Locus 4905

Sequence ID	3R_DroMel_CAF1
Location	12,886,339 – 12,886,486
Length	147
Max. P	0.798850

overview

Window 8

Location	12,886,339 – 12,886,446
Length	107
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	94.28
Mean single sequence MFE	-30.02
Consensus MFE	-27.38
Energy contribution	-27.98
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.27
Structure conservation index	0.91
SVM decision value	0.61
SVM RNA-class probability	0.798850
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12886339 107 + 27905053
CCGUCGCCACCAGCUAGUUGGCGCACCGUUUAGAGAUCCCAUUCGCACUAUGUACAUUCGGGCAAAUAUCGGAGCAUGUGCAUGU------------ACAUCGUACAUAUGUGCAUUAC
..(((((((.(.....).))))).))..................(((((((((((.(((((.......)))))(.(((((....)------------)))))))))))).))))..... ( -28.60)
>DroSec_CAF1 4076 107 + 1
CCGUCGCCACCAGCUAGUUGGCGCACCGUUUAGAGAUCCCAUUCGCACUAUGUACAUUCGGGCAAACAUCGGAGCAUGUGCAUGU------------ACAUCGUACAUAUGUGCAUUAC
..(((((((.(.....).))))).))..................(((((((((((.(((((.......)))))(.(((((....)------------)))))))))))).))))..... ( -28.60)
>DroSim_CAF1 3145 107 + 1
CCGUCGCCACCAGCUAGUUGGCGCACCGUUUAGAGAUCCCAUUCGCACUAUGUACAUUCGGGCAAACAUCGGAGCAUGUGCAUGU------------ACAUCGUACAUAUGUGCAUUAC
..(((((((.(.....).))))).))..................(((((((((((.(((((.......)))))(.(((((....)------------)))))))))))).))))..... ( -28.60)
>DroEre_CAF1 2547 107 + 1
CCGUCGCCACCAGCUAGUUGGCGCACCGUUUAAAAAUCCCAUUCGCACUAUGUACAUUCGGGCAAACAUCGGAGCAUGUGCAUGU------------ACAUCGUACAUAUGUGCAUUAC
..(((((((.(.....).))))).))..................(((((((((((.(((((.......)))))(.(((((....)------------)))))))))))).))))..... ( -28.60)
>DroYak_CAF1 4100 119 + 1
CCGUCGCCACCAGCUAGUUGGCGCACCGUUUAAAAAUCCCAUUCGCACUAUGUACAUUCGGGCAAACAUCGGAGCAUGUGCAUGUACAUACAUAUGUACAUCGUACAUAUGUGCAUUAC
..(((((((.(.....).))))).))..................(((((((((((.(((((.......)))))(.((((((((((......)))))))))))))))))).))))..... ( -35.70)
>consensus
CCGUCGCCACCAGCUAGUUGGCGCACCGUUUAGAGAUCCCAUUCGCACUAUGUACAUUCGGGCAAACAUCGGAGCAUGUGCAUGU____________ACAUCGUACAUAUGUGCAUUAC
..(((((((.(.....).))))).))..................(((((((((((.(((((.......)))))((....))(((((((......))))))).))))))).))))..... (-27.38 = -27.98 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	12,886,379 – 12,886,486
Length	107
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	85.95
Mean single sequence MFE	-28.03
Consensus MFE	-19.47
Energy contribution	-22.57
Covariance contribution	3.10
Combinations/Pair	1.12
Mean z-score	-2.85
Structure conservation index	0.69
SVM decision value	-0.03
SVM RNA-class probability	0.519154
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12886379 107 + 27905053
AUUCGCACUAUGUACAUUCGGGCAAAUAUCGGAGCAUGUGCAUGU------------ACAUCGUACAUAUGUGCAUUACAUACAUGUGCGCUUUCCGAUUUGUUUGUUUUUAUUUUUAG
.......(((.(((.(..(((((((..(((((((..((..(((((------------(....((((....))))......))))))..))..))))))))))))))..).)))...))) ( -29.10)
>DroSec_CAF1 4116 107 + 1
AUUCGCACUAUGUACAUUCGGGCAAACAUCGGAGCAUGUGCAUGU------------ACAUCGUACAUAUGUGCAUUACAUACAUGUGCGCUUUCCGAUUUGUUUGUUUUUAUUUUUAG
...................(((((((((((((((..((..(((((------------(....((((....))))......))))))..))..))))))..))))))))).......... ( -29.50)
>DroSim_CAF1 3185 107 + 1
AUUCGCACUAUGUACAUUCGGGCAAACAUCGGAGCAUGUGCAUGU------------ACAUCGUACAUAUGUGCAUUACAUACAUGUGCGCUUUCCGAUUUGUUUGUUUUUAUUUUUAG
...................(((((((((((((((..((..(((((------------(....((((....))))......))))))..))..))))))..))))))))).......... ( -29.50)
>DroEre_CAF1 2587 107 + 1
AUUCGCACUAUGUACAUUCGGGCAAACAUCGGAGCAUGUGCAUGU------------ACAUCGUACAUAUGUGCAUUACAUACAUGUGCGCUUUCCGAUUUGUUUGUUUUUAUUUUUAG
...................(((((((((((((((..((..(((((------------(....((((....))))......))))))..))..))))))..))))))))).......... ( -29.50)
>DroYak_CAF1 4140 119 + 1
AUUCGCACUAUGUACAUUCGGGCAAACAUCGGAGCAUGUGCAUGUACAUACAUAUGUACAUCGUACAUAUGUGCAUUACAUACAUGUGCGCUUUCCGAUUUGUUUGUUUUUAUUUUUAG
...................(((((((((((((((((((((.(((((..(((((((((((...)))))))))))...))))).)))))))....)))))..))))))))).......... ( -37.10)
>DroPer_CAF1 4238 83 + 1
ACUCGCACUAUGUAUA------CAUA------------UGUAUGU------------ACA---UACAUA--UGCAUU-CAUACAAAUGUAUUUUCUGAUUUGUUUGUUUUUAUUUUUAG
....(((.((((((((------(((.------------...))))------------)..---))))))--)))...-...(((((((.(((....))).)))))))............ ( -13.50)
>consensus
AUUCGCACUAUGUACAUUCGGGCAAACAUCGGAGCAUGUGCAUGU____________ACAUCGUACAUAUGUGCAUUACAUACAUGUGCGCUUUCCGAUUUGUUUGUUUUUAUUUUUAG
...................(((((((((((((((.(((((((((((((......))))))).))))))..((((((.........)))))).))))))..))))))))).......... (-19.47 = -22.57 +   3.10)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:42 2006