Locus 3239

Sequence ID 3R_DroMel_CAF1
Location 8,650,426 – 8,650,546
Length 120
Max. P 0.683421
window5238 window5239

overview

Window 8

Location 8,650,426 – 8,650,520
Length 94
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 78.40
Mean single sequence MFE -19.62
Consensus MFE -10.85
Energy contribution -11.60
Covariance contribution 0.75
Combinations/Pair 1.24
Mean z-score -2.06
Structure conservation index 0.55
SVM decision value 0.31
SVM RNA-class probability 0.683421
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8650426 94 + 27905053
CAAUGUAUUCUUGGGU-UAUAAAAAUCAGGGUGGAAACCAAAAAAAAAAAAAAAAAAACCGAAAAUCGA----------GCAAUUGCUUAAAGUUGCUGGUUCUA
........((((((..-........))))))(((((.((....................((.....))(----------((((((......)))))))))))))) ( -14.80)
>DroSec_CAF1 77303 91 + 1
CAAUGUAUUUUUAGGC-UAUAAAAAUCAGGGUGGAAUCCCAAAAAAAAA---AUGAAACCGAAAAUGGA----------GUAACUGCUUAAAGUUGCUGGCUCUA
...........(((((-(..........(((......))).........---......((......))(----------((((((......)))))))))).))) ( -16.10)
>DroSim_CAF1 93575 89 + 1
CAAUGUAUUUUUAGGC-UAUAAAAAUCAGGGUGGAAACCCAAAAAAAAA-----GAAACCGAAAAUGGA----------GCACCUGCUUAAAGUUGCUGGCUCUA
...((.(((((((...-..)))))))))((((....)))).........-----...........((((----------((....((........))..)))))) ( -20.20)
>DroYak_CAF1 82749 102 + 1
CAAUGUAUUUUUGUGUCCUUAAAAAUGUGGCUAGAAAGCCAAAAAAAAA---CAAGAAACGAGAAUGGAGCCACCGAAGGCAACUGCUUAAAGUUGCCAGCUCUA
......((((((((.((..........(((((....)))))........---...)).))))))))(((((.......(((((((......))))))).))))). ( -27.40)
>consensus
CAAUGUAUUUUUAGGC_UAUAAAAAUCAGGGUGGAAACCCAAAAAAAAA___AAAAAACCGAAAAUGGA__________GCAACUGCUUAAAGUUGCUGGCUCUA
......(((((((......)))))))..((((....)))).......................................((((((......))))))........ (-10.85 = -11.60 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 8,650,453 – 8,650,546
Length 93
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 82.04
Mean single sequence MFE -23.03
Consensus MFE -14.76
Energy contribution -16.57
Covariance contribution 1.81
Combinations/Pair 1.17
Mean z-score -1.77
Structure conservation index 0.64
SVM decision value 0.18
SVM RNA-class probability 0.621108
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8650453 93 + 27905053
GGGUGGAAACCAAAAAAAAAAAAAAAAAAACCGAAAAUCGA----------GCAAUUGCUUAAAGUUGCUGGUUCUAAUUAUUGUCCUCGUUCCCGGUUGUGA
.(((....))).................(((((..((.(((----------((((((......)))))).((..(........).)))))))..))))).... ( -17.80)
>DroSec_CAF1 77330 90 + 1
GGGUGGAAUCCCAAAAAAAAA---AUGAAACCGAAAAUGGA----------GUAACUGCUUAAAGUUGCUGGCUCUAAUUAUUGUCCUCGUUCUCGGUUGUGA
(((......))).........---....((((((.((((((----------((((((......)))))))(((..........))).))))).)))))).... ( -23.10)
>DroSim_CAF1 93602 88 + 1
GGGUGGAAACCCAAAAAAAAA-----GAAACCGAAAAUGGA----------GCACCUGCUUAAAGUUGCUGGCUCUAAUUAUUGUCCUCGUUCUCGGUUGUGA
((((....)))).........-----..((((((.((((((----------(((.((......)).))))(((..........))).))))).)))))).... ( -24.30)
>DroYak_CAF1 82777 100 + 1
GGCUAGAAAGCCAAAAAAAAA---CAAGAAACGAGAAUGGAGCCACCGAAGGCAACUGCUUAAAGUUGCCAGCUCUAAUUAUUGUCCUCGUUCUCAGUUGUGA
((((....)))).........---((...((((((((((((((.......(((((((......))))))).)))).............))))))).))).)). ( -26.91)
>consensus
GGGUGGAAACCCAAAAAAAAA___AAAAAACCGAAAAUGGA__________GCAACUGCUUAAAGUUGCUGGCUCUAAUUAUUGUCCUCGUUCUCGGUUGUGA
((((....))))................((((((.(((((...........((((((......)))))).(((..........))).))))).)))))).... (-14.76 = -16.57 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:26 2006