Locus 5467

Sequence ID 3R_DroMel_CAF1
Location 14,446,376 – 14,446,486
Length 110
Max. P 0.979719
window8900 window8901

overview

Window 0

Location 14,446,376 – 14,446,486
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.87
Mean single sequence MFE -28.06
Consensus MFE -20.88
Energy contribution -21.76
Covariance contribution 0.88
Combinations/Pair 1.10
Mean z-score -2.67
Structure conservation index 0.74
SVM decision value 1.63
SVM RNA-class probability 0.968826
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14446376 110 + 27905053
UUUGUUUGGUCCAA----------AAGAAGAGAAUGUUUUUUGUUUUGAAAACAUUUUUAUUUACUUUUAUUGUUUGAUAACUUGAAAAGAUUGGGGGAAAACCGGACUAAGAAAGUGUU
....((((((((..----------.(((.((((((((((((......)))))))))))).))).(((((...(((....)))...)))))....((......))))))))))........ ( -25.40)
>DroSec_CAF1 3502 108 + 1
UUAGUUUGGUCCAA----------AAGAAGAGAAUGUUUUUUGUUUUGAAAACAUUUUUAUUUACUUUUAUUGUUUGAUAACUUGAAAAGGUUGGGG--AAACCGGACCAAGAAAGUGUU
....((((((((((----------(((((((((((((((((......))))))))))))..)).))))).........((((((....))))))((.--...))))))))))........ ( -31.70)
>DroSim_CAF1 3815 108 + 1
UUAGUUUCGUCCAA----------AAGAAGAGAAUGUUUUUUGUUUUGAAAACAUUUUUAUUUACUUUUAUUGUUUGAUAACUUGAAAAGGUUGGGG--AAACCGGACCAAGAAAGUGUU
..(((((((..(((----------.((((((((((((((((......)))))))))))......))))).)))..))).))))......((((.((.--...)).))))........... ( -27.80)
>DroEre_CAF1 3462 117 + 1
UUAGUUUGGUCCAAACCGGUGACAAAGAAAAGAAUGCGUUUUGUUUUGAAAACACU-UUAGUUACUUUUAUUGUGUGAUAACUUGAAAAGGUUGGGG--AAACCGGACCAAGAAAGUAUU
....((((((((.....((((((((((....(....)(((((......))))).))-)).))))))............((((((....))))))((.--...))))))))))........ ( -29.50)
>DroYak_CAF1 3648 118 + 1
UUAGUUUGGUCCAAAACGGUGACAAAGAGAAGAAUGCGUUUUGUUUUGGAAACAUUUUUAGUUACUUUUAUUGUAUGACAACUUUAAAAGGUUGGUG--AAACCGGACCAAGAAAUUGUU
....((((((((......(((((.((((.((((.....)))).))))(....).......)))))(((((..((......))..)))))((((....--.))))))))))))........ ( -25.90)
>consensus
UUAGUUUGGUCCAA__________AAGAAGAGAAUGUUUUUUGUUUUGAAAACAUUUUUAUUUACUUUUAUUGUUUGAUAACUUGAAAAGGUUGGGG__AAACCGGACCAAGAAAGUGUU
....((((((((.................((((((((((((......)))))))))))).....(((((...((......))...)))))...((.......))))))))))........ (-20.88 = -21.76 +   0.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,446,376 – 14,446,486
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.87
Mean single sequence MFE -16.95
Consensus MFE -13.30
Energy contribution -13.74
Covariance contribution 0.44
Combinations/Pair 1.16
Mean z-score -2.52
Structure conservation index 0.78
SVM decision value 1.84
SVM RNA-class probability 0.979719
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14446376 110 - 27905053
AACACUUUCUUAGUCCGGUUUUCCCCCAAUCUUUUCAAGUUAUCAAACAAUAAAAGUAAAUAAAAAUGUUUUCAAAACAAAAAACAUUCUCUUCUU----------UUGGACCAAACAAA
............((((((.......))........................(((((........((((((((........)))))))).....)))----------))))))........ ( -10.92)
>DroSec_CAF1 3502 108 - 1
AACACUUUCUUGGUCCGGUUU--CCCCAACCUUUUCAAGUUAUCAAACAAUAAAAGUAAAUAAAAAUGUUUUCAAAACAAAAAACAUUCUCUUCUU----------UUGGACCAAACUAA
.........(((((((((((.--....))))....................(((((........((((((((........)))))))).....)))----------)))))))))..... ( -18.62)
>DroSim_CAF1 3815 108 - 1
AACACUUUCUUGGUCCGGUUU--CCCCAACCUUUUCAAGUUAUCAAACAAUAAAAGUAAAUAAAAAUGUUUUCAAAACAAAAAACAUUCUCUUCUU----------UUGGACGAAACUAA
.........((.((((((((.--....))))....................(((((........((((((((........)))))))).....)))----------)))))).))..... ( -14.22)
>DroEre_CAF1 3462 117 - 1
AAUACUUUCUUGGUCCGGUUU--CCCCAACCUUUUCAAGUUAUCACACAAUAAAAGUAACUAA-AGUGUUUUCAAAACAAAACGCAUUCUUUUCUUUGUCACCGGUUUGGACCAAACUAA
.........(((((((((...--..))((((......((((((............))))))..-.(((((((......)))))))..................)))).)))))))..... ( -22.90)
>DroYak_CAF1 3648 118 - 1
AACAAUUUCUUGGUCCGGUUU--CACCAACCUUUUAAAGUUGUCAUACAAUAAAAGUAACUAAAAAUGUUUCCAAAACAAAACGCAUUCUUCUCUUUGUCACCGUUUUGGACCAAACUAA
.........(((((((((...--..))...((((((..((......))..))))))......................((((((....(........)....)))))))))))))..... ( -18.10)
>consensus
AACACUUUCUUGGUCCGGUUU__CCCCAACCUUUUCAAGUUAUCAAACAAUAAAAGUAAAUAAAAAUGUUUUCAAAACAAAAAACAUUCUCUUCUU__________UUGGACCAAACUAA
.........(((((((((((.......)))).................................((((((((........))))))))....................)))))))..... (-13.30 = -13.74 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:30 2006