Locus 3118

Sequence ID 3L_DroMel_CAF1
Location 9,060,242 – 9,060,450
Length 208
Max. P 0.976157
window4860 window4861

overview

Window 0

Location 9,060,242 – 9,060,336
Length 94
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 69.24
Mean single sequence MFE -21.88
Consensus MFE -11.70
Energy contribution -11.96
Covariance contribution 0.25
Combinations/Pair 1.40
Mean z-score -2.07
Structure conservation index 0.54
SVM decision value 1.76
SVM RNA-class probability 0.976157
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9060242 94 + 23771897
-----AUCAGGCACCUUUUCAAAAUAAUGGAGGUUACCAACCAUCCUACCAAGGCAAUGGAGGUUACACACCAACAUACCAAAACCCUUUUGAGGGUUA---
-----....((.((((((..........))))))..))..(((((((....)))..)))).(((.....)))..........((((((....)))))).--- ( -19.80)
>DroSec_CAF1 5667 99 + 1
AGGUUACCAGGCACCUUCUCAAAAUAAUGGAGGUUACCAACCAACCUACCAAGGUAAUGGAGGUUACACACCAACCUAUCAAAACACUUUUGAUGGUUA---
.(((.(((.((.((((((..........))))))..))..(((((((....))))..))).))).....)))((((.((((((.....)))))))))).--- ( -26.30)
>DroEre_CAF1 5685 96 + 1
AGGCUACCA---GCCACCCCAAGCUAAUGGAGGCUACCAGCCACCCCACCAACCUAAUGGAGGCUACCAACCACCCUACCAAG---CUAAUGGAGGCUACAG
.(((.....---))).(((((((((..(((.(((.....)))...((.(((......))).))...............)))))---))..))).))...... ( -24.80)
>DroYak_CAF1 5605 86 + 1
--------AGCCGACUUCUCAAAACAAUGGAGGUUACCAGACACCUUACCAAACUAAUGGAGGUUACCAAGAACCCUACCAAG---CUAAUGGAGGU-----
--------((((((((((.((......)))))))).............(((......))).)))).........(((.(((..---....)))))).----- ( -16.60)
>consensus
_____ACCAGGCACCUUCUCAAAAUAAUGGAGGUUACCAACCACCCUACCAAGCUAAUGGAGGUUACAAACCAACCUACCAAA___CUAAUGAAGGUUA___
............((((((.........((((((((.........(((.(((......)))))).........))))).)))..........))))))..... (-11.70 = -11.96 +   0.25)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 1

Location 9,060,336 – 9,060,450
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 81.43
Mean single sequence MFE -19.60
Consensus MFE -12.35
Energy contribution -12.97
Covariance contribution 0.62
Combinations/Pair 1.06
Mean z-score -1.84
Structure conservation index 0.63
SVM decision value 0.26
SVM RNA-class probability 0.655702
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9060336 114 + 23771897
CCACCAACCCAAUCAAUCAUCGUAUCAAACAAAUGGUGGAUACCAGCCACCCUUACCACCUCAUGGAGGUUACCAACCACCUUCUCAAACUUAUGGAGGUUUCCAACAACCUAA
...(((............................(((((.......))))).............((((((........)))))).........)))(((((......))))).. ( -20.00)
>DroSec_CAF1 5766 114 + 1
CCACCAACCCAAUCAAUCUUCGCUUCAAACAAAUGGAGGAUAUCAGCCACCCUUACCACCUCAUGGAGGUUACCAACCACCUUCUCAAACUUAUGGAGGUUUCCAACAACCUAA
...(((.............((.(((((......)))))))........................((((((........)))))).........)))(((((......))))).. ( -17.00)
>DroEre_CAF1 5781 114 + 1
CCACCAACCCAAUCAAUCAGCAGUUCAAUCAAAUGGAGGAUACCAGCCACCUUUACCAGCCUAUGGAGGUUACCAACCACCUUCUCAACCGUUUGGAGGCUUCCAGCAGCCUAA
............................((((((((.((.......))................((((((........))))))....))))))))(((((......))))).. ( -22.00)
>DroYak_CAF1 5691 101 + 1
-CACCAGCCAUAU------------CAAGCAAACGGAGGAUACCAGCCACCCUUACCAGCCUAUGGAGGUUACCAACAACCUGCUCAAUCAUAUGGAGCUGUCCACCAACCCAA
-.....((.....------------...))....((.(((((.............(((.....)))(((((......)))))((((.........))))))))).))....... ( -19.40)
>consensus
CCACCAACCCAAUCAAUCAUCG_UUCAAACAAAUGGAGGAUACCAGCCACCCUUACCACCCCAUGGAGGUUACCAACCACCUUCUCAAACUUAUGGAGGUUUCCAACAACCUAA
...(((............................((.((.......)).)).............((((((........)))))).........)))(((((......))))).. (-12.35 = -12.97 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:58 2006