Locus 1740

Sequence ID 3R_DroMel_CAF1
Location 5,022,574 – 5,022,669
Length 95
Max. P 0.899454
window2862 window2863

overview

Window 2

Location 5,022,574 – 5,022,669
Length 95
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 82.68
Mean single sequence MFE -20.97
Consensus MFE -12.79
Energy contribution -14.35
Covariance contribution 1.56
Combinations/Pair 1.12
Mean z-score -1.99
Structure conservation index 0.61
SVM decision value -0.03
SVM RNA-class probability 0.517451
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5022574 95 + 27905053
CCCCAACAAAAUCCAAUUGCAUUUAAGU-AAGCCAAUGCUUCAAGUAAAUAG-----GGAGAAUAAUUGAAGCAUUGCAACCGGAAGGAAAAUUGGUUGAG
......(((...((((((..........-..((.((((((((((........-----.........))))))))))))..((....))..))))))))).. ( -23.13)
>DroSec_CAF1 129144 95 + 1
CCCCAACAAAAUCCAAUUGCAUUUAAGU-AAGCCAAUGCUUCAAGUAAAUAG-----GGAGAAUAAUUGAAGCAUUGCAACCGGAAGGAAAAUUAGUUGAG
...((((.........((((......))-))((.((((((((((........-----.........))))))))))))..((....)).......)))).. ( -22.63)
>DroSim_CAF1 133592 95 + 1
CCCCAACAAAAUCCAAUUGCAUUUAAGU-AAGCCAAUGCUUCAAGUAAAUAG-----GGAGAAUAAUUGAAGCAUUGCAACCGGAAGGAAAAUUGGUUGAG
......(((...((((((..........-..((.((((((((((........-----.........))))))))))))..((....))..))))))))).. ( -23.13)
>DroEre_CAF1 130787 95 + 1
CCCCAACAAAAUCCAAUUGCAUUUAAGU-AAGCCAAUGCUUGAAGUAAAUAG-----GGAGAAUAAUUGAAGCAUUGCAACCGGAAGGAAAAUUGGUUGAG
...((((....(((..((((.(((((((-(......))))))))))))....-----)))....................((....)).......)))).. ( -19.20)
>DroYak_CAF1 133045 95 + 1
CCCCAACAAAAUCCAAUUGCAUUUAAGU-AAGCCAAUGCUUCAAGUAAAUAG-----GGGGAAUAAUUGAAGCAUUGCAACCGGAAGGAAAAUUGGUUGAG
......(((...((((((..........-..((.((((((((((........-----.........))))))))))))..((....))..))))))))).. ( -23.13)
>DroAna_CAF1 128591 91 + 1
--ACUAUAAAUUCUAUAUACAUUUCUUUCUAGCAGACUCUCAAAGCGAAUAGAAAAAGGGGAUCAUUUGAGGCU--------UGAACUUAAAUUGGUUGCC
--.......................((((((...(.((.....)))...))))))..((.(((((((((((...--------....)))))).))))).)) ( -14.60)
>consensus
CCCCAACAAAAUCCAAUUGCAUUUAAGU_AAGCCAAUGCUUCAAGUAAAUAG_____GGAGAAUAAUUGAAGCAUUGCAACCGGAAGGAAAAUUGGUUGAG
...((((..........................(((((((((((......................)))))))))))...((....)).......)))).. (-12.79 = -14.35 +   1.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,022,574 – 5,022,669
Length 95
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 82.68
Mean single sequence MFE -23.15
Consensus MFE -17.18
Energy contribution -18.74
Covariance contribution 1.56
Combinations/Pair 1.22
Mean z-score -2.89
Structure conservation index 0.74
SVM decision value 1.01
SVM RNA-class probability 0.899454
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5022574 95 - 27905053
CUCAACCAAUUUUCCUUCCGGUUGCAAUGCUUCAAUUAUUCUCC-----CUAUUUACUUGAAGCAUUGGCUU-ACUUAAAUGCAAUUGGAUUUUGUUGGGG
.....(((((......(((((((((((((((((((.((......-----.....)).))))))))))(....-.)......)))))))))....))))).. ( -27.00)
>DroSec_CAF1 129144 95 - 1
CUCAACUAAUUUUCCUUCCGGUUGCAAUGCUUCAAUUAUUCUCC-----CUAUUUACUUGAAGCAUUGGCUU-ACUUAAAUGCAAUUGGAUUUUGUUGGGG
((((((..........(((((((((((((((((((.((......-----.....)).))))))))))(....-.)......)))))))))....)))))). ( -25.94)
>DroSim_CAF1 133592 95 - 1
CUCAACCAAUUUUCCUUCCGGUUGCAAUGCUUCAAUUAUUCUCC-----CUAUUUACUUGAAGCAUUGGCUU-ACUUAAAUGCAAUUGGAUUUUGUUGGGG
.....(((((......(((((((((((((((((((.((......-----.....)).))))))))))(....-.)......)))))))))....))))).. ( -27.00)
>DroEre_CAF1 130787 95 - 1
CUCAACCAAUUUUCCUUCCGGUUGCAAUGCUUCAAUUAUUCUCC-----CUAUUUACUUCAAGCAUUGGCUU-ACUUAAAUGCAAUUGGAUUUUGUUGGGG
.....(((((......((((((((((((((((.((.((......-----.....)).)).)))))))(....-.)......)))))))))....))))).. ( -20.80)
>DroYak_CAF1 133045 95 - 1
CUCAACCAAUUUUCCUUCCGGUUGCAAUGCUUCAAUUAUUCCCC-----CUAUUUACUUGAAGCAUUGGCUU-ACUUAAAUGCAAUUGGAUUUUGUUGGGG
.....(((((......(((((((((((((((((((.((......-----.....)).))))))))))(....-.)......)))))))))....))))).. ( -27.00)
>DroAna_CAF1 128591 91 - 1
GGCAACCAAUUUAAGUUCA--------AGCCUCAAAUGAUCCCCUUUUUCUAUUCGCUUUGAGAGUCUGCUAGAAAGAAAUGUAUAUAGAAUUUAUAGU--
(....).....(((((((.--------...(((((((((..............))).))))))..(((.......)))..........)))))))....-- ( -11.14)
>consensus
CUCAACCAAUUUUCCUUCCGGUUGCAAUGCUUCAAUUAUUCUCC_____CUAUUUACUUGAAGCAUUGGCUU_ACUUAAAUGCAAUUGGAUUUUGUUGGGG
.....(((((......(((((((((((((((((((.((................)).))))))))))(......)......)))))))))....))))).. (-17.18 = -18.74 +   1.56)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:10 2006