Locus 4554

Sequence ID	3L_DroMel_CAF1
Location	13,102,394 – 13,102,490
Length	96
Max. P	0.737964

overview

Window 0

Location	13,102,394 – 13,102,490
Length	96
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	83.54
Mean single sequence MFE	-27.33
Consensus MFE	-20.58
Energy contribution	-21.02
Covariance contribution	0.43
Combinations/Pair	1.16
Mean z-score	-2.10
Structure conservation index	0.75
SVM decision value	0.42
SVM RNA-class probability	0.728082
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13102394 96 + 23771897
CGAACUUUGUUCGAAUUCCGUCCUCAUGUGGCUCCCAAUUGCUGGCACUGCAAUUGCUUCUUGGCCAUUUAAUGAGCCAAGAACUUGCUUUCGGAC
(((((...)))))......((((......(((...(((((((.......))))))).(((((((((((...))).))))))))...)))...)))) ( -28.70)
>DroSec_CAF1 90055 96 + 1
CGAACUUUGUUCGAAUUCCGUCCUCAUGUGGCUCCCAAUUGCUGGCACUGCAAUUGCUUCUUGGCCAUUUAAUGAGCCAAGAACAUGCUUUCGGAC
(((((...)))))...((((....(((((......(((((((.......)))))))..((((((((((...))).))))))))))))....)))). ( -31.90)
>DroSim_CAF1 87806 96 + 1
CGAACUUUGUUCGAAUUCCGUCCUCAUGUGGCUCCCAAUUGCUGGCACUGCAAUUGCUUCUUGGCCAUUUAAUGAGCCAAGAACUUGCUUUCGGAC
(((((...)))))......((((......(((...(((((((.......))))))).(((((((((((...))).))))))))...)))...)))) ( -28.70)
>DroEre_CAF1 86527 95 + 1
CGAACUUUGUUCGAAUUCCGUCCUCAUGUGGCUUCCAAUUGCUGGCACUGCAAUUGCUGCUUGGCCGUUUAAUGAGCCAAGAACUUGCUUUCGG-C
(((((...)))))....(((....((.((......(((((((.......)))))))...(((((((((...))).)))))).)).))....)))-. ( -23.50)
>DroYak_CAF1 89690 96 + 1
CGAACUUUGUUCGAAUUCCGUUCACAUGUGGUUCCCAAUUGCUGGCACUGCAAUUGCUUCUUGGCCUUUUAAUGAGCCAAGAACUUGCUUUCGGAC
(((((...)))))...((((....((.((......(((((((.......)))))))..((((((((.......).))))))))).))....)))). ( -26.70)
>DroAna_CAF1 83009 77 + 1
CG-----------------GUCGUUAUGGGCCUGCCAAUUGCUUUCGCUGCAAUUGCUUUUUGGCUUUGGAAUGGGCCAAGAAUAAGU--AUGGGC
.(-----------------(((......)))).(((((((((.......))))))..((((((((((......)))))))))).....--...))) ( -24.50)
>consensus
CGAACUUUGUUCGAAUUCCGUCCUCAUGUGGCUCCCAAUUGCUGGCACUGCAAUUGCUUCUUGGCCAUUUAAUGAGCCAAGAACUUGCUUUCGGAC
(((((...)))))......((((............(((((((.......))))))).(((((((((.......).)))))))).........)))) (-20.58 = -21.02 +   0.43)

alignment

secondary structure

dotplot

Window 1

Location	13,102,394 – 13,102,490
Length	96
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	83.54
Mean single sequence MFE	-27.27
Consensus MFE	-20.44
Energy contribution	-22.07
Covariance contribution	1.62
Combinations/Pair	1.00
Mean z-score	-2.16
Structure conservation index	0.75
SVM decision value	0.44
SVM RNA-class probability	0.737964
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13102394 96 - 23771897
GUCCGAAAGCAAGUUCUUGGCUCAUUAAAUGGCCAAGAAGCAAUUGCAGUGCCAGCAAUUGGGAGCCACAUGAGGACGGAAUUCGAACAAAGUUCG
((((....((...(((((((((........))))))))).(((((((.......)))))))...)).......))))......(((((...))))) ( -29.30)
>DroSec_CAF1 90055 96 - 1
GUCCGAAAGCAUGUUCUUGGCUCAUUAAAUGGCCAAGAAGCAAUUGCAGUGCCAGCAAUUGGGAGCCACAUGAGGACGGAAUUCGAACAAAGUUCG
((((.....(((((((((((((........))))))))..(((((((.......)))))))......))))).))))......(((((...))))) ( -31.70)
>DroSim_CAF1 87806 96 - 1
GUCCGAAAGCAAGUUCUUGGCUCAUUAAAUGGCCAAGAAGCAAUUGCAGUGCCAGCAAUUGGGAGCCACAUGAGGACGGAAUUCGAACAAAGUUCG
((((....((...(((((((((........))))))))).(((((((.......)))))))...)).......))))......(((((...))))) ( -29.30)
>DroEre_CAF1 86527 95 - 1
G-CCGAAAGCAAGUUCUUGGCUCAUUAAACGGCCAAGCAGCAAUUGCAGUGCCAGCAAUUGGAAGCCACAUGAGGACGGAAUUCGAACAAAGUUCG
.-(((...((((((((((((((........))))))).)))..)))).(((((((...))))....))).......)))....(((((...))))) ( -23.80)
>DroYak_CAF1 89690 96 - 1
GUCCGAAAGCAAGUUCUUGGCUCAUUAAAAGGCCAAGAAGCAAUUGCAGUGCCAGCAAUUGGGAACCACAUGUGAACGGAAUUCGAACAAAGUUCG
.((((...(((..(((((((((........))))))))).(((((((.......))))))).........)))...))))...(((((...))))) ( -29.80)
>DroAna_CAF1 83009 77 - 1
GCCCAU--ACUUAUUCUUGGCCCAUUCCAAAGCCAAAAAGCAAUUGCAGCGAAAGCAAUUGGCAGGCCCAUAACGAC-----------------CG
(((...--........((((......)))).(((((...((....)).((....))..))))).)))..........-----------------.. ( -19.70)
>consensus
GUCCGAAAGCAAGUUCUUGGCUCAUUAAAUGGCCAAGAAGCAAUUGCAGUGCCAGCAAUUGGGAGCCACAUGAGGACGGAAUUCGAACAAAGUUCG
((((.........(((((((((........))))))))).(((((((.......)))))))............))))......(((((...))))) (-20.44 = -22.07 +   1.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:24 2006