Locus 1852

Sequence ID 3L_DroMel_CAF1
Location 5,197,674 – 5,197,775
Length 101
Max. P 0.670244
window2888 window2889

overview

Window 8

Location 5,197,674 – 5,197,775
Length 101
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 89.74
Mean single sequence MFE -21.97
Consensus MFE -18.51
Energy contribution -18.70
Covariance contribution 0.19
Combinations/Pair 1.07
Mean z-score -1.53
Structure conservation index 0.84
SVM decision value 0.29
SVM RNA-class probability 0.670244
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5197674 101 + 23771897
GCAUGAAUAUGCAUAGAUUGCAAAUGAAAUAAA-AAAUUUGUUUGGCAGAGUAGGCGACUCUGUUGCUAUUUGUUGCUUCGAAAAUUUUAUGCAAACAUUUU
(((((((..((((.....))))..((((.(((.-((((..((..((((((((.....)))))))))).)))).))).)))).....)))))))......... ( -23.20)
>DroSec_CAF1 62641 100 + 1
GAAUGAAUAUGCAUAGCUUGCAAAUGAAACAA--AAAUUUGUUUGGCAGAGUAGACGACUCUGUUGCUAUUUGUUGCCUCGAAAAUGUUAUGCAAACGUUUU
(((((....((((((((..(((((((((((((--....))))))((((((((.....))))))))..)))))))............))))))))..))))). ( -24.74)
>DroEre_CAF1 63088 97 + 1
GAAUGAAUAUGCAUAUCUUGCAAAUGAAACAAAAAAAUUUGUUUGGCAGAGAAGACGACCCUGUUGCUAUUUGUUGCUUCGCAAAUGUUAUGCAAAC-----
.........((((((..((((...(.(((((((....))))))).)....((((.((((...((....))..))))))))))))....))))))...----- ( -20.10)
>DroYak_CAF1 62728 96 + 1
GAAUGAAUAUGCAUAUCUUGCAAAUGAAACAAA-AAAUUUAUUUGGCAGAGUAGGCGACUCUGUUGCUAUUUGUUGCUUCGAAAAUGUUAUGCAAAC-----
.((..((((.(((.......((((((((.....-...))))))))(((((((.....))))))))))))))..))((..............))....----- ( -19.84)
>consensus
GAAUGAAUAUGCAUAGCUUGCAAAUGAAACAAA_AAAUUUGUUUGGCAGAGUAGACGACUCUGUUGCUAUUUGUUGCUUCGAAAAUGUUAUGCAAAC_____
.........((((((((...((((((((.........))))))))(((((((((.((((...))))))))))..))).........))))))))........ (-18.51 = -18.70 +   0.19)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 5,197,674 – 5,197,775
Length 101
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 89.74
Mean single sequence MFE -17.97
Consensus MFE -13.79
Energy contribution -13.60
Covariance contribution -0.19
Combinations/Pair 1.12
Mean z-score -1.65
Structure conservation index 0.77
SVM decision value 0.23
SVM RNA-class probability 0.643886
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5197674 101 - 23771897
AAAAUGUUUGCAUAAAAUUUUCGAAGCAACAAAUAGCAACAGAGUCGCCUACUCUGCCAAACAAAUUU-UUUAUUUCAUUUGCAAUCUAUGCAUAUUCAUGC
....((((((...............((........))..((((((.....)))))).)))))).....-...........((((.....))))......... ( -14.90)
>DroSec_CAF1 62641 100 - 1
AAAACGUUUGCAUAACAUUUUCGAGGCAACAAAUAGCAACAGAGUCGUCUACUCUGCCAAACAAAUUU--UUGUUUCAUUUGCAAGCUAUGCAUAUUCAUUC
........((((((.(........(....).....((((((((((.....))))))..((((((....--))))))...))))..).))))))......... ( -19.40)
>DroEre_CAF1 63088 97 - 1
-----GUUUGCAUAACAUUUGCGAAGCAACAAAUAGCAACAGGGUCGUCUUCUCUGCCAAACAAAUUUUUUUGUUUCAUUUGCAAGAUAUGCAUAUUCAUUC
-----...((((((...((((((((((........))..(((((.......)))))..(((((((....)))))))..)))))))).))))))......... ( -21.20)
>DroYak_CAF1 62728 96 - 1
-----GUUUGCAUAACAUUUUCGAAGCAACAAAUAGCAACAGAGUCGCCUACUCUGCCAAAUAAAUUU-UUUGUUUCAUUUGCAAGAUAUGCAUAUUCAUUC
-----...((((((........(((((((.((((.....((((((.....))))))........))))-.)))))))..........))))))......... ( -16.39)
>consensus
_____GUUUGCAUAACAUUUUCGAAGCAACAAAUAGCAACAGAGUCGCCUACUCUGCCAAACAAAUUU_UUUGUUUCAUUUGCAAGAUAUGCAUAUUCAUUC
........((((((.(......(......).....(((((((((.......)))))..(((((((....)))))))...))))..).))))))......... (-13.79 = -13.60 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:19 2006