Locus 3988

Sequence ID	3R_DroMel_CAF1
Location	10,828,739 – 10,828,832
Length	93
Max. P	0.969650

overview

Window 6

Location	10,828,739 – 10,828,832
Length	93
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	91.40
Mean single sequence MFE	-24.04
Consensus MFE	-18.30
Energy contribution	-18.90
Covariance contribution	0.60
Combinations/Pair	1.08
Mean z-score	-1.65
Structure conservation index	0.76
SVM decision value	0.16
SVM RNA-class probability	0.613336
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10828739 93 + 27905053
AAUUCGAGUGUGCGCUCUAGCGUAAAGGCCAAACUGCACCUGCACCUCAAAAAGAUGUAGUAAUCUGUGCACAUCAGUUACAAACUAUCGGCC--
..........(((((....)))))..((((....((((((((((.((.....)).)))))......)))))....(((.....)))...))))-- ( -21.80)
>DroSec_CAF1 98216 93 + 1
GAUUCGAGUGUGCGCUCUAGCGUAAAGGCCAAACUGCACCUGCACCUCAAAAAGAUGCAGUAAUCUGUGCACAUUAGUUACAAACUAUCGGCC--
..........(((((....)))))..((((....((((((((((.((.....)).)))))......)))))...((((.....))))..))))-- ( -24.90)
>DroSim_CAF1 104330 93 + 1
GAUUCGAGUGUGCGCUCUAGCGUAAAGGCCAAACUGCACCUGCACCUCAAAAAGAUGCAGUAAUCUGUGCACAUCAGUAACAAACUAUCGGCC--
..........(((((....)))))..((((....((((((((((.((.....)).)))))......)))))....(((.....)))...))))-- ( -24.00)
>DroEre_CAF1 100661 93 + 1
AAUUCGAGUGUGCGCUCUAGCGUAAAGGCCAAAAUGCACCUGCACCUCAAAAAUAUGCAGUAAUCUGUGCACAUCAGUUACAAACUC--GGAUGU
.((((((((.(((((....)))))..........((((((((((...........)))))......)))))............))))--)))).. ( -24.20)
>DroYak_CAF1 103762 93 + 1
AAUUCGAGUGUGCGCUCUAGCGUAAAGGCCAAACUGCACCUGCACCUCAAACAGAUGCAGUAAUCUUUGCACAUCAGUUACAAACUG--GAAUGU
.((((..((((((((....))..(((((....((((((.(((.........))).))))))..)))))))))))((((.....))))--)))).. ( -25.30)
>consensus
AAUUCGAGUGUGCGCUCUAGCGUAAAGGCCAAACUGCACCUGCACCUCAAAAAGAUGCAGUAAUCUGUGCACAUCAGUUACAAACUAUCGGCC__
..........(((((....)))))..((((....((((((((((.((.....)).)))))......)))))....(((.....)))...)))).. (-18.30 = -18.90 +   0.60)

alignment

secondary structure

dotplot

Window 7

Location	10,828,739 – 10,828,832
Length	93
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	91.40
Mean single sequence MFE	-29.18
Consensus MFE	-24.40
Energy contribution	-25.00
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.95
Structure conservation index	0.84
SVM decision value	1.65
SVM RNA-class probability	0.969650
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10828739 93 - 27905053
--GGCCGAUAGUUUGUAACUGAUGUGCACAGAUUACUACAUCUUUUUGAGGUGCAGGUGCAGUUUGGCCUUUACGCUAGAGCGCACACUCGAAUU
--...(((((((((((.((....))..))))))))((.((((((...)))))).))((((..((((((......))))))..))))..))).... ( -24.30)
>DroSec_CAF1 98216 93 - 1
--GGCCGAUAGUUUGUAACUAAUGUGCACAGAUUACUGCAUCUUUUUGAGGUGCAGGUGCAGUUUGGCCUUUACGCUAGAGCGCACACUCGAAUC
--...(((((((((((.((....))..))))))))(((((((((...)))))))))((((..((((((......))))))..))))..))).... ( -30.90)
>DroSim_CAF1 104330 93 - 1
--GGCCGAUAGUUUGUUACUGAUGUGCACAGAUUACUGCAUCUUUUUGAGGUGCAGGUGCAGUUUGGCCUUUACGCUAGAGCGCACACUCGAAUC
--...((((((((((((((....))).))))))))(((((((((...)))))))))((((..((((((......))))))..))))..))).... ( -31.50)
>DroEre_CAF1 100661 93 - 1
ACAUCC--GAGUUUGUAACUGAUGUGCACAGAUUACUGCAUAUUUUUGAGGUGCAGGUGCAUUUUGGCCUUUACGCUAGAGCGCACACUCGAAUU
.....(--(((((((((.((((((((((........))))))))....)).)))))((((.(((((((......))))))).))))))))).... ( -28.70)
>DroYak_CAF1 103762 93 - 1
ACAUUC--CAGUUUGUAACUGAUGUGCAAAGAUUACUGCAUCUGUUUGAGGUGCAGGUGCAGUUUGGCCUUUACGCUAGAGCGCACACUCGAAUU
..((((--((((.....)))).(((((........((((((((((.......))))))))))((((((......))))))..)))))...)))). ( -30.50)
>consensus
__GGCCGAUAGUUUGUAACUGAUGUGCACAGAUUACUGCAUCUUUUUGAGGUGCAGGUGCAGUUUGGCCUUUACGCUAGAGCGCACACUCGAAUU
.........(((((((.((....))..))))))).((((((((.....))))))))((((..((((((......))))))..))))......... (-24.40 = -25.00 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:19 2006