Locus 4241

Sequence ID 3R_DroMel_CAF1
Location 11,377,855 – 11,378,015
Length 160
Max. P 0.971006
window6878 window6879

overview

Window 8

Location 11,377,855 – 11,377,975
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.50
Mean single sequence MFE -44.56
Consensus MFE -40.48
Energy contribution -40.88
Covariance contribution 0.40
Combinations/Pair 1.05
Mean z-score -1.56
Structure conservation index 0.91
SVM decision value 1.31
SVM RNA-class probability 0.940996
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11377855 120 - 27905053
AUGGCGGCAGAGUGACCAUGGAGGAGGUGGAGAACUCCUUCGGCGGAAACAUUUGUCGCUGCACUGGAUAUCGUCCCAUUCUGGAUGCCAUGAAGUCCUUUGCGGUGGACAGCACCGUUG
..(((((((((((..((.((((((((........))))))))..))..)).)))))))))(((..((((.((((..((((...))))..)))).))))..)))((((.....)))).... ( -47.20)
>DroSec_CAF1 125497 120 - 1
AUGGCGGCAGAGUGACCAUGGAGGAGGUGGAGAACUCCUUCGGUGGAAACAUUUGUCGCUGCACUGGAUAUCGUCCCAUUCUGGAUGCCAUGAAGUCCUUUGCGGUGGACAGCACCAUUG
..(((((((((((..(((((((((((........))))))).))))..)).)))))))))(((..((((.((((..((((...))))..)))).))))..)))((((.....)))).... ( -48.30)
>DroSim_CAF1 116501 120 - 1
AUGGCGGCAGAGUGACCAUGGAGGAGGUGGAGAACUCCUUUGGUGGAAACAUUUGUCGCUGCACUGGAUAUCGUCCAAUUCUGGAUGCCAUGAAGUCCUUUGCUGUGGACAGCACCAUUG
..(((((((((((..((((.((((((........)))).)).))))..)).)))))))))((..(((....((((((....)))))))))....((((........)))).))....... ( -43.20)
>DroEre_CAF1 113050 120 - 1
AUGGCGGCAGAGUGACCAUGGAGCAGGUGGAGAACUCCUUCGGUGGAAACAUUUGUCGCUGCACUGGAUACCGUCCCAUUCUGGAUGCCAUGAAGUCCUUUGCGGUGGACAGCACUGUUG
...((.((((((.((((((((.((((..(((....)))...((((....)))).....)))).........(((((......))))))))))..))))))))).)).((((....)))). ( -39.60)
>DroYak_CAF1 115590 120 - 1
AUGGCGGCAGAGUGACCAUGGAGGAGGUGGAGAACUCCUUUGGUGGAAACAUUUGUCGCUGCACUGGAUAUCGGCCCAUUCUGGAUGCCAUGAAGUCCUUUGCGGUGGACAGCACUAUUG
..(((((((((((..((((.((((((........)))).)).))))..)).)))))))))(((..((((.(((((((.....))..)))..)).))))..)))((((.....)))).... ( -44.50)
>consensus
AUGGCGGCAGAGUGACCAUGGAGGAGGUGGAGAACUCCUUCGGUGGAAACAUUUGUCGCUGCACUGGAUAUCGUCCCAUUCUGGAUGCCAUGAAGUCCUUUGCGGUGGACAGCACCAUUG
..(((((((((((..(((((((((((........))))))).))))..)).)))))))))(((..((((..(((((......))))).......))))..)))((((.....)))).... (-40.48 = -40.88 +   0.40)

alignment

Postscript

secondary structure

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dotplot

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Window 9

Location 11,377,895 – 11,378,015
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.50
Mean single sequence MFE -43.76
Consensus MFE -38.52
Energy contribution -39.28
Covariance contribution 0.76
Combinations/Pair 1.03
Mean z-score -1.82
Structure conservation index 0.88
SVM decision value 1.67
SVM RNA-class probability 0.971006
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11377895 120 - 27905053
CCGGGAUUCGUGAUGAACAUGUAUGGGUUGAUGGAACAGCAUGGCGGCAGAGUGACCAUGGAGGAGGUGGAGAACUCCUUCGGCGGAAACAUUUGUCGCUGCACUGGAUAUCGUCCCAUU
........((((.....)))).(((((.(((((...(((..((((((((((((..((.((((((((........))))))))..))..)).))))))))))..)))..))))).))))). ( -45.10)
>DroSec_CAF1 125537 120 - 1
CCGGGAUUCGUGAUGAACAUGUAUGGGUUGAUGGAGCAGCAUGGCGGCAGAGUGACCAUGGAGGAGGUGGAGAACUCCUUCGGUGGAAACAUUUGUCGCUGCACUGGAUAUCGUCCCAUU
........((((.....)))).(((((.(((((...(((..((((((((((((..(((((((((((........))))))).))))..)).))))))))))..)))..))))).))))). ( -45.10)
>DroSim_CAF1 116541 120 - 1
CCGGGAUUCGUGAUGAACAUGUAUGGGUUGAUGGAGCAGCAUGGCGGCAGAGUGACCAUGGAGGAGGUGGAGAACUCCUUUGGUGGAAACAUUUGUCGCUGCACUGGAUAUCGUCCAAUU
...((((....((((..(((((....((((......))))..(((((((((((..((((.((((((........)))).)).))))..)).)))))))))))).))..)))))))).... ( -38.80)
>DroEre_CAF1 113090 120 - 1
CCGGGAUUCGUGAUGAACAUGUAUGGCUUGAUGGAGCAGCAUGGCGGCAGAGUGACCAUGGAGCAGGUGGAGAACUCCUUCGGUGGAAACAUUUGUCGCUGCACUGGAUACCGUCCCAUU
..(((((..(((.....(((((...((((....)))).)))))((((((((((..((((.(((..(((.....)))..))).))))..)).))))))))..))).((...)))))))... ( -41.60)
>DroYak_CAF1 115630 120 - 1
CCGGGAUUCGUGAUGAACAUGUACGGGCUGAUGGAGCAGCAUGGCGGCAGAGUGACCAUGGAGGAGGUGGAGAACUCCUUUGGUGGAAACAUUUGUCGCUGCACUGGAUAUCGGCCCAUU
........((((.....))))...(((((((((...(((..((((((((((((..((((.((((((........)))).)).))))..)).))))))))))..)))..)))))))))... ( -48.20)
>consensus
CCGGGAUUCGUGAUGAACAUGUAUGGGUUGAUGGAGCAGCAUGGCGGCAGAGUGACCAUGGAGGAGGUGGAGAACUCCUUCGGUGGAAACAUUUGUCGCUGCACUGGAUAUCGUCCCAUU
..(((((.((((.....))))........((((...(((..((((((((((((..(((((((((((........))))))).))))..)).))))))))))..)))..)))))))))... (-38.52 = -39.28 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:12 2006