Locus 5945

Sequence ID 2R_DroMel_CAF1
Location 18,747,742 – 18,747,845
Length 103
Max. P 0.999011
window9538 window9539

overview

Window 8

Location 18,747,742 – 18,747,845
Length 103
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 77.60
Mean single sequence MFE -24.10
Consensus MFE -11.96
Energy contribution -13.40
Covariance contribution 1.44
Combinations/Pair 1.05
Mean z-score -2.00
Structure conservation index 0.50
SVM decision value 0.53
SVM RNA-class probability 0.772080
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18747742 103 + 20766785
UCCACGAAUAUGUUCGUGAUCAUAAAAUUAUAAUUUAUGAACAAAAAGCAGCGGGCAGGAGCAUGCAGUUUGGAGUGUGGAGUCUGGAGUGUGGAGUAUGGAG------
(((((...(((((((.((.(((((((.......))))))).))....((.....))..))))))).(.((..((.(....).))..)).))))))........------ ( -23.80)
>DroSec_CAF1 110495 89 + 1
UCCACGAAUAUGUUCGUGAUCAUAAAAUUAUAAUUUAUGAACAAAAAGCAGCGGGCAGGAGCAUGCAGUUUGGAGUG--------------UGGAGUAUGGAG------
((((((....(((((((((...............)))))))))..((((.(((.((....)).))).))))....))--------------))))........------ ( -21.46)
>DroSim_CAF1 111270 96 + 1
UCCACGAAUAUGUUCGUGAUCAUAAAAUUAUAAUUUAUGAACAAAAAGCAGCGGGCAGGAGCAUGCAGUUUGGAGUGUGG-------AGUGUGGAGUAUGGAG------
((((((..((..(((....(((((((.......))))))).((((..(((((........)).)))..)))))))..)).-------..))))))........------ ( -25.80)
>DroMoj_CAF1 171624 94 + 1
UCCACGAAUAUGUUCGUGAUCAUAAAAUUAUAAUUUAUGAACAAAGGCGAACGCGU-GGAGCAU-------GGAGUGUGG-------AGUGUGGAGCGUGGAGCGGCCC
((((((..(((((((.((.(((((((.......))))))).))...((....))..-.))))))-------)...)))))-------)....((.((.....))..)). ( -26.80)
>DroAna_CAF1 107089 80 + 1
UCCACGAAUAUGUUCGUGAUCAUAAAAUUAUAAUUUAUGAACAAAAAGAAGCGGGCCAGAGGGGCC-----GGGGUG---------------GGACU---GGG------
(((((.....(((((((((...............)))))))))........(.((((.....))))-----.).)))---------------))...---...------ ( -22.66)
>consensus
UCCACGAAUAUGUUCGUGAUCAUAAAAUUAUAAUUUAUGAACAAAAAGCAGCGGGCAGGAGCAUGCAGUUUGGAGUGUGG_______AGUGUGGAGUAUGGAG______
(((((.....(((((((((...............))))))))).......(((.((....)).)))........................))))).............. (-11.96 = -13.40 +   1.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,747,742 – 18,747,845
Length 103
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 77.60
Mean single sequence MFE -18.86
Consensus MFE -10.80
Energy contribution -10.80
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.12
Structure conservation index 0.57
SVM decision value 3.33
SVM RNA-class probability 0.999011
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18747742 103 - 20766785
------CUCCAUACUCCACACUCCAGACUCCACACUCCAAACUGCAUGCUCCUGCCCGCUGCUUUUUGUUCAUAAAUUAUAAUUUUAUGAUCACGAACAUAUUCGUGGA
------......................(((((....((((..(((.((........)))))..)))).(((((((.......)))))))..............))))) ( -18.10)
>DroSec_CAF1 110495 89 - 1
------CUCCAUACUCCA--------------CACUCCAAACUGCAUGCUCCUGCCCGCUGCUUUUUGUUCAUAAAUUAUAAUUUUAUGAUCACGAACAUAUUCGUGGA
------........((((--------------(....((((..(((.((........)))))..)))).(((((((.......)))))))..............))))) ( -18.10)
>DroSim_CAF1 111270 96 - 1
------CUCCAUACUCCACACU-------CCACACUCCAAACUGCAUGCUCCUGCCCGCUGCUUUUUGUUCAUAAAUUAUAAUUUUAUGAUCACGAACAUAUUCGUGGA
------...............(-------((((....((((..(((.((........)))))..)))).(((((((.......)))))))..............))))) ( -18.10)
>DroMoj_CAF1 171624 94 - 1
GGGCCGCUCCACGCUCCACACU-------CCACACUCC-------AUGCUCC-ACGCGUUCGCCUUUGUUCAUAAAUUAUAAUUUUAUGAUCACGAACAUAUUCGUGGA
((..((.....))..))....(-------((((.....-------..((...-..))(((((....((.(((((((.......))))))).)))))))......))))) ( -22.10)
>DroAna_CAF1 107089 80 - 1
------CCC---AGUCC---------------CACCCC-----GGCCCCUCUGGCCCGCUUCUUUUUGUUCAUAAAUUAUAAUUUUAUGAUCACGAACAUAUUCGUGGA
------...---....(---------------(((...-----((((.....))))........((((((((((((.......)))))))..))))).......)))). ( -17.90)
>consensus
______CUCCAUACUCCACACU_______CCACACUCCAAACUGCAUGCUCCUGCCCGCUGCUUUUUGUUCAUAAAUUAUAAUUUUAUGAUCACGAACAUAUUCGUGGA
.....................................................................(((((((.......)))))))(((((((....))))))). (-10.80 = -10.80 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:43 2006