Locus 736

Sequence ID 2L_DroMel_CAF1
Location 2,124,524 – 2,124,702
Length 178
Max. P 0.834668
window1213 window1214

overview

Window 3

Location 2,124,524 – 2,124,625
Length 101
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 84.52
Mean single sequence MFE -24.85
Consensus MFE -16.12
Energy contribution -17.40
Covariance contribution 1.28
Combinations/Pair 1.07
Mean z-score -1.80
Structure conservation index 0.65
SVM decision value 0.02
SVM RNA-class probability 0.545398
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2124524 101 + 22407834
AAAUUGAUUUGUUUCACUGCUUU------------UUUGCACACCAAAAGCCGCUUAGCAAAUUGAAUGCACAUUGUGAGUUUGUGCAUCUGAUAGGAGCUCACAAAAAAAUA
...(..(((((((...(.(((((------------(.........)))))).)...)))))))..).......((((((((((.(((....).)).))))))))))....... ( -24.20)
>DroSec_CAF1 124810 99 + 1
AAAUUGAUUUGUUUCGCUGCUUU------------UU-GCACACCUAAAGCCGCUUAGCAAAUUGAAUGCACAUUGUGAGUUUGUGCAUCUGAUAGGAGCUCACAAAAAA-CA
...(..(((((((..((.(((((------------..-........))))).))..)))))))..).......((((((((((.(((....).)).))))))))))....-.. ( -28.10)
>DroSim_CAF1 124588 100 + 1
AAAUUGAUUUGUUUCGCUGCUUU------------UUCGCACACCUAAAGCCGCUUAGCAAAUUGAAUGCACUUUGUGAGUUUGUGCAUCUGAUAGGAGCUCNNNNNNNN-NN
...(..(((((((..((.(((((------------...........))))).))..)))))))..)((((((...........)))))).....................-.. ( -21.10)
>DroEre_CAF1 127615 111 + 1
AAAUUGAUUUGUUUCACUGCUUUUG-UUUUUUUUUUUUGCACACCUAAAGCCGCUUAGCAAAUUGAAUGCACAUUGUGCGUUUGUGCAUCUGAUAAGAGCUGACAAAAAA-UA
.......((((((.....(((((((-((.........(((((.......((......)).....((((((((...)))))))))))))...))))))))).))))))...-.. ( -26.20)
>DroYak_CAF1 129936 112 + 1
AAAUUGAUUUGUUUCACUGUUUUGGGUUUUUUUUGUUUGCACACCUAAAGCCGCUUAGCAAAUUGAAUGCACAUUGUGAGCUGGUGCAUCUGAUAAGAGCUGACAAAAAA-UA
...(..(((((((...(.(((((((((...............))))))))).)...)))))))..).......((((.((((..(((....).))..)))).))))....-.. ( -24.66)
>consensus
AAAUUGAUUUGUUUCACUGCUUU____________UUUGCACACCUAAAGCCGCUUAGCAAAUUGAAUGCACAUUGUGAGUUUGUGCAUCUGAUAGGAGCUCACAAAAAA_UA
...(..(((((((...(.(((((.......................))))).)...)))))))..).......((((((((((.(((....).)).))))))))))....... (-16.12 = -17.40 +   1.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 2,124,585 – 2,124,702
Length 117
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 86.24
Mean single sequence MFE -25.10
Consensus MFE -19.83
Energy contribution -19.95
Covariance contribution 0.12
Combinations/Pair 1.14
Mean z-score -1.88
Structure conservation index 0.79
SVM decision value 0.73
SVM RNA-class probability 0.834668
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2124585 117 + 22407834
UUGUGAGUUUGUGCAUCUGAUAGGAGCUCACAAAAAAAUAAACCC--UAAAAACAAUAAAACAUGACUAUAUCGCCGAAAGGUUGCAGGACUCACAGGGUGCAAACAGCCAGGAUAACA
.(((((((((.((((...((((..((.(((...............--................))))).))))(((....))))))))))))))))((.((....)).))......... ( -26.58)
>DroSec_CAF1 124870 116 + 1
UUGUGAGUUUGUGCAUCUGAUAGGAGCUCACAAAAAA-CAAACCA--UAAAAACAAUAAAACAUGGCUAUAUCGCCGAAAGGUUGCAGAACUCACAGGGUGCAAACAGCCAGGAUAACA
.(((((((((.((((...((((..((((.........-.......--.................)))).))))(((....))))))))))))))))((.((....)).))......... ( -29.41)
>DroEre_CAF1 127687 105 + 1
UUGUGCGUUUGUGCAUCUGAUAAGAGCUGACAAAAAA-UAAACCA--UAAAAAGAGUAAAACAUGACAAUAUCGCCGAAAGGUUGCAGGACUCACAGG-----------CAGGAUAACA
((.((((((...((.(((....))))).)))......-.......--......((((....(.((.((.....(((....)))))))).))))....)-----------)).))..... ( -19.20)
>DroYak_CAF1 130009 118 + 1
UUGUGAGCUGGUGCAUCUGAUAAGAGCUGACAAAAAA-UAAAUAAUAUAAAACCAAUAAAACAUGACUAUAUCGCCGAAAGGUUGAAGCACUCACAGGGUGCAAACAGCCGGGAUAACA
((((.((((..(((....).))..)))).))))....-...............................((((.((....(((((..(((((.....)))))...)))))))))))... ( -25.20)
>consensus
UUGUGAGUUUGUGCAUCUGAUAAGAGCUCACAAAAAA_UAAACCA__UAAAAACAAUAAAACAUGACUAUAUCGCCGAAAGGUUGCAGGACUCACAGGGUGCAAACAGCCAGGAUAACA
.((((((.((.(((((((....)))................................................(((....))))))).))))))))((.((....)).))......... (-19.83 = -19.95 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:22 2006