Locus 5541

Sequence ID 2R_DroMel_CAF1
Location 17,691,738 – 17,691,858
Length 120
Max. P 0.999848
window8891 window8892

overview

Window 1

Location 17,691,738 – 17,691,858
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.50
Mean single sequence MFE -47.00
Consensus MFE -38.46
Energy contribution -38.38
Covariance contribution -0.08
Combinations/Pair 1.10
Mean z-score -2.33
Structure conservation index 0.82
SVM decision value 1.91
SVM RNA-class probability 0.982421
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17691738 120 + 20766785
UUAUAGCCUACGCUUGUCCAGAUGGUGCUGGCAGCCAACUGGAGCAAUGGACAUUGACACGCCGUCACCAAAGUGUCCACGCCCUUCUCCAGGGUGGAGGAGGUGCCAACAACAAGCCAA
...........((((((((((.((((.......)))).)))))....(((((((((((.....)))).....))))))).((((((((((.....)))))))).))......)))))... ( -45.40)
>DroSec_CAF1 1360 120 + 1
UUAUAGCCUACGCUUGUCCAGAUGGUGCUGGCAGCCAACUGGAGCAAUGGACAUUGACACGCCGUCACCAAAGUGUCCACACCCUGCUCCAGGGUGGCGGAGGAGCCAACAAUAAGCCAA
...........((((((...(.((((.((....((((.((((((((.(((((((((((.....)))).....))))))).....))))))))..))))...)).)))).).))))))... ( -43.90)
>DroSim_CAF1 557 120 + 1
UUAUAGCCUACGCUUGUCCAGAUGGUGCUGGCAGCCAACUGGAGCAAUGGACAUUGACACGCCGUCACCAAAGUGUCCACGCCCUGCUUCAGGGUGGCGGAGGUGCCAACAACAAGCCAA
...........((((((...(.(((..((....((((.((((((((.(((((((((((.....)))).....))))))).....))))))))..))))...))..))).).))))))... ( -46.40)
>DroEre_CAF1 1178 120 + 1
UCAUAGCCUACGCUUGUCCGGAUGGUGCUGGAAGCCAACUGGAGCAAUGGACGUUGACACGCCGGCACCAAAGUGUCCACGCCCUGCUCCAGGGUGGAGGAGGUGCCAACAACAAGCCAA
...........((((((...(.(((..((.....(((.((((((((..((.(((.(((((...(....)...))))).))))).))))))))..)))....))..))).).))))))... ( -49.80)
>DroYak_CAF1 1057 120 + 1
UCAUAGCCUACGCUUGUCCGGAUGGUGCUGGCAGUCAACUGGAGCAGUGGACGUUGACACGCCGGCACCAAAGUGUGCACGCCCUGCUCCAGGGUGGAGGAGGUGCCAACAACAAGCCAA
...........((((((...(.(((..((..(..(((.(((((((((.((.(((.(.(((((.(....)...))))))))))))))))))))..)))..).))..))).).))))))... ( -49.50)
>consensus
UUAUAGCCUACGCUUGUCCAGAUGGUGCUGGCAGCCAACUGGAGCAAUGGACAUUGACACGCCGUCACCAAAGUGUCCACGCCCUGCUCCAGGGUGGAGGAGGUGCCAACAACAAGCCAA
...........((((((...(.(((..((.....(((.((((((((..((.....(((((............)))))....)).))))))))..)))....))..))).).))))))... (-38.46 = -38.38 +  -0.08)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 17,691,738 – 17,691,858
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.50
Mean single sequence MFE -50.82
Consensus MFE -46.30
Energy contribution -47.30
Covariance contribution 1.00
Combinations/Pair 1.05
Mean z-score -2.66
Structure conservation index 0.91
SVM decision value 4.24
SVM RNA-class probability 0.999848
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17691738 120 - 20766785
UUGGCUUGUUGUUGGCACCUCCUCCACCCUGGAGAAGGGCGUGGACACUUUGGUGACGGCGUGUCAAUGUCCAUUGCUCCAGUUGGCUGCCAGCACCAUCUGGACAAGCGUAGGCUAUAA
...((((((((((((((......(((..((((((..((((((.(((((.(((....))).))))).))))))....)))))).))).))))))))((....))))))))........... ( -50.80)
>DroSec_CAF1 1360 120 - 1
UUGGCUUAUUGUUGGCUCCUCCGCCACCCUGGAGCAGGGUGUGGACACUUUGGUGACGGCGUGUCAAUGUCCAUUGCUCCAGUUGGCUGCCAGCACCAUCUGGACAAGCGUAGGCUAUAA
.(((((((((((((((......((((..(((((((((((..(.(((((.(((....))).))))).)..)))..)))))))).)))).)))))))((....))......))))))))... ( -54.10)
>DroSim_CAF1 557 120 - 1
UUGGCUUGUUGUUGGCACCUCCGCCACCCUGAAGCAGGGCGUGGACACUUUGGUGACGGCGUGUCAAUGUCCAUUGCUCCAGUUGGCUGCCAGCACCAUCUGGACAAGCGUAGGCUAUAA
...((((((((((((((.....((((..(((.((((((((((.(((((.(((....))).))))).))))))..)))).))).))))))))))))((....))))))))........... ( -52.40)
>DroEre_CAF1 1178 120 - 1
UUGGCUUGUUGUUGGCACCUCCUCCACCCUGGAGCAGGGCGUGGACACUUUGGUGCCGGCGUGUCAACGUCCAUUGCUCCAGUUGGCUUCCAGCACCAUCCGGACAAGCGUAGGCUAUGA
...((((((((((((........(((..((((((((((((((.(((((.(((....))).))))).))))))..)))))))).)))...))))))((....))))))))........... ( -48.70)
>DroYak_CAF1 1057 120 - 1
UUGGCUUGUUGUUGGCACCUCCUCCACCCUGGAGCAGGGCGUGCACACUUUGGUGCCGGCGUGUCAACGUCCACUGCUCCAGUUGACUGCCAGCACCAUCCGGACAAGCGUAGGCUAUGA
...(((((((..(((((((((((((.....))))..))).)))).))...((((((.((((.((((((.............)))))))))).))))))....)))))))........... ( -48.12)
>consensus
UUGGCUUGUUGUUGGCACCUCCUCCACCCUGGAGCAGGGCGUGGACACUUUGGUGACGGCGUGUCAAUGUCCAUUGCUCCAGUUGGCUGCCAGCACCAUCUGGACAAGCGUAGGCUAUAA
...((((((((((((((......(((..((((((((((((((.(((((.(((....))).))))).))))))..)))))))).))).))))))))((....))))))))........... (-46.30 = -47.30 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:20 2006