Locus 493

Sequence ID	X_DroMel_CAF1
Location	1,420,815 – 1,420,947
Length	132
Max. P	0.801561

overview

Window 8

Location	1,420,815 – 1,420,916
Length	101
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	89.27
Mean single sequence MFE	-16.49
Consensus MFE	-12.24
Energy contribution	-12.30
Covariance contribution	0.06
Combinations/Pair	1.05
Mean z-score	-2.07
Structure conservation index	0.74
SVM decision value	0.62
SVM RNA-class probability	0.801561
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1420815 101 + 22224390
UAUGACGAAUUUGUGCCCUAAAACUCUAAACGCUAGCUCAUUUGCACACACGCACACUGAGCAUAUCAACAACUUCAUCAUCAUUAGCAUUAGCAUUAGCA
.((((.(((.((((((...............))..(((((..(((......)))...)))))......)))).))).)))).....((....))....... ( -16.56)
>DroSec_CAF1 27224 101 + 1
UAUGACGAAUUUGUGCCCUAAAACUCUAAACGAUAGCUCAUUUGCACACACGCACACUGAGCAUAUCAACAACUUCAUCAUCAUUAGCAUUAGCAUUAGCA
.((((.(((.((((....((......))...(((((((((..(((......)))...))))).)))).)))).))).)))).....((....))....... ( -18.00)
>DroSim_CAF1 17865 101 + 1
UAUGACGAGUUUGUGCCCUAAAACUCUAAACGCUAGCUCAUUUGCACACACGCACACUGAGCAUAUCAACAACUUCAUCAUCAUUAGCAUUAGCAUUAGCA
......((((((........)))))).....(((((((((..(((......)))...)))))........................((....))..)))). ( -21.50)
>DroEre_CAF1 22502 82 + 1
UAUGACGAAUUUGUGCCCUAAAACUCU-------AGCUCAUUUGCACACACGCACACUCAGCAUAUCAACAACUUCAUCAUCAUU------------AGCA
.((((.(((.((((.............-------.((......))......((.......))......)))).))).))))....------------.... (  -9.90)
>consensus
UAUGACGAAUUUGUGCCCUAAAACUCUAAACGCUAGCUCAUUUGCACACACGCACACUGAGCAUAUCAACAACUUCAUCAUCAUUAGCAUUAGCAUUAGCA
.((((.(((.(((((........)...........(((((..(((......)))...)))))......)))).))).)))).................... (-12.24 = -12.30 +   0.06)

alignment

secondary structure

dotplot

Window 9

Location	1,420,815 – 1,420,916
Length	101
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	89.27
Mean single sequence MFE	-24.65
Consensus MFE	-21.60
Energy contribution	-21.85
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.88
SVM decision value	0.33
SVM RNA-class probability	0.692974
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1420815 101 - 22224390
UGCUAAUGCUAAUGCUAAUGAUGAUGAAGUUGUUGAUAUGCUCAGUGUGCGUGUGUGCAAAUGAGCUAGCGUUUAGAGUUUUAGGGCACAAAUUCGUCAUA
.((....))...........((((((((.((((......(((((...((((....))))..)))))..((.(((((....))))))))))).)))))))). ( -24.80)
>DroSec_CAF1 27224 101 - 1
UGCUAAUGCUAAUGCUAAUGAUGAUGAAGUUGUUGAUAUGCUCAGUGUGCGUGUGUGCAAAUGAGCUAUCGUUUAGAGUUUUAGGGCACAAAUUCGUCAUA
.((....))...........((((((((.((((.((((.(((((...((((....))))..))))))))).......(((....))))))).)))))))). ( -27.00)
>DroSim_CAF1 17865 101 - 1
UGCUAAUGCUAAUGCUAAUGAUGAUGAAGUUGUUGAUAUGCUCAGUGUGCGUGUGUGCAAAUGAGCUAGCGUUUAGAGUUUUAGGGCACAAACUCGUCAUA
....((((((((((.(((..((......))..))).)))(((((...((((....))))..))))))))))))..((((((........))))))...... ( -24.50)
>DroEre_CAF1 22502 82 - 1
UGCU------------AAUGAUGAUGAAGUUGUUGAUAUGCUGAGUGUGCGUGUGUGCAAAUGAGCU-------AGAGUUUUAGGGCACAAAUUCGUCAUA
....------------....((((((((.......((((((.......))))))((((....((((.-------...))))....))))...)))))))). ( -22.30)
>consensus
UGCUAAUGCUAAUGCUAAUGAUGAUGAAGUUGUUGAUAUGCUCAGUGUGCGUGUGUGCAAAUGAGCUAGCGUUUAGAGUUUUAGGGCACAAAUUCGUCAUA
....................((((((((.......((((((.......))))))((((....(((((.........)))))....))))...)))))))). (-21.60 = -21.85 +   0.25)

alignment

secondary structure

dotplot

Window 0

Location	1,420,855 – 1,420,947
Length	92
Sequences	4
Columns	92
Reading direction	forward
Mean pairwise identity	90.22
Mean single sequence MFE	-16.57
Consensus MFE	-12.64
Energy contribution	-13.07
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-1.52
Structure conservation index	0.76
SVM decision value	0.01
SVM RNA-class probability	0.540761
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1420855 92 + 22224390
UUUGCACACACGCACACUGAGCAUAUCAACAACUUCAUCAUCAUUAGCAUUAGCAUUAGCACGCAGCAGUUAUGCUCCUGUGUUAGCCCUAA
...........((((((.(((((((.(...................((....))....((.....)).).)))))))..))))..))..... ( -17.50)
>DroSec_CAF1 27264 92 + 1
UUUGCACACACGCACACUGAGCAUAUCAACAACUUCAUCAUCAUUAGCAUUAGCAUUAGCACGCAGCAGUUAUGCUCUUGUGUUAGCCCUAA
...........(((((..(((((((.(...................((....))....((.....)).).))))))).)))))......... ( -17.80)
>DroSim_CAF1 17905 92 + 1
UUUGCACACACGCACACUGAGCAUAUCAACAACUUCAUCAUCAUUAGCAUUAGCAUUAGCACGCAGCAGUUAUGCUCUUGUGUUAGCCUUAA
...........(((((..(((((((.(...................((....))....((.....)).).))))))).)))))......... ( -17.80)
>DroEre_CAF1 22535 80 + 1
UUUGCACACACGCACACUCAGCAUAUCAACAACUUCAUCAUCAUU------------AGCACGAAACAGUUGUGCUCUUGUGUUAGCCCUAA
...((..((((((.......)).......................------------(((((((.....)))))))...))))..))..... ( -13.20)
>consensus
UUUGCACACACGCACACUGAGCAUAUCAACAACUUCAUCAUCAUUAGCAUUAGCAUUAGCACGCAGCAGUUAUGCUCUUGUGUUAGCCCUAA
...........(((((..(((((((.(...................((....))....((.....)).).))))))).)))))......... (-12.64 = -13.07 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:55 2006