Locus 4211

Sequence ID 3R_DroMel_CAF1
Location 11,355,853 – 11,356,029
Length 176
Max. P 0.995205
window6798 window6799

overview

Window 8

Location 11,355,853 – 11,355,949
Length 96
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.46
Mean single sequence MFE -38.40
Consensus MFE -26.90
Energy contribution -27.90
Covariance contribution 1.00
Combinations/Pair 1.16
Mean z-score -2.89
Structure conservation index 0.70
SVM decision value 2.55
SVM RNA-class probability 0.995205
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11355853 96 + 27905053
GCGACGAAUGUCAUUUGUAUCUG------------------UAUCUGUCCCUGGCCUUGUAUCUGCAUCUCACAGAUGCGGACGCU------GAUGCGGAUGCGCGUGUGCCUCGCUAAU
((((.(.....(((.((((((((------------------((((.((.....))...(..((((((((.....))))))))..).------)))))))))))).)))..).)))).... ( -36.60)
>DroSec_CAF1 103435 96 + 1
GCUACGAAUGUCAUUUGUAUCUG------------------CAUCUGCCCCUGGCCUUGUAUCUGCAUCUCGCAGAUGCGAACGCU------GAUGCGGAUGCGCGUGUGCCUCGCUAAU
....(((....(((.((((((((------------------((((.(((...))).((((((((((.....)))))))))).....------)))))))))))).)))....)))..... ( -38.10)
>DroSim_CAF1 94191 92 + 1
----CGAAUGUCAUUUGUAUCUG------------------UAUCUGUCCCUGGCCUUGUAUCUGCAUCUCGCAGAUGCGAACGCU------GAUGCGGAUGCGCGUGUGCCUCGCUAAU
----(((....(((.((((((((------------------((((.......(((.((((((((((.....))))))))))..)))------)))))))))))).)))....)))..... ( -34.21)
>DroEre_CAF1 90860 114 + 1
GCGACGAAUGCCAUUUGUAUCUG------UAUCUGGUUCUGAAUCUGUCCCUGGCCUUGUAUCUGCAUUUCGCAGAUGCGGACGCGGAUGCGGAUGCGGAUGCGCGUGUGUCUCGCUAAU
((((((.((((((((((((((((------((((((((((.......((.....))...((((((((.....)))))))))))).)))))))))))))))))).)))).))))..)).... ( -52.20)
>DroYak_CAF1 93468 108 + 1
ACGACGAAUGUCAUUUGUAUCUGUAAAUGUAUCUGUAUCUGUAUCUGUCCCUGGCCUUGUAUCUGCAUUUCGCAGAUGC------------GGAUGCGAAUGCGCGUGUGCCUCGCUAAU
..(((....)))................((((.(((((((((((((((.....((.........)).....))))))))------------))))))).))))(((.......))).... ( -30.90)
>consensus
GCGACGAAUGUCAUUUGUAUCUG__________________UAUCUGUCCCUGGCCUUGUAUCUGCAUCUCGCAGAUGCGAACGCU______GAUGCGGAUGCGCGUGUGCCUCGCUAAU
((((.(.((((((((((((((.........................((.....)).((((((((((.....))))))))))...........)))))))))).))))...).)))).... (-26.90 = -27.90 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,355,915 – 11,356,029
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.06
Mean single sequence MFE -32.12
Consensus MFE -28.12
Energy contribution -29.20
Covariance contribution 1.08
Combinations/Pair 1.03
Mean z-score -1.62
Structure conservation index 0.88
SVM decision value 1.37
SVM RNA-class probability 0.946790
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11355915 114 - 27905053
AAAGCAGCCUCGAUAAUCACAGGACACAUUUGCAUAUAAACACGCUUCCGGGCUGAUGUCCUUCGCAUGCAAAUGAAAACAUUAGCGAGGCACACGCGCAUCCGCAUC------AGCGUC
...((.((((((.(((((....))..(((((((((........((....((((....))))...)))))))))))......))).))))))....(((....)))...------.))... ( -30.90)
>DroSec_CAF1 103497 114 - 1
AGCGCGGCCUCGAUAAUCACAGGACACAUUUGCAUAUAAACACGCUUCCGGGCUGAUGUCCUUCGCAUGCAAAUGAAAACAUUAGCGAGGCACACGCGCAUCCGCAUC------AGCGUU
.(((((((((((.(((((....))..(((((((((........((....((((....))))...)))))))))))......))).))))))...)))))...(((...------.))).. ( -36.40)
>DroSim_CAF1 94249 114 - 1
AGCGCAGCCUCGAUAAUCACAGGACACAUUUGCAUAUAAACACGCUUCCGGGCUGAUGUCCUUCGCAUGCAAAUGAAAACAUUAGCGAGGCACACGCGCAUCCGCAUC------AGCGUU
(((((.((((((.(((((....))..(((((((((........((....((((....))))...)))))))))))......))).))))))....(((....)))...------.))))) ( -34.00)
>DroEre_CAF1 90934 120 - 1
AGCGCAGCCUCGAUAAUCACAGGACACAUUUGCAUACAAACACGCUUCCGGGCUGAUGUCCUUCGCAUGCAAAUGAAAACAUUAGCGAGACACACGCGCAUCCGCAUCCGCAUCCGCGUC
.((((................(((..(((((((((........((....((((....))))...))))))))))).........(((.(.....).))).)))((....))....)))). ( -28.00)
>DroYak_CAF1 93547 109 - 1
AGCGCAGCCUCGAUAAUCACAGGACACAUUUGCAUAUAAACACGCUUCCGGGCUGAUGUCCUUCGCAUGCAAAUGAAAACAUUAGCGAGGCACACGCGCAUUCGCAUCC-----------
.((((.((((((.(((((....))..(((((((((........((....((((....))))...)))))))))))......))).))))))....))))..........----------- ( -31.30)
>consensus
AGCGCAGCCUCGAUAAUCACAGGACACAUUUGCAUAUAAACACGCUUCCGGGCUGAUGUCCUUCGCAUGCAAAUGAAAACAUUAGCGAGGCACACGCGCAUCCGCAUC______AGCGUC
.((((.((((((.(((((....))..(((((((((........((....((((....))))...)))))))))))......))).))))))....(((....)))..........)))). (-28.12 = -29.20 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:52 2006