Locus 16

Sequence ID	4_DroMel_CAF1
Location	180,777 – 180,977
Length	200
Max. P	0.788774

overview

Window 8

Location	180,777 – 180,897
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.75
Mean single sequence MFE	-31.66
Consensus MFE	-23.56
Energy contribution	-23.76
Covariance contribution	0.20
Combinations/Pair	1.23
Mean z-score	-1.84
Structure conservation index	0.74
SVM decision value	0.41
SVM RNA-class probability	0.723946
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 180777 120 + 1281640
UAGGAGGUAGGUGACCAUUAAAGUGUCAUUCGUUUUAGCAAAAACACUUUGUAGUUGCACACCGUGAAAUAUAUCCCUGUAAUCAGAUUGCAUAACCAUGCGAUCGGCGGCUUCCAAUAA
..((((((..(..((...((((((((..((.((....))))..))))))))..))..).(.((.(((..((((....)))).)))((((((((....)))))))))).)))))))..... ( -31.90)
>DroSec_CAF1 7109 120 + 1
UAGGAGGUAGGUGACCAUUAAAGUGUCAUUCGUCUUAGCAAACACACUUUGUAGUUUCACACCGUGAAAUAUAUCCCUAUAAUCAGAUUGCAUAACCAUGCGAUCGGCGGCUUCCAAUAA
..((((((.(((((((......).))))))((((...(((((.....))))).(((((((...)))))))...............((((((((....))))))))))))))))))..... ( -32.80)
>DroSim_CAF1 4896 120 + 1
UAGGAGGCAGGUGACCAUUAAAGUGUCAUUCGUCCCAGCAAACACACUUUGUAGUUUCCCACCGUGAACUAUAUCCCUAUAAUCAGAUUGCAUAACCAUGCGAUCGGCGGCUUCCAAUAA
..((((((.(((((((......).))))))((((...............(((((((..(....)..)))))))............((((((((....))))))))))))))))))..... ( -34.00)
>DroEre_CAF1 9653 120 + 1
UAGGAGGUAGGUGACCAUUAACGUGUCAUUCGUUUUAGUCAAAGCAGUUAGUAGUUGCACACCGUGAAAUAUAUCCCUAUAAUCAGAUUGCAUAACCAUGCGAUCAGCGGCUUCUAACAA
...((((..(((((((......).))))))..))))..........(((((.((((((......(((..((((....)))).)))((((((((....)))))))).)))))).))))).. ( -30.70)
>DroYak_CAF1 6859 120 + 1
AAGGAGGUAGGUGAUCAAUAACGUUUUCUUGGUUUGAGUCAAAGCUGUUAGUAGUUGCACACCGUGAAAUAUAUCUCUAUAAUCAGAUUGCAUUACCAUGCGAUCGGCGGCUUCCAACAA
..((((((.((((..((((.((.......((((((......))))))...)).))))..))))......................((((((((....))))))))....))))))..... ( -28.90)
>consensus
UAGGAGGUAGGUGACCAUUAAAGUGUCAUUCGUUUUAGCAAAAACACUUUGUAGUUGCACACCGUGAAAUAUAUCCCUAUAAUCAGAUUGCAUAACCAUGCGAUCGGCGGCUUCCAAUAA
..((((((.(((((((......).))))))((((...((((..((.....))..))))...........................((((((((....))))))))))))))))))..... (-23.56 = -23.76 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	180,857 – 180,977
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.92
Mean single sequence MFE	-25.73
Consensus MFE	-19.76
Energy contribution	-19.92
Covariance contribution	0.16
Combinations/Pair	1.14
Mean z-score	-1.82
Structure conservation index	0.77
SVM decision value	0.58
SVM RNA-class probability	0.788774
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 180857 120 + 1281640
AAUCAGAUUGCAUAACCAUGCGAUCGGCGGCUUCCAAUAAUAUUUUACUAAUAUGUCGAUAUUCUAUUAAGGAAUUACUUUUUAUGUUAUUGCUGAAUUUUAAUAAAUGGUUUUCCGUCC
.....((((((((....))))))))(((((...(((...(((((.....)))))(.(((((...((..(((......)))..))...))))))..............)))....))))). ( -23.40)
>DroSec_CAF1 7189 120 + 1
AAUCAGAUUGCAUAACCAUGCGAUCGGCGGCUUCCAAUAAUAUUUUACUAAUAUGUCGAUAUAAGGAUAAGGAAUUUCUUUUUGUUUUAUUGCUGAAUUUUAAUAAAUGGUUUUCCGCCC
.....((((((((....))))))))(((((...(((...(((((.....)))))(.(((((.((.((.((((....)))).)).)).))))))..............)))....))))). ( -27.10)
>DroSim_CAF1 4976 120 + 1
AAUCAGAUUGCAUAACCAUGCGAUCGGCGGCUUCCAAUAAUAUUUUACUAGUAUGUCGAUAUAAGGAUAAGGAAUUACUUUUUGUAUUAUUGCUGAAUUUUAAUAAAUGGUUUUCCGCCC
.....((((((((....))))))))(((((...(((............(((((....(((((((((((((....))).))))))))))..)))))............)))....))))). ( -28.75)
>DroEre_CAF1 9733 120 + 1
AAUCAGAUUGCAUAACCAUGCGAUCAGCGGCUUCUAACAAUAUUUUACUAUUAUGUCGAUAUUCGAUUGAGGAAUUACUUUUGUUUUUAUUGCUGAGAUUUAAUAGGUAACUUUCCGCCC
.....((((((((....))))))))...(((.......................((((.....))))...((((((((((..(((((.......))))).....))))))..))))))). ( -24.20)
>DroYak_CAF1 6939 120 + 1
AAUCAGAUUGCAUUACCAUGCGAUCGGCGGCUUCCAACAAUAUUUUACUAAUAUUUCGAUAUUCGAUUGAAAAAUUACUUUUUCUUUUAUUGCUGAAUUUUAAUAAGUGACUUUCCGCCC
.....((((((((....))))))))(((((..................((((.(((((((.....))))))).)))).....((.(((((((........))))))).))....))))). ( -25.20)
>consensus
AAUCAGAUUGCAUAACCAUGCGAUCGGCGGCUUCCAAUAAUAUUUUACUAAUAUGUCGAUAUUCGAUUAAGGAAUUACUUUUUGUUUUAUUGCUGAAUUUUAAUAAAUGGUUUUCCGCCC
.....((((((((....))))))))(((((...(((...(((((.....)))))..(((((.......(((......))).......)))))...............)))....))))). (-19.76 = -19.92 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:26 2006