Locus 7112

Sequence ID	2L_DroMel_CAF1
Location	19,950,624 – 19,950,756
Length	132
Max. P	0.845744

overview

Window 3

Location	19,950,624 – 19,950,738
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	85.31
Mean single sequence MFE	-46.48
Consensus MFE	-34.53
Energy contribution	-37.24
Covariance contribution	2.71
Combinations/Pair	1.06
Mean z-score	-2.04
Structure conservation index	0.74
SVM decision value	0.77
SVM RNA-class probability	0.845744
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19950624 114 + 22407834
GGCGGGACUGACCACGGCGCACAUGCAGAGCAUGGGCGUCCAGACCCAGGGUCAAGGUCAGGUUCAGGGUCAGGCGCUGGGUCAGGCGCUGGGUCAGCCGGGUUCGGAUCAGAA
..(.((.((((((.((((((.(((((...)))))((((((..(((((.(..((.......))..).))))).)))))).......)))))))))))))).)............. ( -52.70)
>DroSec_CAF1 133624 102 + 1
GGCGGGACUGACCACGGCGCACAUGCAGAGCAUGGGCGUCCAGACCCAGGGUCAAGGUCAGGUUCAAGGCCAGGC------------GCUGGGUCAGCCGGGCUCGGAUCAGAA
.....((((((((.((((((.(((((...))))).)).....(((((((.(((..((((........)))).)))------------.))))))).)))))).)))).)).... ( -47.80)
>DroSim_CAF1 136133 102 + 1
GGCGGGACUGACCACGGCGCACAUGCAGAGCAUGGGCGUCCAGACCCAGGGUCAAGGUCAGGUUCAGGGCCAGGC------------GCUGGGUCAGCCGGGCUCGGAUCAAAA
.....((((((((.((((((.(((((...))))).)).....(((((((.(((..((((........)))).)))------------.))))))).)))))).)))).)).... ( -47.70)
>DroEre_CAF1 132046 90 + 1
GGCGGGACUGACCACGGCGCACAUGCAGAGCAUGGGCGUCCAGACCCAGGGUCAAGGUCAGCUGCAG------------------------GGUCAGCCGGGCUCAGAGCAGAA
.((((..((((((..(((((.(((((...))))).)))))..((((...))))..)))))))))).(------------------------((((.....)))))......... ( -38.10)
>DroYak_CAF1 132607 96 + 1
GGCGGGACUGACCACGGCGCACAUGCAGAGCAUGGGUGUCCAGACCCAGGGUCAAGGUCAGCUUCAG------GC------------CCUGGGUCAGCCGGCCUCAGACCAGAA
(((.((.((......(((((.(((((...))))).)))))..(((((((((((.(((....)))..)------))------------)))))))))))).)))........... ( -46.10)
>consensus
GGCGGGACUGACCACGGCGCACAUGCAGAGCAUGGGCGUCCAGACCCAGGGUCAAGGUCAGGUUCAGGG_CAGGC____________GCUGGGUCAGCCGGGCUCGGAUCAGAA
((((((.((((((..(((((.(((((...))))).)))))..((((...))))..)))))).)))..((((.((((((......)))))).)))).)))............... (-34.53 = -37.24 +   2.71)

alignment

secondary structure

dotplot

Window 4

Location	19,950,664 – 19,950,756
Length	92
Sequences	4
Columns	92
Reading direction	forward
Mean pairwise identity	83.33
Mean single sequence MFE	-37.53
Consensus MFE	-20.81
Energy contribution	-21.30
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.32
Structure conservation index	0.55
SVM decision value	0.11
SVM RNA-class probability	0.589502
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19950664 92 + 22407834
CAGACCCAGGGUCAAGGUCAGGUUCAGGGUCAGGCGCUGGGUCAGGCGCUGGGUCAGCCGGGUUCGGAUCAGAAGCCACCGAACUCGGGUUC
..(((((((.(((.......((..(((.(.....).)))..)).))).)))))))..((((((((((...........)))))))))).... ( -41.30)
>DroSec_CAF1 133664 80 + 1
CAGACCCAGGGUCAAGGUCAGGUUCAAGGCCAGGC------------GCUGGGUCAGCCGGGCUCGGAUCAGAAGCCACCGAACUCGGGUUC
..(((((((.(((..((((........)))).)))------------.)))))))..(((((.((((...........)))).))))).... ( -36.10)
>DroSim_CAF1 136173 80 + 1
CAGACCCAGGGUCAAGGUCAGGUUCAGGGCCAGGC------------GCUGGGUCAGCCGGGCUCGGAUCAAAAGCCACCGAACUCGGGUUC
..(((((((.(((..((((........)))).)))------------.)))))))..(((((.((((...........)))).))))).... ( -36.00)
>DroYak_CAF1 132647 74 + 1
CAGACCCAGGGUCAAGGUCAGCUUCAG------GC------------CCUGGGUCAGCCGGCCUCAGACCAGAAGCCACCGACCUCGGGCUC
..(((((((((((.(((....)))..)------))------------))))))))(((((((.((......)).)))..((....)))))). ( -36.70)
>consensus
CAGACCCAGGGUCAAGGUCAGGUUCAGGGCCAGGC____________GCUGGGUCAGCCGGGCUCGGAUCAGAAGCCACCGAACUCGGGUUC
..(((((((.......................................)))))))..(((((.((((...........)))).))))).... (-20.81 = -21.30 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:45 2006