Locus 200

Sequence ID 2R_DroMel_CAF1
Location 1,462,800 – 1,462,960
Length 160
Max. P 0.973728
window462 window463

overview

Window 2

Location 1,462,800 – 1,462,920
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.33
Mean single sequence MFE -32.76
Consensus MFE -27.88
Energy contribution -27.16
Covariance contribution -0.72
Combinations/Pair 1.19
Mean z-score -1.27
Structure conservation index 0.85
SVM decision value -0.04
SVM RNA-class probability 0.513986
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1462800 120 + 20766785
AAUGGGGACAACGACUUCAUCCGCAGGAACGGGAACAAAUGGUUAAAGUACAAAAGUUGUUCUGAGCUGAAGUUGCACUUCAGUGCUCUUCGGUGCAUAAAGCGAUGCGGCUUGACAAAU
..((....))......(((.(((((......(((((((...((......)).....)))))))..(((((((..((((....)))).)))))))((.....))..)))))..)))..... ( -34.40)
>DroSec_CAF1 83319 120 + 1
AAUGGGGACAAAGACUUCAUCCGCAGGAACGGGAACAAAUGGUUAAAGUACAAAAGUUGUUCUGAGCUGAAGUUGCACUUUAGUGUUCUUCGGUGCAUAAAGCGAUGCGGCUUGACAAAU
..((....))......(((.(((((......(((((((...((......)).....)))))))..(((((((..((((....)))).)))))))((.....))..)))))..)))..... ( -32.70)
>DroSim_CAF1 82798 120 + 1
AAUGGGGACAACGACUUCAUCCGCAGGAACGGGAACAAAUGGUUAAAGUACAAAAGUUGUUCUGAGCUGAAGUUGCACUUUAGUGCUCUUCGGUGCAUAAAGCGAUGCGGCUUGACAAAU
..((....))......(((.(((((......(((((((...((......)).....)))))))..(((((((..((((....)))).)))))))((.....))..)))))..)))..... ( -34.40)
>DroEre_CAF1 94311 120 + 1
AAUGGGGACAACGGCUUCAUCCACAGGAACAGGAACAAAUGGUUAAAGUACAAAAGUUGUUCUGAGCUGAAGUUGCACUUCAGUGCUCUUUGGUGCACAAAGCGAUGCGGCUUGACAAAU
..((....)).((((((..(((...)))...(((((((...((......)).....)))))))))))))(((((((((((..((((.(....).)))).)))...))))))))....... ( -31.20)
>DroYak_CAF1 89385 120 + 1
AAUAGGGACAACGACUUCAUCCACAGGAACAGGAACAAAUGGUUAAAGUACAAAAGUUGUCCUGAGCUGAAAUUGCACUUCAGUGCUCUUUGGCGCAUAAAGCGAUGCGGCUUGACAAAU
....((((((((.((((...(((...(........)...)))...))))......))))))))((((((..(((((......(((((....))))).....))))).))))))....... ( -31.10)
>consensus
AAUGGGGACAACGACUUCAUCCGCAGGAACGGGAACAAAUGGUUAAAGUACAAAAGUUGUUCUGAGCUGAAGUUGCACUUCAGUGCUCUUCGGUGCAUAAAGCGAUGCGGCUUGACAAAU
....((((((((.((((...(((...(........)...)))...))))......))))))))(.(((((((..((((....)))).))))))).)...((((......))))....... (-27.88 = -27.16 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,462,840 – 1,462,960
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.83
Mean single sequence MFE -32.21
Consensus MFE -26.92
Energy contribution -28.52
Covariance contribution 1.60
Combinations/Pair 1.11
Mean z-score -1.99
Structure conservation index 0.84
SVM decision value 1.72
SVM RNA-class probability 0.973728
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1462840 120 + 20766785
GGUUAAAGUACAAAAGUUGUUCUGAGCUGAAGUUGCACUUCAGUGCUCUUCGGUGCAUAAAGCGAUGCGGCUUGACAAAUUAGCGUCUUAAUAAGGAGAUGCUAGAACAUACAUAUAUUU
.(((...((....(((((((((...(((((((..((((....)))).)))))))((.....)))).))))))).))...((((((((((......)))))))))))))............ ( -35.70)
>DroSec_CAF1 83359 120 + 1
GGUUAAAGUACAAAAGUUGUUCUGAGCUGAAGUUGCACUUUAGUGUUCUUCGGUGCAUAAAGCGAUGCGGCUUGACAAAUUAGCGUCUUAAUAAAGAGAUGCUAGAACAUGCAUCUAUUU
((((..((.(((.....))).)).))))((((..((((....)))).))))(((((((.((((......))))......((((((((((......))))))))))...)))))))..... ( -34.00)
>DroSim_CAF1 82838 120 + 1
GGUUAAAGUACAAAAGUUGUUCUGAGCUGAAGUUGCACUUUAGUGCUCUUCGGUGCAUAAAGCGAUGCGGCUUGACAAAUUAGCGUCUUAAUAAGGAGAUGCUAGAACAUGCAUAUAUUU
.(((...((....(((((((((...(((((((..((((....)))).)))))))((.....)))).))))))).))...((((((((((......)))))))))))))............ ( -35.70)
>DroEre_CAF1 94351 120 + 1
GGUUAAAGUACAAAAGUUGUUCUGAGCUGAAGUUGCACUUCAGUGCUCUUUGGUGCACAAAGCGAUGCGGCUUGACAAAUUAGCGUCUUAAUAAGGAGAUGCUAGAGCAUACAUUUAUUU
.(((((.((......((((((.((.((..(((..((((....)))).)))..))...)).))))))...)))))))...((((((((((......))))))))))............... ( -33.50)
>DroYak_CAF1 89425 107 + 1
GGUUAAAGUACAAAAGUUGUCCUGAGCUGAAAUUGCACUUCAGUGCUCUUUGGCGCAUAAAGCGAUGCGGCUUGACAAAUUAGCGUCGUAAUAAA-------------AUACAUAUAUUU
.......(((............((.((..((...((((....))))..))..)).))....(((((((..............)))))))......-------------.)))........ ( -22.14)
>consensus
GGUUAAAGUACAAAAGUUGUUCUGAGCUGAAGUUGCACUUCAGUGCUCUUCGGUGCAUAAAGCGAUGCGGCUUGACAAAUUAGCGUCUUAAUAAGGAGAUGCUAGAACAUACAUAUAUUU
.......(((...(((((((((...(((((((..((((....)))).)))))))((.....)))).)))))))......((((((((((......))))))))))....)))........ (-26.92 = -28.52 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:19 2006