Locus 8662

Sequence ID	3R_DroMel_CAF1
Location	23,153,324 – 23,153,483
Length	159
Max. P	0.818925

overview

Window 9

Location	23,153,324 – 23,153,444
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.92
Mean single sequence MFE	-39.42
Consensus MFE	-34.42
Energy contribution	-34.18
Covariance contribution	-0.25
Combinations/Pair	1.11
Mean z-score	-1.76
Structure conservation index	0.87
SVM decision value	0.67
SVM RNA-class probability	0.818925
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23153324 120 + 27905053
UGGAAUGCCGGAUGAAGUGGUCCUUGGUCCGAAAAGUUAAGCAGGAUCCCGGUUGAAUGGUUAAUAUCAGGAGACCGGGAGCUGCACUAUCAGAUCCAGCUCCAACAAUUGAACGAACGC
((((..((.(((((((((((.(....).))..........((((..((((((((...((((....))))...)))))))).))))))).)))..))).))))))................ ( -39.60)
>DroSec_CAF1 4149 120 + 1
UGGAAUGCCGGAUAUAGUGGUCCUUGGUCCGAAAAGUUAAGCAGAACCCCGGUUGAAUGGUUAAUAUCAGGAGACCGGGAGCUGCACUAUCGGAUCCAGCUCCAACAAUUGAACGAACGC
((((..((.((((......)))).((((((((..(((...((((...(((((((...((((....))))...)))))))..))))))).))))).)))))))))................ ( -41.10)
>DroSim_CAF1 8626 120 + 1
UGGAAUGCCGGAUGAAGUGGUCCUUGGUCCGAAAAGUUAAGCAGAACCCCGGUUGAAUGGUUAAUAUCAGGAGACCGGGAGCUGCACUAUCGGAUCCAGCUCCAACAAUUGAACGAACGC
((((..((.((((......)))).((((((((..(((...((((...(((((((...((((....))))...)))))))..))))))).))))).)))))))))................ ( -40.80)
>DroYak_CAF1 8591 118 + 1
GGGAAUGCCGGAUGAAGUGGUCCUUGCUCCGAAAAGUUAAGCAGGACUCCGGUUGAAUGGUUAAUAUCGGGAGACCGGGAACUGCACUAUCCGAUCCUG-UCCAGCAAUUGCA-AAACGC
(.((.(((.((((...(..(((((.(((...........))))))))..)(((((.(((((.....((((....)))).......))))).)))))..)-))).))).)).).-...... ( -36.20)
>consensus
UGGAAUGCCGGAUGAAGUGGUCCUUGGUCCGAAAAGUUAAGCAGAACCCCGGUUGAAUGGUUAAUAUCAGGAGACCGGGAGCUGCACUAUCGGAUCCAGCUCCAACAAUUGAACGAACGC
((((....(((((.(((.....))).))))).........((((...(((((((...((((....))))...)))))))..)))).........))))...................... (-34.42 = -34.18 +  -0.25)

alignment

secondary structure

dotplot

Window 0

Location	23,153,364 – 23,153,483
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.89
Mean single sequence MFE	-39.52
Consensus MFE	-32.08
Energy contribution	-33.45
Covariance contribution	1.37
Combinations/Pair	1.07
Mean z-score	-1.98
Structure conservation index	0.81
SVM decision value	0.57
SVM RNA-class probability	0.786856
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23153364 119 + 27905053
GCAGGAUCCCGGUUGAAUGGUUAAUAUCAGGAGACCGGGAGCUGCACUAUCAGAUCCAGCUCCAACAAUUGAACGAACGCAUC-GCUUGAAAAAGCAGUCGAGUGUGCACGCUGUGGAAA
((((..((((((((...((((....))))...)))))))).)))).........((((((..((.....)).......(((.(-((((((........))))))))))..)))).))... ( -40.90)
>DroSec_CAF1 4189 119 + 1
GCAGAACCCCGGUUGAAUGGUUAAUAUCAGGAGACCGGGAGCUGCACUAUCGGAUCCAGCUCCAACAAUUGAACGAACGCAUC-GCUUGAAAAAGCAGUCGAGUGUGCACGCUGUGGAAA
((((...(((((((...((((....))))...)))))))..)))).........((((((..((.....)).......(((.(-((((((........))))))))))..)))).))... ( -38.90)
>DroSim_CAF1 8666 119 + 1
GCAGAACCCCGGUUGAAUGGUUAAUAUCAGGAGACCGGGAGCUGCACUAUCGGAUCCAGCUCCAACAAUUGAACGAACGCAUC-GCUUGAAAAAGCAGUCGAGUGUGCACGCUGUGGAAA
((((...(((((((...((((....))))...)))))))..)))).........((((((..((.....)).......(((.(-((((((........))))))))))..)))).))... ( -38.90)
>DroYak_CAF1 8631 118 + 1
GCAGGACUCCGGUUGAAUGGUUAAUAUCGGGAGACCGGGAACUGCACUAUCCGAUCCUG-UCCAGCAAUUGCA-AAACGCAUCUGCAUGAAAAGGCAGUGGAGUGUGCACGCUGUGGAAA
((((...(((((((...((((....))))...)))))))...(((((..((((..(((.-..(((((..(((.-....)))..))).))...)))...))))..)))))..))))..... ( -39.40)
>consensus
GCAGAACCCCGGUUGAAUGGUUAAUAUCAGGAGACCGGGAGCUGCACUAUCGGAUCCAGCUCCAACAAUUGAACGAACGCAUC_GCUUGAAAAAGCAGUCGAGUGUGCACGCUGUGGAAA
((((...(((((((...((((....))))...)))))))..))))...............((((....................((((....)))).....((((....)))).)))).. (-32.08 = -33.45 +   1.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:16:36 2006