Locus 2913

Sequence ID 2R_DroMel_CAF1
Location 10,123,468 – 10,123,582
Length 114
Max. P 0.929129
window4802 window4803

overview

Window 2

Location 10,123,468 – 10,123,582
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.43
Mean single sequence MFE -33.37
Consensus MFE -22.62
Energy contribution -24.46
Covariance contribution 1.84
Combinations/Pair 1.26
Mean z-score -1.78
Structure conservation index 0.68
SVM decision value 0.68
SVM RNA-class probability 0.821743
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10123468 114 + 20766785
GCUUAAAGAAUCCAAGUCCGCCGAAA------UGGUAGUGGAAGAGGAACUGCCUGAAACUACGGGAGUGGAAGUAGAUGGGUCCACGGUUGUGGGAUGAUUAAAUAGACCUGGAUCAGG
..........((((..((((......------.((((((.........))))))........))))..))))........((((((.((((.(((.....)))....))))))))))... ( -30.46)
>DroSec_CAF1 7271 114 + 1
GCUUAAAGAAUCCAAGGUCGCCGAAA------UGGUAGUGGAAGAGGAACUGCCUGGAACUACGGGAGUGGAAGUGGACGGGUCCACGGUUGUGGGAUGAUUAAAUGGACUUGGAGCAGG
((((.(((..((((.(((((((....------.((((((.........)))))).....((((....))))..(((((....))))).......)).)))))...))))))).))))... ( -34.70)
>DroSim_CAF1 7072 114 + 1
GCUUAAAGAAUCCAAGGUCGCCGAAU------UGGUAGUGGAAGAGGAACUGCCUGGAACUACGGGAGUGGAAGUGGACGGGUCCACGGUUGUGGGAUGAUUAAAUGGACUUGGAGCAGG
((((.(((..((((.(((((((....------.((((((.........)))))).....((((....))))..(((((....))))).......)).)))))...))))))).))))... ( -34.70)
>DroEre_CAF1 7461 105 + 1
GCUUAGGGAAUCCAAGUUCGCCGAAAUUAGCAUUGAAGUGGGAGACGAGCUAGGUGGAACUACGGG---------------AUCCACGCUUGUGGGAAUAUUAAAGGAACCUGGAGCAGG
((((.(((..(((..((((.(((.....(((.....(((.(....)..)))..(((((.(....).---------------.))))))))..)))))))......))).))).))))... ( -30.10)
>DroYak_CAF1 7381 120 + 1
GCUAAGGGAAUCCAAGUUCGCCGAAAUCAGCAUGGAAGUGGGAGAGAGACUUGGCGGAACUACGGGAGUGGAAGUGGAUGGACCCACGCAUGUGGGAAUAUUAAAGGAACUUGGAGCCGG
.....((...((((((((((((((..((..(((....))).)).......)))))....((((....)))).....((((..(((((....)))))..))))....))))))))).)).. ( -36.90)
>consensus
GCUUAAAGAAUCCAAGUUCGCCGAAA______UGGUAGUGGAAGAGGAACUGCCUGGAACUACGGGAGUGGAAGUGGACGGGUCCACGGUUGUGGGAUGAUUAAAUGGACUUGGAGCAGG
..........(((((((((.(((..........((((((.........)))))).....((((....)))).......))).(((((....)))))..........)))))))))..... (-22.62 = -24.46 +   1.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 10,123,468 – 10,123,582
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.43
Mean single sequence MFE -23.74
Consensus MFE -16.66
Energy contribution -17.50
Covariance contribution 0.84
Combinations/Pair 1.24
Mean z-score -1.96
Structure conservation index 0.70
SVM decision value 1.20
SVM RNA-class probability 0.929129
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10123468 114 - 20766785
CCUGAUCCAGGUCUAUUUAAUCAUCCCACAACCGUGGACCCAUCUACUUCCACUCCCGUAGUUUCAGGCAGUUCCUCUUCCACUACCA------UUUCGGCGGACUUGGAUUCUUUAAGC
...(((((((((((...................(((((..........)))))....(((((....((.((.....)).)))))))..------.......)))))))))))........ ( -25.50)
>DroSec_CAF1 7271 114 - 1
CCUGCUCCAAGUCCAUUUAAUCAUCCCACAACCGUGGACCCGUCCACUUCCACUCCCGUAGUUCCAGGCAGUUCCUCUUCCACUACCA------UUUCGGCGACCUUGGAUUCUUUAAGC
.....(((((((((...................(((((....)))))..........(((((....((.((.....)).)))))))..------.....).)).)))))).......... ( -20.80)
>DroSim_CAF1 7072 114 - 1
CCUGCUCCAAGUCCAUUUAAUCAUCCCACAACCGUGGACCCGUCCACUUCCACUCCCGUAGUUCCAGGCAGUUCCUCUUCCACUACCA------AUUCGGCGACCUUGGAUUCUUUAAGC
.....(((((((((...................(((((....)))))..........(((((....((.((.....)).)))))))..------.....).)).)))))).......... ( -20.80)
>DroEre_CAF1 7461 105 - 1
CCUGCUCCAGGUUCCUUUAAUAUUCCCACAAGCGUGGAU---------------CCCGUAGUUCCACCUAGCUCGUCUCCCACUUCAAUGCUAAUUUCGGCGAACUUGGAUUCCCUAAGC
.....(((((((((.............((.((((((((.---------------........)))))...))).)).............(((......)))))))))))).......... ( -22.80)
>DroYak_CAF1 7381 120 - 1
CCGGCUCCAAGUUCCUUUAAUAUUCCCACAUGCGUGGGUCCAUCCACUUCCACUCCCGUAGUUCCGCCAAGUCUCUCUCCCACUUCCAUGCUGAUUUCGGCGAACUUGGAUUCCCUUAGC
..((.(((((((((..........(((((....)))))...........................((((((((...................))))).))))))))))))..))...... ( -28.81)
>consensus
CCUGCUCCAAGUCCAUUUAAUCAUCCCACAACCGUGGACCCAUCCACUUCCACUCCCGUAGUUCCAGGCAGUUCCUCUUCCACUACCA______UUUCGGCGAACUUGGAUUCUUUAAGC
.....(((((((((...........((((....))))....................(((((...(((.....))).....)))))...............))))))))).......... (-16.66 = -17.50 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:33 2006