Locus 1277

Sequence ID 2L_DroMel_CAF1
Location 3,400,020 – 3,400,116
Length 96
Max. P 0.992294
window2085 window2086

overview

Window 5

Location 3,400,020 – 3,400,116
Length 96
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 80.86
Mean single sequence MFE -23.00
Consensus MFE -15.70
Energy contribution -15.20
Covariance contribution -0.50
Combinations/Pair 1.23
Mean z-score -2.74
Structure conservation index 0.68
SVM decision value 2.32
SVM RNA-class probability 0.992294
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3400020 96 + 22407834
AUUUCAAUCAAUACAUUUGCUUGCAAUUAAAGGUGGUUCUUUUGUUGCAAGUAUUGGUUCGCCUUCGAUAAUAUACUUGCAA---------CACAAAUGUAAUUU--------
...........((((((((.........(((((....)))))((((((((((((....(((....)))....))))))))))---------))))))))))....-------- ( -26.20)
>DroSec_CAF1 22454 96 + 1
AUUUCAAUCAAUACAUUUACUUGCAAUUAAAGCUGGUUCUUUUGUUGCAAGUAUUGGCUAGUCUUCGAUAAUAUACUUGCCA---------CACAAAUGUAACUU--------
...........((((((((((((((((.((((......)))).)))))))))..((((.(((.(........).))).))))---------...)))))))....-------- ( -23.50)
>DroSim_CAF1 22672 96 + 1
AUUUCAAUCAAUACAUUUACUUGCAAUUAAAGCUGGUUCUUUUGUUGCAAGUAUUGGCUUGCCUUCGAUAAUAUACUUGCAA---------CACAAAUGUAACUU--------
...........((((((((((.((.......)).))).....((((((((((((.((....)).........))))))))))---------)).)))))))....-------- ( -22.90)
>DroEre_CAF1 22509 113 + 1
AUUUCAAUCAAUACGUUUGUUCGCCAUUAAGGCUGGUUCUUUGGUUGCAAGUAUGGGCUUUCCUUCGAUAAAAUACCGGCAUACUACUACUUCUAAAUGUAACUUUGAUAUAU
......(((((((((((((............((((((...((((..(.((((....)))).)..))))......)))))).............))))))))...))))).... ( -19.41)
>consensus
AUUUCAAUCAAUACAUUUACUUGCAAUUAAAGCUGGUUCUUUUGUUGCAAGUAUUGGCUUGCCUUCGAUAAUAUACUUGCAA_________CACAAAUGUAACUU________
...........((((((((((((((((.((((......)))).)))))))))...((....))...............................)))))))............ (-15.70 = -15.20 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,400,020 – 3,400,116
Length 96
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 80.86
Mean single sequence MFE -22.40
Consensus MFE -11.46
Energy contribution -12.14
Covariance contribution 0.69
Combinations/Pair 1.11
Mean z-score -2.52
Structure conservation index 0.51
SVM decision value 0.32
SVM RNA-class probability 0.686452
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3400020 96 - 22407834
--------AAAUUACAUUUGUG---------UUGCAAGUAUAUUAUCGAAGGCGAACCAAUACUUGCAACAAAAGAACCACCUUUAAUUGCAAGCAAAUGUAUUGAUUGAAAU
--------....((((((((((---------((((((((((....(((....)))....))))))))))).((((......))))........)))))))))........... ( -26.60)
>DroSec_CAF1 22454 96 - 1
--------AAGUUACAUUUGUG---------UGGCAAGUAUAUUAUCGAAGACUAGCCAAUACUUGCAACAAAAGAACCAGCUUUAAUUGCAAGUAAAUGUAUUGAUUGAAAU
--------....((((((....---------((((.(((...((....)).))).)))).(((((((((..((((......))))..)))))))))))))))........... ( -22.60)
>DroSim_CAF1 22672 96 - 1
--------AAGUUACAUUUGUG---------UUGCAAGUAUAUUAUCGAAGGCAAGCCAAUACUUGCAACAAAAGAACCAGCUUUAAUUGCAAGUAAAUGUAUUGAUUGAAAU
--------....((((((((((---------((((((((((.((....))((....)).)))))))))))).........((.......))...))))))))........... ( -22.20)
>DroEre_CAF1 22509 113 - 1
AUAUAUCAAAGUUACAUUUAGAAGUAGUAGUAUGCCGGUAUUUUAUCGAAGGAAAGCCCAUACUUGCAACCAAAGAACCAGCCUUAAUGGCGAACAAACGUAUUGAUUGAAAU
.....((((...(((........((.((((((((..(((.((((......)))).)))))))).))).))..........(((.....)))........)))....))))... ( -18.20)
>consensus
________AAGUUACAUUUGUG_________UUGCAAGUAUAUUAUCGAAGGCAAGCCAAUACUUGCAACAAAAGAACCAGCUUUAAUUGCAAGCAAAUGUAUUGAUUGAAAU
............((((((((.............((((((((..................)))))))).............((.......))...))))))))........... (-11.46 = -12.14 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:24 2006