Locus 5440

Sequence ID 2R_DroMel_CAF1
Location 17,490,448 – 17,490,568
Length 120
Max. P 0.646192
window8682

overview

Window 2

Location 17,490,448 – 17,490,568
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.17
Mean single sequence MFE -33.80
Consensus MFE -29.90
Energy contribution -30.28
Covariance contribution 0.38
Combinations/Pair 1.09
Mean z-score -1.56
Structure conservation index 0.88
SVM decision value 0.23
SVM RNA-class probability 0.646192
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17490448 120 + 20766785
CAAGGCAGAGGUGGCAAGCACACAGUUUGCCACAUUAUUCACAGUUUCUGCCAGUGCAUUUGUGCGGCUUUUAACAAGUUGUGGCUUUCUUUUGGGAAAUAAAAAAUUAAGUGGAAGCAG
...((((((((((((((((.....)))))))))............))))))).(..(....)..).(((((((...((((.....(((((....))))).....))))...))))))).. ( -36.20)
>DroSec_CAF1 18273 120 + 1
CAAGGCAAAGGUGGCUAGCACACAGUUUGCCACAUUAUUCACAGUUUCUGCCAGUGCAUUUGUGCGGCUUUUAACAAGUUGUGGCUUUCUUUUGGAAUAUACAAAAUUAAGUGGAAGCAG
....((....(((((.(((.....))).)))))....(((((.(((...(((.(..(....)..))))....)))...(((((..((((....))))..)))))......))))).)).. ( -32.00)
>DroSim_CAF1 31142 120 + 1
CAAGGCAGAGGUGGCUAGCACACAGUUUGCCACAUUAUUCACAGUUUCUGCCAGUGCAUUUGUGCGGCUUUUAACAAGUUGUGGCUUUCUUUUGGAAUAUACAAAAUUAAGUGGAAGCAG
...((((((((((((.(((.....))).)))))............))))))).(..(....)..).(((((((.....(((((..((((....))))..))))).......))))))).. ( -34.20)
>DroYak_CAF1 27313 120 + 1
CGAGGCAAAGGUGGCUAGCAAACAGCUUGCCACAUUAUUCACAGUUUCUGCCAGUGCAUUUGUGCGGCUUUUAACAAGUUGCGACUUUCUUUUGGGAAAUACAAAAUUAACUGAAAGCUG
.(((......(((((.(((.....))).)))))....))).((((((....((((...((((((((((((.....)))))))...(((((....))))).)))))....)))).)))))) ( -32.80)
>consensus
CAAGGCAAAGGUGGCUAGCACACAGUUUGCCACAUUAUUCACAGUUUCUGCCAGUGCAUUUGUGCGGCUUUUAACAAGUUGUGGCUUUCUUUUGGAAAAUACAAAAUUAAGUGGAAGCAG
...((((((((((((.(((.....))).)))))............))))))).(..(....)..).(((((((.....(((((..((((....))))..))))).......))))))).. (-29.90 = -30.28 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:57 2006