Locus 2230

Sequence ID 2R_DroMel_CAF1
Location 8,234,078 – 8,234,216
Length 138
Max. P 0.999161
window3671 window3672

overview

Window 1

Location 8,234,078 – 8,234,191
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.53
Mean single sequence MFE -23.93
Consensus MFE -21.76
Energy contribution -21.72
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -1.41
Structure conservation index 0.91
SVM decision value 0.82
SVM RNA-class probability 0.859567
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8234078 113 + 20766785
AUUUGGCACGGCAUCUCAAACCAAGUAAUUAAACAUCAUUCC-GAAAGCAUUUCCAUCAGUAAUGCCAAUCUAAUCCAAAGUAGAUUGGCAAAUACAGCAUUUUAAUUGGAUGG------
((((((..............))))))...............(-....).....(((((.(((.((((((((((........))))))))))..)))..((.......)))))))------ ( -22.84)
>DroSec_CAF1 21509 114 + 1
AUUUGGCACGGCAUCUCAUCCCAAGUAAUUAAACCUCAUUCCCAAAAGCAUUUCCAUCAGUAAUGCCAAUCUAAUCCAAAGUAGAUUGGCAAAUACAGCAUUUUAAUUGGAUGG------
((((((...((....))...))))))...........................(((((.(((.((((((((((........))))))))))..)))..((.......)))))))------ ( -22.40)
>DroSim_CAF1 23536 114 + 1
AUUUGGCACGGCAUCUCAUCCCAAGUAAUUAAACCCCAUUCCCAAAAGCAUUUCCAUCAGUAAUGCCAAUCUAAUCCAAAGUAGAUUGGCAAAUACAGCAUUUUAAUUGGAUGG------
((((((...((....))...))))))...........................(((((.(((.((((((((((........))))))))))..)))..((.......)))))))------ ( -22.40)
>DroEre_CAF1 21091 113 + 1
AUUUGGCUCGGCAAGGCAUCCCAAGUAAUUAAACAUCAUUCC-GAAAGCAUUUCCCUCAGUAAUGCCAAUCUAAUCCAGAGUGGAUUGGCAAAUACAGCAUUUUAAUUGGAUGG------
((((((....((...))...)))))).......((((....(-....)...........(((.((((((((((........))))))))))..))).............)))).------ ( -24.00)
>DroYak_CAF1 22044 119 + 1
AUUUGGCUUGGCUACGCAUCCCAAGUAAUUAAACUUCAGUCC-GAAAGCAUUCCCAUCAGUAAUGCCAAUCUAAUCCAGAGUGGAUUGGCAAAUACAGCAUUUUAAUUGGAUGGCAAAUG
(((((((((((.........))))))................-..........(((((.(((.((((((((((........))))))))))..)))..((.......)))))))))))). ( -28.00)
>consensus
AUUUGGCACGGCAUCUCAUCCCAAGUAAUUAAACAUCAUUCC_GAAAGCAUUUCCAUCAGUAAUGCCAAUCUAAUCCAAAGUAGAUUGGCAAAUACAGCAUUUUAAUUGGAUGG______
((((((....(.....)...))))))...........................(((((.(((.((((((((((........))))))))))..)))..((.......)))))))...... (-21.76 = -21.72 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,234,118 – 8,234,216
Length 98
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 89.95
Mean single sequence MFE -24.36
Consensus MFE -21.56
Energy contribution -21.36
Covariance contribution -0.20
Combinations/Pair 1.08
Mean z-score -2.52
Structure conservation index 0.88
SVM decision value 3.41
SVM RNA-class probability 0.999161
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8234118 98 + 20766785
CC-GAAAGCAUUUCCAUCAGUAAUGCCAAUCUAAUCCAAAGUAGAUUGGCAAAUACAGCAUUUUAAUUGGAUGG-------CAAAAAUGGGAUUUAGCAC----------AUUCAA
..-....((..((((((..(((.((((((((((........))))))))))..)))..(((((.....))))).-------.....))))))....))..----------...... ( -23.50)
>DroSec_CAF1 21549 99 + 1
CCCAAAAGCAUUUCCAUCAGUAAUGCCAAUCUAAUCCAAAGUAGAUUGGCAAAUACAGCAUUUUAAUUGGAUGG-------CAAAAAUGGGAUUUAGCAC----------AUUCAA
((((.........(((((.(((.((((((((((........))))))))))..)))..((.......)))))))-------......)))).........----------...... ( -24.36)
>DroSim_CAF1 23576 99 + 1
CCCAAAAGCAUUUCCAUCAGUAAUGCCAAUCUAAUCCAAAGUAGAUUGGCAAAUACAGCAUUUUAAUUGGAUGG-------CAAAAAUGGGUUUUAGCAC----------AUUCAA
((((.........(((((.(((.((((((((((........))))))))))..)))..((.......)))))))-------......)))).........----------...... ( -23.86)
>DroEre_CAF1 21131 98 + 1
CC-GAAAGCAUUUCCCUCAGUAAUGCCAAUCUAAUCCAGAGUGGAUUGGCAAAUACAGCAUUUUAAUUGGAUGG-------CAAAAAUGGGUUUUAGCAC----------AUUCAA
.(-....)...........(((.((((((((((........))))))))))..)))..........((((((((-------(.((((....)))).)).)----------)))))) ( -23.20)
>DroYak_CAF1 22084 115 + 1
CC-GAAAGCAUUCCCAUCAGUAAUGCCAAUCUAAUCCAGAGUGGAUUGGCAAAUACAGCAUUUUAAUUGGAUGGCAAAUGGCAAAAAUGGGUUUUAGCACAUUCGAGCACAUUCAA
..-(((..((((.(((((.(((.((((((((((........))))))))))..)))..((.......)))))))..))))((...((((.((....)).))))...))...))).. ( -26.90)
>consensus
CC_GAAAGCAUUUCCAUCAGUAAUGCCAAUCUAAUCCAAAGUAGAUUGGCAAAUACAGCAUUUUAAUUGGAUGG_______CAAAAAUGGGUUUUAGCAC__________AUUCAA
.......((...(((((..(((.((((((((((........))))))))))..)))..(((((.....))))).............))))).....)).................. (-21.56 = -21.36 +  -0.20)

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 10:24:24 2006