Locus 2362

Sequence ID 2L_DroMel_CAF1
Location 6,405,942 – 6,406,086
Length 144
Max. P 0.617304
window3804 window3805

overview

Window 4

Location 6,405,942 – 6,406,057
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.62
Mean single sequence MFE -28.62
Consensus MFE -22.68
Energy contribution -22.92
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.62
Structure conservation index 0.79
SVM decision value 0.17
SVM RNA-class probability 0.617304
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6405942 115 + 22407834
CUCUGAGGGAUGAUCCAAAUCAAUGUCAG-----AGGAAAGGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCUGCCUACUUCCCCGAAACAUUUCCGGCU
((((((.(..((((....)))).).))))-----))....(((((..(((....)))......(..(((((((.((((((......)))))).)))).)))..).......))))).... ( -25.30)
>DroSec_CAF1 34296 115 + 1
CUCUGAGGGAUGAUCCAAAUCAAUGUCAG-----AGGAAAGGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCAGCCUACUACCCCGAAACAUUUCCGUGC
((((((.(..((((....)))).).))))-----))....(((((..(((....)))..........(((((((((((((......))))))))))).))...........))))).... ( -28.60)
>DroSim_CAF1 34816 115 + 1
CUCUGAGGGAUGAUCCAAAUCAAUGUCAG-----AGGAAAGGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCAGCCUACUACCCCGAAACAUUUCCGUGC
((((((.(..((((....)))).).))))-----))....(((((..(((....)))..........(((((((((((((......))))))))))).))...........))))).... ( -28.60)
>DroEre_CAF1 32784 115 + 1
CUCUGAGGGAUGAUCCAAAUCAAUGUCAG-----AGCAAAGGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCAGCCUACUGCUCCGAAACAUUUCCGGGC
((((((.(..((((....)))).).))))-----))....(((((..(((....))).((..((.((..(((((((((((......)))))))))))..))))..))....))))).... ( -29.60)
>DroYak_CAF1 38109 120 + 1
CUCUGGGGGAUGAUCCAAAUCAAUGUCAGUGGAAAGGAAAGGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCAGCCUACUUCUCCGAAACAUUUCCGGAC
.((((((((.....)).....(((((...((((.(((...(....).......................(((((((((((......))))))))))).))).))))..))))))))))). ( -31.00)
>consensus
CUCUGAGGGAUGAUCCAAAUCAAUGUCAG_____AGGAAAGGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCAGCCUACUACCCCGAAACAUUUCCGGGC
..((((.(..((((....)))).).))))......((((((....).....................(((((((((((((......))))))))))).))...........))))).... (-22.68 = -22.92 +   0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,405,977 – 6,406,086
Length 109
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 91.62
Mean single sequence MFE -29.30
Consensus MFE -24.25
Energy contribution -24.61
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -1.34
Structure conservation index 0.83
SVM decision value 0.11
SVM RNA-class probability 0.586507
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6405977 109 + 22407834
GGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCUGCCUACUUCCCCGAAACAUUUCCGGCUUGAA------AUAGGUGAGUUG--GGGGAAGCGACGU
(....).................(((...((((.((((((......)))))).)))).((((((((((....)))((((((...------......))))))--))))))).))).. ( -30.10)
>DroSec_CAF1 34331 109 + 1
GGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCAGCCUACUACCCCGAAACAUUUCCGUGCUGAA------AUAGGUGAGUUG--AGGGAAGCGACGU
(....).................(((.(((((((((((((......))))))))))).))..(((..(((.((.((........------...)).))))).--.)))....))).. ( -26.90)
>DroSim_CAF1 34851 109 + 1
GGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCAGCCUACUACCCCGAAACAUUUCCGUGCUGAA------AUAGGUGAGUUG--GGGGAAGCGACGU
(....).................(((.(((((((((((((......))))))))))).)).((((((.(((((((......)))------))..))...)))--))).....))).. ( -30.50)
>DroEre_CAF1 32819 109 + 1
GGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCAGCCUACUGCUCCGAAACAUUUCCGGGCUUCU------AUAGGUGAGUUG--GGGGAAGCGACGU
(....).................(((.(((((((((((((......))))))))))).))(((........(..((.(((((..------......))))).--))..))))))).. ( -28.50)
>DroYak_CAF1 38149 117 + 1
GGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCAGCCUACUUCUCCGAAACAUUUCCGGACUACUACGAGUAUAGGUGAGUUGUGGGGUAAGCGACGU
(....).................(((...(((((((((((......))))))))))).((((((((.(((.((.((..(((......)))...)).))))).))))).))).))).. ( -30.50)
>consensus
GGAAACAUAAGAAAUUACUCAAAGUCAAGAGGUUGUUGAAACUAUGUUUAGCAGCCUACUACCCCGAAACAUUUCCGGGCUGAA______AUAGGUGAGUUG__GGGGAAGCGACGU
(....).................(((...(((((((((((......))))))))))).((.((((..(((.((.((.................)).)))))...)))).)).))).. (-24.25 = -24.61 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:12 2006