Locus 3842

Sequence ID X_DroMel_CAF1
Location 10,211,851 – 10,211,971
Length 120
Max. P 0.857719
window6322 window6323

overview

Window 2

Location 10,211,851 – 10,211,971
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.42
Mean single sequence MFE -43.02
Consensus MFE -37.04
Energy contribution -37.32
Covariance contribution 0.28
Combinations/Pair 1.11
Mean z-score -1.25
Structure conservation index 0.86
SVM decision value 0.13
SVM RNA-class probability 0.597148
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10211851 120 + 22224390
ACCACAUUGGUGACCGCGUAGUUGCAAGCCAGCAGGGUGGCCUGCACAUUGUUGGCGUCCGUAAAUCGAGCAAUCGCACAACCCACUCGGUUAUUUCGCUCGUUGACCAUGGUGGUGAAG
(((((..(((((((.(((..(((((..((((((((.(((.....))).))))))))...((.....)).)))))..)..((((.....)))).....))..))).))))..))))).... ( -41.40)
>DroSec_CAF1 8180 120 + 1
ACCACAUUGGUGACCGCGUAGUUGCAGGCCAACAGGGUGGCCUGCACAUUGUUGGCGUCCGUAAAUCGGGCAAUCGCACAUCCAACUCGGUUAUUUCGCUCGUUGACCAUGGUGGUGAAG
(((((..((((....((((((((((((((((......))))))))).)))).....(((((.....)))))...))).....((((.(((.....)))...))))))))..))))).... ( -43.70)
>DroSim_CAF1 8649 120 + 1
ACCACAUUGGUGACCGCGUAGUUGCAGGCCAACAGGGUGGCCUGCACAUUGUUGGCGUCCGUAAAUCGGGCAAUCGCACAUCCCACUCGGUUAUUUCGCUCGUUGACCAUGGUGGUGAAG
(((.....))).(((((.....(((((((((......)))))))))(((.((..(((((((.....)))))(((((...........))))).........))..)).)))))))).... ( -43.00)
>DroEre_CAF1 9343 120 + 1
AGCACAUUGGUGACCGCGUAAUUGCAGGCCAACAGGGUGGCCUGCACGUUGUUGGCGUCCGUAAAUCGGGCAAUCGCACAACCCACUCUGUUGUUACGCUCGUUGACCAUGGUGGUGAAG
..(((..(((((((.(((((((.((((((((((((.(((.....))).))))))))(((((.....)))))................)))).)))))))..))).))))..)))...... ( -48.80)
>DroYak_CAF1 9327 120 + 1
AACACAUUGGUGACCGCGUAAUUGCAGACCAACAGAGUGGCCUGCACGUUAUUGGCGUCCGUAAAACGGGCAAUCGCACAUCCCACUCGGUUAUUACGUUCGUUGACCAUCGUGGUGAAG
..(((..(((((((.(((((((....((((....((((((..(((..((.....))(((((.....)))))....)))....)))))))))))))))))..))).))))..)))...... ( -38.20)
>consensus
ACCACAUUGGUGACCGCGUAGUUGCAGGCCAACAGGGUGGCCUGCACAUUGUUGGCGUCCGUAAAUCGGGCAAUCGCACAUCCCACUCGGUUAUUUCGCUCGUUGACCAUGGUGGUGAAG
(((((..(((((((.(((.(((.((..((((((((.(((.....))).))))))))(((((.....)))))..................)).))).)))..))).))))..))))).... (-37.04 = -37.32 +   0.28)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 10,211,851 – 10,211,971
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.42
Mean single sequence MFE -41.58
Consensus MFE -35.58
Energy contribution -36.10
Covariance contribution 0.52
Combinations/Pair 1.09
Mean z-score -1.50
Structure conservation index 0.86
SVM decision value 0.81
SVM RNA-class probability 0.857719
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10211851 120 - 22224390
CUUCACCACCAUGGUCAACGAGCGAAAUAACCGAGUGGGUUGUGCGAUUGCUCGAUUUACGGACGCCAACAAUGUGCAGGCCACCCUGCUGGCUUGCAACUACGCGGUCACCAAUGUGGU
....(((((..((((...(((((((.((((((.....))))))....)))))))......(..(((........(((((((((......))))))))).....)))..)))))..))))) ( -44.92)
>DroSec_CAF1 8180 120 - 1
CUUCACCACCAUGGUCAACGAGCGAAAUAACCGAGUUGGAUGUGCGAUUGCCCGAUUUACGGACGCCAACAAUGUGCAGGCCACCCUGUUGGCCUGCAACUACGCGGUCACCAAUGUGGU
....(((((..((((..((..(((..........(((((.(((((....))(((.....)))))))))))....(((((((((......)))))))))....))).)).))))..))))) ( -43.10)
>DroSim_CAF1 8649 120 - 1
CUUCACCACCAUGGUCAACGAGCGAAAUAACCGAGUGGGAUGUGCGAUUGCCCGAUUUACGGACGCCAACAAUGUGCAGGCCACCCUGUUGGCCUGCAACUACGCGGUCACCAAUGUGGU
....(((((..((((......(((......((....))....)))(((((((((.....)))............(((((((((......))))))))).....))))))))))..))))) ( -40.60)
>DroEre_CAF1 9343 120 - 1
CUUCACCACCAUGGUCAACGAGCGUAACAACAGAGUGGGUUGUGCGAUUGCCCGAUUUACGGACGCCAACAACGUGCAGGCCACCCUGUUGGCCUGCAAUUACGCGGUCACCAAUGUGCU
......(((..((((..((..((((((.......((..((((.(((.....(((.....))).))))))).)).(((((((((......))))))))).)))))).)).))))..))).. ( -41.20)
>DroYak_CAF1 9327 120 - 1
CUUCACCACGAUGGUCAACGAACGUAAUAACCGAGUGGGAUGUGCGAUUGCCCGUUUUACGGACGCCAAUAACGUGCAGGCCACUCUGUUGGUCUGCAAUUACGCGGUCACCAAUGUGUU
......((((.((((............((((.((((((..((..((((((((((.....)))..).))))..))..))..)))))).))))(.((((......)))).))))).)))).. ( -38.10)
>consensus
CUUCACCACCAUGGUCAACGAGCGAAAUAACCGAGUGGGAUGUGCGAUUGCCCGAUUUACGGACGCCAACAAUGUGCAGGCCACCCUGUUGGCCUGCAACUACGCGGUCACCAAUGUGGU
....(((((..((((...................((((((((.((....)).))))))))(..(((........(((((((((......))))))))).....)))..)))))..))))) (-35.58 = -36.10 +   0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:04 2006