Locus 7276

Sequence ID	X_DroMel_CAF1
Location	18,119,230 – 18,119,417
Length	187
Max. P	0.980142

overview

Window 5

Location	18,119,230 – 18,119,344
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.88
Mean single sequence MFE	-36.30
Consensus MFE	-31.34
Energy contribution	-32.02
Covariance contribution	0.69
Combinations/Pair	1.09
Mean z-score	-1.64
Structure conservation index	0.86
SVM decision value	0.54
SVM RNA-class probability	0.773204
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18119230 114 - 22224390
GCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAUCUUUGGCAUAUUAAAUUGUUGAAUCAGUCACCGAGAAGGAGUCGGAGUAGGAGUAGCUGAUGCAGUUGGAGAUG------
((((((((((..((((.....))))))))))))))..((((((..((.((((......((((.((..((.....))..)).))))......))))((....)).))..))))))------ ( -37.30)
>DroSec_CAF1 1844 114 - 1
GCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAUCUUUGGCAUAUUAAAUUGUUGAAUCAGUCACCGAGAAGGAGUCGGAGUAGGAGUCACAGAUGGAGAUGGAGGUG------
((((((((((..((((.....))))))))))))))(((((((.((((.......((((......))))..((((.......)))).......)))).)))))))..........------ ( -37.20)
>DroSim_CAF1 2115 120 - 1
GCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAUCUUUGGCAUAUUAAAUUGUUGAAUCAGUCACCGAGAAGGAGUCGGAGUAGGAGUCACAGAUGGAGAUGGAGGUGGAGAUG
((((((((((..((((.....))))))))))))))((((((((..(((........)))..))((.(((.(((.....((.((.......)).)).....))).))).)))))))).... ( -38.40)
>DroEre_CAF1 1769 113 - 1
GAGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAUCUUUGGCAUAUUAAAUUGUUGAAUCAGUCACCGAGAAGGAGUCGGAGUCAGAGUCG-GGAUCGGGAUCGGGAUG------
..((((((((..((((.....)))))))))))).(((.(((((..(((........)))..)).......((((....((.((.......)).)).-...))))))).)))...------ ( -32.30)
>consensus
GCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAUCUUUGGCAUAUUAAAUUGUUGAAUCAGUCACCGAGAAGGAGUCGGAGUAGGAGUCACAGAUGGAGAUGGAGAUG______
((((((((((..((((.....))))))))))))))(((((((.((((.......((((......))))..((((.......)))).......)))).)))))))................ (-31.34 = -32.02 +   0.69)

alignment

secondary structure

dotplot

Window 6

Location	18,119,264 – 18,119,378
Length	114
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	88.74
Mean single sequence MFE	-38.40
Consensus MFE	-30.25
Energy contribution	-32.38
Covariance contribution	2.12
Combinations/Pair	1.06
Mean z-score	-3.13
Structure conservation index	0.79
SVM decision value	1.85
SVM RNA-class probability	0.980142
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18119264 114 - 22224390
AUCUUUACUGGAGACGC---AGACAGAGAUGGAGAUGGCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAUCUUUGGCAUAUUAAAUUGUUGAAUCAGUCACCGAGAAGGA
.(((((..(((.(((..---...((((((((((....((((((((((..((((.....))))))))))))))))))))))))(((........))).......))).)))..))))) ( -42.00)
>DroSec_CAF1 1878 114 - 1
AUCUUUACUGGAGACGC---AGACAGAGAUGGAGAUGGCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAUCUUUGGCAUAUUAAAUUGUUGAAUCAGUCACCGAGAAGGA
.(((((..(((.(((..---...((((((((((....((((((((((..((((.....))))))))))))))))))))))))(((........))).......))).)))..))))) ( -42.00)
>DroSim_CAF1 2155 114 - 1
AUCUUUACUGGAGACGC---AGACAGAGAUGGAGAUGGCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAUCUUUGGCAUAUUAAAUUGUUGAAUCAGUCACCGAGAAGGA
.(((((..(((.(((..---...((((((((((....((((((((((..((((.....))))))))))))))))))))))))(((........))).......))).)))..))))) ( -42.00)
>DroYak_CAF1 2068 101 - 1
AUCUUAACUGGAGACGGAGA---------------UGGAGAAUGGGAAUGGGAAUGCAUCUCUCUCUGUCGCUCUAUCUUUGGCAUAUUAAAUUGUUGAAUCAGUCACCGAGAAGG-
..(((...(((.(((.((((---------------(((((....(((..((((.....))))..)))....)))))))((..(((........)))..)))).))).)))..))).- ( -27.60)
>consensus
AUCUUUACUGGAGACGC___AGACAGAGAUGGAGAUGGCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAUCUUUGGCAUAUUAAAUUGUUGAAUCAGUCACCGAGAAGGA
.(((((..(((.(((............(((((....(((((((((((..((((.....))))))))))))))))))))((..(((........)))..))...))).)))..))))) (-30.25 = -32.38 +   2.12)

alignment

secondary structure

dotplot

Window 7

Location	18,119,304 – 18,119,417
Length	113
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	87.83
Mean single sequence MFE	-36.28
Consensus MFE	-26.85
Energy contribution	-28.10
Covariance contribution	1.25
Combinations/Pair	1.07
Mean z-score	-2.39
Structure conservation index	0.74
SVM decision value	1.07
SVM RNA-class probability	0.910372
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18119304 113 - 22224390
GCCGCAGGGAGAGCACACAAUAAAAUCAGACC-GAUAACCAUCUUUACUGGAGACGC---AGACAGAGAUGGAGAUGGCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAU
.((....))(((((..............(.((-.((..((((((((.(((......)---))..))))))))..)))))((((((((..((((.....))))))))))))))))).. ( -36.70)
>DroSec_CAF1 1918 113 - 1
GCCACAGGGAGAGCACACAAUAAAAUCAGACC-GAUAACCAUCUUUACUGGAGACGC---AGACAGAGAUGGAGAUGGCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAU
.((....))(((((..............(.((-.((..((((((((.(((......)---))..))))))))..)))))((((((((..((((.....))))))))))))))))).. ( -36.50)
>DroSim_CAF1 2195 113 - 1
GCCGCAGGGAGAGCACACAAUAAAAUCAGACC-GAUAACCAUCUUUACUGGAGACGC---AGACAGAGAUGGAGAUGGCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAU
.((....))(((((..............(.((-.((..((((((((.(((......)---))..))))))))..)))))((((((((..((((.....))))))))))))))))).. ( -36.70)
>DroYak_CAF1 2107 102 - 1
GCCGCAGGGAGAGCACACAAUAAAAUCAGUCCUGAUAACCAUCUUAACUGGAGACGGAGA---------------UGGAGAAUGGGAAUGGGAAUGCAUCUCUCUCUGUCGCUCUAU
((.((((((((((....((.(....(((.(((((.(..((((((...(((....))))))---------------)))..).))))).))).).))...)))))))))).))..... ( -35.20)
>consensus
GCCGCAGGGAGAGCACACAAUAAAAUCAGACC_GAUAACCAUCUUUACUGGAGACGC___AGACAGAGAUGGAGAUGGCGAUGGAGAAUGGGAAUGCAUCCCUCUCUGUCGCUCUAU
.((....))(((((........................(((((((....(....)........((....))))))))).((((((((..((((.....))))))))))))))))).. (-26.85 = -28.10 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:53 2006