Locus 2234

Sequence ID 3L_DroMel_CAF1
Location 6,205,404 – 6,205,523
Length 119
Max. P 0.974045
window3458 window3459

overview

Window 8

Location 6,205,404 – 6,205,523
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.39
Mean single sequence MFE -38.42
Consensus MFE -30.87
Energy contribution -32.09
Covariance contribution 1.23
Combinations/Pair 1.05
Mean z-score -3.63
Structure conservation index 0.80
SVM decision value 1.72
SVM RNA-class probability 0.974045
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6205404 119 + 23771897
AAAGAGAAUUUAUAGUGGGAU-CCACCAAAAUCUCCGUCGGGUUUUUAUAUGGUUAGCCUAAAGGGCAACCGAAAAAUCCGCCGGUGUUAUAGCUUAUUGAGUGCUACUUGGUAAAUUUG
.....((((((((.((((...-))))(((...(.(((.(((((((((...(((((.(((.....))))))))))))))))).))).)...((((.........)))).))))))))))). ( -33.60)
>DroSec_CAF1 7196 120 + 1
AAAGAGAAUUUAUAGUGGGAUUCCAGCGGAAUCUCCGACGGGCUUUUAAAUGGUUAGUCGAAAGUUUAACCAAGAAAUCCGUCGGUGUUAUGAAAUUUGGAGUGCUACUUGGUAAAUUUG
.....(((((((((((((.(((((((((....(.(((((((..((((...(((((((.(....).)))))))))))..))))))).)...))....))))))).)))))..)))))))). ( -43.60)
>DroSim_CAF1 7098 120 + 1
AAAGAUAAUUUAUAGUGGGAUUCCAGUGGAAUCUCCGACGGCGUUUUAAAUGGUUAGUCGAAAGUUCAACCAAGAAAUCCGUCGGUGUUAUGAAAUUUGGAGUGCUACUUGGUAAAUUUG
......((((((((((((.(((((((......(.(((((((.(((((...(((((...(....)...))))).)))))))))))).).........))))))).)))))..))))))).. ( -38.06)
>consensus
AAAGAGAAUUUAUAGUGGGAUUCCAGCGGAAUCUCCGACGGGCUUUUAAAUGGUUAGUCGAAAGUUCAACCAAGAAAUCCGUCGGUGUUAUGAAAUUUGGAGUGCUACUUGGUAAAUUUG
.....(((((((((((((.(((((((......(.(((((((..((((...(((((...(....)...)))))))))..))))))).).........))))))).)))))..)))))))). (-30.87 = -32.09 +   1.23)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,205,404 – 6,205,523
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.39
Mean single sequence MFE -26.68
Consensus MFE -19.26
Energy contribution -19.60
Covariance contribution 0.34
Combinations/Pair 1.12
Mean z-score -2.76
Structure conservation index 0.72
SVM decision value 0.85
SVM RNA-class probability 0.865448
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6205404 119 - 23771897
CAAAUUUACCAAGUAGCACUCAAUAAGCUAUAACACCGGCGGAUUUUUCGGUUGCCCUUUAGGCUAACCAUAUAAAAACCCGACGGAGAUUUUGGUGG-AUCCCACUAUAAAUUCUCUUU
...((((((((((((((.........)))))....(((.(((.(((((.(((((((.....))).))))....))))).))).))).....)))))))-))................... ( -29.90)
>DroSec_CAF1 7196 120 - 1
CAAAUUUACCAAGUAGCACUCCAAAUUUCAUAACACCGACGGAUUUCUUGGUUAAACUUUCGACUAACCAUUUAAAAGCCCGUCGGAGAUUCCGCUGGAAUCCCACUAUAAAUUCUCUUU
............((((...................(((((((.(((..((((((..........))))))....)))..))))))).((((((...))))))...))))........... ( -25.10)
>DroSim_CAF1 7098 120 - 1
CAAAUUUACCAAGUAGCACUCCAAAUUUCAUAACACCGACGGAUUUCUUGGUUGAACUUUCGACUAACCAUUUAAAACGCCGUCGGAGAUUCCACUGGAAUCCCACUAUAAAUUAUCUUU
..((((((...(((.....................(((((((.....((((((((....))))))))............))))))).((((((...))))))..))).))))))...... ( -25.03)
>consensus
CAAAUUUACCAAGUAGCACUCCAAAUUUCAUAACACCGACGGAUUUCUUGGUUGAACUUUCGACUAACCAUUUAAAAACCCGUCGGAGAUUCCGCUGGAAUCCCACUAUAAAUUCUCUUU
............((((...................(((((((.(((..((((((..........))))))...)))...))))))).((((((...))))))...))))........... (-19.26 = -19.60 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:29 2006