Locus 4958

Sequence ID	X_DroMel_CAF1
Location	12,950,368 – 12,950,510
Length	142
Max. P	0.802076

overview

Window 9

Location	12,950,368 – 12,950,472
Length	104
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.58
Mean single sequence MFE	-32.25
Consensus MFE	-21.52
Energy contribution	-24.02
Covariance contribution	2.50
Combinations/Pair	1.00
Mean z-score	-1.74
Structure conservation index	0.67
SVM decision value	0.23
SVM RNA-class probability	0.645891
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12950368 104 - 22224390
--------GAUCCGCGGAUCUGCCUUAACUUUCACAUUGGGCACCUAAUUGUGCGCCUUAAUCUCGGUUAAUUUGCUCCAGUUUUGAUCCGCGCUUGUGGCGCACAGAAA--------GC
--------((((....))))........(((((..(((((....)))))((((((((.(((.(.(((((((...((....)).)))).))).).))).))))))))))))--------). ( -33.50)
>DroSec_CAF1 8615 104 - 1
--------GAUCCGCGGAUCUGCCUUAACUUUCACAUUGGGCACCUAAUUGUGCGCCUUAAUCUCGGUUAAUUUGCUCCAGUUUUGAUCCGCGCUUGCGGCGCACAGAAA--------GC
--------((((....))))........(((((..(((((....)))))((((((((.(((.(.(((((((...((....)).)))).))).).))).))))))))))))--------). ( -33.50)
>DroEre_CAF1 7956 112 - 1
GAUCUGCCGAUCUGCGGAUCUGCCUUAACUUUCACAUUGGGCACCUAAUUGUGGGCCUUAAUCUCGGUUAAUUUGCUCCAGUUUUGAUCCGCGCUUGUGGCGCACAGAAA--------GC
(((((((......)))))))........(((((..(((((....)))))((((.(((.(((.(.(((((((...((....)).)))).))).).))).))).))))))))--------). ( -34.40)
>DroYak_CAF1 8248 110 - 1
GAUCUUCGGAUCUUUGGAUCUGCCUUAACUUUCACAUUGGGCCCCUAAUUGUGGGCCUUAAUCUCGGUUAAUUUGCUCCAGUUUUGAUC----------ACACACAGAAAAGCCAGCUGC
((((....)))).((((.((((................(((((((.....).)))))).......((((((...((....)).))))))----------.....))))....)))).... ( -27.60)
>consensus
________GAUCCGCGGAUCUGCCUUAACUUUCACAUUGGGCACCUAAUUGUGCGCCUUAAUCUCGGUUAAUUUGCUCCAGUUUUGAUCCGCGCUUGUGGCGCACAGAAA________GC
........((((....)))).((((.............))))......(((((((((.(((.(.(((((((...((....)).)))).))).).))).)))))))))............. (-21.52 = -24.02 +   2.50)

alignment

secondary structure

dotplot

Window 0

Location	12,950,400 – 12,950,510
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.65
Mean single sequence MFE	-36.50
Consensus MFE	-27.69
Energy contribution	-29.50
Covariance contribution	1.81
Combinations/Pair	1.06
Mean z-score	-2.13
Structure conservation index	0.76
SVM decision value	0.62
SVM RNA-class probability	0.802076
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12950400 110 - 22224390
--AAGAAGCAACAGGUUUCCAGCUGGCGUUCGGAUCUUCG--------GAUCCGCGGAUCUGCCUUAACUUUCACAUUGGGCACCUAAUUGUGCGCCUUAAUCUCGGUUAAUUUGCUCCA
--..(.(((((..(((.((((((....)))((((((....--------)))))).)))...)))((((((........((((((......)))).))........)))))).))))).). ( -33.09)
>DroSec_CAF1 8647 110 - 1
--AAGAAGCAACAGGUUUCCAGCUGGCGUUCGGAUCUUCG--------GAUCCGCGGAUCUGCCUUAACUUUCACAUUGGGCACCUAAUUGUGCGCCUUAAUCUCGGUUAAUUUGCUCCA
--..(.(((((..(((.((((((....)))((((((....--------)))))).)))...)))((((((........((((((......)))).))........)))))).))))).). ( -33.09)
>DroEre_CAF1 7988 118 - 1
--AAGAAGCAACAGGUUUCCAGCUGGCGUUCGGAUCUUCGGAUCUGCCGAUCUGCGGAUCUGCCUUAACUUUCACAUUGGGCACCUAAUUGUGGGCCUUAAUCUCGGUUAAUUUGCUCCA
--..(.(((((((((((..(((.((((....(((((....)))))))))..)))..))))))..((((((........((((.((.......)))))).......)))))).))))).). ( -37.66)
>DroYak_CAF1 8278 120 - 1
AAAAGAAGCAACAGGUUUCCAACUGGCGUUCGGAUCCGCGGAUCUUCGGAUCUUUGGAUCUGCCUUAACUUUCACAUUGGGCCCCUAAUUGUGGGCCUUAAUCUCGGUUAAUUUGCUCCA
....(.((((((((........))).....((((((((.(((((....))))).))))))))..((((((........(((((((.....).)))))).......)))))).))))).). ( -42.16)
>consensus
__AAGAAGCAACAGGUUUCCAGCUGGCGUUCGGAUCUUCG________GAUCCGCGGAUCUGCCUUAACUUUCACAUUGGGCACCUAAUUGUGCGCCUUAAUCUCGGUUAAUUUGCUCCA
....(.(((((.............(((...(((((((.((((((....)))))).)))))))..........((((((((....)))).)))).)))(((((....))))).))))).). (-27.69 = -29.50 +   1.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:55 2006