Locus 4665

Sequence ID 3R_DroMel_CAF1
Location 12,310,590 – 12,310,750
Length 160
Max. P 0.774698
window7656 window7657 window7658

overview

Window 6

Location 12,310,590 – 12,310,710
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -54.90
Consensus MFE -52.22
Energy contribution -52.33
Covariance contribution 0.11
Combinations/Pair 1.02
Mean z-score -1.72
Structure conservation index 0.95
SVM decision value 0.30
SVM RNA-class probability 0.678927
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12310590 120 + 27905053
AGUGGCGCACGCAGGAGCGCUUCUCGAACCGCGUGUUCUGGUAGUGGGGAUGGUGACUGGGGUGCUGCUGGUGCUGGCGGUGCUCACAAUUGGCACUGCGACAGUUAUGCGCCACCAGUG
.((((((((..(((.((((((((.....((((...........))))....(....).)))))))).)))..((((((((((((.......))))))))..))))..))))))))..... ( -52.50)
>DroSec_CAF1 1883 120 + 1
AGUGGCGCACGCAGGAGCGCUUCUCGAACCGCGUGUUCUGGUAGUGGGGAUGGUGACUGGGGUGCUGCUGGUGUUGGCGGUGCUCACAGUUGGCACUGCGACAGUUGUGCGCCACCAGUG
.(((((((((.(((.((((((((.....((((...........))))....(....).)))))))).))).(((((.(((((((.......))))))))))))...)))))))))..... ( -56.10)
>DroSim_CAF1 1863 120 + 1
AGUGGCGCACGCAGGAGCGCUUCUCGAACCGCGUGUUCUGGUAGUGGGGAUGGUGACUGGGGUGCUGCUGGUGCUGGCGGUGCUCACAGUUGGCACUGCGACAGUUGUGCGCCACCAGUG
.(((((((((.(((.((((((((.....((((...........))))....(....).)))))))).)))..((((((((((((.......))))))))..)))).)))))))))..... ( -56.10)
>consensus
AGUGGCGCACGCAGGAGCGCUUCUCGAACCGCGUGUUCUGGUAGUGGGGAUGGUGACUGGGGUGCUGCUGGUGCUGGCGGUGCUCACAGUUGGCACUGCGACAGUUGUGCGCCACCAGUG
.(((((((((((((.((((((((....((((....((((......)))).))))....)))))))).)))..((((((((((((.......))))))))..))))))))))))))..... (-52.22 = -52.33 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,310,630 – 12,310,750
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -51.23
Consensus MFE -50.00
Energy contribution -50.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.98
SVM decision value 0.54
SVM RNA-class probability 0.774698
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12310630 120 + 27905053
GUAGUGGGGAUGGUGACUGGGGUGCUGCUGGUGCUGGCGGUGCUCACAAUUGGCACUGCGACAGUUAUGCGCCACCAGUGGCUCGUCCGUCUUCAGAGAGUCCUCAUAGGUGUCACUGUU
.(((((((((((((.((((((((((.((((....(.((((((((.......)))))))).)))))...))))).))))).)).))))).......(((....))).......)))))).. ( -52.20)
>DroSec_CAF1 1923 120 + 1
GUAGUGGGGAUGGUGACUGGGGUGCUGCUGGUGUUGGCGGUGCUCACAGUUGGCACUGCGACAGUUGUGCGCCACCAGUGGCUCGUCCGUCUUUAGCGAGUCCUCAUAGGUGUCACUGUU
.(((((((((((((.((((((((((.((.(.(((((.(((((((.......)))))))))))).).))))))).))))).)).))))).............((.....))..)))))).. ( -51.00)
>DroSim_CAF1 1903 120 + 1
GUAGUGGGGAUGGUGACUGGGGUGCUGCUGGUGCUGGCGGUGCUCACAGUUGGCACUGCGACAGUUGUGCGCCACCAGUGGCUCGUCCGUCUUCAGCGAGUCCUCAUAGGUGUCACUGUU
.......(((((((.((((((((((.((((....(.((((((((.......)))))))).)))))...))))).))))).)).))))).....(((.((..((.....))..)).))).. ( -50.50)
>consensus
GUAGUGGGGAUGGUGACUGGGGUGCUGCUGGUGCUGGCGGUGCUCACAGUUGGCACUGCGACAGUUGUGCGCCACCAGUGGCUCGUCCGUCUUCAGCGAGUCCUCAUAGGUGUCACUGUU
.(((((((((((((.((((((((((.((((....(.((((((((.......)))))))).)))))...))))).))))).)).))))).............((.....))..)))))).. (-50.00 = -50.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,310,630 – 12,310,750
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -37.70
Consensus MFE -34.83
Energy contribution -35.61
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -1.76
Structure conservation index 0.92
SVM decision value 0.18
SVM RNA-class probability 0.622995
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12310630 120 - 27905053
AACAGUGACACCUAUGAGGACUCUCUGAAGACGGACGAGCCACUGGUGGCGCAUAACUGUCGCAGUGCCAAUUGUGAGCACCGCCAGCACCAGCAGCACCCCAGUCACCAUCCCCACUAC
....(((((........((.(((((((....)))).))))).(((((((.((.......(((((((....))))))))).)))))))................)))))............ ( -36.71)
>DroSec_CAF1 1923 120 - 1
AACAGUGACACCUAUGAGGACUCGCUAAAGACGGACGAGCCACUGGUGGCGCACAACUGUCGCAGUGCCAACUGUGAGCACCGCCAACACCAGCAGCACCCCAGUCACCAUCCCCACUAC
....(((((........((.((((((......)).))))))..((((((.((.(....)(((((((....))))))))).)))))).................)))))............ ( -35.90)
>DroSim_CAF1 1903 120 - 1
AACAGUGACACCUAUGAGGACUCGCUGAAGACGGACGAGCCACUGGUGGCGCACAACUGUCGCAGUGCCAACUGUGAGCACCGCCAGCACCAGCAGCACCCCAGUCACCAUCCCCACUAC
....(((((........((.(((((((....))).)))))).(((((((.((.(....)(((((((....))))))))).)))))))................)))))............ ( -40.50)
>consensus
AACAGUGACACCUAUGAGGACUCGCUGAAGACGGACGAGCCACUGGUGGCGCACAACUGUCGCAGUGCCAACUGUGAGCACCGCCAGCACCAGCAGCACCCCAGUCACCAUCCCCACUAC
....(((((........((.(((((((....))).)))))).(((((((.((.......(((((((....))))))))).)))))))................)))))............ (-34.83 = -35.61 +   0.78)

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 11:35:51 2006