Locus 1778

Sequence ID 3R_DroMel_CAF1
Location 5,104,355 – 5,104,504
Length 149
Max. P 0.776320
window2921 window2922

overview

Window 1

Location 5,104,355 – 5,104,467
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.67
Mean single sequence MFE -29.25
Consensus MFE -21.17
Energy contribution -22.93
Covariance contribution 1.76
Combinations/Pair 1.09
Mean z-score -2.02
Structure conservation index 0.72
SVM decision value 0.52
SVM RNA-class probability 0.768276
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5104355 112 + 27905053
AAC--------CAGACAAAAAAUAUAUCAUGCAUGCGAAAGCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUACAAUUAUAGCUGGCUUUGCUGGCUAACUGGUUGGCUCUUAAAGUA
(((--------(((......((((..((.(((((((....))))...(((.......)))))).))..)))).........((((..((...))..)))).))))))............. ( -28.80)
>DroSec_CAF1 11128 112 + 1
AAC--------CAGCCAAAAAAUACAUCAUGCAUGCGAUAGCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUACAAUUAUAGCCGGGUUUGCUGGCUAACUGGUUGGCUCUUAAAGUA
..(--------((((((...((((..((.(((((((....))))...(((.......)))))).))..)))).........(((((((.....)))))))..)))))))........... ( -29.30)
>DroSim_CAF1 11366 112 + 1
AUC--------CAGACAAAAAAUACAUCAUGCAUGCGAAAGCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUACAAUUAUAGCCGGGUUUGCUGGCUAACUGGUUGGCUCUUAAAGUA
...--------...........(((.((((..((((....)))))))))))......(((..((((((.......(((((((((((((.....)))))))..))))))))))))..))). ( -29.01)
>DroEre_CAF1 12263 112 + 1
AAG--------CAGACAAAAAAUACAUCAUGCAUGCGAAAGCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUGCAAUUAUAGCUGGCUUUUGGAGCUAACCGGUUGGCUCUUAAAGUG
..(--------(((........(((.((((..((((....))))))))))).......))))...((((((.........)))))).(((((.((((((((....)))))))).))))). ( -32.06)
>DroYak_CAF1 12308 110 + 1
AACCAGACAACCAGACAAAAAAUACAUCAUGCAUGCGCAAGCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUGCAAUUAUUGCUGGCUGUG----------GGUUGGCUCUUAAAGUA
((((..(((.((((.(((..............((((....)))).((.(((((...((((.....))))))))).))....))))))).))).----------))))............. ( -27.10)
>consensus
AAC________CAGACAAAAAAUACAUCAUGCAUGCGAAAGCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUACAAUUAUAGCUGGCUUUGCUGGCUAACUGGUUGGCUCUUAAAGUA
......................(((.((((..((((....)))))))))))......(((..((((((.......(((((((((((((.....)))))))..))))))))))))..))). (-21.17 = -22.93 +   1.76)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,104,387 – 5,104,504
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.88
Mean single sequence MFE -25.73
Consensus MFE -20.21
Energy contribution -21.81
Covariance contribution 1.60
Combinations/Pair 1.12
Mean z-score -1.77
Structure conservation index 0.79
SVM decision value 0.54
SVM RNA-class probability 0.776320
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5104387 117 + 27905053
GCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUACAAUUAUAGCUGGCUUUGCUGGCUAACUGGUUGGCUCUUAAAGUAGUUACACAAAACUGGCAAUAAAAACAA-AAA--AAAAAGA
((...((.((((((...(((..((((((.......((((((((((..((...))..))))..))))))))))))..))))))))).))......))...........-...--....... ( -26.11)
>DroSec_CAF1 11160 119 + 1
GCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUACAAUUAUAGCCGGGUUUGCUGGCUAACUGGUUGGCUCUUAAAGUAGUUACACAAAACUGGCAAUAAAAACAA-AAACAAUAAAGA
((...((.((((((...(((..((((((.......(((((((((((((.....)))))))..))))))))))))..))))))))).))......))...........-............ ( -26.81)
>DroSim_CAF1 11398 120 + 1
GCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUACAAUUAUAGCCGGGUUUGCUGGCUAACUGGUUGGCUCUUAAAGUAGUUACACAAAACUGGCAAUAAAAAUAAAAAACAAAAAAGA
((...((.((((((...(((..((((((.......(((((((((((((.....)))))))..))))))))))))..))))))))).))......))........................ ( -26.81)
>DroEre_CAF1 12295 120 + 1
GCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUGCAAUUAUAGCUGGCUUUUGGAGCUAACCGGUUGGCUCUUAAAGUGGUUACACAAAACUGGCAAUAAAAGAACAAAACAAAAAGAA
((...((.((((((....(.((...(((((.....)))))...)).)(((((.((((((((....)))))))).))))))))))).))......))........................ ( -27.80)
>DroYak_CAF1 12348 105 + 1
GCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUGCAAUUAUUGCUGGCUGUG----------GGUUGGCUCUUAAAGUAGUUGCACAAAACGGGCAAUAAAAGAAUAA-----AAAAGA
.....((.(((((...((((.....))))))))).)).((((((((.(.((((----------.(...(((.....)))...).))))...).))))))))........-----...... ( -21.10)
>consensus
GCAUAUGGGUAACUGAAACUGCAAGAGUUGUUAUACAAUUAUAGCUGGCUUUGCUGGCUAACUGGUUGGCUCUUAAAGUAGUUACACAAAACUGGCAAUAAAAAAAAAAAACAAAAAAGA
((...((.((((((...(((..((((((.......(((((((((((((.....)))))))..))))))))))))..))))))))).))......))........................ (-20.21 = -21.81 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:09 2006