Locus 5962

Sequence ID 2R_DroMel_CAF1
Location 18,780,126 – 18,780,240
Length 114
Max. P 0.721330
window9563 window9564

overview

Window 3

Location 18,780,126 – 18,780,240
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 82.57
Mean single sequence MFE -41.33
Consensus MFE -24.08
Energy contribution -25.75
Covariance contribution 1.67
Combinations/Pair 1.30
Mean z-score -2.47
Structure conservation index 0.58
SVM decision value 0.21
SVM RNA-class probability 0.637443
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18780126 114 + 20766785
UGGGUGGCCAGGUCCAAUUGGAAGGCCACCAAUAGAAUGUCCUUGAUGUUGUGAUCAGUAUGAUCCCACCAAAUGUUGGAAGUAUCACCGGCUCGACGAAUAGACGUUCGCACU
..(((((((...(((....))).)))))))....(((((((..(..(((((.((((.....)))).........(((((........))))).))))).)..)))))))..... ( -37.90)
>DroVir_CAF1 4462 114 + 1
AUAUGUGCCAGUGCCAUUUGAAAGGCCACCAGCAGUAUGUCCAUUAUGUUAUGAUCAGCGCGAUGCCAAAAACAGUCGGUUUCAUCGCGUGUUAACUUGAUGCUGGUGCGCACA
...(((((....(((........)))((((((((...((..(((......)))..))((((((((....((((.....))))))))))))..........)))))))).))))) ( -37.10)
>DroSec_CAF1 41 114 + 1
UGGGUGGCCAGGUCCAAUUGGAAGGCCACCAAUAGAAUGUCCUUGAUGUUGUGAUCAGUAUGAUCCCACCAAAUGUUGGUGGUGUCACCGGCUGGACGAAUAGACGUUCGCACU
..(((((((...(((....))).)))))))....(((((((.......((((..(((((.(((..((((((.....))))))..)))...)))))))))...)))))))..... ( -46.40)
>DroSim_CAF1 41 114 + 1
UGGGUGGCCAGGUCCAAUUGGAAGGCCACCAAUAGAAUGUCCUUGAUGUUGUGAUCAGUAUGAUCCCACCAAAUGUUGGUGGUGUCACCGGCUGGACGAAUAGACGUUCGCACU
..(((((((...(((....))).)))))))....(((((((.......((((..(((((.(((..((((((.....))))))..)))...)))))))))...)))))))..... ( -46.40)
>DroEre_CAF1 41 114 + 1
UGGGUGGCCAGGUCCAAUUGAAAGGCCACCAAUAGAAUAUCCUUGAUGUUGUGAUCAGUAUGAUCCCACCAAAUGUUGGUGGUGUCGCCGGCUGGUCGAAUGGAGGUUCGCACU
..(((((((...((.....))..)))))))....(((...((((.((....((((((((.(((..((((((.....))))))..)))...)))))))).)).)))))))..... ( -44.60)
>DroYak_CAF1 41 114 + 1
UGCGUGGCCAGGUCCAACUGAAAGGCCACCAGUAGAAUAUCCUUGAUGUUGUGAUCGGUAUGAUCCCUCCAAAUGUUGGUGGUAUCGCCGGCUGGUCGAAUAGAGGUUCUCACU
((.((((((...((.....))..))))))))((((((...((((..((((.((((((((.((((.((.(((.....))).)).))))...)))))))))))))))))))).)). ( -35.60)
>consensus
UGGGUGGCCAGGUCCAAUUGAAAGGCCACCAAUAGAAUGUCCUUGAUGUUGUGAUCAGUAUGAUCCCACCAAAUGUUGGUGGUAUCACCGGCUGGACGAAUAGACGUUCGCACU
..(((((((...((.....))..)))))))..((.((((((...)))))).)).(((((.((((.((((((.....)))))).))))...))))).(((((....))))).... (-24.08 = -25.75 +   1.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,780,126 – 18,780,240
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 82.57
Mean single sequence MFE -36.97
Consensus MFE -22.57
Energy contribution -24.05
Covariance contribution 1.48
Combinations/Pair 1.23
Mean z-score -2.55
Structure conservation index 0.61
SVM decision value 0.40
SVM RNA-class probability 0.721330
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18780126 114 - 20766785
AGUGCGAACGUCUAUUCGUCGAGCCGGUGAUACUUCCAACAUUUGGUGGGAUCAUACUGAUCACAACAUCAAGGACAUUCUAUUGGUGGCCUUCCAAUUGGACCUGGCCACCCA
.....(((.((((..((..((...))..))............((((((.((((.....))))....)))))))))).)))....(((((((.(((....)))...))))))).. ( -35.20)
>DroVir_CAF1 4462 114 - 1
UGUGCGCACCAGCAUCAAGUUAACACGCGAUGAAACCGACUGUUUUUGGCAUCGCGCUGAUCAUAACAUAAUGGACAUACUGCUGGUGGCCUUUCAAAUGGCACUGGCACAUAU
(((((.((((((((....(((..(((((((((...((((......))))))))))).))..(((......))))))....))))))))(((........)))....)))))... ( -40.30)
>DroSec_CAF1 41 114 - 1
AGUGCGAACGUCUAUUCGUCCAGCCGGUGACACCACCAACAUUUGGUGGGAUCAUACUGAUCACAACAUCAAGGACAUUCUAUUGGUGGCCUUCCAAUUGGACCUGGCCACCCA
.................((((....((((...((((((.....))))))((((.....))))....))))..))))........(((((((.(((....)))...))))))).. ( -39.80)
>DroSim_CAF1 41 114 - 1
AGUGCGAACGUCUAUUCGUCCAGCCGGUGACACCACCAACAUUUGGUGGGAUCAUACUGAUCACAACAUCAAGGACAUUCUAUUGGUGGCCUUCCAAUUGGACCUGGCCACCCA
.................((((....((((...((((((.....))))))((((.....))))....))))..))))........(((((((.(((....)))...))))))).. ( -39.80)
>DroEre_CAF1 41 114 - 1
AGUGCGAACCUCCAUUCGACCAGCCGGCGACACCACCAACAUUUGGUGGGAUCAUACUGAUCACAACAUCAAGGAUAUUCUAUUGGUGGCCUUUCAAUUGGACCUGGCCACCCA
.....(((..(((..(((.((....)))))..((((((.....))))))((((.....))))..........)))..)))....(((((((.(((....)))...))))))).. ( -37.00)
>DroYak_CAF1 41 114 - 1
AGUGAGAACCUCUAUUCGACCAGCCGGCGAUACCACCAACAUUUGGAGGGAUCAUACCGAUCACAACAUCAAGGAUAUUCUACUGGUGGCCUUUCAGUUGGACCUGGCCACGCA
(((.((((..(((..(((.((....)))))..((.(((.....))).))((((.....))))..........)))..))))))).((((((.(((....)))...))))))... ( -29.70)
>consensus
AGUGCGAACCUCUAUUCGUCCAGCCGGCGACACCACCAACAUUUGGUGGGAUCAUACUGAUCACAACAUCAAGGACAUUCUAUUGGUGGCCUUCCAAUUGGACCUGGCCACCCA
((((.(((..(((...................(((((((...)))))))((((.....))))..........)))..)))))))(((((((.(((....)))...))))))).. (-22.57 = -24.05 +   1.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:08 2006