Locus 8004

Sequence ID 3L_DroMel_CAF1
Location 21,121,599 – 21,121,696
Length 97
Max. P 0.996731
window13071 window13072

overview

Window 1

Location 21,121,599 – 21,121,696
Length 97
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 76.05
Mean single sequence MFE -20.62
Consensus MFE -11.88
Energy contribution -12.25
Covariance contribution 0.38
Combinations/Pair 1.14
Mean z-score -1.91
Structure conservation index 0.58
SVM decision value 0.44
SVM RNA-class probability 0.738021
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21121599 97 + 23771897
CGAAAUAAUAAUAUAUUUGCAUUAAAGCGA-UAU-GUUGAUGA--UGAUGAUUUUGUCCAGUGCAAGAAGUUCGUUUGCAUUGGAAAUAUUUAGAGAAAAG
..(((((.(((((((((.((......))))-)))-))))....--...........(((((((((((.......)))))))))))..)))))......... ( -21.40)
>DroSec_CAF1 172275 92 + 1
UGAAAUAAUAAUAUAUUUGCAUUCAA-------GUGAUGAGAG--AUAUGAUUUUGUGCAGUGCAAGAAGUUCGUUUGCACUGGAAAUAUUUAGAGACAAG
..(((((....(((((((.((((...-------..))))..))--)))))........(((((((((.......)))))))))....)))))......... ( -16.50)
>DroSim_CAF1 83955 98 + 1
CGAAAUAAUAAUAUAUUUGCAUUAGAGCAU-UAGAGAUGACAG--AUAUGAUUUUGUGCAGUGCAAGAAGUUCGUUUGCACUGGAAAUAUUUAGAGAAAAG
..(((((....((((((((((((.......-....)))).)))--)))))........(((((((((.......)))))))))....)))))......... ( -19.30)
>DroEre_CAF1 94812 93 + 1
CGAAU-------AUAU-UGAAUUUUAGCGAAUAAAGUUCCUAUUGCUCUAAUUUCUCCCAGUGCAAGAAGUUCGUUUGCACUGGAAAUAUUUAGAGAAGAG
.....-------....-.((((((((.....))))))))......((((((......((((((((((.......))))))))))......))))))..... ( -25.30)
>consensus
CGAAAUAAUAAUAUAUUUGCAUUAAAGCGA_UAGAGAUGAUAG__AUAUGAUUUUGUCCAGUGCAAGAAGUUCGUUUGCACUGGAAAUAUUUAGAGAAAAG
................................................(((.....(((((((((((.......))))))))))).....)))........ (-11.88 = -12.25 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 21,121,599 – 21,121,696
Length 97
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 76.05
Mean single sequence MFE -14.57
Consensus MFE -10.26
Energy contribution -10.82
Covariance contribution 0.56
Combinations/Pair 1.10
Mean z-score -2.41
Structure conservation index 0.70
SVM decision value 2.74
SVM RNA-class probability 0.996731
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21121599 97 - 23771897
CUUUUCUCUAAAUAUUUCCAAUGCAAACGAACUUCUUGCACUGGACAAAAUCAUCA--UCAUCAAC-AUA-UCGCUUUAAUGCAAAUAUAUUAUUAUUUCG
...........(((((((((.(((((.........))))).))))...........--........-...-..((......)).)))))............ ( -11.10)
>DroSec_CAF1 172275 92 - 1
CUUGUCUCUAAAUAUUUCCAGUGCAAACGAACUUCUUGCACUGCACAAAAUCAUAU--CUCUCAUCAC-------UUGAAUGCAAAUAUAUUAUUAUUUCA
.((((.............((((((((.........)))))))).............--...(((....-------.)))..))))................ ( -11.20)
>DroSim_CAF1 83955 98 - 1
CUUUUCUCUAAAUAUUUCCAGUGCAAACGAACUUCUUGCACUGCACAAAAUCAUAU--CUGUCAUCUCUA-AUGCUCUAAUGCAAAUAUAUUAUUAUUUCG
...........(((((..((((((((.........)))))))).............--............-.(((......))))))))............ ( -12.60)
>DroEre_CAF1 94812 93 - 1
CUCUUCUCUAAAUAUUUCCAGUGCAAACGAACUUCUUGCACUGGGAGAAAUUAGAGCAAUAGGAACUUUAUUCGCUAAAAUUCA-AUAU-------AUUCG
((.((((((((.(.((((((((((((.........)))))))))))).).)))))).)).))(((.((((.....)))).))).-....-------..... ( -23.40)
>consensus
CUUUUCUCUAAAUAUUUCCAGUGCAAACGAACUUCUUGCACUGCACAAAAUCAUAU__CUAUCAACUCUA_UCGCUUUAAUGCAAAUAUAUUAUUAUUUCG
................((((((((((.........))))))))))........................................................ (-10.26 = -10.82 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:03:34 2006