Locus 4059

Sequence ID 2R_DroMel_CAF1
Location 13,394,491 – 13,394,611
Length 120
Max. P 0.929231
window6540 window6541

overview

Window 0

Location 13,394,491 – 13,394,611
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.50
Mean single sequence MFE -42.78
Consensus MFE -32.77
Energy contribution -33.83
Covariance contribution 1.06
Combinations/Pair 1.18
Mean z-score -2.16
Structure conservation index 0.77
SVM decision value 0.16
SVM RNA-class probability 0.612905
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13394491 120 + 20766785
UUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCCGUCAGUCGCUCCUGACAGCCGCUAGCAUAGUAGCUCCAAGUGGCACGGAAAACCGAAUCCC
...(((......(((((((.((.((.((((((..(((((.(..(((.(((((......)).))).)))..).))))).)))))).)).)).)))))))..))).(((....)))...... ( -42.70)
>DroGri_CAF1 15280 120 + 1
UCUUAUCCUUGAUCUGUUGCACAAAGUCAGCAUGCUGCUCGAUGCGACGACGUAUGUCCAGUUGCCGCUUCUUGCAGCCGCUGGCAAAGUAACUCCAAUAGGCCCGGAACAGUGAGUCCG
......(((......(((((.....((((((..(((((..((.(((.((((.........)))).))).))..))))).))))))...)))))......)))..((((........)))) ( -37.60)
>DroSec_CAF1 12091 120 + 1
UUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCCGUCAGUCGCUCCUGACAGCCGCUAGCAUAGUAGCUCCAAGUGGCCCGGAAAACCGAAUCCC
..((((......(((((((.((.((.((((((..(((((.(..(((.(((((......)).))).)))..).))))).)))))).)).)).)))))))..))))(((....)))...... ( -44.90)
>DroSim_CAF1 12895 120 + 1
UUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCAGUCAGUCGCUCUUGACAGCCGCUAGCAUAGUAGCUCCAAGUGGCCCGGAAAACCGAAUCCC
..((((......(((((((.((.((.((((((..(((((.((.(((.((((........).))).)))))..))))).)))))).)).)).)))))))..))))(((....)))...... ( -42.10)
>DroEre_CAF1 12490 120 + 1
UUGGCUCCUUAUUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGCCCGUCAGUCGCUCCUGACAGCCGUUAGCAUAGUAGCUCCAUGUGGCCCGGAACAGCGAAUCCC
..(((..(.....((((((.((.((.((((((..(((((.(..(((.(((((......)).))).)))..).))))).)))))).)).)).)))))).)..))).(((........))). ( -41.30)
>DroYak_CAF1 12516 120 + 1
UUGGCUCUUUGCUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGCCCGUCAGUCGCUCCUGACAGCCGUUAGCAUAGUAGCUCCAAGUGGCCCGGAACACCGAGUCCC
..(((((.(..((((((((.((.((.((((((..(((((.(..(((.(((((......)).))).)))..).))))).)))))).)).)).))))))))..)...((....))))))).. ( -48.10)
>consensus
UUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCCGUCAGUCGCUCCUGACAGCCGCUAGCAUAGUAGCUCCAAGUGGCCCGGAAAACCGAAUCCC
..((((......(((((((.((.((.((((((..(((((.(..(((.(((((......)).))).)))..).))))).)))))).)).)).)))))))..)))).(((........))). (-32.77 = -33.83 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 13,394,491 – 13,394,611
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.50
Mean single sequence MFE -46.32
Consensus MFE -39.59
Energy contribution -40.48
Covariance contribution 0.90
Combinations/Pair 1.22
Mean z-score -2.42
Structure conservation index 0.85
SVM decision value 1.20
SVM RNA-class probability 0.929231
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13394491 120 - 20766785
GGGAUUCGGUUUUCCGUGCCACUUGGAGCUACUAUGCUAGCGGCUGUCAGGAGCGACUGACGGACAUUCGCAGGCGCAUCGAACAGAACGCUAGAAUUGUGGCUCCAAUUAAAGAGCCAA
.((.((((((.......)))..((((((((((....((((((.((((..(..(((.(((.(((....)))))).)))..)..))))..))))))....)))))))))).....))))).. ( -49.60)
>DroGri_CAF1 15280 120 - 1
CGGACUCACUGUUCCGGGCCUAUUGGAGUUACUUUGCCAGCGGCUGCAAGAAGCGGCAACUGGACAUACGUCGUCGCAUCGAGCAGCAUGCUGACUUUGUGCAACAGAUCAAGGAUAAGA
(((((.....).))))..((....)).....(((((((((..(((((.....)))))..))))......(((((.((((.((((((....))).))).)))).)).))))))))...... ( -36.70)
>DroSec_CAF1 12091 120 - 1
GGGAUUCGGUUUUCCGGGCCACUUGGAGCUACUAUGCUAGCGGCUGUCAGGAGCGACUGACGGACAUUCGCAGGCGCAUCGAACAGAACGCUAGAAUUGUGGCUCCAAUUAAAGAGCCAA
.((.(((((....)))))))..((((((((((....((((((.((((..(..(((.(((.(((....)))))).)))..)..))))..))))))....))))))))))............ ( -50.20)
>DroSim_CAF1 12895 120 - 1
GGGAUUCGGUUUUCCGGGCCACUUGGAGCUACUAUGCUAGCGGCUGUCAAGAGCGACUGACUGACAUUCGCAGGCGCAUCGAACAGAACGCUAGAAUUGUGGCUCCAAUUAAAGAGCCAA
.((.(((((....)))))))..((((((((((....((((((.((((...(((((.(((.(........)))).))).))..))))..))))))....))))))))))............ ( -46.30)
>DroEre_CAF1 12490 120 - 1
GGGAUUCGCUGUUCCGGGCCACAUGGAGCUACUAUGCUAACGGCUGUCAGGAGCGACUGACGGGCAUUCGCAGGCGCAUCGAACAGAACGCUAGAAUUGUGGCUCCAAAUAAGGAGCCAA
..(((((.((((((.(.(((.(((((.....))))).....(.(((((((......))))))).).......))).)...)))))).......))))).(((((((......))))))). ( -45.20)
>DroYak_CAF1 12516 120 - 1
GGGACUCGGUGUUCCGGGCCACUUGGAGCUACUAUGCUAACGGCUGUCAGGAGCGACUGACGGGCAUUCGCAGGCGCAUCGAACAGAACGCUAGAAUUGUGGCUCCAAGCAAAGAGCCAA
(((((.....))))).((((.(((((((((((..(((.((.(.(((((((......))))))).).)).)))((((..((.....)).))))......)))))))))))....).))).. ( -49.90)
>consensus
GGGAUUCGGUGUUCCGGGCCACUUGGAGCUACUAUGCUAGCGGCUGUCAGGAGCGACUGACGGACAUUCGCAGGCGCAUCGAACAGAACGCUAGAAUUGUGGCUCCAAUUAAAGAGCCAA
.((.(((((....)))))))..((((((((((....((((((.((((..((.(((.(((.((......))))).))).))..))))..))))))....))))))))))............ (-39.59 = -40.48 +   0.90)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:48 2006