Locus 1414

Sequence ID 3L_DroMel_CAF1
Location 4,116,067 – 4,116,183
Length 116
Max. P 0.866656
window2196 window2197

overview

Window 6

Location 4,116,067 – 4,116,162
Length 95
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 88.47
Mean single sequence MFE -14.82
Consensus MFE -14.06
Energy contribution -13.90
Covariance contribution -0.16
Combinations/Pair 1.06
Mean z-score -1.29
Structure conservation index 0.95
SVM decision value 0.30
SVM RNA-class probability 0.677973
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4116067 95 + 23771897
--AAUACCGCCGCCCCCGCUUCAAAUUUGCCUAUGUGCAAAAUGGGCGAACAACAAAAAAAA--CAAAUGAUAAAAGGAAAAUAGAAAGCAAAUUGCUA
--....((...((....))......(((((((((.......)))))))))............--............)).........(((.....))). ( -14.90)
>DroSec_CAF1 17541 95 + 1
AGAAUACAGCCGCCCCCGCUUCAAAUUUGCCUAUGUGCCAAAUGGGCGAACAACAAAAAAA----AAAUGAUAAAAGGAAAAUAGAAAGCAAAUUGCUA
.........((((....))......(((((((((.......)))))))))...........----...........)).........(((.....))). ( -14.60)
>DroSim_CAF1 17939 92 + 1
ACAAUAACGCCGCCCCCGCUUCAAAUUUGCCUAUGUGCCAAAUGGGCGAACAACACA---A----AAAUGAUAAAAGGAAAAUAGAAAGCAAAUUGCUA
.........((((....))......(((((((((.......))))))))).......---.----...........)).........(((.....))). ( -14.60)
>DroEre_CAF1 17762 88 + 1
--AAUGCCGCCGCCCCCGCUACAAAUUUGCUUAUGUGCAAAAUGGGCGAACAAAAAA---------AAUUAUAAAAGGAAAAUAGAAAGCAAAUAGCUA
--.....((((((....))......(((((......)))))...)))).........---------.....................(((.....))). ( -14.20)
>DroYak_CAF1 17978 97 + 1
--AAUACCGCCGCCCCCGCUUCAAAUUUGCCUAUGUGCAAAAUGGGCGAACAAAAAAAAAAUGCAAAAUAAUAAAAGGAAAAUAGAAAGCAAAUGGCUA
--......(((((....))......(((((((((.......)))))))))............................................))).. ( -15.80)
>consensus
__AAUACCGCCGCCCCCGCUUCAAAUUUGCCUAUGUGCAAAAUGGGCGAACAACAAAAAAA____AAAUGAUAAAAGGAAAAUAGAAAGCAAAUUGCUA
.........((((....))......(((((((((.......)))))))))..........................)).........(((.....))). (-14.06 = -13.90 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,116,087 – 4,116,183
Length 96
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 80.74
Mean single sequence MFE -16.45
Consensus MFE -11.68
Energy contribution -12.13
Covariance contribution 0.45
Combinations/Pair 1.32
Mean z-score -2.03
Structure conservation index 0.71
SVM decision value 0.85
SVM RNA-class probability 0.866656
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4116087 96 + 23771897
AAAUUUGCCUAUGUGCAAAAUGGGCGAACAACAAAAAAAA--CAAAUGAUAAAAGGAAAAUAGAAAGCAAAUUGCUAAUGCAGGCGCACAUUUUGUUC
...(((((((((.......))))))))).(((((((....--.......................(((.....)))..(((....)))..))))))). ( -18.00)
>DroSec_CAF1 17563 94 + 1
AAAUUUGCCUAUGUGCCAAAUGGGCGAACAACAAAAAAA----AAAUGAUAAAAGGAAAAUAGAAAGCAAAUUGCUAAUGCAGGCGCACAUUUUGUUC
...(((((((((.......))))))))).(((((((...----......................(((.....)))..(((....)))..))))))). ( -18.00)
>DroSim_CAF1 17961 91 + 1
AAAUUUGCCUAUGUGCCAAAUGGGCGAACAACACA---A----AAAUGAUAAAAGGAAAAUAGAAAGCAAAUUGCUAAUGCAGGCGCACAUUUUGUUC
...(((((((((.......))))))))).......---(----(((((.................(((.....)))..(((....))))))))).... ( -17.60)
>DroEre_CAF1 17782 89 + 1
AAAUUUGCUUAUGUGCAAAAUGGGCGAACAAAAAA---------AAUUAUAAAAGGAAAAUAGAAAGCAAAUAGCUAAUGCAAGCGCACAUUUUGUUC
......((((((.......))))))((((((((..---------.....................(((.....)))..(((....)))..)))))))) ( -15.50)
>DroYak_CAF1 17998 98 + 1
AAAUUUGCCUAUGUGCAAAAUGGGCGAACAAAAAAAAAAUGCAAAAUAAUAAAAGGAAAAUAGAAAGCAAAUGGCUAAUGCAAGCGCACAUUUUGUUC
......((((((.......))))))((((((((................................(((.....)))..(((....)))..)))))))) ( -18.20)
>DroAna_CAF1 18477 75 + 1
--ACUUGCGAA-----AAAAAGGGGGGGCCUCAAAAUA---------GGCGAAAAAAAAAUAGAAAGCAA-------AUGCAAGCGCACAUUUUGUUC
--...((((..-----...........((((......)---------)))................((..-------..))...)))).......... ( -11.40)
>consensus
AAAUUUGCCUAUGUGCAAAAUGGGCGAACAACAAAAAAA____AAAUGAUAAAAGGAAAAUAGAAAGCAAAUUGCUAAUGCAAGCGCACAUUUUGUUC
...(((((((((.......)))))))))...................(((((((...........(((.....)))..(((....)))..))))))). (-11.68 = -12.13 +   0.45)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:53 2006