Max. P	0.999827

overview

Window 3

Location	20,629,964 – 20,630,065
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	95.45
Mean single sequence MFE	-35.00
Consensus MFE	-33.80
Energy contribution	-34.60
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.28
Structure conservation index	0.97
SVM decision value	4.18
SVM RNA-class probability	0.999827
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20629964 101 + 20766785
UCCGCAGCAAUGGAGUCACUGCGGCCAGCUUCCUUUGGCUGCCUUCACGCAACGAUGCAAGCGAAAUGCGUAUGCAAAUUUUAAACUGACUCUUGCGGAAG
((((((.....(((((((..((((((((......))))))))......(((...(((((.......))))).)))...........))))))))))))).. ( -36.80)
>DroSec_CAF1 80524 101 + 1
UCCGCAGCAAUGGAGUCACUGCGGCCAGCUUCCUUUGGCUGCCUUCACGCAACGAUGCAAGCGAAAUGCGUAUGCAAAUUUUGAACUGACUCUUGCGGAAG
((((((.....(((((((..((((((((......))))))))......(((...(((((.......))))).)))...........))))))))))))).. ( -36.80)
>DroSim_CAF1 81336 101 + 1
UCCGCAGCAAUGGAGUCACUGCGGCCAGCUUCCUUUGGCUGCCUUCACGCAACGAUGCAAGCGAAAUGCGUAUGCAAAUUUUGAACUGACUCUUGCGGAAG
((((((.....(((((((..((((((((......))))))))......(((...(((((.......))))).)))...........))))))))))))).. ( -36.80)
>DroEre_CAF1 111776 101 + 1
UCCGCAGUAAUGGAGUCACUGCGGCCAGCUUCCUUUGGCUGCCUUCACGCAACGAUGCAAGCGAAAUGCGUAUGCAAAUUUCCUUCUGACUCUAACGGAAG
((((((....))((((((..((((((((......))))))))......(((...(((((.......))))).)))...........))))))...)))).. ( -32.30)
>DroYak_CAF1 84661 101 + 1
UCCGCAGUAAUGGAGUCACUGCGGCCAGCUUCCUUUGGCUGCCUUCACGCAACGAUGCAAGCGAAAUGCGUAUGCAAAUUCUCUUCUGACUCUAACGGAAG
((((((....))((((((..((((((((......))))))))......(((...(((((.......))))).)))...........))))))...)))).. ( -32.30)
>consensus
UCCGCAGCAAUGGAGUCACUGCGGCCAGCUUCCUUUGGCUGCCUUCACGCAACGAUGCAAGCGAAAUGCGUAUGCAAAUUUUCAACUGACUCUUGCGGAAG
((((((.....(((((((..((((((((......))))))))......(((...(((((.......))))).)))...........))))))))))))).. (-33.80 = -34.60 +   0.80)

alignment

secondary structure

dotplot

Window 4

Location	20,629,964 – 20,630,065
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	95.45
Mean single sequence MFE	-34.04
Consensus MFE	-30.57
Energy contribution	-30.49
Covariance contribution	-0.08
Combinations/Pair	1.07
Mean z-score	-1.58
Structure conservation index	0.90
SVM decision value	1.42
SVM RNA-class probability	0.951788
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20629964 101 - 20766785
CUUCCGCAAGAGUCAGUUUAAAAUUUGCAUACGCAUUUCGCUUGCAUCGUUGCGUGAAGGCAGCCAAAGGAAGCUGGCCGCAGUGACUCCAUUGCUGCGGA
..((((((.(.((((((((....((((.....(((.......)))...(((((......)))))))))..)))))))))((((((....)))))))))))) ( -36.10)
>DroSec_CAF1 80524 101 - 1
CUUCCGCAAGAGUCAGUUCAAAAUUUGCAUACGCAUUUCGCUUGCAUCGUUGCGUGAAGGCAGCCAAAGGAAGCUGGCCGCAGUGACUCCAUUGCUGCGGA
..((((((.(.((((((((......((((...((.....)).))))..(((((......))))).....).))))))))((((((....)))))))))))) ( -34.90)
>DroSim_CAF1 81336 101 - 1
CUUCCGCAAGAGUCAGUUCAAAAUUUGCAUACGCAUUUCGCUUGCAUCGUUGCGUGAAGGCAGCCAAAGGAAGCUGGCCGCAGUGACUCCAUUGCUGCGGA
..((((((.(.((((((((......((((...((.....)).))))..(((((......))))).....).))))))))((((((....)))))))))))) ( -34.90)
>DroEre_CAF1 111776 101 - 1
CUUCCGUUAGAGUCAGAAGGAAAUUUGCAUACGCAUUUCGCUUGCAUCGUUGCGUGAAGGCAGCCAAAGGAAGCUGGCCGCAGUGACUCCAUUACUGCGGA
(((((((..((((.((...((((..(((....))))))).)).)).))...))).)))).((((........)))).(((((((((.....))))))))). ( -31.80)
>DroYak_CAF1 84661 101 - 1
CUUCCGUUAGAGUCAGAAGAGAAUUUGCAUACGCAUUUCGCUUGCAUCGUUGCGUGAAGGCAGCCAAAGGAAGCUGGCCGCAGUGACUCCAUUACUGCGGA
(((((((..((((.((....(((..(((....))).))).)).)).))...))).)))).((((........)))).(((((((((.....))))))))). ( -32.50)
>consensus
CUUCCGCAAGAGUCAGUUCAAAAUUUGCAUACGCAUUUCGCUUGCAUCGUUGCGUGAAGGCAGCCAAAGGAAGCUGGCCGCAGUGACUCCAUUGCUGCGGA
((((((((((...............(((....))).....)))))...(((((......)))))....)))))....(((((((((.....))))))))). (-30.57 = -30.49 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:37 2006