Locus 9546

Sequence ID 3R_DroMel_CAF1
Location 25,229,878 – 25,229,988
Length 110
Max. P 0.976216
window15268 window15269

overview

Window 8

Location 25,229,878 – 25,229,988
Length 110
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 83.69
Mean single sequence MFE -26.61
Consensus MFE -18.74
Energy contribution -18.97
Covariance contribution 0.23
Combinations/Pair 1.10
Mean z-score -2.74
Structure conservation index 0.70
SVM decision value 1.28
SVM RNA-class probability 0.939596
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25229878 110 + 27905053
UUGACCAAAAGCCACUUAAAGGCACGCAAAGAAAAAGUUACUUAGGUACAAAAACGUCGCGUUUGACAGUUAGCAUGGUCACACUUUCCACCAGUGUGACCAUGCAGUAG---
((((((....(((.......))).(.....).............))).))).(((((((....)))).))).(((((((((((((.......))))))))))))).....--- ( -33.30)
>DroSec_CAF1 88267 105 + 1
UUGCCCAAUAGCCACUUAAGGACACGUAAAGAAAAAGUUCCUUAAGUAAAAAAACA--------GUCAGUUAGCACGGUGACACUUUCCAUCAGUGCGACCAUGCACUAAAAC
........(((..(((((((((.((...........))))))))))).........--------........(((.(((..((((.......))))..))).))).))).... ( -22.10)
>DroSim_CAF1 88390 105 + 1
UUGACCAAUAGCCACUUAAGGACACGCAAAGAAAAAGUUCCUUAAGUAAAAAAACA--------GUCAGUUAGCACGGUGACACUUUCCAUCAGUGCGACCAUGCACUAAAAC
(((((........(((((((((.((...........))))))))))).........--------)))))...(((.(((..((((.......))))..))).)))........ ( -24.43)
>consensus
UUGACCAAUAGCCACUUAAGGACACGCAAAGAAAAAGUUCCUUAAGUAAAAAAACA________GUCAGUUAGCACGGUGACACUUUCCAUCAGUGCGACCAUGCACUAAAAC
.............(((((((((.((...........))))))))))).........................(((.(((..((((.......))))..))).)))........ (-18.74 = -18.97 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 25,229,878 – 25,229,988
Length 110
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 83.69
Mean single sequence MFE -34.50
Consensus MFE -24.49
Energy contribution -24.83
Covariance contribution 0.34
Combinations/Pair 1.12
Mean z-score -3.20
Structure conservation index 0.71
SVM decision value 1.77
SVM RNA-class probability 0.976216
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25229878 110 - 27905053
---CUACUGCAUGGUCACACUGGUGGAAAGUGUGACCAUGCUAACUGUCAAACGCGACGUUUUUGUACCUAAGUAACUUUUUCUUUGCGUGCCUUUAAGUGGCUUUUGGUCAA
---.....(((((((((((((.......)))))))))))))....(((((((.((.((......(((((.(((.........))).).))))......)).)).))))).)). ( -36.70)
>DroSec_CAF1 88267 105 - 1
GUUUUAGUGCAUGGUCGCACUGAUGGAAAGUGUCACCGUGCUAACUGAC--------UGUUUUUUUACUUAAGGAACUUUUUCUUUACGUGUCCUUAAGUGGCUAUUGGGCAA
...((((((((((((.(((((.......))))).)))))))..))))).--------........((((((((((((...........)).))))))))))(((....))).. ( -33.00)
>DroSim_CAF1 88390 105 - 1
GUUUUAGUGCAUGGUCGCACUGAUGGAAAGUGUCACCGUGCUAACUGAC--------UGUUUUUUUACUUAAGGAACUUUUUCUUUGCGUGUCCUUAAGUGGCUAUUGGUCAA
........(((((((.(((((.......))))).)))))))....((((--------((.....(((((((((((((...........)).)))))))))))....)))))). ( -33.80)
>consensus
GUUUUAGUGCAUGGUCGCACUGAUGGAAAGUGUCACCGUGCUAACUGAC________UGUUUUUUUACUUAAGGAACUUUUUCUUUGCGUGUCCUUAAGUGGCUAUUGGUCAA
........(((((((.(((((.......))))).)))))))........................((((((((((((...........)).))))))))))............ (-24.49 = -24.83 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:36:53 2006