Locus 6629

Sequence ID 2R_DroMel_CAF1
Location 20,722,350 – 20,722,502
Length 152
Max. P 0.980260
window10556 window10557

overview

Window 6

Location 20,722,350 – 20,722,462
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.40
Mean single sequence MFE -17.82
Consensus MFE -11.56
Energy contribution -11.04
Covariance contribution -0.52
Combinations/Pair 1.22
Mean z-score -1.91
Structure conservation index 0.65
SVM decision value 0.16
SVM RNA-class probability 0.613264
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20722350 112 + 20766785
U--AAGCAAUACGCCAUUUCAUAGGUAAUAUUGAUCAAACUCCGCCUAUU--UUUUACUCAUAACAGUAUACACCCAAAUACAU----ACAUACACACAUGUGUGUAUUUCAGAAAUAUA
.--..((.....)).(((((((((((.................)))))).--...((((......)))).......((((((((----((((......))))))))))))..)))))... ( -18.13)
>DroSec_CAF1 155696 112 + 1
U--AGGCAGUACGCCAUUUCAUAGGUAAUAUUGAUCAAACUCCGCCUUUU--UCUUACUCAUAUCAGUAUACACACAAAUACAU----ACAUACACACAUGUGUGUAUUUCAGAAAUAUA
.--.(((.....)))(((((....(((.(((((((...............--..........))))))))))....((((((((----((((......))))))))))))..)))))... ( -22.61)
>DroSim_CAF1 160774 116 + 1
U--AGGCAAUACGCCAUUUCAUAGGUAAUAUUGAUCAAACUCCGCCUUUU--UCUUACUCAUAUCAGUAUACACACAAAUACAUAUGUACAUACACACAUGUGUGUAUUUCAGAAAUAUA
.--.(((.....)))(((((....(((.(((((((...............--..........))))))))))......((((((((((........))))))))))......)))))... ( -21.21)
>DroEre_CAF1 196825 109 + 1
UAAUAGCAGUACGCCAUUUCAUAGGUAAUAUCGAUCAAACUCCGCCUUUUUAUUUGACUCAUA---CAGUGCAUACAAAUACAU----UC----AUACAUGUGUGUAUUUCAGAAAUAUA
........(((((((........)))......(((((((.............))))).))...---..))))....((((((((----.(----(....)).)))))))).......... ( -13.92)
>DroYak_CAF1 162011 112 + 1
UCAAAGCAGUACACCAUUUCAUAGGUAAUAUCGAUCAAACUCCGCCUUCCUUUUUUACUCAUAUCACAGUACGCACAAAUACAA----AC----AUACAUGUGUGUAUUUUAGAAAUAUA
...............(((((..((((.................))))....................((((((((((..((...----..----.))..))))))))))...)))))... ( -13.23)
>consensus
U__AAGCAGUACGCCAUUUCAUAGGUAAUAUUGAUCAAACUCCGCCUUUU__UUUUACUCAUAUCAGUAUACACACAAAUACAU____ACAUACACACAUGUGUGUAUUUCAGAAAUAUA
...............(((((..((((.................)))).....................(((((((((......................)))))))))....)))))... (-11.56 = -11.04 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,722,388 – 20,722,502
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.91
Mean single sequence MFE -21.24
Consensus MFE -15.07
Energy contribution -15.51
Covariance contribution 0.44
Combinations/Pair 1.20
Mean z-score -2.94
Structure conservation index 0.71
SVM decision value 1.86
SVM RNA-class probability 0.980260
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20722388 114 + 20766785
UCCGCCUAUU--UUUUACUCAUAACAGUAUACACCCAAAUACAU----ACAUACACACAUGUGUGUAUUUCAGAAAUAUAAAUAGAUUUCCCAACGCUAAAUAAUGAGUUAAAGGGUAAA
...((((.((--(...((((((..............((((((((----((((......))))))))))))..(((((........))))).............)))))).)))))))... ( -22.50)
>DroSec_CAF1 155734 114 + 1
UCCGCCUUUU--UCUUACUCAUAUCAGUAUACACACAAAUACAU----ACAUACACACAUGUGUGUAUUUCAGAAAUAUAAAUAGAUUUCCCAACGCUAAAUAAAGAGUUAAAGGGUAAA
...(((((((--....((((................((((((((----((((......))))))))))))..(((((........)))))...............)))).)))))))... ( -23.90)
>DroSim_CAF1 160812 118 + 1
UCCGCCUUUU--UCUUACUCAUAUCAGUAUACACACAAAUACAUAUGUACAUACACACAUGUGUGUAUUUCAGAAAUAUAAAUAGAUUUCCCAACGCUAAAUAAAGAGUUAAAGGGUAAA
...(((((((--....((((..................((((((((((........))))))))))......(((((........)))))...............)))).)))))))... ( -22.50)
>DroEre_CAF1 196865 109 + 1
UCCGCCUUUUUAUUUGACUCAUA---CAGUGCAUACAAAUACAU----UC----AUACAUGUGUGUAUUUCAGAAAUAUAAAUAAAUUUCCCAGCGCUAAAUAAAGAGUUAAAGAGCAAA
...((.......((((((((...---.(((((....((((((((----.(----(....)).))))))))..(((((........)))))...))))).......))))))))..))... ( -20.30)
>DroYak_CAF1 162051 112 + 1
UCCGCCUUCCUUUUUUACUCAUAUCACAGUACGCACAAAUACAA----AC----AUACAUGUGUGUAUUUUAGAAAUAUAAAUCAAUUCCCCAACGCUAAAUAAAGAGUUAAAGAGCAAA
.........((((((.((((.......((((((((((..((...----..----.))..)))))))))).((....))...........................)))).)))))).... ( -17.00)
>consensus
UCCGCCUUUU__UUUUACUCAUAUCAGUAUACACACAAAUACAU____ACAUACACACAUGUGUGUAUUUCAGAAAUAUAAAUAGAUUUCCCAACGCUAAAUAAAGAGUUAAAGGGUAAA
...(((((((......((((........(((((((((......................)))))))))....(((((........)))))...............)))).)))))))... (-15.07 = -15.51 +   0.44)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:38 2006