Locus 180

Sequence ID 4_DroMel_CAF1
Location 1,104,930 – 1,105,072
Length 142
Max. P 0.894810
window290 window291

overview

Window 0

Location 1,104,930 – 1,105,037
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.60
Mean single sequence MFE -23.40
Consensus MFE -18.25
Energy contribution -18.88
Covariance contribution 0.62
Combinations/Pair 1.24
Mean z-score -1.98
Structure conservation index 0.78
SVM decision value 0.98
SVM RNA-class probability 0.894810
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1104930 107 - 1281640
CACAAAGUAUGCAAUGUCAUUUAGCAACCAACGGAGAUACAAAAUAUUGUUUCCGUGCUAAAAGGAAAAGCAUAAUACAUUUAUAAAUCGUGAAAAUGUGAUA-------------GUGU
(((....(((((....((.((((((.....(((((((((........))))))))))))))).))....))))).(((((((.((.....)).)))))))...-------------))). ( -25.20)
>DroSec_CAF1 18438 107 - 1
CACAAAGUAUGCAAUGUCAUUUAGCAACCGACGGAGAUACAAAAUAUUGUUUCCUUGUUGAAAGAAAAAGUAUAAUACAUUUAUAAAUCGUGAAGAUGUGAUA-------------GUGU
(((....(((((....((.((((((((.....(((((((........))))))))))))))).))....))))).(((((((.((.....)).)))))))...-------------))). ( -20.30)
>DroEre_CAF1 18646 120 - 1
CACAAAGUAUGCAAUGUCAUUUAGCAACCGACGGAGAUACAAUAUAUUGUUUCUAUGCUGAAAGAAAAAGCAAAAAACGUGUACAAAACGUGAAAAUGUGAUAUUUCUUACAGAGAGUGU
((((.....(((....((.(((((((.((...))(((.((((....)))).))).))))))).))....)))....((((.......)))).....))))...((((.....)))).... ( -22.30)
>DroYak_CAF1 9746 120 - 1
CACAAAGUAUGCAAUGUCAUUUAACAACCGACGGAGAUAUUAUAUAUUGUUUCCUUGGUGAAAGAAAAAGCAGAAUACAAUUAUAUAACGUGAAAAUGUGAUACUUUUUACAGAAAGUGU
......((((....(((..(((....(((((.(((((((........)))))))))))).....)))..)))..)))).........((((....)))).((((((((....)))))))) ( -25.80)
>consensus
CACAAAGUAUGCAAUGUCAUUUAGCAACCGACGGAGAUACAAAAUAUUGUUUCCUUGCUGAAAGAAAAAGCAUAAUACAUUUAUAAAACGUGAAAAUGUGAUA_____________GUGU
(((....(((((....((.((((((((.....(((((((........))))))))))))))).))....))))).(((((((.((.....)).)))))))................))). (-18.25 = -18.88 +   0.62)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,104,957 – 1,105,072
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.66
Mean single sequence MFE -24.27
Consensus MFE -19.13
Energy contribution -19.50
Covariance contribution 0.38
Combinations/Pair 1.16
Mean z-score -1.70
Structure conservation index 0.79
SVM decision value 0.44
SVM RNA-class probability 0.738752
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1104957 115 - 1281640
AAGCUUUUGAAAAGCUUAAAGUGUCAUCUUAG-----UUUCACAAAGUAUGCAAUGUCAUUUAGCAACCAACGGAGAUACAAAAUAUUGUUUCCGUGCUAAAAGGAAAAGCAUAAUACAU
((((((.....))))))...(((..((....)-----)..)))....(((((....((.((((((.....(((((((((........))))))))))))))).))....)))))...... ( -25.60)
>DroSec_CAF1 18465 115 - 1
AAGCUUUUAAAAAGCUUUAAGUGUCAUCUUAG-----UUUCACAAAGUAUGCAAUGUCAUUUAGCAACCGACGGAGAUACAAAAUAUUGUUUCCUUGUUGAAAGAAAAAGUAUAAUACAU
((((((.....))))))...(((..((....)-----)..)))....(((((....((.((((((((.....(((((((........))))))))))))))).))....)))))...... ( -20.00)
>DroEre_CAF1 18686 115 - 1
AAGCUUUUGAAAAGCUUUGAGUGUCACCGUAG-----UCUCACAAAGUAUGCAAUGUCAUUUAGCAACCGACGGAGAUACAAUAUAUUGUUUCUAUGCUGAAAGAAAAAGCAAAAAACGU
..((((((.....((((((.(.(.(......)-----.).).))))))........((.(((((((.((...))(((.((((....)))).))).))))))).))))))))......... ( -23.00)
>DroYak_CAF1 9786 120 - 1
AAGCUUUUGAAAAGCUUUAAGUGUCAUCGUAGUAUUGUCUCACAAAGUAUGCAAUGUCAUUUAACAACCGACGGAGAUAUUAUAUAUUGUUUCCUUGGUGAAAGAAAAAGCAGAAUACAA
..((((((........(((((((.(((.(((...(((.....)))....))).))).)))))))..(((((.(((((((........))))))))))))......))))))......... ( -28.50)
>consensus
AAGCUUUUGAAAAGCUUUAAGUGUCAUCGUAG_____UCUCACAAAGUAUGCAAUGUCAUUUAGCAACCGACGGAGAUACAAAAUAUUGUUUCCUUGCUGAAAGAAAAAGCAUAAUACAU
((((((.....))))))...(((.................)))....(((((....((.((((((((.....(((((((........))))))))))))))).))....)))))...... (-19.13 = -19.50 +   0.38)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:26 2006