Locus 5466

Sequence ID 3R_DroMel_CAF1
Location 14,445,759 – 14,445,897
Length 138
Max. P 0.858498
window8898 window8899

overview

Window 8

Location 14,445,759 – 14,445,857
Length 98
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 89.51
Mean single sequence MFE -27.50
Consensus MFE -22.04
Energy contribution -22.35
Covariance contribution 0.31
Combinations/Pair 1.14
Mean z-score -1.97
Structure conservation index 0.80
SVM decision value 0.82
SVM RNA-class probability 0.858498
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14445759 98 - 27905053
---CACAAAGUGCAAUGUGCCGCAUUGCAU-UGCCUUGCGAAAUGCCAACCAUUUCAACGCGGGGCUUUGACCAUCAUCAAUUGCCGUUGACAAUAUGAAAA
---..((((((((((((.....))))))))-)(((((((((((((.....))))))...))))))).)))....((((..((((.......))))))))... ( -27.60)
>DroSec_CAF1 2897 99 - 1
CUCCACAAAGUGCAAUGUGCCGCAUUGCAUUUGCCUUGCGAAAUGCCAAGCAUUUCAACGCGAGGCUUUGACCA---UCAAUUGCCGUUGACAAUAUGAAAA
.......((((((((((.....))))))))))((((((((((((((...)))))))...)))))))........---(((((....)))))........... ( -31.30)
>DroEre_CAF1 2882 95 - 1
---CUCAAAAUGCAAUGUGCCGAAUUGCAU-UGCCUUGUGAAAUGCCAACCAUGGCGACGCGGGGCUUUGACCA---UCAAUUGCCGUUGACAAUAUGAAAA
---.((((((((((((.......)))))))-)((((((((...(((((....))))).)))))))).))))...---(((((....)))))........... ( -27.90)
>DroYak_CAF1 3042 95 - 1
---CUCAAAGUGCAAUGUGCCGAAUUGCAU-GGCCCUGUGAAAUGCCAACCAUUGCGACCCGGGGCUUUGACCA---UCAAUUGCCGUUGACAAUAUGAAAA
---.(((...(((((((.((..(((((((.-(((((((.(...(((........)))..)))))))).))....---.)))))))))))).))...)))... ( -23.20)
>consensus
___CACAAAGUGCAAUGUGCCGAAUUGCAU_UGCCUUGCGAAAUGCCAACCAUUGCAACGCGGGGCUUUGACCA___UCAAUUGCCGUUGACAAUAUGAAAA
.....((((((((((((.....))))))))..((((((((.((((.....))))....)))))))))))).......(((((....)))))........... (-22.04 = -22.35 +   0.31)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 14,445,781 – 14,445,897
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.37
Mean single sequence MFE -26.03
Consensus MFE -20.66
Energy contribution -20.97
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -1.64
Structure conservation index 0.79
SVM decision value 0.36
SVM RNA-class probability 0.704712
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14445781 116 - 27905053
CUUAUGCAAUCCCUGAAUCCACCAACAACAGCUCCCCCAC---CACAAAGUGCAAUGUGCCGCAUUGCAU-UGCCUUGCGAAAUGCCAACCAUUUCAACGCGGGGCUUUGACCAUCAUCA
.............(((........................---.....(((((((((.....))))))))-)(((((((((((((.....))))))...)))))))........)))... ( -26.10)
>DroSec_CAF1 2919 115 - 1
CUUAUGCAAUCCCUGAAUCCACCAA--ACAGCUCUCCCACCUCCACAAAGUGCAAUGUGCCGCAUUGCAUUUGCCUUGCGAAAUGCCAAGCAUUUCAACGCGAGGCUUUGACCA---UCA
......................(((--(...................((((((((((.....))))))))))((((((((((((((...)))))))...)))))))))))....---... ( -30.50)
>DroEre_CAF1 2904 107 - 1
CUUAUGCAAUCCCUGAAUCCACCA---ACAGCUCCCC------CUCAAAAUGCAAUGUGCCGAAUUGCAU-UGCCUUGUGAAAUGCCAACCAUGGCGACGCGGGGCUUUGACCA---UCA
........................---..........------.((((((((((((.......)))))))-)((((((((...(((((....))))).)))))))).))))...---... ( -26.30)
>DroYak_CAF1 3064 107 - 1
CUUAUGCAAUCCCUGAAUCCACCA---ACAGCUCCCC------CUCAAAGUGCAAUGUGCCGAAUUGCAU-GGCCCUGUGAAAUGCCAACCAUUGCGACCCGGGGCUUUGACCA---UCA
......................((---(.((((((..------.......((((((((((......)))(-(((..........))))..)))))))....)))))))))....---... ( -21.22)
>consensus
CUUAUGCAAUCCCUGAAUCCACCA___ACAGCUCCCC______CACAAAGUGCAAUGUGCCGAAUUGCAU_UGCCUUGCGAAAUGCCAACCAUUGCAACGCGGGGCUUUGACCA___UCA
.............................................((((((((((((.....))))))))..((((((((.((((.....))))....)))))))))))).......... (-20.66 = -20.97 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:28 2006