Locus 7799

Sequence ID X_DroMel_CAF1
Location 19,436,411 – 19,436,546
Length 135
Max. P 0.988619
window12795 window12796 window12797

overview

Window 5

Location 19,436,411 – 19,436,517
Length 106
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 80.66
Mean single sequence MFE -22.27
Consensus MFE -16.17
Energy contribution -15.73
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -2.70
Structure conservation index 0.73
SVM decision value 2.13
SVM RNA-class probability 0.988619
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19436411 106 + 22224390
UAAAUAGUGCCCGCACAGGCGCUGCACUCGUACGUAUACGUAAUACGCGUUUACACUUAUGUACAUAAAUAUGUACAUACAU-------GUCCAACAAUCCAACAAUCCGCAU
.....((((((......))))))((.......(((((.....))))).(((.(((..(((((((((....)))))))))..)-------))..))).............)).. ( -25.80)
>DroSec_CAF1 4156 97 + 1
UAAAUAGUGCCCGCACAAGCGCUGCACUCGCACGUAUACGUAAUACGCGUUUUCACGUAUGUAU--------UUACGUACAAUUCAACA--------AUCCAACAAUCCGCAU
.....(((((.(((....)))..))))).((.(((((.....))))).........((((((..--------..)))))).........--------............)).. ( -20.10)
>DroSim_CAF1 4513 105 + 1
UAAAUAGUGCCCGCACAAGCGCUGCACUCGUACGUAUACGUAAUACGCGUUUUCACUUAUGUAU--------UUACGUACAAUCCAACAAUCCAACAAUCCAACAAUCCGCAU
.....(((((.(((....)))..))))).((((((((((((((.............))))))).--------.)))))))................................. ( -20.92)
>consensus
UAAAUAGUGCCCGCACAAGCGCUGCACUCGUACGUAUACGUAAUACGCGUUUUCACUUAUGUAU________UUACGUACAAU_CAACA_UCCAACAAUCCAACAAUCCGCAU
.....(((((.(((....)))..))))).((.(((((.....)))))..........((((((..........))))))..............................)).. (-16.17 = -15.73 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 19,436,411 – 19,436,517
Length 106
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 80.66
Mean single sequence MFE -29.40
Consensus MFE -23.31
Energy contribution -22.87
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -1.76
Structure conservation index 0.79
SVM decision value 0.75
SVM RNA-class probability 0.839711
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19436411 106 - 22224390
AUGCGGAUUGUUGGAUUGUUGGAC-------AUGUAUGUACAUAUUUAUGUACAUAAGUGUAAACGCGUAUUACGUAUACGUACGAGUGCAGCGCCUGUGCGGGCACUAUUUA
.........((((.((((((..((-------((.(((((((((....))))))))).)))).)))((((((.....))))))...))).))))((((....))))........ ( -32.70)
>DroSec_CAF1 4156 97 - 1
AUGCGGAUUGUUGGAU--------UGUUGAAUUGUACGUAA--------AUACAUACGUGAAAACGCGUAUUACGUAUACGUGCGAGUGCAGCGCUUGUGCGGGCACUAUUUA
.(((............--------........((((((((.--------....(((((((....)))))))))))))))((..((((((...))))))..)).)))....... ( -28.40)
>DroSim_CAF1 4513 105 - 1
AUGCGGAUUGUUGGAUUGUUGGAUUGUUGGAUUGUACGUAA--------AUACAUAAGUGAAAACGCGUAUUACGUAUACGUACGAGUGCAGCGCUUGUGCGGGCACUAUUUA
.(((............................(((((((((--------.(((....((....))..))))))))))))((((((((((...)))))))))).)))....... ( -27.10)
>consensus
AUGCGGAUUGUUGGAUUGUUGGA_UGUUG_AUUGUACGUAA________AUACAUAAGUGAAAACGCGUAUUACGUAUACGUACGAGUGCAGCGCUUGUGCGGGCACUAUUUA
................................((((((((.................((....))(((.....))).))))))))(((((..(((....))).)))))..... (-23.31 = -22.87 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 19,436,451 – 19,436,546
Length 95
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 79.19
Mean single sequence MFE -17.83
Consensus MFE -12.32
Energy contribution -12.43
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -1.99
Structure conservation index 0.69
SVM decision value 1.08
SVM RNA-class probability 0.912103
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19436451 95 + 22224390
UAAUACGCGUUUACACUUAUGUACAUAAAUAUGUACAUACAU-------GUCCAACAAUCCAACAAUCCGCAUGGGCGAAAGCAUACUUUGUUUGAAUACCA
........(((.(((..(((((((((....)))))))))..)-------))..)))..((.(((((.((....))((....)).....))))).))...... ( -20.40)
>DroSec_CAF1 4196 86 + 1
UAAUACGCGUUUUCACGUAUGUAU--------UUACGUACAAUUCAACA--------AUCCAACAAUCCGCAUGGGCGAAAGCAUGCUUUGUUUGAAUACCA
......(.((.((((.((((((..--------..)))))).........--------....(((((...((((..((....)))))).))))))))).))). ( -18.20)
>DroSim_CAF1 4553 94 + 1
UAAUACGCGUUUUCACUUAUGUAU--------UUACGUACAAUCCAACAAUCCAACAAUCCAACAAUCCGCAUGGGCGAAAGCAUGCUUUGUUUGAAUACCA
......(.((.((((....(((((--------....)))))....................(((((...((((..((....)))))).))))))))).))). ( -14.90)
>consensus
UAAUACGCGUUUUCACUUAUGUAU________UUACGUACAAU_CAACA_UCCAACAAUCCAACAAUCCGCAUGGGCGAAAGCAUGCUUUGUUUGAAUACCA
.................((((((..........))))))...................((.(((((...((((..((....)))))).))))).))...... (-12.32 = -12.43 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:50 2006