Locus 6012

Sequence ID 3R_DroMel_CAF1
Location 15,836,435 – 15,836,595
Length 160
Max. P 0.941475
window9812 window9813

overview

Window 2

Location 15,836,435 – 15,836,555
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -43.03
Consensus MFE -39.71
Energy contribution -39.93
Covariance contribution 0.23
Combinations/Pair 1.05
Mean z-score -2.53
Structure conservation index 0.92
SVM decision value 1.32
SVM RNA-class probability 0.941475
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15836435 120 + 27905053
GCACCAACAUCAAAGAUGGCGAGCCCGAGAUCAAGGCUGAGAACUGGCCGCCCAAGCUGUUGAUGCAGCUAAUGCCCAAGCACCUAGUUGGCAAUAUUGGUGGGCAGUUUCUCAAGGACU
...((..((((...))))...((((.........))))((((((((.(((((..((((((....))))))..((((..(((.....))))))).....))))).))).)))))..))... ( -41.40)
>DroEre_CAF1 61149 120 + 1
GCACCAACAUCAAAGAUGGCGAGCCCGAGAUCAAGGCUGAGAACUGGCCGCCCAAGCUGUUGAUGCAGCUAAUGCCCAAACACCUAGUUGGCAAUAUCGGUGGUCAGUUUCUCAAGGAUU
...((..((((...))))...((((.........))))((((((((((((((..((((((....))))))..((((..(((.....))))))).....))))))))).)))))..))... ( -43.60)
>DroYak_CAF1 65714 120 + 1
GCACCAACAUUAAAGAUGGGGAACCAGAGAUCAAGGCUGAGAACUGGCCGCCCAAGCUGUUGAUGCAGCUAAUGCCCAAGCACCUGGUUGGCAAUAUCGGUGGUCAGUUUCUCAAGGAUU
...((...........(((....)))...........(((((((((((((((..((((((....))))))..((((.((.(....).)))))).....))))))))).)))))).))... ( -44.10)
>consensus
GCACCAACAUCAAAGAUGGCGAGCCCGAGAUCAAGGCUGAGAACUGGCCGCCCAAGCUGUUGAUGCAGCUAAUGCCCAAGCACCUAGUUGGCAAUAUCGGUGGUCAGUUUCUCAAGGAUU
...((..((((...))))...((((.........))))((((((((((((((..((((((....))))))..((((..(((.....))))))).....))))))))).)))))..))... (-39.71 = -39.93 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 15,836,475 – 15,836,595
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -40.90
Consensus MFE -39.19
Energy contribution -39.63
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.73
Structure conservation index 0.96
SVM decision value 0.45
SVM RNA-class probability 0.739996
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15836475 120 + 27905053
GAACUGGCCGCCCAAGCUGUUGAUGCAGCUAAUGCCCAAGCACCUAGUUGGCAAUAUUGGUGGGCAGUUUCUCAAGGACUCGAAAAUGGUUGUUUUUCGACCCACUCCAGGAGAGGCACU
....((.(((((..((((((....))))))..((((..(((.....))))))).....))))).))(((((((..(((.(((((((.......))))))).....)))..)))))))... ( -41.80)
>DroEre_CAF1 61189 120 + 1
GAACUGGCCGCCCAAGCUGUUGAUGCAGCUAAUGCCCAAACACCUAGUUGGCAAUAUCGGUGGUCAGUUUCUCAAGGAUUCUAAAAUGGUUGUUUUUCGACCCACUCCAGGAGAGGCGCU
....((((((((..((((((....))))))..((((..(((.....))))))).....))))))))(((((((..(((.........(((((.....)))))...)))..)))))))... ( -42.00)
>DroYak_CAF1 65754 120 + 1
GAACUGGCCGCCCAAGCUGUUGAUGCAGCUAAUGCCCAAGCACCUGGUUGGCAAUAUCGGUGGUCAGUUUCUCAAGGAUUCUAAAAUGGUAGUUUUUCGACCCACUCCAGGAGAGGCGCU
....((((((((..((((((....))))))..((((.((.(....).)))))).....))))))))(((((((..(((.........(((.(.....).)))...)))..)))))))... ( -38.90)
>consensus
GAACUGGCCGCCCAAGCUGUUGAUGCAGCUAAUGCCCAAGCACCUAGUUGGCAAUAUCGGUGGUCAGUUUCUCAAGGAUUCUAAAAUGGUUGUUUUUCGACCCACUCCAGGAGAGGCGCU
....((((((((..((((((....))))))..((((..(((.....))))))).....))))))))(((((((..(((.........(((((.....)))))...)))..)))))))... (-39.19 = -39.63 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:27 2006