Locus 1403

Sequence ID 2L_DroMel_CAF1
Location 3,744,713 – 3,744,825
Length 112
Max. P 0.601986
window2290 window2291

overview

Window 0

Location 3,744,713 – 3,744,825
Length 112
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 88.59
Mean single sequence MFE -18.73
Consensus MFE -13.40
Energy contribution -12.77
Covariance contribution -0.62
Combinations/Pair 1.12
Mean z-score -1.46
Structure conservation index 0.72
SVM decision value -0.05
SVM RNA-class probability 0.507965
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3744713 112 + 22407834
UAUUUUAAAUAUUUAACAACCAAAUCUCUAUUCACAUUUCCCGGCGGGUAAAUAUCCAUACAAAUUUAGAACAUUUUUCCAGGUCAAUGUGAAC-ACAUUGAGCUGCACGAAU
..((((((((.........((.....................)).((((....))))......))))))))........(((.(((((((....-))))))).)))....... ( -17.00)
>DroSec_CAF1 206814 112 + 1
UAUUUUAAAUAUUUAACAACAGAAACUUAAUGCACAUUCCCCGGCGGGUAAACAUUCAUAAAAAUUUAGAACAUUUUUCCAGGUCAAUGUGAAC-ACAUUGAGCUGCACGAAU
..((((((((.((((.(....)......((((......(((....)))....))))..)))).))))))))........(((.(((((((....-))))))).)))....... ( -17.50)
>DroSim_CAF1 213953 107 + 1
UAUUUUAAAUAUUUAACAGCAGAAACUCAAUGCACAUUCC-----GGGUAAACAUUCAUAAAAAUUUAGAACAUUUUUCCAGGUCAAUGUGAAC-ACAUUGAGCUGCACGAAU
..................((((...(((((((((((((((-----(((.(((..(((.(((....))))))..))).))).))..))))))...-.)))))))))))...... ( -21.50)
>DroYak_CAF1 224759 113 + 1
UAUUUUAAAUAUUUAACAGCCAAAUCUCUAUACACAUUCCCCAUUGGCUAAACAGCCAUAAAAAUUUAGAACAUUUUUCCAGGUCAAUGUGAACGACAUGGAGCUGCACAAAU
................((((...((.((....((((((..((..(((((....)))))..........(((.....)))..))..))))))...)).))...))))....... ( -18.90)
>consensus
UAUUUUAAAUAUUUAACAACAAAAACUCAAUGCACAUUCCCCGGCGGGUAAACAUCCAUAAAAAUUUAGAACAUUUUUCCAGGUCAAUGUGAAC_ACAUUGAGCUGCACGAAU
..((((((((.(((.......))).....................((((....))))......))))))))........(((.(((((((.....))))))).)))....... (-13.40 = -12.77 +  -0.62)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,744,713 – 3,744,825
Length 112
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 88.59
Mean single sequence MFE -26.85
Consensus MFE -17.82
Energy contribution -18.00
Covariance contribution 0.19
Combinations/Pair 1.15
Mean z-score -2.03
Structure conservation index 0.66
SVM decision value 0.14
SVM RNA-class probability 0.601986
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3744713 112 - 22407834
AUUCGUGCAGCUCAAUGU-GUUCACAUUGACCUGGAAAAAUGUUCUAAAUUUGUAUGGAUAUUUACCCGCCGGGAAAUGUGAAUAGAGAUUUGGUUGUUAAAUAUUUAAAAUA
......((((((...(.(-(((((((((..(((((..((((((((...........)))))))).....))))).)))))))))).).....))))))............... ( -29.00)
>DroSec_CAF1 206814 112 - 1
AUUCGUGCAGCUCAAUGU-GUUCACAUUGACCUGGAAAAAUGUUCUAAAUUUUUAUGAAUGUUUACCCGCCGGGGAAUGUGCAUUAAGUUUCUGUUGUUAAAUAUUUAAAAUA
....(..((..(((((((-....)))))))(((((..((((((((...........)))))))).....)))))...))..)............................... ( -23.10)
>DroSim_CAF1 213953 107 - 1
AUUCGUGCAGCUCAAUGU-GUUCACAUUGACCUGGAAAAAUGUUCUAAAUUUUUAUGAAUGUUUACCC-----GGAAUGUGCAUUGAGUUUCUGCUGUUAAAUAUUUAAAAUA
......(((((((((((.-...((((((...((((..((((((((...........))))))))..))-----)))))))))))))))...)))).................. ( -25.40)
>DroYak_CAF1 224759 113 - 1
AUUUGUGCAGCUCCAUGUCGUUCACAUUGACCUGGAAAAAUGUUCUAAAUUUUUAUGGCUGUUUAGCCAAUGGGGAAUGUGUAUAGAGAUUUGGCUGUUAAAUAUUUAAAAUA
(((((.((((((..((.((...((((((..(((((((.....)))))........(((((....)))))..))..))))))....)).))..))))))))))).......... ( -29.90)
>consensus
AUUCGUGCAGCUCAAUGU_GUUCACAUUGACCUGGAAAAAUGUUCUAAAUUUUUAUGAAUGUUUACCCGCCGGGGAAUGUGCAUAGAGAUUCGGCUGUUAAAUAUUUAAAAUA
......(((((........((.((((((..(((((..((((((((...........))))))))..)))..))..)))))).)).........)))))............... (-17.82 = -18.00 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:49 2006