Locus 493

Sequence ID 2R_DroMel_CAF1
Location 2,707,040 – 2,707,135
Length 95
Max. P 0.907784
window937 window938

overview

Window 7

Location 2,707,040 – 2,707,135
Length 95
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 68.89
Mean single sequence MFE -35.68
Consensus MFE -16.35
Energy contribution -17.66
Covariance contribution 1.31
Combinations/Pair 1.16
Mean z-score -2.10
Structure conservation index 0.46
SVM decision value 0.85
SVM RNA-class probability 0.865376
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2707040 95 + 20766785
GACUUAU-----------AUAGUGUACAUAGUGGGAUGCGGUGGAAGCGGUGGAA--AAAGCGA--GGAGCUG-----GCGCAAUUUCAGUGCUCUGCUCUGGCGAGCUCCGCUU
.......-----------...((...(((.((.....)).)))...))((((((.--...((..--(((((.(-----((((.......)))))..))))).))....)))))). ( -28.30)
>DroSec_CAF1 3362 105 + 1
GGCUUAUACAUAGUGUACAUAGUGUACAUAGUGGGAUGCGGUGGAAGCGGCGGAA---AAGCGA--GGAGCUG-----GCGCAAUUUCAGAGCUCUGCUCUGGCGAGCUCCGCUU
.((((...(((.((((((.....)))))).)))...(((.((....)).)))...---))))..--((((((.-----((.......((((((...)))))))).)))))).... ( -38.91)
>DroYak_CAF1 3571 97 + 1
GGCUUAU-----------AAAGUGUGCAUAGUGAAAUACGCUGGAAGCGGUGGAA--UAAGCGAGUGGAGCUA-----GCGCAAUUUUAGAGCUCUGCUUUGGCGAGCUCCGCUU
.((((((-----------..(.(((...(((((.....)))))...))).)...)--)))))((((((((((.-----((.(((...(((....)))..))))).)))))))))) ( -35.30)
>DroAna_CAF1 3131 93 + 1
UG----G-----------GAGCUGGGCGCUGAG-----AGCUGGGAGUAAUGUAAGGCAAGCGA--GUGGCUGCAUUUCAGCAAUUUUAGUGCUCUGCUACGGCGAGCUCCGCUU
..----(-----------(((((((((((((((-----(((((..(..........(((.((..--...))))).)..))))..)))))))))))(((....))))))))).... ( -40.20)
>consensus
GGCUUAU___________AAAGUGUACAUAGUGGGAUGCGCUGGAAGCGGUGGAA___AAGCGA__GGAGCUG_____GCGCAAUUUCAGAGCUCUGCUCUGGCGAGCUCCGCUU
............................................((((((((.......(((.......))).......))).......((((((.((....))))))))))))) (-16.35 = -17.66 +   1.31) 

alignment

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secondary structure

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dotplot

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Window 8

Location 2,707,040 – 2,707,135
Length 95
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 68.89
Mean single sequence MFE -24.98
Consensus MFE -13.90
Energy contribution -14.40
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.56
SVM decision value 1.06
SVM RNA-class probability 0.907784
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2707040 95 - 20766785
AAGCGGAGCUCGCCAGAGCAGAGCACUGAAAUUGCGC-----CAGCUCC--UCGCUUU--UUCCACCGCUUCCACCGCAUCCCACUAUGUACACUAU-----------AUAAGUC
..((((.((((....)))).((((...((((..(((.-----.......--.)))..)--)))....))))...)))).......((((((...)))-----------))).... ( -22.70)
>DroSec_CAF1 3362 105 - 1
AAGCGGAGCUCGCCAGAGCAGAGCUCUGAAAUUGCGC-----CAGCUCC--UCGCUU---UUCCGCCGCUUCCACCGCAUCCCACUAUGUACACUAUGUACACUAUGUAUAAGCC
..(.(((((((((((((((...)))))).....))).-----.))))))--.)((((---.......((.......)).........(((((.....)))))........)))). ( -28.00)
>DroYak_CAF1 3571 97 - 1
AAGCGGAGCUCGCCAAAGCAGAGCUCUAAAAUUGCGC-----UAGCUCCACUCGCUUA--UUCCACCGCUUCCAGCGUAUUUCACUAUGCACACUUU-----------AUAAGCC
.((.((((((.(((((...((....))....))).))-----.)))))).)).(((((--(......((.....))((((......)))).......-----------)))))). ( -23.60)
>DroAna_CAF1 3131 93 - 1
AAGCGGAGCUCGCCGUAGCAGAGCACUAAAAUUGCUGAAAUGCAGCCAC--UCGCUUGCCUUACAUUACUCCCAGCU-----CUCAGCGCCCAGCUC-----------C----CA
..(.((((((.(.(((.(.(((((........(((......)))((...--..))...................)))-----))).))).).)))))-----------)----). ( -25.60)
>consensus
AAGCGGAGCUCGCCAGAGCAGAGCACUAAAAUUGCGC_____CAGCUCC__UCGCUU___UUCCACCGCUUCCACCGCAUCCCACUAUGCACACUAU___________AUAAGCC
(((((((((((((....)).)))))).......((.........))......))))).......................................................... (-13.90 = -14.40 +   0.50) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:05 2006