Locus 2474

Sequence ID	X_DroMel_CAF1
Location	6,591,279 – 6,591,432
Length	153
Max. P	0.761223

overview

Window 3

Location	6,591,279 – 6,591,392
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.14
Mean single sequence MFE	-37.50
Consensus MFE	-28.59
Energy contribution	-28.34
Covariance contribution	-0.25
Combinations/Pair	1.11
Mean z-score	-1.77
Structure conservation index	0.76
SVM decision value	0.50
SVM RNA-class probability	0.761223
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6591279 113 - 22224390
GUGCGUGCCGUAAAUCGGUGCAUACGAUAGCCGCCUAUCCGCCGCUGACUCAUGGAGCUACAAGCUCCAAGCUCCAAGCUCCGAUGUUCGAGCC-------ACAGAUCUCAGCUUCCCCG
(.(((..(((.....)))..)....(((((....))))).)))(((((.((.((((((.....)))))).((((..(((......))).)))).-------...))..)))))....... ( -37.00)
>DroSec_CAF1 6953 106 - 1
GUGCGUGCCGUAAAUCGGUGCAUACGAUAGCCGCCUAUCCGCCGCUGACUCAUGCAG-------CUCCAAGCUCCAAGCUCCGAUCUUUGAGCC-------ACAGAUCUCAGCUUCCCCG
(.(((..(((.....)))..)....(((((....))))).)))(((((....((..(-------(((.(((.((........)).))).)))).-------.))....)))))....... ( -30.00)
>DroEre_CAF1 7093 113 - 1
GUGCGUGCCGUAAAUCGGUGCAUACGAUAGCCGUCUAUCCGCAGCUGACUCAUGGGG-------CUCAGAUCCCCGAUCUCCGAUCUUGGAGCCUCGGAUCACAGAUCUCAGCUGCCCCU
(((.(..(((.....)))..).)))(((((....))))).((((((((....(((((-------((((((((..........)))))..))))))))((((...)))))))))))).... ( -44.70)
>DroYak_CAF1 6209 106 - 1
GUGCGUGCCGUAAAUCGGUGCACACGAUAGCCGCCUAUCCGCAGCUGACUCAUGGAG-------CACCGAGCUCCAAGCUCCGAUCUUUGAGCC-------ACAGAUCUCAGCUUCCCCG
(((.(..(((.....)))..).)))(((((....))))).(.((((((.((.(((((-------(.....)))))).((((........)))).-------...))..)))))).).... ( -38.30)
>consensus
GUGCGUGCCGUAAAUCGGUGCAUACGAUAGCCGCCUAUCCGCAGCUGACUCAUGGAG_______CUCCAAGCUCCAAGCUCCGAUCUUUGAGCC_______ACAGAUCUCAGCUUCCCCG
(((.(..(((.....)))..).)))(((((....)))))....(((((.((.(((((..............))))).((((........))))...........))..)))))....... (-28.59 = -28.34 +  -0.25)

alignment

secondary structure

dotplot

Window 4

Location	6,591,312 – 6,591,432
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.32
Mean single sequence MFE	-31.33
Consensus MFE	-22.00
Energy contribution	-21.56
Covariance contribution	-0.44
Combinations/Pair	1.18
Mean z-score	-1.67
Structure conservation index	0.70
SVM decision value	0.25
SVM RNA-class probability	0.651572
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6591312 120 - 22224390
CCAUCCAUCGCGCACUAUCAUUACUACCAAGGAAACACAUGUGCGUGCCGUAAAUCGGUGCAUACGAUAGCCGCCUAUCCGCCGCUGACUCAUGGAGCUACAAGCUCCAAGCUCCAAGCU
.........(((..(((((...........(....)....(((.(..(((.....)))..).)))))))).))).........(((......((((((.....)))))).......))). ( -33.82)
>DroSec_CAF1 6986 113 - 1
CCAUCCAUCGCACACUAUCAUUAAUACCAAGGAAACUCAUGUGCGUGCCGUAAAUCGGUGCAUACGAUAGCCGCCUAUCCGCCGCUGACUCAUGCAG-------CUCCAAGCUCCAAGCU
.........((...(((((..........((....))...(((.(..(((.....)))..).))))))))..)).........((((.(....))))-------)....(((.....))) ( -25.10)
>DroEre_CAF1 7133 104 - 1
CUAU------CGCACUAUCAUU---ACCAUGGAAACACAUGUGCGUGCCGUAAAUCGGUGCAUACGAUAGCCGUCUAUCCGCAGCUGACUCAUGGGG-------CUCAGAUCCCCGAUCU
..((------(((.........---..((((......))))((((..(((.....)))..)....(((((....))))).)))))........((((-------.......))))))).. ( -27.10)
>DroYak_CAF1 6242 104 - 1
CUUC------GGCACUAUCAUU---ACCAAGGAAACUCGUGUGCGUGCCGUAAAUCGGUGCACACGAUAGCCGCCUAUCCGCAGCUGACUCAUGGAG-------CACCGAGCUCCAAGCU
..((------(((.(((((...---....((....)).((((((..((((.....)))))))))))))))..((......)).)))))....(((((-------(.....)))))).... ( -39.30)
>consensus
CCAU______CGCACUAUCAUU___ACCAAGGAAACACAUGUGCGUGCCGUAAAUCGGUGCAUACGAUAGCCGCCUAUCCGCAGCUGACUCAUGGAG_______CUCCAAGCUCCAAGCU
...........((.(((((...........(....)....(((.(..(((.....)))..).))))))))..((......)).)).......(((((..............))))).... (-22.00 = -21.56 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:40 2006