Locus 1523

Sequence ID 3R_DroMel_CAF1
Location 4,348,137 – 4,348,257
Length 120
Max. P 0.995966
window2531 window2532

overview

Window 1

Location 4,348,137 – 4,348,257
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.42
Mean single sequence MFE -46.58
Consensus MFE -41.96
Energy contribution -42.96
Covariance contribution 1.00
Combinations/Pair 1.05
Mean z-score -1.51
Structure conservation index 0.90
SVM decision value 1.33
SVM RNA-class probability 0.942639
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4348137 120 + 27905053
CGCAUGGUUGCCAGCACUUUUGGUGAGCUCCAUAUCGCUAGCAGUCGAGCGUCCGCAGCGCCGUGCUCCACUGGCAUUGUAUGUGGCCAAUGUGGGCAUCGAAACGCUAUGGAAAAUGUU
(((.((..(((.(((.....(((......)))....))).)))..)).)))((((.((((.(((((.((((((((..........))))..))))))).))...)))).))))....... ( -42.20)
>DroSec_CAF1 35385 120 + 1
AGCCUGGGUGCCAGCUCUUUUGGUGAGCUCCAUAUCGCUGGCAGUCGAGCGUCCGCAGCGCCGUGCUCCACUGGCAUUGUAUGUGGCCAAUGUGGGCAUCGAAACGCUGUGGAAAAUGCU
.((.(((.(((((((.....(((......)))....))))))).))).)).(((((((((.(((((.((((((((..........))))..))))))).))...)))))))))....... ( -53.70)
>DroSim_CAF1 25711 120 + 1
AGCCUGGGUGCCAGCUCUUUUGGUGAGCUCCAUAUCGCUGGCAGUCGAGCGUCCGCAGCGCCGUGCUCCACUGGCAAUGUACGUGGCCAAUGUGGGCAUCGAAACGCUGUGGAAAAUGCU
.((.(((.(((((((.....(((......)))....))))))).))).)).(((((((((.(((((.((((((((.((....)).))))..))))))).))...)))))))))....... ( -54.70)
>DroEre_CAF1 35491 120 + 1
AACCUGGUUGCCUGCACUUUUGGUGAGCUCCAUAUCGCUGGCAGUCGAGCGUCCGGAGCGCCGUACUCCACUGGCAUUGUAUGUGGCCAAUGUGGGCAUCGAAACGCUGUGGAAAAUGCU
....((..((((.((.....(((......)))....)).))))..))((((((((.((((.((...(((((((((..........))))..)))))...))...)))).))))...)))) ( -39.50)
>DroYak_CAF1 27283 120 + 1
AACCUGGUUGCCAGCACUCUUGGUGAGCUCCAUAUCGCUGGCAGUCGAGCGUCCGGAGCGACGUACUCCACUGGCAUUGUAUGUGGCCAAUGUUGGCAUCGAAACGCUUUGGAAAAUGUU
....((..(((((((.....(((......)))....)))))))..))....(((((((((((((((............)))))).((((....)))).......)))))))))....... ( -42.80)
>consensus
AGCCUGGUUGCCAGCACUUUUGGUGAGCUCCAUAUCGCUGGCAGUCGAGCGUCCGCAGCGCCGUGCUCCACUGGCAUUGUAUGUGGCCAAUGUGGGCAUCGAAACGCUGUGGAAAAUGCU
....((..(((((((.....(((......)))....)))))))..))(((((((((((((.(((((.((((((((..........))))..))))))).))...)))))))))...)))) (-41.96 = -42.96 +   1.00)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 4,348,137 – 4,348,257
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.42
Mean single sequence MFE -42.80
Consensus MFE -40.68
Energy contribution -41.16
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -1.75
Structure conservation index 0.95
SVM decision value 2.64
SVM RNA-class probability 0.995966
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4348137 120 - 27905053
AACAUUUUCCAUAGCGUUUCGAUGCCCACAUUGGCCACAUACAAUGCCAGUGGAGCACGGCGCUGCGGACGCUCGACUGCUAGCGAUAUGGAGCUCACCAAAAGUGCUGGCAACCAUGCG
.......(((.((((((..((.(((((((..((((..........)))))))).))))))))))).)))(((..(..((((((((...(((......)))....))))))))..)..))) ( -43.50)
>DroSec_CAF1 35385 120 - 1
AGCAUUUUCCACAGCGUUUCGAUGCCCACAUUGGCCACAUACAAUGCCAGUGGAGCACGGCGCUGCGGACGCUCGACUGCCAGCGAUAUGGAGCUCACCAAAAGAGCUGGCACCCAGGCU
.......(((.((((((..((.(((((((..((((..........)))))))).))))))))))).))).((..(..(((((((....(((......))).....)))))))..)..)). ( -48.20)
>DroSim_CAF1 25711 120 - 1
AGCAUUUUCCACAGCGUUUCGAUGCCCACAUUGGCCACGUACAUUGCCAGUGGAGCACGGCGCUGCGGACGCUCGACUGCCAGCGAUAUGGAGCUCACCAAAAGAGCUGGCACCCAGGCU
.......(((.((((((..((.(((((((..((((..........)))))))).))))))))))).))).((..(..(((((((....(((......))).....)))))))..)..)). ( -48.20)
>DroEre_CAF1 35491 120 - 1
AGCAUUUUCCACAGCGUUUCGAUGCCCACAUUGGCCACAUACAAUGCCAGUGGAGUACGGCGCUCCGGACGCUCGACUGCCAGCGAUAUGGAGCUCACCAAAAGUGCAGGCAACCAGGUU
.(((((((((((.((((....))))...(((((........)))))...)))))....((.((((((..((((.(....).))))...))))))...))..)))))).(....)...... ( -35.50)
>DroYak_CAF1 27283 120 - 1
AACAUUUUCCAAAGCGUUUCGAUGCCAACAUUGGCCACAUACAAUGCCAGUGGAGUACGUCGCUCCGGACGCUCGACUGCCAGCGAUAUGGAGCUCACCAAGAGUGCUGGCAACCAGGUU
.......(((..((((...((.(((...(((((((..........)))))))..))))).))))..))).((..(..((((((((...(((......)))....))))))))..)..)). ( -38.60)
>consensus
AGCAUUUUCCACAGCGUUUCGAUGCCCACAUUGGCCACAUACAAUGCCAGUGGAGCACGGCGCUGCGGACGCUCGACUGCCAGCGAUAUGGAGCUCACCAAAAGUGCUGGCAACCAGGCU
.......(((.((((((..((.(((...(((((((..........)))))))..))))))))))).))).((..(..((((((((...(((......)))....))))))))..)..)). (-40.68 = -41.16 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:47 2006