Locus 5937

Sequence ID 2R_DroMel_CAF1
Location 18,731,762 – 18,731,855
Length 93
Max. P 0.992234
window9522 window9523

overview

Window 2

Location 18,731,762 – 18,731,855
Length 93
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 77.54
Mean single sequence MFE -23.16
Consensus MFE -14.40
Energy contribution -15.23
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.62
SVM decision value 1.16
SVM RNA-class probability 0.924740
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18731762 93 + 20766785
GAGUUGGUAAA---------AAAAAAGGUAUAAGCAG---AGCGCAGAGCGGAAAACAAAAUGUUUAUCUUGUGCAAGCAUUUUGCUUUCCAAAU-------CCACUUCCAG
(((.(((....---------.................---.((.....))(((((.((((((((((.........)))))))))).)))))....-------))).)))... ( -19.80)
>DroSec_CAF1 94622 84 + 1
GAGUUGGGAA-------------AAAGGUAU-----G---AGAGCAGAGCGGAAAACAAAAUGUUUAUCUUGUGCAAGCAUUUUGCUUUCCAAAU-------CCAAUUCCAG
((((((((..-------------........-----.---...((...))(((((.((((((((((.........)))))))))).)))))...)-------)))))))... ( -22.90)
>DroSim_CAF1 95450 84 + 1
GAGUGGGGAA-------------AAAGCUAU-----G---AGAGCAGAGCGGAAAACAAAAUGUUUAUCUUGUGCAAGCAUUUUGCUUUCCAAAU-------CCACUUCCAG
(((((((...-------------...(((.(-----(---....)).)))(((((.((((((((((.........)))))))))).)))))...)-------)))))).... ( -25.90)
>DroEre_CAF1 95791 84 + 1
GAGUUGG-------------AGAAAAGGUAUA--------AGAGCAGAGCGGAAAACAAAAUGUUUAUCUUGUGCAAGCAUUUUGCUUUCCAAAU-------CCACUUCCAG
(((.(((-------------(...........--------...((...))(((((.((((((((((.........)))))))))).)))))...)-------))).)))... ( -19.80)
>DroYak_CAF1 96737 112 + 1
GAGUUGGGAAAAUAGGUAUGAAAAAAGGUAUGAUGAGAGUAGAGCAGAGCGGAAAACAAAAUGUUUAUCUUGUGCAAGCAUUUUGCUUUCCAAAUCCACAAUCCACUUCCAG
(..((((((..................((...((....))...)).....(((((.((((((((((.........)))))))))).)))))...))).)))..)........ ( -21.80)
>DroAna_CAF1 93242 91 + 1
GAGGAGGGCCAGUGGAGGUG------GAAAU-----A---AAAGCUGGGCGACAAACAAAAUAUUUAUCUUGUGCAAGCAUUUUGCUUUCCAAAU-------CCACUUCCAU
.....(((..((((((..((------(((((-----(---((((((..((.((((..............)))))).))).))))).))))))..)-------)))))))).. ( -28.74)
>consensus
GAGUUGGGAA_____________AAAGGUAU_____G___AGAGCAGAGCGGAAAACAAAAUGUUUAUCUUGUGCAAGCAUUUUGCUUUCCAAAU_______CCACUUCCAG
(((.(((....................................((...))(((((.((((((((((.........)))))))))).)))))...........))).)))... (-14.40 = -15.23 +   0.83)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,731,762 – 18,731,855
Length 93
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 77.54
Mean single sequence MFE -24.25
Consensus MFE -15.51
Energy contribution -15.40
Covariance contribution -0.11
Combinations/Pair 1.10
Mean z-score -3.28
Structure conservation index 0.64
SVM decision value 2.32
SVM RNA-class probability 0.992234
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18731762 93 - 20766785
CUGGAAGUGG-------AUUUGGAAAGCAAAAUGCUUGCACAAGAUAAACAUUUUGUUUUCCGCUCUGCGCU---CUGCUUAUACCUUUUUU---------UUUACCAACUC
..(((((..(-------(...(((((((((((((.((((....).))).)))))))))))))((.....)))---)..)))...))......---------........... ( -22.60)
>DroSec_CAF1 94622 84 - 1
CUGGAAUUGG-------AUUUGGAAAGCAAAAUGCUUGCACAAGAUAAACAUUUUGUUUUCCGCUCUGCUCU---C-----AUACCUUU-------------UUCCCAACUC
..((((..((-------....(((((((((((((.((((....).))).)))))))))))))((...))...---.-----...))...-------------))))...... ( -21.00)
>DroSim_CAF1 95450 84 - 1
CUGGAAGUGG-------AUUUGGAAAGCAAAAUGCUUGCACAAGAUAAACAUUUUGUUUUCCGCUCUGCUCU---C-----AUAGCUUU-------------UUCCCCACUC
.....(((((-------....(((((((((((((.((((....).))).)))))))))))))(((.((....---)-----).)))...-------------....))))). ( -24.40)
>DroEre_CAF1 95791 84 - 1
CUGGAAGUGG-------AUUUGGAAAGCAAAAUGCUUGCACAAGAUAAACAUUUUGUUUUCCGCUCUGCUCU--------UAUACCUUUUCU-------------CCAACUC
.((((((..(-------(..((((((((((((((.((((....).))).)))))))))))))).))..))..--------...........)-------------))).... ( -22.61)
>DroYak_CAF1 96737 112 - 1
CUGGAAGUGGAUUGUGGAUUUGGAAAGCAAAAUGCUUGCACAAGAUAAACAUUUUGUUUUCCGCUCUGCUCUACUCUCAUCAUACCUUUUUUCAUACCUAUUUUCCCAACUC
.((..((((((..(..((..((((((((((((((.((((....).))).)))))))))))))).))..)))))))..))................................. ( -28.40)
>DroAna_CAF1 93242 91 - 1
AUGGAAGUGG-------AUUUGGAAAGCAAAAUGCUUGCACAAGAUAAAUAUUUUGUUUGUCGCCCAGCUUU---U-----AUUUC------CACCUCCACUGGCCCUCCUC
..((.(((((-------(..((((((..((((.(((.((....(((((((.....)))))))))..))))))---)-----.))))------))..))))))..))...... ( -26.50)
>consensus
CUGGAAGUGG_______AUUUGGAAAGCAAAAUGCUUGCACAAGAUAAACAUUUUGUUUUCCGCUCUGCUCU___C_____AUACCUUU_____________UUCCCAACUC
..((.................(((((((((((((.((((....).))).)))))))))))))((...))....................................))..... (-15.51 = -15.40 +  -0.11)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:29 2006