Locus 3494

Sequence ID	X_DroMel_CAF1
Location	9,386,949 – 9,387,108
Length	159
Max. P	0.680837

overview

Window 9

Location	9,386,949 – 9,387,068
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.98
Mean single sequence MFE	-21.30
Consensus MFE	-14.57
Energy contribution	-15.88
Covariance contribution	1.31
Combinations/Pair	1.04
Mean z-score	-2.14
Structure conservation index	0.68
SVM decision value	0.31
SVM RNA-class probability	0.680837
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9386949 119 + 22224390
UAGCACUAAGCUGUGCAUAAUAAAAUUUAAAACUAGUUUCUUUCAAUUCUUUAUUUCCGCCUCCCUCAAAAGUUUAACAAAAAAUA-AAAAAAAAAAGAAUUAAGGGAACCGGAAGCCUA
..((((......)))).....................................((((((..(((((....(((((...........-..........))))).)))))..)))))).... ( -18.20)
>DroSec_CAF1 956 120 + 1
UAGCACUAAGCUGUGCAUAAUACAAUUUAAAACUAGUUUCUUUCAAUUCUUUAUUUUCGCCCCUAUCAAAAGUUUUUAAAAAAAAACCAAAAAAAAAGAAUUGAGGGAACCGGAAGCCUA
..((((......))))................(..(((.(((((((((((((.((((.(............((((((....))))))).)))).))))))))))))))))..)....... ( -23.40)
>DroSim_CAF1 4032 119 + 1
UAGCACUAAGCUGUGCAUAAUACAAUUUAAAACUAGUUUCUUUCAAUUCUUUAUUUCCGCCCCUCUCAAAAGUUUGUUAAAAAAAA-CAAAAAAAAAGAAUUGAGGGAACCGGAAGCCUA
..((((......))))................(..(((.(((((((((((((..........((......))((((((......))-))))...))))))))))))))))..)....... ( -24.20)
>DroYak_CAF1 4441 110 + 1
UAGCGCUAAGCUGUGCAUAAUACAAUUUAAAACUAGUUUCUUUCAAUUCCUUAUUUCCGCCCCUCUCAAAAGUUUGUUAACG------AAAAAAAAAGA----AGGGAAACGGAAGCCUA
..((((......)))).....................................(((((((((.(((......((((....))------))......)))----.)))...)))))).... ( -19.40)
>consensus
UAGCACUAAGCUGUGCAUAAUACAAUUUAAAACUAGUUUCUUUCAAUUCUUUAUUUCCGCCCCUCUCAAAAGUUUGUUAAAAAAAA_CAAAAAAAAAGAAUUGAGGGAACCGGAAGCCUA
..((((......))))...................(.(((((((((((((((.(((..................................))).))))))))))))))).)......... (-14.57 = -15.88 +   1.31)

alignment

secondary structure

dotplot

Window 0

Location	9,386,989 – 9,387,108
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.01
Mean single sequence MFE	-25.27
Consensus MFE	-18.78
Energy contribution	-19.97
Covariance contribution	1.19
Combinations/Pair	1.11
Mean z-score	-1.45
Structure conservation index	0.74
SVM decision value	0.02
SVM RNA-class probability	0.545097
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9386989 119 + 22224390
UUUCAAUUCUUUAUUUCCGCCUCCCUCAAAAGUUUAACAAAAAAUA-AAAAAAAAAAGAAUUAAGGGAACCGGAAGCCUAGUCAUAAAAUUCGUUUAGCUGGCAGGCAAUGGUGAAAGUG
(((((.........(((((..(((((....(((((...........-..........))))).)))))..)))))((((.((((((((.....))))..)))))))).....)))))... ( -23.20)
>DroSec_CAF1 996 120 + 1
UUUCAAUUCUUUAUUUUCGCCCCUAUCAAAAGUUUUUAAAAAAAAACCAAAAAAAAAGAAUUGAGGGAACCGGAAGCCUAGUCAUAAAAUUCGUUUAGCUGGCAGGCAAUGGAGAAAGUG
......(((((((((((((.((((.......((((((....))))))(((..........)))))))...)))).((((.((((((((.....))))..))))))))))))))))).... ( -22.80)
>DroSim_CAF1 4072 119 + 1
UUUCAAUUCUUUAUUUCCGCCCCUCUCAAAAGUUUGUUAAAAAAAA-CAAAAAAAAAGAAUUGAGGGAACCGGAAGCCUAGUCAUGAAAUUCGUUUAGCUGGCAGGCAAAGGAGAAAGUG
((((..((((((..(((((.(((((((.....((((((......))-))))......))...)))))...)))))((((.((((..(((....)))...))))))))))))))))))... ( -29.10)
>DroYak_CAF1 4481 110 + 1
UUUCAAUUCCUUAUUUCCGCCCCUCUCAAAAGUUUGUUAACG------AAAAAAAAAGA----AGGGAAACGGAAGCCUAGUCAUGAAAUUCGUUUAGCUGGCAGGCAGUGGAGAAAGUG
......((((....((((((((.(((......((((....))------))......)))----.)))...)))))((((.((((..(((....)))...))))))))...))))...... ( -26.00)
>consensus
UUUCAAUUCUUUAUUUCCGCCCCUCUCAAAAGUUUGUUAAAAAAAA_CAAAAAAAAAGAAUUGAGGGAACCGGAAGCCUAGUCAUAAAAUUCGUUUAGCUGGCAGGCAAUGGAGAAAGUG
......(((((((((((((...(((((((...(((..................)))....)))))))...)))))((((.((((((((.....))))..)))))))).)))))))).... (-18.78 = -19.97 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:39 2006