Locus 9507

Sequence ID 3R_DroMel_CAF1
Location 25,121,978 – 25,122,098
Length 120
Max. P 0.619614
window15218 window15219

overview

Window 8

Location 25,121,978 – 25,122,098
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.17
Mean single sequence MFE -42.38
Consensus MFE -30.22
Energy contribution -31.50
Covariance contribution 1.28
Combinations/Pair 1.23
Mean z-score -1.71
Structure conservation index 0.71
SVM decision value 0.18
SVM RNA-class probability 0.619614
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25121978 120 + 27905053
UGGCUCGACAGACUUGUGGGGCACGGCAGCCAGUUUCUUCCGUAUGCUCAGUAGGAGCUUUGCCGAACUGGAAAGACCCUUUUCCAGGGCCCUCACCUCGUCUGAACUGGGUUCGAAUUU
.((((((.(((((..(((((((.((((((..(((((((.(.(......).).)))))))))))))..((((((((....)))))))).)))).)))...)))))...))))))....... ( -45.10)
>DroSec_CAF1 50485 120 + 1
UGGAUCAGCAGACUUGUAGGGCACGGCAUCCACUUUCUUUCGGAUGCUUAGUAGAAGCUUUGCCGAACUGGAAAGACCCUUCUCCAGUGCCCUCACCUCGUCUGAACUGGGUUCGAAUUC
.(((((..(((((..((((((((((((((((..........)))))))..(.(((((((((.((.....))))))...))))).).))))))).))...))))).....)))))...... ( -41.50)
>DroSim_CAF1 53032 120 + 1
UGGCUCGGCAGACAUGUAGGGUACGGCAUCCACUUUCUUUCGGAUGCUUAGUAGAAGCUUUGCCGAACUGGAAAGACCCUUCUCCAGUGCCCUCACCUCGUCUGAACUGGGUUCGAAUUC
.((((((((((((..((((((((((((((((..........)))))))..(.(((((((((.((.....))))))...))))).).))))))).))...)))))..)))))))....... ( -40.70)
>DroEre_CAF1 53162 120 + 1
UGGCCUGGCGGAUUUGCAGGCCACUGCAGUCAGUUUCUGCCGCAUGCUCAGCAGGAGCUUUGCCGCCCUGGAAAGACCCUUUUCCAGUGCCCGCAUCUCGUCCAAACUGGGACUGGAUUU
.(((..(((((..((((((....))))))..(((((((((.(......).)))))))))...)))))((((((((....)))))))).)))...((((.((((......)))).)))).. ( -47.60)
>DroYak_CAF1 52484 120 + 1
UGGCAUGGCAGAUAUGCAGGGCACUGCAGUCAGUUUCUUUCGCAUGCUCAGUAGGAGCUUUGCCGACCUGGAAAGUCCCUUUUCCAGUGCCCUCAUCUCGUCUAAACUGGGUAUGGAUUU
.(((((((((((.((((((((.((((....)))).))))..))))((((.....)))))))))))..((((((((....)))))))))))).((((((((.......)))).)))).... ( -37.00)
>consensus
UGGCUCGGCAGACUUGUAGGGCACGGCAGCCAGUUUCUUUCGCAUGCUCAGUAGGAGCUUUGCCGAACUGGAAAGACCCUUUUCCAGUGCCCUCACCUCGUCUGAACUGGGUUCGAAUUU
.((((((((((((.((.(((((.(((((...(((((((..............))))))).)))))..((((((((....)))))))).)))))))....)))))..)))))))....... (-30.22 = -31.50 +   1.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 25,121,978 – 25,122,098
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.17
Mean single sequence MFE -41.42
Consensus MFE -29.84
Energy contribution -29.96
Covariance contribution 0.12
Combinations/Pair 1.20
Mean z-score -1.69
Structure conservation index 0.72
SVM decision value 0.17
SVM RNA-class probability 0.618621
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25121978 120 - 27905053
AAAUUCGAACCCAGUUCAGACGAGGUGAGGGCCCUGGAAAAGGGUCUUUCCAGUUCGGCAAAGCUCCUACUGAGCAUACGGAAGAAACUGGCUGCCGUGCCCCACAAGUCUGUCGAGCCA
...(((((........(((((...(((.((((.(((((((......)))))))..(((((..((((.....))))...(....)........))))).)))))))..))))))))))... ( -43.20)
>DroSec_CAF1 50485 120 - 1
GAAUUCGAACCCAGUUCAGACGAGGUGAGGGCACUGGAGAAGGGUCUUUCCAGUUCGGCAAAGCUUCUACUAAGCAUCCGAAAGAAAGUGGAUGCCGUGCCCUACAAGUCUGCUGAUCCA
...........(((..(((((...((.(((((((((((((......)))))))).((((...((((.....))))(((((........))))))))).)))))))..))))))))..... ( -42.40)
>DroSim_CAF1 53032 120 - 1
GAAUUCGAACCCAGUUCAGACGAGGUGAGGGCACUGGAGAAGGGUCUUUCCAGUUCGGCAAAGCUUCUACUAAGCAUCCGAAAGAAAGUGGAUGCCGUACCCUACAUGUCUGCCGAGCCA
.............((((.(..((.(((((((.((((((((......)))))))).((((...((((.....))))(((((........)))))))))..)))).))).))..).)))).. ( -37.50)
>DroEre_CAF1 53162 120 - 1
AAAUCCAGUCCCAGUUUGGACGAGAUGCGGGCACUGGAAAAGGGUCUUUCCAGGGCGGCAAAGCUCCUGCUGAGCAUGCGGCAGAAACUGACUGCAGUGGCCUGCAAAUCCGCCAGGCCA
..(((..((((......))))..)))...(((.(((((((......)))))))(((((....((((.....)))).((((((....((((....)))).))).)))...)))))..))). ( -47.90)
>DroYak_CAF1 52484 120 - 1
AAAUCCAUACCCAGUUUAGACGAGAUGAGGGCACUGGAAAAGGGACUUUCCAGGUCGGCAAAGCUCCUACUGAGCAUGCGAAAGAAACUGACUGCAGUGCCCUGCAUAUCUGCCAUGCCA
...........((...((((....((((((((((((......((.....)).((((((....((((.....))))...(....)...)))))).))))))))).))).))))...))... ( -36.10)
>consensus
AAAUUCGAACCCAGUUCAGACGAGGUGAGGGCACUGGAAAAGGGUCUUUCCAGUUCGGCAAAGCUCCUACUGAGCAUCCGAAAGAAACUGGCUGCCGUGCCCUACAAGUCUGCCGAGCCA
................(((((...(((.((((((((((((......)))))))..(((((..((((.....))))...(....)........)))))))))))))..)))))........ (-29.84 = -29.96 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:36:09 2006