Locus 4102

Sequence ID 3L_DroMel_CAF1
Location 11,977,033 – 11,977,149
Length 116
Max. P 0.656387
window6381 window6382

overview

Window 1

Location 11,977,033 – 11,977,149
Length 116
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 87.50
Mean single sequence MFE -37.42
Consensus MFE -23.09
Energy contribution -25.90
Covariance contribution 2.81
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.62
SVM decision value 0.01
SVM RNA-class probability 0.538372
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11977033 116 + 23771897
UUUGACUCGCUAUAGCAGCCGCCUAGAGGGCGCCAGGGAAACUAUGAAAGUUGGUGAGCGAUGGCAACACUAGACUUUCAGCUGUUCGCUGACAGUCAAACAAAUAUAUUUAUUUC
((((..(((((.((.((((((((.....))))...((....))......)))).)))))))((....))...((((.(((((.....))))).))))...))))............ ( -35.00)
>DroSim_CAF1 7307 116 + 1
AUUGACUUGCAAUAGCAGCCGCCUAGAGGGCGCCAGGGAAACUGUGAAAAUUCGUGAGCGGUGACAACUCUAGACUUUCAGCUGUUCGCUGGCAGUCAAACAAAUAUAUUUAUUUC
.(((((((((....)))...(((.....)))(((((.(((...((..(((.((..(((.(....)..)))..)).)))..))..))).)))))))))))................. ( -33.10)
>DroEre_CAF1 4944 115 + 1
CUUGACUUGCUACAACUGCCGCCUAGAGGGCGCCAGUGA-ACUGUGAAAGUUCGUGAGCGGUGGCAGCUCUGUACUUUCAGCUGUUUGCUGGCAAGCAAGCAAAUUUAUUUAUUUC
.(((.((((((.........(((.....)))(((((..(-((.((((((((.((.((((.......)))))).))))))).).)))..))))).)))))))))............. ( -45.70)
>DroYak_CAF1 4720 114 + 1
CUU-ACUUGCUACAACCGCCGCC-AGAGGGCGCCAGUGAAACUGUGAAAGUUCGUGAGCGGUGGCAACUCUUGACUUUCAGCUGUUCGCUGGCAAGCAAACAAAUUUAUUUAUUUC
...-..(((((.........(((-....)))(((((((((....((((((((...(((..(...)..)))..))))))))....))))))))).)))))................. ( -35.90)
>consensus
CUUGACUUGCUACAACAGCCGCCUAGAGGGCGCCAGGGAAACUGUGAAAGUUCGUGAGCGGUGGCAACUCUAGACUUUCAGCUGUUCGCUGGCAAGCAAACAAAUAUAUUUAUUUC
.((((((..........(((........)))(((((((((....((((((((...(((.........)))..))))))))....)))))))))))))))................. (-23.09 = -25.90 +   2.81)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,977,033 – 11,977,149
Length 116
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 87.50
Mean single sequence MFE -33.52
Consensus MFE -25.34
Energy contribution -24.90
Covariance contribution -0.44
Combinations/Pair 1.26
Mean z-score -1.61
Structure conservation index 0.76
SVM decision value 0.26
SVM RNA-class probability 0.656387
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11977033 116 - 23771897
GAAAUAAAUAUAUUUGUUUGACUGUCAGCGAACAGCUGAAAGUCUAGUGUUGCCAUCGCUCACCAACUUUCAUAGUUUCCCUGGCGCCCUCUAGGCGGCUGCUAUAGCGAGUCAAA
...........(((((((.((((.(((((.....))))).))))((((...(((...(((....((((.....)))).....)))(((.....)))))).)))).))))))).... ( -30.80)
>DroSim_CAF1 7307 116 - 1
GAAAUAAAUAUAUUUGUUUGACUGCCAGCGAACAGCUGAAAGUCUAGAGUUGUCACCGCUCACGAAUUUUCACAGUUUCCCUGGCGCCCUCUAGGCGGCUGCUAUUGCAAGUCAAU
.................((((((((((((.....)))....((((((((.......((((...(((..........)))...))))..)))))))))))(((....))))))))). ( -30.20)
>DroEre_CAF1 4944 115 - 1
GAAAUAAAUAAAUUUGCUUGCUUGCCAGCAAACAGCUGAAAGUACAGAGCUGCCACCGCUCACGAACUUUCACAGU-UCACUGGCGCCCUCUAGGCGGCAGUUGUAGCAAGUCAAG
................(((((((((((((.....))))....((((..((((((...(((...(((((.....)))-))...)))(((.....)))))))))))))))))).)))) ( -38.80)
>DroYak_CAF1 4720 114 - 1
GAAAUAAAUAAAUUUGUUUGCUUGCCAGCGAACAGCUGAAAGUCAAGAGUUGCCACCGCUCACGAACUUUCACAGUUUCACUGGCGCCCUCU-GGCGGCGGUUGUAGCAAGU-AAG
.................((((((((((((.....))))............(((.(((((.............(((.....))).((((....-))))))))).)))))))))-)). ( -34.30)
>consensus
GAAAUAAAUAAAUUUGUUUGACUGCCAGCGAACAGCUGAAAGUCUAGAGUUGCCACCGCUCACGAACUUUCACAGUUUCACUGGCGCCCUCUAGGCGGCUGCUAUAGCAAGUCAAG
...........(((((((...(((((.((.......(((((((...((((.......))))....)))))))(((.....)))))(((.....))))))))....))))))).... (-25.34 = -24.90 +  -0.44)

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 11:14:32 2006