Locus 2549

Sequence ID X_DroMel_CAF1
Location 6,830,258 – 6,830,387
Length 129
Max. P 0.725557
window4160 window4161

overview

Window 0

Location 6,830,258 – 6,830,366
Length 108
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 86.01
Mean single sequence MFE -27.25
Consensus MFE -18.48
Energy contribution -18.48
Covariance contribution -0.00
Combinations/Pair 1.04
Mean z-score -1.67
Structure conservation index 0.68
SVM decision value 0.16
SVM RNA-class probability 0.611631
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6830258 108 - 22224390
CAAUUGGCCAGCACAAAA-AAAGGCCAAGACAAGC-----CAAGCCCACGACUUGGUAAUUGAAAGCCAAGCGGGU-UUCUCGUUUUGGACUGAUAUAUGGCUACACCCGUAACU
....((((((........-..((.(((((((.((.-----.((((((..(.((((((........)))))))))))-)))).))))))).))......))))))........... ( -30.89)
>DroSec_CAF1 10484 113 - 1
CAAUUGGCCAGCACAAAA-AAAGUCCAAGACAAGCCAAGCCAAGCCCACGACUUGGUAAUUGAAAGCCAAGCGGGU-UUCUCAUUUUGGACUGAUAUACGGCUACACCCGUAACU
...(((.......)))..-..(((((((((...((((((.(........).))))))....((((.((....)).)-)))...)))))))))....(((((......)))))... ( -28.80)
>DroSim_CAF1 10505 114 - 1
CAAUUGGCCAGCACAAAAAAAAGUCCAAGACAAGCCAAGCCAAGCCCACGACUUGGUAAUUGAAAGCCAAGCGGGU-UUCUCAUUUUGGACUGAUAUACGGCUACACCCGUAACU
...(((.......))).....(((((((((...((((((.(........).))))))....((((.((....)).)-)))...)))))))))....(((((......)))))... ( -28.80)
>DroYak_CAF1 10753 91 - 1
CAAUUGGCCAGCACAAAA------------------------AGCCCAAGACUUGGUAAUUGAAAGCCAAGCGGGUUUUCUCAUUUUGGACUGAUAUAUUGCUACACCCGUAACU
..((..(((((.....((------------------------(((((..(.((((((........))))))))))))))......)))).)..))...((((.......)))).. ( -20.50)
>consensus
CAAUUGGCCAGCACAAAA_AAAGUCCAAGACAAGC_____CAAGCCCACGACUUGGUAAUUGAAAGCCAAGCGGGU_UUCUCAUUUUGGACUGAUAUACGGCUACACCCGUAACU
........(((..(((((...............................(.((((((........)))))))(((....))).)))))..)))...(((((......)))))... (-18.48 = -18.48 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,830,293 – 6,830,387
Length 94
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 84.03
Mean single sequence MFE -20.45
Consensus MFE -13.73
Energy contribution -13.72
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.67
SVM decision value 0.41
SVM RNA-class probability 0.725557
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6830293 94 - 22224390
AAGUAUACCAGUACCAUCAACCAAUUGGCCAGCACAAAA-AAAGGCCAAGACAAGC-----CAAGCCCACGACUUGGUAAUUGAAAGCCAAGCGGGU-UUC
..((((....))))..........((((((.........-...)))))).......-----.((((((..(.((((((........)))))))))))-)). ( -22.30)
>DroSec_CAF1 10519 99 - 1
AAGAAUACCAGUACCAUCAACCAAUUGGCCAGCACAAAA-AAAGUCCAAGACAAGCCAAGCCAAGCCCACGACUUGGUAAUUGAAAGCCAAGCGGGU-UUC
..................((((..(((((...((.....-...(((...)))..((((((.(........).))))))...))...)))))...)))-).. ( -19.70)
>DroSim_CAF1 10540 100 - 1
AAGAAUACCAGUACCAUCAACCAAUUGGCCAGCACAAAAAAAAGUCCAAGACAAGCCAAGCCAAGCCCACGACUUGGUAAUUGAAAGCCAAGCGGGU-UUC
..................((((..(((((...((.........(((...)))..((((((.(........).))))))...))...)))))...)))-).. ( -19.70)
>DroYak_CAF1 10788 77 - 1
AAGUAUACCAGUACCGCCAACCAAUUGGCCAGCACAAAA------------------------AGCCCAAGACUUGGUAAUUGAAAGCCAAGCGGGUUUUC
..((((....)))).(((((....)))))........((------------------------(((((..(.((((((........)))))))))))))). ( -20.10)
>consensus
AAGAAUACCAGUACCAUCAACCAAUUGGCCAGCACAAAA_AAAGUCCAAGACAAGC_____CAAGCCCACGACUUGGUAAUUGAAAGCCAAGCGGGU_UUC
.......(((((...........)))))....................................((((..(.((((((........))))))))))).... (-13.73 = -13.72 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:25 2006