Locus 6800

Sequence ID	2L_DroMel_CAF1
Location	19,012,438 – 19,012,605
Length	167
Max. P	0.996461

overview

Window 4

Location	19,012,438 – 19,012,543
Length	105
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	89.72
Mean single sequence MFE	-25.71
Consensus MFE	-21.06
Energy contribution	-21.02
Covariance contribution	-0.04
Combinations/Pair	1.15
Mean z-score	-1.52
Structure conservation index	0.82
SVM decision value	0.42
SVM RNA-class probability	0.727724
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19012438 105 - 22407834
CACAGGCAUGGAAUGCCUAAAUCCACCAGACUUCCACAAUGGAACCAUCAAAAGGGGUUUGGCAUUGUUGAAUACCCUAAGACAAAUAGCAGGUGAAAAUAUUUA-
...((((((...)))))).....((((.((.((((.....))))...))...(((((((..((...))..))).)))).............))))..........- ( -24.50)
>DroSec_CAF1 17085 105 - 1
CACAGGCAUGGAAUGCCUAAAUCCACCAGACUUCCACCAUGGAACCAUCAA-GGGGGUUUGGCAUUGUUGAAUACCCUAAGACAAAUAGCAGGUGAAAAUAUAUAU
...((((((...)))))).....((((.((.((((.....))))...)).(-(((..((..((...))..))..)))).............))))........... ( -25.90)
>DroSim_CAF1 13075 105 - 1
CACAGGCAUGGAAUGCCUAAAUCCACCAGACUUCCACCAUGGAACCAUCAA-GGGGGUUUGGCAUUGUUGAAUACCCUAAGACAAAUAGCAGGUGAAAAUAUAUAU
...((((((...)))))).....((((.((.((((.....))))...)).(-(((..((..((...))..))..)))).............))))........... ( -25.90)
>DroEre_CAF1 15609 102 - 1
CACAGGCAUGGAAUGCCUAAAUCCACCAGGCUUCCACAAUGGAACUCUCCG-AGGGGUUGGGC-UUGUUGAAUACCCUAAGACGCAUAACAGG-GAAAAUAUAUA-
.((((((.(((((.((((.........)))))))))......((((((...-.))))))..))-))))......((((............)))-)..........- ( -25.30)
>DroYak_CAF1 12412 103 - 1
CUCAGGCAUGGAAUGCCUAAGUCCGCCAGACUUCUACAAUGGAA-UAUCAA-AGGGGUUUGGCAUUGUUACAUACCCUAGGACAAGUAGCAGGUGAAAAUAUAUA-
((.((((((...)))))).)).(((((((((((((.........-......-)))))))))))..((((((....(....)....))))))))............- ( -26.96)
>consensus
CACAGGCAUGGAAUGCCUAAAUCCACCAGACUUCCACAAUGGAACCAUCAA_AGGGGUUUGGCAUUGUUGAAUACCCUAAGACAAAUAGCAGGUGAAAAUAUAUA_
...((((((...)))))).....((((....((((.....))))...((...(((((((((((...))))))).))))..)).........))))........... (-21.06 = -21.02 +  -0.04)

alignment

secondary structure

dotplot

Window 5

Location	19,012,506 – 19,012,605
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	93.62
Mean single sequence MFE	-36.36
Consensus MFE	-32.32
Energy contribution	-31.80
Covariance contribution	-0.52
Combinations/Pair	1.12
Mean z-score	-2.05
Structure conservation index	0.89
SVM decision value	2.70
SVM RNA-class probability	0.996461
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19012506 99 + 22407834
GUGGAAGUCUGGUGGAUUUAGGCAUUCCAUGCCUGUGCUGUGCCGUUGAUGGUUCUCCAUUCUGGUUGAAGCCCUGAAGCCUUCUGCUUUUGCCGGGCA
((((((((((((.....)))))).))))))(((((.(((..((((..(((((....))))).))))...)))...(((((.....)))))...))))). ( -34.20)
>DroSec_CAF1 17153 96 + 1
GUGGAAGUCUGGUGGAUUUAGGCAUUCCAUGCCUGUGCUGUGCCGUGGAUGGUUCUGCAUUCUGGUU---GCCCUGAAGCCUUCUGCUUUUGCCGGGCA
......((((((..((....(((((..(((....)))..)))))(..((.(((((.(((.......)---))...).)))).))..).))..)))))). ( -34.20)
>DroSim_CAF1 13143 96 + 1
GUGGAAGUCUGGUGGAUUUAGGCAUUCCAUGCCUGUGCUGUGCCGUGGAUGGUUCUGCAUUCUGGUU---GCCCUGAAGCCUUCUGCUUUUGCCGGGCA
......((((((..((....(((((..(((....)))..)))))(..((.(((((.(((.......)---))...).)))).))..).))..)))))). ( -34.20)
>DroEre_CAF1 15674 96 + 1
GUGGAAGCCUGGUGGAUUUAGGCAUUCCAUGCCUGUGCGGUGCCGUGGAUGCUUCUGCAUUCUGGUU---GCCCUGAAGCCUUCUGCUUUUGCCAGGCA
((((((((((((.....)))))).))))))(((((.(((((((((.((((((....))))))))).)---)))..(((((.....))))).))))))). ( -43.80)
>DroYak_CAF1 12478 96 + 1
GUAGAAGUCUGGCGGACUUAGGCAUUCCAUGCCUGAGCUUUGCCGUGGAUGGUUCUGCAUUCUGGUU---GCCCUGAAGCCUUCUGUUUUUGCCAGGCA
(((((((((((((((((((((((((...))))))))).))))))..))))..))))))..((((((.---.....(((((.....))))).)))))).. ( -35.40)
>consensus
GUGGAAGUCUGGUGGAUUUAGGCAUUCCAUGCCUGUGCUGUGCCGUGGAUGGUUCUGCAUUCUGGUU___GCCCUGAAGCCUUCUGCUUUUGCCGGGCA
......(((((((((...(((((((...))))))).((...((((.(((((......)))))))))....)))).(((((.....))))).))))))). (-32.32 = -31.80 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:15 2006