Locus 1749

Sequence ID	X_DroMel_CAF1
Location	4,863,597 – 4,863,692
Length	95
Max. P	0.999665

overview

Window 5

Location	4,863,597 – 4,863,692
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	87.37
Mean single sequence MFE	-21.28
Consensus MFE	-18.16
Energy contribution	-18.00
Covariance contribution	-0.16
Combinations/Pair	1.19
Mean z-score	-2.66
Structure conservation index	0.85
SVM decision value	2.87
SVM RNA-class probability	0.997483
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4863597 95 + 22224390
AACUAAAAACAAAAAAAAAAAAAACCACUUGCAAUCCAAUUCGGACGGGAAGGAACCAUUUCAAUCGGGCCGCAAGUGGAUUUGAAUUGAGAUCU
........................((((((((..(((.(((..((.((.......)).))..))).)))..))))))))................ ( -20.30)
>DroSec_CAF1 15352 85 + 1
AACCAAA----------AAAGAAACCACUUGCAAUCCAAUCCGGACGGAAAGGAACCAUUUCAAUCGGGCCGCAAGUGGAUUUGAAUUGAGAUCU
...(((.----------...(((.((((((((..(((..(((....)))..))).((.........))...)))))))).)))...)))...... ( -22.60)
>DroSim_CAF1 15339 85 + 1
AACCAAA----------AAAGAAACCACUUGCAAUCCAAUCGGGACGGAAAGGAACCAUUUCAAUCGGGCCGCAAGUGGAUUUGAAUUGAGAUCU
...(((.----------...(((.((((((((..(((.((.(..(.((.......)).)..).)).)))..)))))))).)))...)))...... ( -21.10)
>DroEre_CAF1 18309 80 + 1
AACUAAA---------------AACCACUUGCAAUCCAACCCAGACGGGAAGGAACCAUUUCAAUCAGGUCGCAAGUGGAUUUGAAUUGAGAUCU
.......---------------..((((((((..(((..(((....)))..)))(((..........))).))))))))................ ( -23.80)
>DroYak_CAF1 15540 82 + 1
AACAAAA----------A---AAAACACUUGCAAUCCAAUCCGGACGGGAAGGAACCAUUUCAAUCAGGCCGCAAGUGGAUUUGAAUUGAGAUCU
..(((..----------(---((..(((((((..(((..(((....)))..))).((..........))..)))))))..)))...)))...... ( -18.60)
>consensus
AACCAAA__________AAA_AAACCACUUGCAAUCCAAUCCGGACGGGAAGGAACCAUUUCAAUCGGGCCGCAAGUGGAUUUGAAUUGAGAUCU
........................((((((((..(((..(((....)))..))).((..........))..))))))))................ (-18.16 = -18.00 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	4,863,597 – 4,863,692
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	87.37
Mean single sequence MFE	-24.74
Consensus MFE	-22.44
Energy contribution	-21.92
Covariance contribution	-0.52
Combinations/Pair	1.20
Mean z-score	-2.90
Structure conservation index	0.91
SVM decision value	3.86
SVM RNA-class probability	0.999665
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4863597 95 - 22224390
AGAUCUCAAUUCAAAUCCACUUGCGGCCCGAUUGAAAUGGUUCCUUCCCGUCCGAAUUGGAUUGCAAGUGGUUUUUUUUUUUUUUGUUUUUAGUU
....((.((..((((.(((((((((..((((((...((((.......))))...))))))..)))))))))...........))))..)).)).. ( -23.80)
>DroSec_CAF1 15352 85 - 1
AGAUCUCAAUUCAAAUCCACUUGCGGCCCGAUUGAAAUGGUUCCUUUCCGUCCGGAUUGGAUUGCAAGUGGUUUCUUU----------UUUGGUU
.....((((.......(((((((((..((((((...((((.......))))...))))))..))))))))).......----------.)))).. ( -25.76)
>DroSim_CAF1 15339 85 - 1
AGAUCUCAAUUCAAAUCCACUUGCGGCCCGAUUGAAAUGGUUCCUUUCCGUCCCGAUUGGAUUGCAAGUGGUUUCUUU----------UUUGGUU
.....((((.......(((((((((..(((((((..((((.......))))..)))))))..))))))))).......----------.)))).. ( -29.16)
>DroEre_CAF1 18309 80 - 1
AGAUCUCAAUUCAAAUCCACUUGCGACCUGAUUGAAAUGGUUCCUUCCCGUCUGGGUUGGAUUGCAAGUGGUU---------------UUUAGUU
.......((((.(((.((((((((((.(..(((.(.((((.......)))).).)))..).)))))))))).)---------------)).)))) ( -24.80)
>DroYak_CAF1 15540 82 - 1
AGAUCUCAAUUCAAAUCCACUUGCGGCCUGAUUGAAAUGGUUCCUUCCCGUCCGGAUUGGAUUGCAAGUGUUUU---U----------UUUUGUU
......(((...(((..((((((((..(..(((...((((.......))))...)))..)..))))))))..))---)----------..))).. ( -20.20)
>consensus
AGAUCUCAAUUCAAAUCCACUUGCGGCCCGAUUGAAAUGGUUCCUUCCCGUCCGGAUUGGAUUGCAAGUGGUUU_UUU__________UUUAGUU
................((((((((((.((((((...((((.......))))...)))))).))))))))))........................ (-22.44 = -21.92 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:05 2006