Locus 149

Sequence ID	3L_DroMel_CAF1
Location	460,472 – 460,614
Length	142
Max. P	0.688762

overview

Window 3

Location	460,472 – 460,574
Length	102
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	87.48
Mean single sequence MFE	-26.81
Consensus MFE	-19.21
Energy contribution	-19.02
Covariance contribution	-0.19
Combinations/Pair	1.11
Mean z-score	-1.44
Structure conservation index	0.72
SVM decision value	-0.02
SVM RNA-class probability	0.524065
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 460472 102 + 23771897
AGGCCAAAUGUCAGUUUUCAUUGGCAAAGACCUGCAAUUUUUAGGGCUUCUCAUAGAG-GAACGCCUUCAAGAUAGCUUGAGCUGCCAGCCAUUUCUUUCACC
.(((..((((........))))((((.......((.(((((.(((((((((......)-))).))))).))))).))......)))).)))............ ( -25.12)
>DroSec_CAF1 41473 102 + 1
AGGCCAAAUGUCAGUUUUCAUUGGCAAAGACCUGCAAUUUUUAGGGCUUCUCAUAGAG-GAACGCCUUCAAGAUAGCUUGAGCUGCCAGCCAUUUCUUUCACC
.(((..((((........))))((((.......((.(((((.(((((((((......)-))).))))).))))).))......)))).)))............ ( -25.12)
>DroEre_CAF1 43405 102 + 1
AGGCCAAAUGUCAGUUUUCAUUGGCAGAGACCUGCAAUUUUUAGGGCUUCUCAUAGAA-GAACGCCUUCGAGAUAGUUUGGGCUGCCAGCAAUUUCUUUUGCC
.(((.....))).........((((((...((.((.(((((.(((((((((......)-))).))))).))))).))..)).))))))((((......)))). ( -30.40)
>DroYak_CAF1 42975 92 + 1
AGGCCAAAUGUCAGUUUUCAUUGGCAGAGACCUGCAAUUUCUAGGGCUUCUUAUAGAAGGAACGCCUUCGAGAUAGUU-GAGC----------UCUUUUAACC
..(((((.((........)))))))((((..(.((.(((((.((((((((((.....))))).))))).))))).)).-)..)----------)))....... ( -26.60)
>consensus
AGGCCAAAUGUCAGUUUUCAUUGGCAAAGACCUGCAAUUUUUAGGGCUUCUCAUAGAA_GAACGCCUUCAAGAUAGCUUGAGCUGCCAGCCAUUUCUUUCACC
.((((((.(((((((....))))))).......((.(((((.((((((((.........))).))))).))))).))))).)))................... (-19.21 = -19.02 +  -0.19)

alignment

secondary structure

dotplot

Window 4

Location	460,495 – 460,614
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	79.05
Mean single sequence MFE	-32.88
Consensus MFE	-18.05
Energy contribution	-20.68
Covariance contribution	2.63
Combinations/Pair	1.10
Mean z-score	-2.13
Structure conservation index	0.55
SVM decision value	0.32
SVM RNA-class probability	0.688762
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 460495 119 + 23771897
GCAAAGACCUGCAAUUUUUAGGGCUUCUCAUAGAG-GAACGCCUUCAAGAUAGCUUGAGCUGCCAGCCAUUUCUUUCACCAAAGUAGGCUGGUCACAACGGCUUGCAUUCAAAUCCCAUU
((((.(.((.((.(((((.(((((((((......)-))).))))).))))).))....(..(((((((....((((....))))..)))))))..)...))))))).............. ( -32.90)
>DroSec_CAF1 41496 119 + 1
GCAAAGACCUGCAAUUUUUAGGGCUUCUCAUAGAG-GAACGCCUUCAAGAUAGCUUGAGCUGCCAGCCAUUUCUUUCACCAAAGUUGGCUGGUCGCAACGGCUUGCAUUCAAAUCCCAUU
((((.(.((.((.(((((.(((((((((......)-))).))))).))))).))....((.((((((((...((((....)))).)))))))).))...))))))).............. ( -39.20)
>DroEre_CAF1 43428 118 + 1
GCAGAGACCUGCAAUUUUUAGGGCUUCUCAUAGAA-GAACGCCUUCGAGAUAGUUUGGGCUGCCAGCAAUUUCUUUUGCCAAAGUAGGCUGGUCGCAA-GCCUUCCACUCAAAUUCCAUU
((((....)))).(((((.(((((((((......)-))).))))).)))))(((..(((((((((((.....((((....))))...))))))....)-))))...)))........... ( -33.90)
>DroYak_CAF1 42998 95 + 1
GCAGAGACCUGCAAUUUCUAGGGCUUCUUAUAGAAGGAACGCCUUCGAGAUAGUU-GAGC----------UCUUUUAACCAAAGAAGGCCGAUU--------------CCAAAUUCCAUU
((((....)))).(((((.((((((((((.....))))).))))).)))))((((-(.((----------.(((((......))))))))))))--------------............ ( -25.50)
>consensus
GCAAAGACCUGCAAUUUUUAGGGCUUCUCAUAGAA_GAACGCCUUCAAGAUAGCUUGAGCUGCCAGCCAUUUCUUUCACCAAAGUAGGCUGGUCGCAA_GGCUUGCAUUCAAAUCCCAUU
((((....)))).(((((.((((((((.........))).))))).))))).......((.(((((((....((((....))))..))))))).))........................ (-18.05 = -20.68 +   2.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:53 2006