Locus 4185

Sequence ID 3R_DroMel_CAF1
Location 11,341,788 – 11,341,883
Length 95
Max. P 0.632714
window6731 window6732

overview

Window 1

Location 11,341,788 – 11,341,883
Length 95
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 84.27
Mean single sequence MFE -18.00
Consensus MFE -14.65
Energy contribution -14.90
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.81
SVM decision value 0.20
SVM RNA-class probability 0.632714
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11341788 95 + 27905053
UUCUCCGCCAGCAUCCUUCCGCCAUCUGCCCCCGCAACUCCCCCUUCAGC-----UCAACUCCUUUGCCAUUGGCAGUCGCACUUUGGUUUACAUGGCUC
......((((....((....((...(((((...((((.............-----.........))))....)))))..)).....))......)))).. ( -18.25)
>DroSim_CAF1 79179 95 + 1
UUCUCCGCCAGCAUCCUUCCGCCAUCUGCCCCUGCAACGCCCCCCUCAGC-----ACAACUCCUUUGCCAUUGGCAGUCGCACUUUGGUUUACAUGGCUC
......((((..........((((..(((..((((...((........))-----.(((.....)))......))))..)))...)))).....)))).. ( -18.66)
>DroEre_CAF1 76334 81 + 1
UUCUCCGCCAGCUUCCUUCCCCCGUCUGCCCCCGCC-------------------UCAACUCCUUUGCCAUUGGCAGUCGCACUCUGGUUUACAUGGCUC
......((((....((......((.(((((...((.-------------------...........))....))))).))......))......)))).. ( -18.00)
>DroYak_CAF1 78202 100 + 1
UUCUCCGCCAGCUUCCUUCCGCCAUCUGCCCCCGCCACCGCCCCCUCAGCUCACCACAACUCCCUUGCCAUUGGCAGUCGCACUCUGGUUUACAUGGCUC
......((((....((....((...(((((...((....)).......((................))....)))))..)).....))......)))).. ( -17.09)
>consensus
UUCUCCGCCAGCAUCCUUCCGCCAUCUGCCCCCGCAAC_CCCCCCUCAGC_____ACAACUCCUUUGCCAUUGGCAGUCGCACUCUGGUUUACAUGGCUC
......((((....((....((...(((((...((...............................))....)))))..)).....))......)))).. (-14.65 = -14.90 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 11,341,788 – 11,341,883
Length 95
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 84.27
Mean single sequence MFE -26.87
Consensus MFE -17.36
Energy contribution -19.18
Covariance contribution 1.81
Combinations/Pair 1.05
Mean z-score -1.61
Structure conservation index 0.65
SVM decision value -0.02
SVM RNA-class probability 0.521155
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11341788 95 - 27905053
GAGCCAUGUAAACCAAAGUGCGACUGCCAAUGGCAAAGGAGUUGA-----GCUGAAGGGGGAGUUGCGGGGGCAGAUGGCGGAAGGAUGCUGGCGGAGAA
..((((.(((..((....(((((((.((..((((...........-----))))....)).))))))).))........(....)..)))))))...... ( -25.40)
>DroSim_CAF1 79179 95 - 1
GAGCCAUGUAAACCAAAGUGCGACUGCCAAUGGCAAAGGAGUUGU-----GCUGAGGGGGGCGUUGCAGGGGCAGAUGGCGGAAGGAUGCUGGCGGAGAA
..(((.......((..((..(((((.((.........))))))).-----.))...)).((((((((....))......(....))))))))))...... ( -29.20)
>DroEre_CAF1 76334 81 - 1
GAGCCAUGUAAACCAGAGUGCGACUGCCAAUGGCAAAGGAGUUGA-------------------GGCGGGGGCAGACGGGGGAAGGAAGCUGGCGGAGAA
..((((.((...((.(..(((..(((((...(((......)))..-------------------)))))..)))..)..)).......))))))...... ( -21.60)
>DroYak_CAF1 78202 100 - 1
GAGCCAUGUAAACCAGAGUGCGACUGCCAAUGGCAAGGGAGUUGUGGUGAGCUGAGGGGGCGGUGGCGGGGGCAGAUGGCGGAAGGAAGCUGGCGGAGAA
..((((.((...(((...(((..((((((((.((((.....)))).))..(((.....)))..))))))..)))..)))(....)...))))))...... ( -31.30)
>consensus
GAGCCAUGUAAACCAAAGUGCGACUGCCAAUGGCAAAGGAGUUGA_____GCUGAGGGGGG_GUGGCGGGGGCAGAUGGCGGAAGGAAGCUGGCGGAGAA
..((((.((...(((...(((..((((((..........(((........)))..........))))))..)))..)))(....)...))))))...... (-17.36 = -19.18 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:48 2006