Locus 8664

Sequence ID	X_DroMel_CAF1
Location	21,952,144 – 21,952,280
Length	136
Max. P	0.951739

overview

Window 3

Location	21,952,144 – 21,952,264
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.80
Mean single sequence MFE	-30.36
Consensus MFE	-27.02
Energy contribution	-26.74
Covariance contribution	-0.28
Combinations/Pair	1.12
Mean z-score	-1.38
Structure conservation index	0.89
SVM decision value	0.79
SVM RNA-class probability	0.850727
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21952144 120 + 22224390
UUCAAAGUUAUGACAGUCGAACAGGCGUAGCGGUGAGUGCGUGUGCAUAAAAUCAGAUAUCAAAAAUUGUUUACAAAUAAUUUAAUAGCCGCAGCGCACGCACGUCACGCAUUCGUGUGC
.(((..((((((...(.....)...))))))..)))((((((((((.........(....)..((((((((....))))))))..........))))))))))..(((((....))))). ( -34.00)
>DroSec_CAF1 10600 114 + 1
UUCAAAGUUAUGACAGUCGAACAGGCGUAGCGGUGAGUGUGUGUGCAUAAAAUCAGAUAUCAAAAAUUGUUUACAAAUAAUUUAAUAGCCGCAGCGCACGCACGUCAC------GUGUGC
......((((((...(.....)...)))))).((((((((((((((.........(....)..((((((((....))))))))..........)))))))))).))))------...... ( -29.00)
>DroSim_CAF1 2262 114 + 1
UUCAAAGUUAUGACAGUCGAACAGGCGUAGCGGUGAGUGUGUGUGCAUAAAAUCAGAUAUCAAAAAUUGUUUACAAAUAAUUUAAUAGCCGCAGCGCACGCACGUCAC------GUGUGC
......((((((...(.....)...)))))).((((((((((((((.........(....)..((((((((....))))))))..........)))))))))).))))------...... ( -29.00)
>DroEre_CAF1 2191 120 + 1
UUCAAAGUUAUGACAGUCGAACAGGCGUAGCGGCGAGUGUGUGUGCAUAAAAUCAGAUAUCAAAAAUUGUUUACAAAUAAUUUAAUAGCCACAGCGCACGCACGUCACGCAUUCGUGUGC
............(((..((((...((((..(((((.(((((((.((.........(....)..((((((((....))))))))....)))))).))).))).))..)))).))))))).. ( -30.90)
>DroYak_CAF1 10204 120 + 1
AUCGAAGUUAUGACAGCCGAACAGGCGAGGCAGUAAGAGUGUGUGCAUAAAAUCAGAUAUCAAAAAUUGUUUACAAAUAAUUUAAUAGCCACAGCACACGCACGUCACGCAUUCGUGUGC
..((((....((((.(((.....)))............((((((((.........(....)..((((((((....))))))))..........))))))))..))))....))))..... ( -28.90)
>consensus
UUCAAAGUUAUGACAGUCGAACAGGCGUAGCGGUGAGUGUGUGUGCAUAAAAUCAGAUAUCAAAAAUUGUUUACAAAUAAUUUAAUAGCCGCAGCGCACGCACGUCACGCAUUCGUGUGC
..........((((.(((.....)))..........((((((((((.........(....)..((((((((....))))))))..........))))))))))))))............. (-27.02 = -26.74 +  -0.28)

alignment

secondary structure

dotplot

Window 4

Location	21,952,184 – 21,952,280
Length	96
Sequences	4
Columns	98
Reading direction	forward
Mean pairwise identity	91.62
Mean single sequence MFE	-20.80
Consensus MFE	-19.61
Energy contribution	-19.42
Covariance contribution	-0.19
Combinations/Pair	1.05
Mean z-score	-1.89
Structure conservation index	0.94
SVM decision value	1.41
SVM RNA-class probability	0.951739
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21952184 96 + 22224390
GUGUGCAUAAAAUCAGAUAUCAAAAAUUGUUUACAAAUAAUUUAAUAGCCGCAGCGCACGCACGUCACGCAUUCGUGUGCGCCGUAAAAACAGGAC--
((((((.................((((((((....))))))))....((....)))))))).((.(((((....)))))))((.........))..-- ( -21.10)
>DroSec_CAF1 10640 87 + 1
GUGUGCAUAAAAUCAGAUAUCAAAAAUUGUUUACAAAUAAUUUAAUAGCCGCAGCGCACGCACGUCAC------GUGUGCGCCGUAAAAACA---C--
(((.((.........(....)..((((((((....))))))))....))))).((((((((.......------))))))))..........---.-- ( -20.50)
>DroSim_CAF1 2302 87 + 1
GUGUGCAUAAAAUCAGAUAUCAAAAAUUGUUUACAAAUAAUUUAAUAGCCGCAGCGCACGCACGUCAC------GUGUGCGCCGUAAAAACA---C--
(((.((.........(....)..((((((((....))))))))....))))).((((((((.......------))))))))..........---.-- ( -20.50)
>DroEre_CAF1 2231 98 + 1
GUGUGCAUAAAAUCAGAUAUCAAAAAUUGUUUACAAAUAAUUUAAUAGCCACAGCGCACGCACGUCACGCAUUCGUGUGCGCCGCAAAAACAGGACUC
((((((.........(....)..((((((((....))))))))..........))))))((.((.(((((....)))))))..))............. ( -21.10)
>consensus
GUGUGCAUAAAAUCAGAUAUCAAAAAUUGUUUACAAAUAAUUUAAUAGCCGCAGCGCACGCACGUCAC______GUGUGCGCCGUAAAAACA___C__
(((.((.........(....)..((((((((....))))))))....))))).((((((((.............))))))))................ (-19.61 = -19.42 +  -0.19)

alignment

secondary structure

dotplot

Window 5

Location	21,952,184 – 21,952,280
Length	96
Sequences	4
Columns	98
Reading direction	reverse
Mean pairwise identity	91.62
Mean single sequence MFE	-23.97
Consensus MFE	-19.61
Energy contribution	-19.55
Covariance contribution	-0.06
Combinations/Pair	1.04
Mean z-score	-1.55
Structure conservation index	0.82
SVM decision value	0.14
SVM RNA-class probability	0.604982
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21952184 96 - 22224390
--GUCCUGUUUUUACGGCGCACACGAAUGCGUGACGUGCGUGCGCUGCGGCUAUUAAAUUAUUUGUAAACAAUUUUUGAUAUCUGAUUUUAUGCACAC
--((.((((....)))).)).((((....))))..(((((((.....(((.(((((((....(((....)))..))))))).)))....))))))).. ( -24.20)
>DroSec_CAF1 10640 87 - 1
--G---UGUUUUUACGGCGCACAC------GUGACGUGCGUGCGCUGCGGCUAUUAAAUUAUUUGUAAACAAUUUUUGAUAUCUGAUUUUAUGCACAC
--(---(((.....((((((((.(------(.....)).))))))))(((.(((((((....(((....)))..))))))).))).......)))).. ( -24.70)
>DroSim_CAF1 2302 87 - 1
--G---UGUUUUUACGGCGCACAC------GUGACGUGCGUGCGCUGCGGCUAUUAAAUUAUUUGUAAACAAUUUUUGAUAUCUGAUUUUAUGCACAC
--(---(((.....((((((((.(------(.....)).))))))))(((.(((((((....(((....)))..))))))).))).......)))).. ( -24.70)
>DroEre_CAF1 2231 98 - 1
GAGUCCUGUUUUUGCGGCGCACACGAAUGCGUGACGUGCGUGCGCUGUGGCUAUUAAAUUAUUUGUAAACAAUUUUUGAUAUCUGAUUUUAUGCACAC
..((.((((....)))).)).((((....))))..(((((((.....(((.(((((((....(((....)))..))))))).)))....))))))).. ( -22.30)
>consensus
__G___UGUUUUUACGGCGCACAC______GUGACGUGCGUGCGCUGCGGCUAUUAAAUUAUUUGUAAACAAUUUUUGAUAUCUGAUUUUAUGCACAC
................((((.((((....))))..))))(((((...(((.(((((((....(((....)))..))))))).)))......))))).. (-19.61 = -19.55 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:48 2006