Locus 315

Sequence ID 3R_DroMel_CAF1
Location 1,218,729 – 1,218,866
Length 137
Max. P 0.879649
window532 window533 window534

overview

Window 2

Location 1,218,729 – 1,218,830
Length 101
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 79.04
Mean single sequence MFE -22.27
Consensus MFE -15.95
Energy contribution -17.33
Covariance contribution 1.38
Combinations/Pair 1.08
Mean z-score -1.89
Structure conservation index 0.72
SVM decision value 0.91
SVM RNA-class probability 0.879649
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1218729 101 + 27905053
GGUAGCGGGUUCUCGAAAUAAUUGCGCAUUUGCUAGUGAAUAUCCUUUCUCUUAAACAGAAGAGAAAGUUUUCCUAGAAAUUAAAUGCUUUAUUGCAAAAU
.(((((((.............))))(((((((((((.(((....(((((((((......)))))))))..)))))))....))))))).....)))..... ( -23.52)
>DroSec_CAF1 9581 101 + 1
GGUAGCGGGUUCUCGAAAUAAUUGCGCAUUUGCUAGUGCAUAUCCUUUCUCGUAAAAAGAAGAGAAAGUUUAUGUAGAAAGUAAAUGCUUUAUUGGAAAAA
....((((.............))))(((((((((..((((((..(((((((..........)))))))..))))))...)))))))))............. ( -27.82)
>DroSim_CAF1 9713 101 + 1
GGUAGCGGGUUCUCGAAAUAAUUGCGCAUUUGCUAGUGCAUAUCCUUUCUCGUAAAAAGAAGAGAAAGUUUAUGUAGAAAGUAAAUGCUUUAUUGGAAAAA
....((((.............))))(((((((((..((((((..(((((((..........)))))))..))))))...)))))))))............. ( -27.82)
>DroYak_CAF1 13189 77 + 1
GGUAGCAUGUCCUCGAAAUAAUUGCGCAUUUGCUAUUCCAUAUUCUUUGUUGUUAAAAGAAGAGAAAGUUUAUCUAC------------------------
(((((((.((.(.(((.....))).).)).)))))..))...((((((.......))))))................------------------------ (  -9.90)
>consensus
GGUAGCGGGUUCUCGAAAUAAUUGCGCAUUUGCUAGUGCAUAUCCUUUCUCGUAAAAAGAAGAGAAAGUUUAUCUAGAAAGUAAAUGCUUUAUUGGAAAAA
..((((((((.(.(((.....))).).)))))))).((((((..(((((((..........)))))))..))))))......................... (-15.95 = -17.33 +   1.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 1,218,753 – 1,218,866
Length 113
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 90.72
Mean single sequence MFE -29.25
Consensus MFE -21.33
Energy contribution -23.33
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -3.79
Structure conservation index 0.73
SVM decision value 0.78
SVM RNA-class probability 0.849287
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1218753 113 + 27905053
CGCAUUUGCUAGUGAAUAUCCUUUCUCUUAAACAGAAGAGAAAGUUUUCCUAGAAAUUAAAUGCUUUAUUGCAAAAU-CUCAAACGGAAAAUGGA-UAUUUAUAAAUUUGAUUUA
.((....))..((((((((((((((((((......))))))))(((((((...........(((......)))....-.......))))))))))-)))))))............ ( -27.65)
>DroSec_CAF1 9605 115 + 1
CGCAUUUGCUAGUGCAUAUCCUUUCUCGUAAAAAGAAGAGAAAGUUUAUGUAGAAAGUAAAUGCUUUAUUGGAAAAACAUCAAACGGAAAAUGGAAUUUUUUUAAAUUUGAGUUA
.(((((((((..((((((..(((((((..........)))))))..))))))...)))))))))...........(((.(((((..(((((.......)))))...)))))))). ( -31.30)
>DroSim_CAF1 9737 115 + 1
CGCAUUUGCUAGUGCAUAUCCUUUCUCGUAAAAAGAAGAGAAAGUUUAUGUAGAAAGUAAAUGCUUUAUUGGAAAAACAUGAAACGGAAAAUGGAAUUUUUUUAAAUUUGAGUUA
.(((((((((..((((((..(((((((..........)))))))..))))))...)))))))))....((((((((((((..........)))...))))))))).......... ( -28.80)
>consensus
CGCAUUUGCUAGUGCAUAUCCUUUCUCGUAAAAAGAAGAGAAAGUUUAUGUAGAAAGUAAAUGCUUUAUUGGAAAAACAUCAAACGGAAAAUGGAAUUUUUUUAAAUUUGAGUUA
.(((((((((..((((((..(((((((..........)))))))..))))))...)))))))))...............(((((..(((((.......)))))...))))).... (-21.33 = -23.33 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 1,218,753 – 1,218,866
Length 113
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 90.72
Mean single sequence MFE -23.00
Consensus MFE -16.30
Energy contribution -16.97
Covariance contribution 0.67
Combinations/Pair 1.07
Mean z-score -3.29
Structure conservation index 0.71
SVM decision value 0.49
SVM RNA-class probability 0.757337
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1218753 113 - 27905053
UAAAUCAAAUUUAUAAAUA-UCCAUUUUCCGUUUGAG-AUUUUGCAAUAAAGCAUUUAAUUUCUAGGAAAACUUUCUCUUCUGUUUAAGAGAAAGGAUAUUCACUAGCAAAUGCG
...............((((-(((.((((((....(((-(((.(((......)))...))))))..)))))).((((((((......))))))))))))))).....((....)). ( -28.20)
>DroSec_CAF1 9605 115 - 1
UAACUCAAAUUUAAAAAAAUUCCAUUUUCCGUUUGAUGUUUUUCCAAUAAAGCAUUUACUUUCUACAUAAACUUUCUCUUCUUUUUACGAGAAAGGAUAUGCACUAGCAAAUGCG
.(((((((((..((((........))))..)))))).)))...........((((((.((.....((((..(((((((..........)))))))..))))....)).)))))). ( -22.30)
>DroSim_CAF1 9737 115 - 1
UAACUCAAAUUUAAAAAAAUUCCAUUUUCCGUUUCAUGUUUUUCCAAUAAAGCAUUUACUUUCUACAUAAACUUUCUCUUCUUUUUACGAGAAAGGAUAUGCACUAGCAAAUGCG
...................................................((((((.((.....((((..(((((((..........)))))))..))))....)).)))))). ( -18.50)
>consensus
UAACUCAAAUUUAAAAAAAUUCCAUUUUCCGUUUGAUGUUUUUCCAAUAAAGCAUUUACUUUCUACAUAAACUUUCUCUUCUUUUUACGAGAAAGGAUAUGCACUAGCAAAUGCG
....((((((..((((........))))..))))))...............((((((.((.....((((..(((((((..........)))))))..))))....)).)))))). (-16.30 = -16.97 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:15 2006