Locus 2486

Sequence ID	3L_DroMel_CAF1
Location	6,981,663 – 6,981,812
Length	149
Max. P	0.644166

overview

Window 3

Location	6,981,663 – 6,981,778
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.40
Mean single sequence MFE	-26.40
Consensus MFE	-23.38
Energy contribution	-23.30
Covariance contribution	-0.08
Combinations/Pair	1.20
Mean z-score	-1.31
Structure conservation index	0.89
SVM decision value	0.18
SVM RNA-class probability	0.622393
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6981663 115 - 23771897
AUGGAUGAGCGAUAAAGGCCCAAAGCGUAAUUCGAUAUUGGCCAGCUGACAACCAAAAUCGGAGGUGAUGAGUGGGUUUUCGUUGCAGAGGCAUAA-----UAAUUAUAAAUUGAUGAUA
........((((..((((((((...(((..((((((.((((...........)))).))))))....)))..))))))))..))))..........-----..(((((......))))). ( -29.10)
>DroSec_CAF1 51497 115 - 1
AUGGAAGAGCGAUAAAGGCCCAAAGCGUAAUUCGAUAUUGGCCAGCUGACAACCAAAAUCGGAGGUGAGGAGUGGAUUUUGGUGGCAAACAAAUAA-----UAAUUAUAAAUGUAUGAUA
........((......((((.....((.....)).....))))........(((((((((.(..........).))))))))).))..........-----..((((((....)))))). ( -21.30)
>DroSim_CAF1 51273 115 - 1
AUGGAUGAGCGAUAAAGGCCUAAAGCGUAAUUCGAUAUUGGCCAGCUGACAACCAAAAUCGGAGGUAAAGAGUGGGUUUUGGUUGCAGAGACAUAA-----UAAUUAUAAAUGGAUGAUA
....(((.........((((.....((.....)).....))))..(((.(((((((((((.(..........).))))))))))))))...)))..-----..(((((......))))). ( -26.60)
>DroEre_CAF1 51306 115 - 1
CUGGAUGAGCGAUAAAGGCCUAAAGCGUAAUUCGAUAUUGGCCAGCUGGCAGUCAAAUUCGGAGGUGAAGAGUGGGCUUUGGUUGCAGAGACAAAA-----UAAUUAUAAAUGUAUGAAA
.((..(..(((((.((((((((.....((.(((((..((((((....)))...)))..)))))..)).....)))))))).)))))..)..))...-----................... ( -26.40)
>DroYak_CAF1 53141 120 - 1
AUGGAUGAGCGAUAAAGGCCCAAAGCGUAAUUCGAUAUUGGCCAGCUGGCAACCAAAAUCGGAGGUGAAGAGUGGGUUUCGAUUGCAGAGAUAUAAUACCAUAAUUAUAAAUGUAUGAUA
........(((((..(((((((.....((.((((((.((((((....)))...))).))))))..)).....)))))))..))))).....((((((......))))))........... ( -28.60)
>consensus
AUGGAUGAGCGAUAAAGGCCCAAAGCGUAAUUCGAUAUUGGCCAGCUGACAACCAAAAUCGGAGGUGAAGAGUGGGUUUUGGUUGCAGAGACAUAA_____UAAUUAUAAAUGUAUGAUA
........(((((.((((((((.....((.((((((.((((...........)))).))))))..)).....)))))))).))))).................................. (-23.38 = -23.30 +  -0.08)

alignment

secondary structure

dotplot

Window 4

Location	6,981,698 – 6,981,812
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.39
Mean single sequence MFE	-21.54
Consensus MFE	-17.62
Energy contribution	-18.02
Covariance contribution	0.40
Combinations/Pair	1.14
Mean z-score	-1.43
Structure conservation index	0.82
SVM decision value	0.23
SVM RNA-class probability	0.644166
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6981698 114 + 23771897
AAAACCCACUCAUCACCUCCGAUUUUGGUUGUCAGCUGGCCAAUAUCGAAUUACGCUUUGGGCCUUUAUCGCUCAUCCAUCCAA--UUCACACUCAC----ACACUUUUGGCCAGCAUGC
..((((.....(((......)))...))))....(((((((((....(((((......(((((.......))))).......))--)))........----......))))))))).... ( -24.29)
>DroSec_CAF1 51532 118 + 1
AAAAUCCACUCCUCACCUCCGAUUUUGGUUGUCAGCUGGCCAAUAUCGAAUUACGCUUUGGGCCUUUAUCGCUCUUCCAUCCGA--UUCACACUCACACACACACUUUUGGCCAGCAUGC
..............((..(((....)))..))..(((((((((....(((((.......((((.......))))........))--)))..................))))))))).... ( -21.71)
>DroSim_CAF1 51308 118 + 1
AAAACCCACUCUUUACCUCCGAUUUUGGUUGUCAGCUGGCCAAUAUCGAAUUACGCUUUAGGCCUUUAUCGCUCAUCCAUCCGA--UUCACACUCACACACACACUUUUGGCCAGCAUGC
..............((..(((....)))..))..(((((((((...........((.....))....((((..........)))--)....................))))))))).... ( -20.00)
>DroEre_CAF1 51341 114 + 1
AAAGCCCACUCUUCACCUCCGAAUUUGACUGCCAGCUGGCCAAUAUCGAAUUACGCUUUAGGCCUUUAUCGCUCAUCCAGCCAA--UCAACACUCAC----ACACUUUCGGCCAGCAUGC
..................................(((((((......((.....((.....)).....))(((.....)))...--...........----........))))))).... ( -18.80)
>DroYak_CAF1 53181 116 + 1
GAAACCCACUCUUCACCUCCGAUUUUGGUUGCCAGCUGGCCAAUAUCGAAUUACGCUUUGGGCCUUUAUCGCUCAUCCAUCCAAAUCCAACACUCAC----ACACUUUUGGCCAGCAUGC
..((((......((......))....))))....(((((((((...((.....))...(((((.......)))))......................----......))))))))).... ( -22.90)
>consensus
AAAACCCACUCUUCACCUCCGAUUUUGGUUGUCAGCUGGCCAAUAUCGAAUUACGCUUUGGGCCUUUAUCGCUCAUCCAUCCAA__UUCACACUCAC____ACACUUUUGGCCAGCAUGC
..((((......((......))....))))....(((((((((...((.....))...(((((.......)))))................................))))))))).... (-17.62 = -18.02 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:48 2006