Locus 2904

Sequence ID	3R_DroMel_CAF1
Location	7,782,176 – 7,782,410
Length	234
Max. P	0.934448

overview

Window 2

Location	7,782,176 – 7,782,292
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.67
Mean single sequence MFE	-26.27
Consensus MFE	-19.49
Energy contribution	-20.68
Covariance contribution	1.19
Combinations/Pair	1.10
Mean z-score	-2.42
Structure conservation index	0.74
SVM decision value	1.24
SVM RNA-class probability	0.934448
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7782176 116 - 27905053
AAUAGAGGAGCUUCGUCGACGGAGAGUCAAUUCUAUUCAAACAAGUAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAA----CAAUCUGC
((((((.((.(((((....)))))..))...)))))).......(((...((........(((.(((....))).)))..............((((.....))))...----))...))) ( -24.80)
>DroSec_CAF1 4649 120 - 1
AAUAGAGCCGCUUCGUUCCCAGAGCGUCAAUUCAAUUCAAACAAGCAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAACAAACAAUCUGC
..((((((.(((((((((...)))))..................((..(((((.....))))).(((....)))..))........))))))((((.....))))..........)))). ( -26.00)
>DroSim_CAF1 4656 120 - 1
AAUAGAGCCGCUUCGUUCCCAGAACGUCAAUUCAAUUCAAACAAGCAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAACAAACAAUCUGC
..((((((.(((((((((...)))))..................((..(((((.....))))).(((....)))..))........))))))((((.....))))..........)))). ( -26.00)
>DroEre_CAF1 4857 116 - 1
AAUAUGGCCGCUUGGUGCUCCCAGCGUCAAUUCAAUUAAAUCAAGCAAACUGAAAACAUCGCUGAGCGGAAGCUAAGCAACCAAAUAAGCGCAGCUGAACAAGCUAAACAAA----CUGC
......((.((((((((((..(((((....((((................)))).....)))))(((....))).))).))))....)))))((((.....)))).......----.... ( -28.29)
>consensus
AAUAGAGCCGCUUCGUUCCCAGAGCGUCAAUUCAAUUCAAACAAGCAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAACAAACAAUCUGC
......(.(((((((....))))))).)................(((.............(((.(((....))).)))..............((((.....))))............))) (-19.49 = -20.68 +   1.19)

alignment

secondary structure

dotplot

Window 3

Location	7,782,292 – 7,782,410
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.20
Mean single sequence MFE	-40.52
Consensus MFE	-27.33
Energy contribution	-28.70
Covariance contribution	1.37
Combinations/Pair	1.16
Mean z-score	-1.57
Structure conservation index	0.67
SVM decision value	0.05
SVM RNA-class probability	0.558814
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7782292 118 + 27905053
UAUACUCCG-GCGCUCUUUUCGCGAACAUUCGAGGCGCGCUCUCUCGAAGCAACGAGAACAGUGCGCCGUUUACUGUGUGACAGAGUGAGAGAGCAAUAGUA-CAAAGAGGGAGAGUCAC
....((((.-..(((((((.(((..........((((((((.(((((......)))))..)))))))).....(((.....))).)))))))))).......-(.....)))))...... ( -41.70)
>DroSec_CAF1 4769 118 + 1
UAUACUCCGGGCGCUCUUUUCGCGAACAUUCGAGGCGCGCUCUCUCGAAGCAACGAGAACAGUAUGCCG-UUACUGUGUGUCAGAGUGAGAGAGCAUUAGUG-CAGAGAGGGAGAGCCAC
.........(((.((((((((.(((....)))..(((((((((((((.....(((...((((((.....-.)))))).))).....)))))))))....)))-).)))).)))).))).. ( -42.50)
>DroSim_CAF1 4776 119 + 1
UAUACUCCGGGCGCUCUUUUCGCGAACAUUCGAGUCGCGCUCUCUCGAAGCAACGAGAACAGUAUGCCGCUUACUGUGUGUCAGAGUGAGAGAGCAUUAGUG-CAGAGAGGGAGAGCCAC
.........(((.((((((((((((.(......)))))(((((((((.....(((...((((((.......)))))).))).....))))))))).......-..)))).)))).))).. ( -42.50)
>DroEre_CAF1 4973 108 + 1
UAUACUCCG-GCGCUCUCUUCGCGAACGUUCGAGACGUUCUCUCUCGAAGCUGCGAGAACAGUAUGCUGUUUAGUAUGUG--AGAAUGA--GAGCAAUAGUGUCUGGGAGGGA-------
....(((((-((((((((..((....))...)))).(((((((((((....(((..((((((....)))))).)))..))--)))..))--))))....)))))..))))...------- ( -35.40)
>consensus
UAUACUCCG_GCGCUCUUUUCGCGAACAUUCGAGGCGCGCUCUCUCGAAGCAACGAGAACAGUAUGCCGUUUACUGUGUGUCAGAGUGAGAGAGCAAUAGUG_CAGAGAGGGAGAGCCAC
....((((....(((((((.(((..((((....((((((((.(((((......)))))..)))))))).......))))......))))))))))........(.....)))))...... (-27.33 = -28.70 +   1.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:30 2006