Locus 4844

Sequence ID 3L_DroMel_CAF1
Location 13,578,949 – 13,579,052
Length 103
Max. P 0.930535
window7640 window7641

overview

Window 0

Location 13,578,949 – 13,579,052
Length 103
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 91.12
Mean single sequence MFE -18.40
Consensus MFE -13.31
Energy contribution -13.43
Covariance contribution 0.12
Combinations/Pair 1.05
Mean z-score -1.77
Structure conservation index 0.72
SVM decision value -0.02
SVM RNA-class probability 0.522047
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13578949 103 + 23771897
UUGCUUAUCUUCCCAACCCAGAUCCUGCAUCCUUAAUCCACCAUCCACUUUCCAGU-----UCCCAGCUGCAUCUUUCCGGGUUUU------CCCCGUCCUCCAGGGCAAAGUA
.(((..((((.........))))...))).................(((((.((((-----.....)))).........(((....------.)))((((....))))))))). ( -16.10)
>DroSec_CAF1 60366 103 + 1
UUGCUUAUCUUCCCAACCCAGAUCCUGCAUCCUUAAUCCACCAUCCACUUUCCAGU-----UCCCAGCUGCAUCUUUCCGGGCUUU------CCCCGCCCUCCAGGGCAAAGUA
.(((..((((.........))))...))).................(((((.((((-----.....)))).........(((....------.)))((((....))))))))). ( -18.50)
>DroEre_CAF1 61889 109 + 1
UUGCUUAUCUUCCCAACCCAGAUCCUGCAUCCUUAAUCCACCAACCACUUUCCAGUGGAAAACCCAGCUGCAUCUUUCCGGGUUUUU-----GCCCGUCCUCCAGGGUAAAGUA
.(((((........(((((.((...((((.......(((((.............))))).........))))....)).)))))..(-----((((........)))))))))) ( -23.91)
>DroYak_CAF1 63328 109 + 1
UUGCUUAUCUUCCCAGCCCAGAUCCUGCAUCCUUAAUCCACCAACCACUUUCCAGU-----ACCCAGCUGCAUCUUUCCGGGUUUUUUUUUCCCCCGUCCUCCAGGGUAAAGUA
.(((..((((.........))))...)))..(((.((((.............((((-----.....))))........((((...........)))).......)))).))).. ( -15.10)
>consensus
UUGCUUAUCUUCCCAACCCAGAUCCUGCAUCCUUAAUCCACCAACCACUUUCCAGU_____ACCCAGCUGCAUCUUUCCGGGUUUU______CCCCGUCCUCCAGGGCAAAGUA
.(((((........(((((.((...((((.......................................))))....)).))))).........(((........)))..))))) (-13.31 = -13.43 +   0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,578,949 – 13,579,052
Length 103
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 91.12
Mean single sequence MFE -31.70
Consensus MFE -24.67
Energy contribution -25.05
Covariance contribution 0.38
Combinations/Pair 1.04
Mean z-score -2.78
Structure conservation index 0.78
SVM decision value 1.21
SVM RNA-class probability 0.930535
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13578949 103 - 23771897
UACUUUGCCCUGGAGGACGGGG------AAAACCCGGAAAGAUGCAGCUGGGA-----ACUGGAAAGUGGAUGGUGGAUUAAGGAUGCAGGAUCUGGGUUGGGAAGAUAAGCAA
..((((.(((((.....)))))------..((((((((....((((((((...-----(((....)))...))))..........))))...))))))))..))))........ ( -29.60)
>DroSec_CAF1 60366 103 - 1
UACUUUGCCCUGGAGGGCGGGG------AAAGCCCGGAAAGAUGCAGCUGGGA-----ACUGGAAAGUGGAUGGUGGAUUAAGGAUGCAGGAUCUGGGUUGGGAAGAUAAGCAA
..((((((((....))))))))------..((((((((....((((((((...-----(((....)))...))))..........))))...)))))))).............. ( -31.70)
>DroEre_CAF1 61889 109 - 1
UACUUUACCCUGGAGGACGGGC-----AAAAACCCGGAAAGAUGCAGCUGGGUUUUCCACUGGAAAGUGGUUGGUGGAUUAAGGAUGCAGGAUCUGGGUUGGGAAGAUAAGCAA
..((((..((((.....)))).-----...((((((((....((((.((..((((.(((((....))))).....))))..))..))))...))))))))..))))........ ( -33.60)
>DroYak_CAF1 63328 109 - 1
UACUUUACCCUGGAGGACGGGGGAAAAAAAAACCCGGAAAGAUGCAGCUGGGU-----ACUGGAAAGUGGUUGGUGGAUUAAGGAUGCAGGAUCUGGGCUGGGAAGAUAAGCAA
.......(((((.....)))))..........(((((..((((.(.((..(.(-----(((....)))).)..))(.(((...))).).).))))...)))))........... ( -31.90)
>consensus
UACUUUACCCUGGAGGACGGGG______AAAACCCGGAAAGAUGCAGCUGGGA_____ACUGGAAAGUGGAUGGUGGAUUAAGGAUGCAGGAUCUGGGUUGGGAAGAUAAGCAA
..((((.(((((.....)))))........((((((((....((((.((.........(((....))).............))..))))...))))))))..))))........ (-24.67 = -25.05 +   0.38)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:59 2006