Locus 4548

Sequence ID 3R_DroMel_CAF1
Location 12,050,348 – 12,050,461
Length 113
Max. P 0.971804
window7428 window7429

overview

Window 8

Location 12,050,348 – 12,050,461
Length 113
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 86.53
Mean single sequence MFE -41.61
Consensus MFE -32.83
Energy contribution -33.50
Covariance contribution 0.67
Combinations/Pair 1.10
Mean z-score -3.89
Structure conservation index 0.79
SVM decision value 1.68
SVM RNA-class probability 0.971804
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12050348 113 + 27905053
GGCUCUUCGUUCGGCCUGGCUCUCAUAAAUGACAUAGAGAGAGAGAGAGAGGAAAAGAGGGAGGUGG------AUGACGGUUGGUAACUGUGGGAGAGCGUGGGCCAAACAAAGAGCCA
(((((((.(((.((((((((((((........(((............................))).------.(.(((((.....))))).))))))).)))))).))).))))))). ( -38.29)
>DroSim_CAF1 21709 111 + 1
GGCUCUUCGUUCGGCCUGGCUCUCAUAAAUGAA--CGAGAGAGAGAGAGAGGAAAAGAGGGAGGUGG------AUGACGGUUGGUAACUGUGGGAGAGCCUGGGCCAAACAAAGAGCCA
(((((((.(((.((((((((((((.........--(....)..........................------.(.(((((.....))))).)))))))).))))).))).))))))). ( -43.10)
>DroYak_CAF1 21440 117 + 1
GGCUCUCCGUUCGGCUCGGCUCUCAUGAAAGAG--AGAGAGAGAGCGAGUGGAAGGGAGGGAGGUGGAGGUCGAUGUUGGUUGGUAACUGUGGGAGAACCUGGGCCAAACAAAGAGCCA
((((((((.(((.(((((.(((((.........--.....)))))))))).))).)))....(((..(((((.....((((.....)))).....).))))..))).......))))). ( -43.44)
>consensus
GGCUCUUCGUUCGGCCUGGCUCUCAUAAAUGAA__AGAGAGAGAGAGAGAGGAAAAGAGGGAGGUGG______AUGACGGUUGGUAACUGUGGGAGAGCCUGGGCCAAACAAAGAGCCA
(((((((.(((.((((((((((((.......................................((........)).(((((.....)))))..))))))).))))).))).))))))). (-32.83 = -33.50 +   0.67)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 9

Location 12,050,348 – 12,050,461
Length 113
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 86.53
Mean single sequence MFE -37.00
Consensus MFE -33.16
Energy contribution -33.05
Covariance contribution -0.11
Combinations/Pair 1.09
Mean z-score -5.73
Structure conservation index 0.90
SVM decision value 1.09
SVM RNA-class probability 0.913020
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12050348 113 - 27905053
UGGCUCUUUGUUUGGCCCACGCUCUCCCACAGUUACCAACCGUCAU------CCACCUCCCUCUUUUCCUCUCUCUCUCUCUCUAUGUCAUUUAUGAGAGCCAGGCCGAACGAAGAGCC
.((((((((((((((((...((((((..((.((.....)).))...------................................(((.....)))))))))..)))))))))))))))) ( -35.60)
>DroSim_CAF1 21709 111 - 1
UGGCUCUUUGUUUGGCCCAGGCUCUCCCACAGUUACCAACCGUCAU------CCACCUCCCUCUUUUCCUCUCUCUCUCUCUCG--UUCAUUUAUGAGAGCCAGGCCGAACGAAGAGCC
.((((((((((((((((..(((((((....................------................................--.........))))))).)))))))))))))))) ( -38.65)
>DroYak_CAF1 21440 117 - 1
UGGCUCUUUGUUUGGCCCAGGUUCUCCCACAGUUACCAACCAACAUCGACCUCCACCUCCCUCCCUUCCACUCGCUCUCUCUCU--CUCUUUCAUGAGAGCCGAGCCGAACGGAGAGCC
.(((((((((((((((.(.(((.((.....))..)))....................................((((((.....--.........)))))).).))))))))))))))) ( -36.74)
>consensus
UGGCUCUUUGUUUGGCCCAGGCUCUCCCACAGUUACCAACCGUCAU______CCACCUCCCUCUUUUCCUCUCUCUCUCUCUCU__CUCAUUUAUGAGAGCCAGGCCGAACGAAGAGCC
.(((((((((((((((...(((((((.....................................................................)))))))..))))))))))))))) (-33.16 = -33.05 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:03 2006