Locus 2038

Sequence ID	X_DroMel_CAF1
Location	5,600,443 – 5,600,608
Length	165
Max. P	0.520319

overview

Window 7

Location	5,600,443 – 5,600,541
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	87.23
Mean single sequence MFE	-29.24
Consensus MFE	-20.28
Energy contribution	-21.32
Covariance contribution	1.04
Combinations/Pair	1.12
Mean z-score	-1.72
Structure conservation index	0.69
SVM decision value	-0.03
SVM RNA-class probability	0.520319
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5600443 98 + 22224390
GCGUCGUAGCAGAGAAACGCGAACCUCUCCGCGACCUCUAUCGUGCUCUCUUUUCCACUCACGGUCGUUUAACGGCGCAUAGAGACAACUCUGCGCUA
........((((((...((((........))))..((((((.(((((.......((......)).........)))))))))))....)))))).... ( -30.19)
>DroSec_CAF1 2006 90 + 1
GCGUCGUAGCGGA--------AACCUCUCCGCGACCUCUAUCGUGCUCUCUCUUCCACUCACGGUCGUUUAACGGCGCAUAGAGACAACUCUGCACUA
(((((((.(((((--------......)))))((((......(((..........)))....)))).....))))))).(((((....)))))..... ( -28.80)
>DroSim_CAF1 2545 90 + 1
GCGUCGUAGCGGA--------AACCUCUCCGCGACCUCUAUCGUGCUCUCUCUUCCACUCACGGUCGUUUAACGGCGCAUAGAGACAACUCUGCACUA
(((((((.(((((--------......)))))((((......(((..........)))....)))).....))))))).(((((....)))))..... ( -28.80)
>DroEre_CAF1 2562 97 + 1
GCGUCGCUGCAAAGCAACGGGACCCUC-CCGCGACCUCUAUCGUGCUCUCUUUUCCGCUCAUGGUCGCUUAACGGCGCAUAGAGACAACUCUGCGCGA
(((((((((..((((..((((.....)-))).((((......(((..........)))....))))))))..)))))...((((....)))))))).. ( -31.00)
>DroYak_CAF1 2580 97 + 1
GCGUCUUAGCAAAGCAAUGGGACCCUC-CCGCGACCUCUAUCGUGCUCUCUUUUCCGCUCACGGUCGCUUAACGGCGCAUAGAGACAACUCUGCGCGA
.(((...(((..(((...(((.....)-))((((......))))))).......(((....)))..)))..)))(((((..(((....)))))))).. ( -27.40)
>consensus
GCGUCGUAGCAGAG_AA_G_GAACCUCUCCGCGACCUCUAUCGUGCUCUCUUUUCCACUCACGGUCGUUUAACGGCGCAUAGAGACAACUCUGCGCUA
(((((((.(.((((..........)))).)((((((......(((..........)))....))))))...))))))).(((((....)))))..... (-20.28 = -21.32 +   1.04)

alignment

secondary structure

dotplot

Window 8

Location	5,600,514 – 5,600,608
Length	94
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	91.81
Mean single sequence MFE	-32.30
Consensus MFE	-24.62
Energy contribution	-25.70
Covariance contribution	1.08
Combinations/Pair	1.11
Mean z-score	-1.53
Structure conservation index	0.76
SVM decision value	-0.04
SVM RNA-class probability	0.511613
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5600514 94 + 22224390
ACGGCGCAUAGAGACAACUCUGCGCUAGG---UCGCCUGCUCUCGUUCGCUCUGGCGCGCAAACGGCACUUGGCACACUUCGCACAGUGGCGCCAAA
..(((((.(((((....))))).((((((---(.(((.......((.(((....))).))....)))))))))).((((......)))))))))... ( -35.20)
>DroSec_CAF1 2069 94 + 1
ACGGCGCAUAGAGACAACUCUGCACUAGG---UCGCCUGCUCUCGUUCGCUCUGGCGCGCAAACGGCACUUGGCACACUUCGCACACUGGCGCCAAA
..(((((..((((....))))((...(((---(.(((((((...((.(((....))).))....))))...))))).))..))......)))))... ( -29.60)
>DroSim_CAF1 2608 97 + 1
ACGGCGCAUAGAGACAACUCUGCACUAAUGAUAGGCCUGCUCUCGUUCGCUCUAGCGCGCAAACGGCACUUGGCACACUUCGCACACUGGCGCCAAA
..(((((..((((....))))((.(((....)))(((((((...((.(((....))).))....))))...))).......))......)))))... ( -28.70)
>DroEre_CAF1 2632 94 + 1
ACGGCGCAUAGAGACAACUCUGCGCGAGG---UCGCCUGCUCUCAUUCGCUCUCGCGCGCAAACAGCACUUGGCACACUUUGCACAGUGACGCCAAA
..(((((..((((....))))(((((((.---.((..((....))..))..))))))))).....(((((..(((.....)))..)))).))))... ( -33.50)
>DroYak_CAF1 2650 94 + 1
ACGGCGCAUAGAGACAACUCUGCGCGAGG---UCGCCUACUCUCAUUCGCUCUCGCGCGCAAACGGCACUUGGCACACUUUGCACAGUGGCGCCAAA
..(((((..((((....))))(((((((.---.((............))..)))))))))....(.((((..(((.....)))..)))).))))... ( -34.50)
>consensus
ACGGCGCAUAGAGACAACUCUGCGCUAGG___UCGCCUGCUCUCGUUCGCUCUCGCGCGCAAACGGCACUUGGCACACUUCGCACAGUGGCGCCAAA
..(((((..((((....))))((((((((.....((..((....))..))))))))))))....(.((((..((.......))..)))).))))... (-24.62 = -25.70 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:47 2006