Locus 4962

Sequence ID 3R_DroMel_CAF1
Location 13,056,507 – 13,056,608
Length 101
Max. P 0.980812
window8121 window8122

overview

Window 1

Location 13,056,507 – 13,056,608
Length 101
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 76.90
Mean single sequence MFE -20.85
Consensus MFE -12.79
Energy contribution -13.23
Covariance contribution 0.45
Combinations/Pair 1.12
Mean z-score -1.36
Structure conservation index 0.61
SVM decision value 0.06
SVM RNA-class probability 0.565191
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13056507 101 + 27905053
GCUUUAAUGCUGCGGCAUAAAUCAUUUUUCCGCAAUUCGUUUCAAUUGCAUAAAAGUAUUUUAUGCACUGCCUUCUUUUGGCUGACUUU----------CAGUGUGUGUAU
((....((((((..(((((((..((((((..((((((......))))))..))))))..)))))))...(((.......))).......----------))))))..)).. ( -23.90)
>DroSec_CAF1 76518 101 + 1
GCUUUAAUGCUGUAACAUAAAUCAUUUUUUCGCAAUUCGUUUCAAUUGCAUAAAAGUAUUUCAUGCACUGCCUUCUUUUGGCUGACUUU----------CAGUGUGUGUAU
((......)).............((((((..((((((......))))))..))))))....(((((((((((.......))).(.....----------)))))))))... ( -18.90)
>DroEre_CAF1 76985 86 + 1
GCUGUAAUGCUGUGGCAUAAAUCAUC-UUCCGCAAUUCGUUUCAAUUGCACAAAAGUAUUUCAUGCACUGCCUUCUGUUGGCUGCCU------------------------
((((.((((((((((......)))).-....((((((......)))))).....)))))).)).))...(((.......))).....------------------------ ( -16.50)
>DroYak_CAF1 78952 101 + 1
GCUUUAAUGCUGUGGCAUAAAUCAUUUUUCCGCAAUUCGUUUCAAUUGCAUAAAAGUAUUUCAUGCACUGCCUUCUUUUGGCUGACUUU----------CAGAGUGUGUAU
......(((((.((((((((((.((((((..((((((......))))))..)))))))))).))))...(((.......))).......----------)).))))).... ( -21.40)
>DroAna_CAF1 78630 105 + 1
GCUUUAAUGCUGUGGCAUAAAUCAUUUUUCCGCAAUUCGUUUCAAUUGCAAAAAAAUACUUUAUGCACUAGCUCCU-UCGGCUGCCGCUGUGGACCAC-CAGA----ACAU
........((((..(((((((..((((((..((((((......))))))..))))))..)))))))..))))(((.-.((((....)))).)))....-....----.... ( -26.40)
>DroPer_CAF1 146075 107 + 1
GCUUUAAUGCUGUGGCAUAAAUCAUUUUUUCGCAAUUCGUUUCAAUUGCAUAAAAAUAUUUCAUGCUGGUGCUGCUUCUGCCUCUGCUUCUGCUUCUUCUGUUGUGU----
........((..((((((((((.((((((..((((((......))))))..)))))))))).))))))..)).((....((....))....))..............---- ( -18.00)
>consensus
GCUUUAAUGCUGUGGCAUAAAUCAUUUUUCCGCAAUUCGUUUCAAUUGCAUAAAAGUAUUUCAUGCACUGCCUUCUUUUGGCUGACUUU__________CAGUGUGUGUAU
((......))....((((((((.((((((..((((((......))))))..)))))))))).)))).(.(((.......))).)........................... (-12.79 = -13.23 +   0.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,056,507 – 13,056,608
Length 101
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 76.90
Mean single sequence MFE -23.60
Consensus MFE -16.52
Energy contribution -16.42
Covariance contribution -0.11
Combinations/Pair 1.24
Mean z-score -2.31
Structure conservation index 0.70
SVM decision value 1.87
SVM RNA-class probability 0.980812
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13056507 101 - 27905053
AUACACACACUG----------AAAGUCAGCCAAAAGAAGGCAGUGCAUAAAAUACUUUUAUGCAAUUGAAACGAAUUGCGGAAAAAUGAUUUAUGCCGCAGCAUUAAAGC
.........(((----------.......(((.......))).(.(((((((.((.((((.(((((((......))))))).)))).)).)))))))).)))......... ( -20.80)
>DroSec_CAF1 76518 101 - 1
AUACACACACUG----------AAAGUCAGCCAAAAGAAGGCAGUGCAUGAAAUACUUUUAUGCAAUUGAAACGAAUUGCGAAAAAAUGAUUUAUGUUACAGCAUUAAAGC
.........(((----------.......(((.......)))...(((((((.((.((((.(((((((......))))))).)))).)).)))))))..)))......... ( -18.70)
>DroEre_CAF1 76985 86 - 1
------------------------AGGCAGCCAACAGAAGGCAGUGCAUGAAAUACUUUUGUGCAAUUGAAACGAAUUGCGGAA-GAUGAUUUAUGCCACAGCAUUACAGC
------------------------..((.(((.......))).(((((((((.((.((((.(((((((......))))))).))-)))).)))))).))).))........ ( -23.70)
>DroYak_CAF1 78952 101 - 1
AUACACACUCUG----------AAAGUCAGCCAAAAGAAGGCAGUGCAUGAAAUACUUUUAUGCAAUUGAAACGAAUUGCGGAAAAAUGAUUUAUGCCACAGCAUUAAAGC
.........(((----------.......(((.......))).(.(((((((.((.((((.(((((((......))))))).)))).)).)))))))).)))......... ( -20.80)
>DroAna_CAF1 78630 105 - 1
AUGU----UCUG-GUGGUCCACAGCGGCAGCCGA-AGGAGCUAGUGCAUAAAGUAUUUUUUUGCAAUUGAAACGAAUUGCGGAAAAAUGAUUUAUGCCACAGCAUUAAAGC
..((----(((.-.((((((.....))..)))).-.)))))..(((((((((.(((((((((((((((......))))))))))))))).)))))).)))........... ( -34.40)
>DroPer_CAF1 146075 107 - 1
----ACACAACAGAAGAAGCAGAAGCAGAGGCAGAAGCAGCACCAGCAUGAAAUAUUUUUAUGCAAUUGAAACGAAUUGCGAAAAAAUGAUUUAUGCCACAGCAUUAAAGC
----..............((....((....((....)).))....(((((((.(((((((.(((((((......))))))).))))))).)))))))....))........ ( -23.20)
>consensus
AUACACACACUG__________AAAGUCAGCCAAAAGAAGGCAGUGCAUGAAAUACUUUUAUGCAAUUGAAACGAAUUGCGGAAAAAUGAUUUAUGCCACAGCAUUAAAGC
.............................(((.......))).(((((((((.((.((((.(((((((......))))))).)))).)).)))))).)))........... (-16.52 = -16.42 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:09 2006