Locus 6275

Sequence ID 3L_DroMel_CAF1
Location 16,721,036 – 16,721,146
Length 110
Max. P 0.943980
window10065 window10066

overview

Window 5

Location 16,721,036 – 16,721,146
Length 110
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 75.68
Mean single sequence MFE -24.22
Consensus MFE -4.66
Energy contribution -5.78
Covariance contribution 1.12
Combinations/Pair 1.21
Mean z-score -1.78
Structure conservation index 0.19
SVM decision value 0.61
SVM RNA-class probability 0.799835
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16721036 110 + 23771897
UAGGGGAAUAUUUGAAGG------AAAAUUUGAAAUGUAUA--UUUUCAAAGAAC-UUCAAAUUUUUCAAACUGAUCCCCUUUGUUUUCAGUGCACCAUUCUCUUUCUCCACGGUCCCG
..((((((.((((((((.------....(((((((......--.)))))))...)-))))))).......(((((............)))))............)))))).((....)) ( -23.40)
>DroSec_CAF1 28460 110 + 1
UAGGGGAAUGUUUGAGGG------GAAAU-CGAGAUGUAUU--UUUUCAAAGAAAUUUUCAAUUUCUCAAACUGUUCCCCUUUGUUUUCAGUGCACCAUUCUCUUUCUCCACGCUCCCC
..(((((.(((..(((((------(((..-.((((......--.))))..((((((.....)))))).......))))))))(((.......)))...............))).))))) ( -25.20)
>DroSim_CAF1 32934 110 + 1
UAGGGGAACGUUUUAAGG------GAAAU-CGAGAUGUAUA--UUUUCAAAGAAAUUUUUAAUUUCUCAAACUGAUCCCCUUUGUUUUCAGUGCACCAUUCUCUUUCUCCACGCUCCCC
..(((((.(((...((((------(((..-.((((..((.(--((((....)))))...))...))))..(((((............)))))......))))))).....))).))))) ( -26.00)
>DroEre_CAF1 29085 117 + 1
UAGGGAUCUGUUUUAAAAAAAUCAGAAAU-CAGAAUAUACGAGUAUAUAUAUAU-UGUAAAAUGCGUUGAACAGAUCCCUUUUGUUUUCCGUGUACCAUUCUCUUUCUCCACGGUCUGG
.((((((((((((........((......-..))...(((.(((((....))))-)))).........))))))))))))........(((((................)))))..... ( -23.49)
>DroYak_CAF1 31262 108 + 1
UAGGGAUCUGUUUUAAAG------GAAAU-CGGAAUAUAUA--UUUUCAAUCAU-UUUUAAAUUGGUUGAACUGUUUGCUUUUGUUUUCAGUGCACCAUUCUCUUUCUCCACGGCCC-G
..(((..((((...((((------..(((-.((........--...(((((((.-........)))))))((((...((....))...))))...)))))..))))....)))))))-. ( -23.00)
>consensus
UAGGGGAAUGUUUUAAGG______GAAAU_CGAAAUGUAUA__UUUUCAAAGAA_UUUUAAAUUUCUCAAACUGAUCCCCUUUGUUUUCAGUGCACCAUUCUCUUUCUCCACGGUCCCG
..((((((.......................((((.........))))......................((((..............))))............))))))......... ( -4.66 =  -5.78 +   1.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,721,036 – 16,721,146
Length 110
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 75.68
Mean single sequence MFE -25.79
Consensus MFE -4.68
Energy contribution -5.96
Covariance contribution 1.28
Combinations/Pair 1.25
Mean z-score -2.07
Structure conservation index 0.18
SVM decision value 1.34
SVM RNA-class probability 0.943980
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16721036 110 - 23771897
CGGGACCGUGGAGAAAGAGAAUGGUGCACUGAAAACAAAGGGGAUCAGUUUGAAAAAUUUGAA-GUUCUUUGAAAA--UAUACAUUUCAAAUUUU------CCUUCAAAUAUUCCCCUA
..(.(((((...........))))).)...........((((((...((((((((((((((((-((....(....)--.....))))))))))).------..)))))))..)))))). ( -27.90)
>DroSec_CAF1 28460 110 - 1
GGGGAGCGUGGAGAAAGAGAAUGGUGCACUGAAAACAAAGGGGAACAGUUUGAGAAAUUGAAAAUUUCUUUGAAAA--AAUACAUCUCG-AUUUC------CCCUCAAACAUUCCCCUA
((((((.(((((((..((((..((....)).....(((((..(.....((..(....)..))..)..)))))....--......)))).-.))))------)......)).)))))).. ( -27.00)
>DroSim_CAF1 32934 110 - 1
GGGGAGCGUGGAGAAAGAGAAUGGUGCACUGAAAACAAAGGGGAUCAGUUUGAGAAAUUAAAAAUUUCUUUGAAAA--UAUACAUCUCG-AUUUC------CCUUAAAACGUUCCCCUA
((((((((((((((..((((.((((.(.((........)).).)))).((.(((((((.....))))))).))...--......)))).-.))))------)......))))))))).. ( -33.40)
>DroEre_CAF1 29085 117 - 1
CCAGACCGUGGAGAAAGAGAAUGGUACACGGAAAACAAAAGGGAUCUGUUCAACGCAUUUUACA-AUAUAUAUAUACUCGUAUAUUCUG-AUUUCUGAUUUUUUUAAAACAGAUCCCUA
.....(((((................)))))........(((((((((((............((-..((((((......))))))..))-.....(((.....))).))))))))))). ( -25.89)
>DroYak_CAF1 31262 108 - 1
C-GGGCCGUGGAGAAAGAGAAUGGUGCACUGAAAACAAAAGCAAACAGUUCAACCAAUUUAAAA-AUGAUUGAAAA--UAUAUAUUCCG-AUUUC------CUUUAAAACAGAUCCCUA
.-(((...((...((((..(((((((.((((..............)))).))..(((((.....-..)))))....--........)).-)))..------))))....))...))).. ( -14.74)
>consensus
CGGGACCGUGGAGAAAGAGAAUGGUGCACUGAAAACAAAGGGGAUCAGUUUGACAAAUUUAAAA_UUCUUUGAAAA__UAUACAUUUCG_AUUUC______CCUUAAAACAUUCCCCUA
..(.(((((...........))))).)...........((((((...((((.......................................................))))..)))))). ( -4.68 =  -5.96 +   1.28)

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 12:14:27 2006