Locus 5146

Sequence ID 2R_DroMel_CAF1
Location 16,742,749 – 16,742,880
Length 131
Max. P 0.677418
window8230 window8231

overview

Window 0

Location 16,742,749 – 16,742,853
Length 104
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 81.40
Mean single sequence MFE -26.01
Consensus MFE -16.78
Energy contribution -17.54
Covariance contribution 0.76
Combinations/Pair 1.08
Mean z-score -1.82
Structure conservation index 0.65
SVM decision value 0.30
SVM RNA-class probability 0.677418
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16742749 104 - 20766785
AUCC-----------AUAAUUAUGAGCCAGAGACAUGCAGCGCCUCUCCACUCGCAUCCAUGCAUGCUUAAUGCUCAUAUGCGAAUUUAGUCAGUCUUCAGCCUUUCAUUGGGAU
((((-----------......((((((..(((((..((...))........((((((....((((.....))))....)))))).........)))))..))...))))..)))) ( -22.60)
>DroSec_CAF1 50539 98 - 1
AUCCAUACUAUAAGCAUAAUUAUGAGGCAGGGACAUGCAGCGCCUCUCCACUCGCAUCCAUGCAUGCUUAAUGCUCAUAUGC-----------------AGUCUUUCAUUGGGAU
((((......(((((((......(((((..(......)...))))).......(((....)))))))))).(((......))-----------------)...........)))) ( -22.90)
>DroSim_CAF1 53134 98 - 1
AUCCUUACUAUACGCAUAAUUAUGAGCCAGGGACAUGCAGCGCCUCUCCACUCGCAUCCAUGCAUGCUUAAUGCUCAUAUGC-----------------AGUCUUUCAUUGGGAU
(((((......(((((((....(((((..(((.(((((((((..........))).....)))))))))...))))))))))-----------------.))........))))) ( -23.24)
>DroEre_CAF1 52091 111 - 1
AUCCAUUCUAUUAGCAUAAUAAUGAGCCAGGGACAUGCAGUGCCCCUCCACUCGCAUCCAUGCAUGCCUAAUGCUCAUAUGCGAAUUUAG----UCCUCAGUCUUUCAUUGGGAA
.............(((((....(((((..(((.((((((((((..........))))...)))))))))...))))))))))........----(((.((((.....))))))). ( -29.40)
>DroYak_CAF1 57694 111 - 1
AUCCAUUCUAUCAGCAUAAUAAUGAGCCAGCGACAUGCAGUGCCUCUCCACUGGCAUCCAUGCAUGCCAAAUGCUCAUAUGCGAAUUUAG----UCCUCAGUCUUUCAUUGGGAC
.............(((((....(((((....(.(((((((((((........)))))...)))))).)....)))))))))).......(----(((.((((.....)))))))) ( -31.90)
>consensus
AUCCAUACUAUAAGCAUAAUUAUGAGCCAGGGACAUGCAGCGCCUCUCCACUCGCAUCCAUGCAUGCUUAAUGCUCAUAUGCGAAUUUAG____UC_UCAGUCUUUCAUUGGGAU
.(((.........(((((....(((((..(((.((((((..((..........)).....)))))))))...))))))))))..................(.....)....))). (-16.78 = -17.54 +   0.76)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,742,785 – 16,742,880
Length 95
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 88.49
Mean single sequence MFE -22.85
Consensus MFE -16.84
Energy contribution -17.20
Covariance contribution 0.36
Combinations/Pair 1.11
Mean z-score -1.70
Structure conservation index 0.74
SVM decision value 0.16
SVM RNA-class probability 0.611465
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16742785 95 - 20766785
UAUUCGCAUAGCGUUUUGGCAUUAUUAAUCC-----------AUAAUUAUGAGCCAGAGACAUGCAGCGCCUCUCCACUCGCAUCCAUGCAUGCUUAAUGCUCAUA
..........((......))...........-----------.....(((((((..(((.(((((((((..........))).....)))))))))...))))))) ( -19.70)
>DroSec_CAF1 50558 106 - 1
UAUUCGCAUAGCGUUUUGGCAUUAUUAAUCCAUACUAUAAGCAUAAUUAUGAGGCAGGGACAUGCAGCGCCUCUCCACUCGCAUCCAUGCAUGCUUAAUGCUCAUA
.....((((.((......)).................(((((((......(((((..(......)...))))).......(((....))))))))))))))..... ( -22.30)
>DroSim_CAF1 53153 106 - 1
UAUUCCCACAGCGUUUUGGCAUUAUUAAUCCUUACUAUACGCAUAAUUAUGAGCCAGGGACAUGCAGCGCCUCUCCACUCGCAUCCAUGCAUGCUUAAUGCUCAUA
..........((((..(((...............))).)))).....(((((((..(((.(((((((((..........))).....)))))))))...))))))) ( -21.86)
>DroEre_CAF1 52123 106 - 1
UAUUCGCAUAGCGUUUCGGCAUUAUUAAUCCAUUCUAUUAGCAUAAUAAUGAGCCAGGGACAUGCAGUGCCCCUCCACUCGCAUCCAUGCAUGCCUAAUGCUCAUA
.........((((((..(((((.............(((((......))))).((...(((..(((((((......)))).))))))..))))))).)))))).... ( -23.60)
>DroYak_CAF1 57726 106 - 1
UAUUCUCAAAGCAUUUUGGCAUUAUUAAUCCAUUCUAUCAGCAUAAUAAUGAGCCAGCGACAUGCAGUGCCUCUCCACUGGCAUCCAUGCAUGCCAAAUGCUCAUA
.........(((((((((((.((((((...................))))))))))..(.(((((((((((........)))))...)))))).)))))))).... ( -26.81)
>consensus
UAUUCGCAUAGCGUUUUGGCAUUAUUAAUCCAUACUAUAAGCAUAAUUAUGAGCCAGGGACAUGCAGCGCCUCUCCACUCGCAUCCAUGCAUGCUUAAUGCUCAUA
..........((......))............................((((((..(((.((((((..((..........)).....)))))))))...)))))). (-16.84 = -17.20 +   0.36)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:44 2006