Locus 6966

Sequence ID 3R_DroMel_CAF1
Location 18,372,643 – 18,372,788
Length 145
Max. P 0.797019
window11295 window11296 window11297

overview

Window 5

Location 18,372,643 – 18,372,748
Length 105
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 79.73
Mean single sequence MFE -45.68
Consensus MFE -26.53
Energy contribution -27.93
Covariance contribution 1.41
Combinations/Pair 1.22
Mean z-score -1.85
Structure conservation index 0.58
SVM decision value 0.30
SVM RNA-class probability 0.672545
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18372643 105 + 27905053
GGUGGUGGUCACCGCCUCGCCGGUAGCAUGUCCUUCGGCGUCCAUGCCGAAAGUGGCUCGAGCCUGGGUGGUUACCUCCACCUCGGCGGGAUGGCUCCCGCCACU
(((((.(((.(((((((.((((..(((....(.(((((((....))))))).)..))))).))..))))))).))).)))))..(((((((....)))))))... ( -56.50)
>DroSec_CAF1 37129 105 + 1
GGUGGUGGUCACAGCCUCGCCGGUAGCGUGUCCUUCGGCGUCCAUCCCGAAAGUGGCUCGAGCCUGGGUGGUUACCUCCACCUCGGCAGGAUGGCUCCCGCCACU
((((((((....((((..(((((.((......)))))))((((..(((....).)).....(((.((((((......)))))).))).)))))))).)))))))) ( -49.70)
>DroSim_CAF1 38410 105 + 1
GGUGGUGGUCACAGCCUCGCCGGUAGCGUGUCCUUCGGCGUCCAUCCCGAAAGUGGCUCGAGCCUGAGUGGUUACCUCCACCUCGGCGGGAUGGCUCCCGCCACU
(((((.(((...((((.(.(.(((..((.(((((((((.(.....)))).))).))).)).))).).).))))))).)))))..(((((((....)))))))... ( -47.20)
>DroEre_CAF1 38152 105 + 1
GGUGGUGGUCACUGCCUCCUCGGUAGCAUGUCCUUCGGCGUCCAUGCCAAAAGUGGCACGAGCCUGGGUGGUUACCUCUACUUCGGCGGGAUGGCUCCCGCCACU
(((((.(((.((..(((.((((...(.(((((....))))).).(((((....)))))))))...)))..)).))).)))))..(((((((....)))))))... ( -47.40)
>DroYak_CAF1 38100 90 + 1
AGUGGUGGUCACUGCCUCCCCGGUAGCAUGUCCUUCGGCGUCCAUGCCAAAAGUGGCACGGGCCUGGGUGGUUACCUCCACUUCGGCGG---------------C
(((((.(((.((..(((.((((...(.(((((....))))).).(((((....)))))))))...)))..)).))).))))).......---------------. ( -37.00)
>DroAna_CAF1 48837 93 + 1
GGUGGUGGUCACCGCGUCGGCGGUAGCAUGACCCAAGGCAUCCAUGCCAAACUUGGUGCUAGCGGUGGUUUUGACCUCCACUUCAGCA------------UCGUU
(((.(((.(.(((((....)))))).))).)))...((((....))))......((((((((.((.(((....))).)).))..))))------------))... ( -36.30)
>consensus
GGUGGUGGUCACAGCCUCGCCGGUAGCAUGUCCUUCGGCGUCCAUGCCAAAAGUGGCUCGAGCCUGGGUGGUUACCUCCACCUCGGCGGGAUGGCUCCCGCCACU
(((((.(((.((.((((....((((..(((((....)))))...))))......(((....))).)))).)).))).)))))..(((.(((....))).)))... (-26.53 = -27.93 +   1.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 18,372,643 – 18,372,748
Length 105
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 79.73
Mean single sequence MFE -42.85
Consensus MFE -29.82
Energy contribution -32.53
Covariance contribution 2.71
Combinations/Pair 1.21
Mean z-score -1.61
Structure conservation index 0.70
SVM decision value 0.60
SVM RNA-class probability 0.797019
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18372643 105 - 27905053
AGUGGCGGGAGCCAUCCCGCCGAGGUGGAGGUAACCACCCAGGCUCGAGCCACUUUCGGCAUGGACGCCGAAGGACAUGCUACCGGCGAGGCGGUGACCACCACC
..((((((((....)))))))).(((((.(((.(((.(((.(((....))).((((((((......))))))))....((.....))).)).))).))).))))) ( -54.50)
>DroSec_CAF1 37129 105 - 1
AGUGGCGGGAGCCAUCCUGCCGAGGUGGAGGUAACCACCCAGGCUCGAGCCACUUUCGGGAUGGACGCCGAAGGACACGCUACCGGCGAGGCUGUGACCACCACC
..((((((((....)))))))).(((((.(((....)))..((.(((((((.(((((((........)))))))...(((.....))).)))).))))).))))) ( -46.30)
>DroSim_CAF1 38410 105 - 1
AGUGGCGGGAGCCAUCCCGCCGAGGUGGAGGUAACCACUCAGGCUCGAGCCACUUUCGGGAUGGACGCCGAAGGACACGCUACCGGCGAGGCUGUGACCACCACC
..((((((((....)))))))).(((((.(((.((..(((.(((....))).(((((((........)))))))....((.....)))))...)).))).))))) ( -47.90)
>DroEre_CAF1 38152 105 - 1
AGUGGCGGGAGCCAUCCCGCCGAAGUAGAGGUAACCACCCAGGCUCGUGCCACUUUUGGCAUGGACGCCGAAGGACAUGCUACCGAGGAGGCAGUGACCACCACC
..((((((((....)))))))).....(.(((....)))).((.(((((((.(((((((((((..(......)..)))))))..)))).)))).)))))...... ( -41.90)
>DroYak_CAF1 38100 90 - 1
G---------------CCGCCGAAGUGGAGGUAACCACCCAGGCCCGUGCCACUUUUGGCAUGGACGCCGAAGGACAUGCUACCGGGGAGGCAGUGACCACCACU
.---------------.......(((((.(((..((.(((.(((((((((((....))))))))..)))...((........)).))).)).....))).))))) ( -36.00)
>DroAna_CAF1 48837 93 - 1
AACGA------------UGCUGAAGUGGAGGUCAAAACCACCGCUAGCACCAAGUUUGGCAUGGAUGCCUUGGGUCAUGCUACCGCCGACGCGGUGACCACCACC
.....------------.......((((.((((.........((..((.((((....((((....))))))))))...)).(((((....))))))))).)))). ( -30.50)
>consensus
AGUGGCGGGAGCCAUCCCGCCGAAGUGGAGGUAACCACCCAGGCUCGAGCCACUUUCGGCAUGGACGCCGAAGGACAUGCUACCGGCGAGGCAGUGACCACCACC
..((((((((....)))))))).(((((.(((.........(((....))).((((((((......)))))))).((((((.(....).))).)))))).))))) (-29.82 = -32.53 +   2.71)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 18,372,677 – 18,372,788
Length 111
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 77.75
Mean single sequence MFE -42.20
Consensus MFE -28.98
Energy contribution -30.82
Covariance contribution 1.84
Combinations/Pair 1.23
Mean z-score -1.11
Structure conservation index 0.69
SVM decision value 0.10
SVM RNA-class probability 0.582741
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18372677 111 + 27905053
UCGGCGUCCAUGCCGAAAGUGGCUCGAGCCUGGGUGGUUACCUCCACCUCGGCGGGAUGGCUCCCGCCACUCACAUCAGCCGCUGAGCCCUGUUGCUCGAGGAGAUUAGUG
((((((....)))))).(((((((.(((((.((((((......)))))).)))(((.((((....)))))))...)))))))))((((......))))............. ( -50.10)
>DroSec_CAF1 37163 111 + 1
UCGGCGUCCAUCCCGAAAGUGGCUCGAGCCUGGGUGGUUACCUCCACCUCGGCAGGAUGGCUCCCGCCACUCACAUCAGCCGCUGAGCCCUGUUGCUCCAGAAGAUUGGUG
((((.(.....))))).(((((((.(((((.((((((......)))))).))).(..((((....))))..)...)))))))))((((......))))............. ( -43.90)
>DroSim_CAF1 38444 111 + 1
UCGGCGUCCAUCCCGAAAGUGGCUCGAGCCUGAGUGGUUACCUCCACCUCGGCGGGAUGGCUCCCGCCACUCCCAUCAGCCGCUGAGCCCUGUUGCUCCAGAAGAUUGGUG
((((.(.....))))).(((((((.(((((.((((((......))).))))))((((((((....)))).)))).)))))))))((((......))))............. ( -44.40)
>DroEre_CAF1 38186 111 + 1
UCGGCGUCCAUGCCAAAAGUGGCACGAGCCUGGGUGGUUACCUCUACUUCGGCGGGAUGGCUCCCGCCACUCACAUCAGCCGCUGAGCCCUGACGCUCCAGGAGAUUUGUG
..((((....))))...((((((....(((..(((((......)))))..)))((((....))))))))))((((....((...((((......))))..)).....)))) ( -42.90)
>DroYak_CAF1 38134 96 + 1
UCGGCGUCCAUGCCAAAAGUGGCACGGGCCUGGGUGGUUACCUCCACUUCGGCGG---------------CCACAUCAGCCGCUGAGCCGUGUGGCUCCAGGAGAUUGGUG
..(((..((.(((((....))))).))(((..(((((......)))))..))).)---------------)).(((((.((...(((((....)))))..))....))))) ( -42.40)
>DroAna_CAF1 48871 99 + 1
AAGGCAUCCAUGCCAAACUUGGUGCUAGCGGUGGUUUUGACCUCCACUUCAGCA------------UCGUUCAGAUCGUUCGUGGAGUUGUGUCGCUCGAGAAGAUUCGAU
..((((....))))......((((((((.((.(((....))).)).))..))))------------))..((..(((.(((.(.((((......)))).)))))))..)). ( -29.50)
>consensus
UCGGCGUCCAUGCCAAAAGUGGCUCGAGCCUGGGUGGUUACCUCCACCUCGGCGGGAUGGCUCCCGCCACUCACAUCAGCCGCUGAGCCCUGUUGCUCCAGAAGAUUGGUG
..((((....))))...((((((....(((.((((((......)))))).)))(((.((((....)))))))......))))))((((......))))............. (-28.98 = -30.82 +   1.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:23 2006