Locus 5315

Sequence ID	X_DroMel_CAF1
Location	13,902,160 – 13,902,301
Length	141
Max. P	0.590023

overview

Window 1

Location	13,902,160 – 13,902,261
Length	101
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	87.41
Mean single sequence MFE	-24.23
Consensus MFE	-21.84
Energy contribution	-22.53
Covariance contribution	0.69
Combinations/Pair	1.08
Mean z-score	-1.36
Structure conservation index	0.90
SVM decision value	0.11
SVM RNA-class probability	0.590023
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13902160 101 + 22224390
UUCCAAGGUGCGAUACCCCAAACUAGUGGGCACGUCAACUGCCACAAGGAAAUUGCAACUGGCAACUGGCGACUUGCAACUUGCAACUAGCAACUCGUAAC
...((((.(((((...((((......))))..(((((..((((((((.....)))....)))))..)))))..))))).)))).................. ( -25.70)
>DroSec_CAF1 2774 87 + 1
UUCCAAGGUGCGAUACCCCAAACUAGUGGGCACGUCAACUGCCACAAGGAAAUUGCAACUGGCAACUGGCGACUUGCAACUUGCAAC--------------
...((((.(((((...((((......))))..(((((..((((((((.....)))....)))))..)))))..))))).))))....-------------- ( -25.70)
>DroSim_CAF1 24538 82 + 1
UUCCAAGGUGCGAUACCCCAAACUAGUGGGCACGUCAACUGCCACAAGGAAAUUGCAACUGGCAACUGGCGACUCGCAACUU-------------------
....(((.(((((...((((......))))..(((((..((((((((.....)))....)))))..)))))..))))).)))------------------- ( -24.80)
>DroYak_CAF1 12756 87 + 1
UUCCAAGGUGCGAUACCCCAAACUAGUGGGCACGUCAACUGCCACAAGGAAAUUGCAACUGGCAACUUGCAACUGGCGACUUGCAAC--------------
.....((.((((((..((((......))((((.(....)))))....))..)))))).)).((((.((((.....)))).))))...-------------- ( -20.70)
>consensus
UUCCAAGGUGCGAUACCCCAAACUAGUGGGCACGUCAACUGCCACAAGGAAAUUGCAACUGGCAACUGGCGACUUGCAACUUGCAAC______________
...((((.(((((...((((......))))..(((((..((((((((.....)))....)))))..)))))..))))).)))).................. (-21.84 = -22.53 +   0.69)

alignment

secondary structure

dotplot

Window 2

Location	13,902,181 – 13,902,301
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.50
Mean single sequence MFE	-28.55
Consensus MFE	-22.29
Energy contribution	-23.73
Covariance contribution	1.44
Combinations/Pair	1.06
Mean z-score	-1.44
Structure conservation index	0.78
SVM decision value	-0.04
SVM RNA-class probability	0.512256
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13902181 120 + 22224390
ACUAGUGGGCACGUCAACUGCCACAAGGAAAUUGCAACUGGCAACUGGCGACUUGCAACUUGCAACUAGCAACUCGUAACUCGCAACUCGCAACUUGCAUCUCGCAAUGUGCAGCAGCAA
....((..((((((((..((((((((.....)))....)))))..))((((..(((((.((((.....((............)).....)))).)))))..)))).)))))).))..... ( -32.70)
>DroSec_CAF1 2795 99 + 1
ACUAGUGGGCACGUCAACUGCCACAAGGAAAUUGCAACUGGCAACUGGCGACUUGCAACUUGCAAC---------------------UUGCAACUUGCAUUUCGCAAUGUACGGCAGCAA
.((.((((.((.(....))))))).))....((((..((((((....((((..(((((.((((...---------------------..)))).)))))..))))..))).)))..)))) ( -31.20)
>DroSim_CAF1 24559 92 + 1
ACUAGUGGGCACGUCAACUGCCACAAGGAAAUUGCAACUGGCAACUGGCGACUCGCAACUU----------------------------GCAACUUGCAUCUCGCAAUGUACGGCAGCAA
....(((((..(((((..((((((((.....)))....)))))..))))).)))))...((----------------------------((.((((((.....)))).))...))))... ( -25.30)
>DroYak_CAF1 12777 99 + 1
ACUAGUGGGCACGUCAACUGCCACAAGGAAAUUGCAACUGGCAACUUGCAACUGGCGACUUGCAAC---------------------UUGCAACUUGCAUCUCACAAUGUUCAGCAGCAA
....(((((((.(....)))))....(.((.((((((...((((.((((.....)))).))))...---------------------)))))).)).)....)))..(((......))). ( -25.00)
>consensus
ACUAGUGGGCACGUCAACUGCCACAAGGAAAUUGCAACUGGCAACUGGCGACUUGCAACUUGCAAC_____________________UUGCAACUUGCAUCUCGCAAUGUACAGCAGCAA
.((.((((.((.(....))))))).))....((((..((((((....((((..(((((.((((((......................)))))).)))))..))))..))).)))..)))) (-22.29 = -23.73 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:40 2006