Locus 4109

Sequence ID 3L_DroMel_CAF1
Location 11,988,667 – 11,988,778
Length 111
Max. P 0.997015
window6390 window6391

overview

Window 0

Location 11,988,667 – 11,988,778
Length 111
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 89.81
Mean single sequence MFE -43.84
Consensus MFE -36.98
Energy contribution -37.86
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -2.52
Structure conservation index 0.84
SVM decision value 2.78
SVM RNA-class probability 0.997015
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11988667 111 + 23771897
GCCCGCGGAUGUCUGAGUGCUCU-------GGUUCUCUUCCUCCAGCGGAUAUGUGGAUGUCUGCAAGUUCUUGAUCUUUCAGUCACGACUACGAGUCGCCCACUUCCGCUGGGGGAU
((.(.(((....))).).))...-------........((((((((((((...((((.((.(((.(((........))).))).))((((.....)))).)))).)))))))))))). ( -44.30)
>DroSec_CAF1 7047 111 + 1
GCCCGCGGAUGUCUGAGUGCUCU-------GGUUCUCUUCCUCCAGCGGAUGUGUGGAUGUCUGCAAGUUCUUGAUCUUUCAGUCACGACUACGAGUCGCCCACUUCCGCUGGAGGAU
((.(.(((....))).).))...-------........((((((((((((.(((.((.((.(((.(((........))).))).))((((.....))))))))).)))))))))))). ( -45.50)
>DroSim_CAF1 6246 111 + 1
GCCCGCGGAUGUCUGAGUGCUCU-------GGUUCUCUUCCUCCAGCGGAUGUGUGGAUGUCUGCAAGUUCUUGAUCUUUCAGUCACGACCACGAGUCGCCCACUUCCGCUGGAGGAU
((.(.(((....))).).))...-------........((((((((((((.(((.((.((.(((.(((........))).))).))((((.....))))))))).)))))))))))). ( -44.80)
>DroEre_CAF1 7104 107 + 1
GCCCGCGGAU----GAGCGCUCU-------GGUUCUCUUGCUCCAGCGGAUACAUGGCUGUCUGGAAGCUCUUGUUCCUUCAGUCAUGACUAUGAGUCGCCCACUUCCGCUGGAGGAU
..((((((..----((((.....-------.))))..))))(((((((((...(((((((...((((.(....)))))..)))))))(((.....))).......))))))))))).. ( -41.80)
>DroYak_CAF1 6376 118 + 1
GCCCGCGGAUGUCUGAGUGCUCUGGUUUCUGGUUCUCUUCCUCCAGCGGAUGUAUGCAUGUCUGGAAGUUCUUGAUCUUUCACUCACGACUAUGAGUCGCCCACUUCCGCUGGAGGAU
.....((((..((.((....)).))..)))).......((((((((((((.((..((.((..((((((........))))))..)).(((.....)))))..)).)))))))))))). ( -42.80)
>consensus
GCCCGCGGAUGUCUGAGUGCUCU_______GGUUCUCUUCCUCCAGCGGAUGUGUGGAUGUCUGCAAGUUCUUGAUCUUUCAGUCACGACUACGAGUCGCCCACUUCCGCUGGAGGAU
..............(((.(((.........))).))).((((((((((((...((((.((.(((.(((........))).))).))((((.....)))).)))).)))))))))))). (-36.98 = -37.86 +   0.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,988,667 – 11,988,778
Length 111
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 89.81
Mean single sequence MFE -39.26
Consensus MFE -34.54
Energy contribution -35.14
Covariance contribution 0.60
Combinations/Pair 1.07
Mean z-score -2.12
Structure conservation index 0.88
SVM decision value 2.45
SVM RNA-class probability 0.994116
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11988667 111 - 23771897
AUCCCCCAGCGGAAGUGGGCGACUCGUAGUCGUGACUGAAAGAUCAAGAACUUGCAGACAUCCACAUAUCCGCUGGAGGAAGAGAACC-------AGAGCACUCAGACAUCCGCGGGC
.(((.((((((((.(((((((((.....)))))..(((.(((........))).)))....))))...)))))))).)))......((-------...((............)).)). ( -37.30)
>DroSec_CAF1 7047 111 - 1
AUCCUCCAGCGGAAGUGGGCGACUCGUAGUCGUGACUGAAAGAUCAAGAACUUGCAGACAUCCACACAUCCGCUGGAGGAAGAGAACC-------AGAGCACUCAGACAUCCGCGGGC
.((((((((((((.(((((((((.....)))))..(((.(((........))).)))....))))...))))))))))))......((-------...((............)).)). ( -42.10)
>DroSim_CAF1 6246 111 - 1
AUCCUCCAGCGGAAGUGGGCGACUCGUGGUCGUGACUGAAAGAUCAAGAACUUGCAGACAUCCACACAUCCGCUGGAGGAAGAGAACC-------AGAGCACUCAGACAUCCGCGGGC
.((((((((((((.(((((((((.....)))))..(((.(((........))).)))....))))...))))))))))))......((-------...((............)).)). ( -42.20)
>DroEre_CAF1 7104 107 - 1
AUCCUCCAGCGGAAGUGGGCGACUCAUAGUCAUGACUGAAGGAACAAGAGCUUCCAGACAGCCAUGUAUCCGCUGGAGCAAGAGAACC-------AGAGCGCUC----AUCCGCGGGC
...((((((((((....((((((.....))).((.(((.(((........))).))).))))).....))))))))))........((-------...(((...----...))).)). ( -36.60)
>DroYak_CAF1 6376 118 - 1
AUCCUCCAGCGGAAGUGGGCGACUCAUAGUCGUGAGUGAAAGAUCAAGAACUUCCAGACAUGCAUACAUCCGCUGGAGGAAGAGAACCAGAAACCAGAGCACUCAGACAUCCGCGGGC
.((((((((((((.(((.(((((((((....))))))(.(((........))).).....))).))).)))))))))))).............((...((............)).)). ( -38.10)
>consensus
AUCCUCCAGCGGAAGUGGGCGACUCGUAGUCGUGACUGAAAGAUCAAGAACUUGCAGACAUCCACACAUCCGCUGGAGGAAGAGAACC_______AGAGCACUCAGACAUCCGCGGGC
.((((((((((((.(((((((((.....)))))..(((.(((........))).)))....))))...))))))))))))..................((............)).... (-34.54 = -35.14 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:41 2006