Locus 678

Sequence ID 3L_DroMel_CAF1
Location 2,013,476 – 2,013,574
Length 98
Max. P 0.783431
window1033 window1034

overview

Window 3

Location 2,013,476 – 2,013,574
Length 98
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 82.12
Mean single sequence MFE -34.49
Consensus MFE -23.23
Energy contribution -24.40
Covariance contribution 1.17
Combinations/Pair 1.12
Mean z-score -2.24
Structure conservation index 0.67
SVM decision value 0.56
SVM RNA-class probability 0.783431
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2013476 98 + 23771897
GGGCGAAAAGCCAGAGUUGGUCUGAAUUCCUGACUAGCAAAUGUCUGGCUAUCGGCCAU-------UGGCCAACGGACAGCACAA--CAAUGGCUGACCAG---CGUCAG
.((((...((((((((((((((.........))))))).....))))))).((((((((-------((.................--))))))))))....---)))).. ( -37.03)
>DroSim_CAF1 79099 98 + 1
GGGCGAAGAGCCAGAGUUGGUCUGAAUUCCUGACUAGCAAAUGUCUGGCUAUCGGCCAU-------UGGCCACCGGACAGCACAA--CAAUGGCUGACCAG---CGUCAG
.((((...((((((((((((((.........))))))).....))))))).((((((((-------((.................--))))))))))....---)))).. ( -37.13)
>DroEre_CAF1 70169 98 + 1
GGGCGAAAAGCCACAGUUGGUCUGAAUUCCUGACUAGCAAAUGUCUGGCUAUCGGCCAU-------UGGCCACCGGACAGCACAA--CAAUGGCUGACCAG---CGUCAG
.((((...(((((..(((((((.........)))))))...(((((((.....((((..-------.)))).)))))))......--...)))))......---)))).. ( -35.00)
>DroWil_CAF1 96867 87 + 1
GGCAGAGAAGCCA--GUCGGGCUGAAUUCCUGACUAGCAAAUGUCUG---------------------GCCACUGGACAGCACAACACAAUGGCUGACCAGUAGUGUCAG
(((......)))(--((((((.......))))))).........(((---------------------((((((((.((((.((......)))))).))))).).))))) ( -32.20)
>DroYak_CAF1 66149 105 + 1
GGGCGAAAAGCCACAGUUGGUCUGAAUUCCUGACUAGCAAAUGUCUGGCUAUCGGCCAUUGGCCAUUGGCCACCGGACAGCACAA--CAAUGGCUGACCAG---CGUCAG
.((((...(((((..((((..(((...(((.(((........)))((((((..((((...))))..))))))..))))))..)))--)..)))))......---)))).. ( -40.00)
>DroAna_CAF1 61183 84 + 1
GAGCCAAAAGCCAGAGCCGAUCUGAAUUCCUGACUGGCAAAUGUCUG---------------------GCCGCCGGACAACACAA--CAAUGGCUGACCAG---CGUCAG
.(((((...(((((....((.......))....)))))...((((((---------------------(...)))))))......--...)))))(((...---.))).. ( -25.60)
>consensus
GGGCGAAAAGCCAGAGUUGGUCUGAAUUCCUGACUAGCAAAUGUCUGGCUAUCGGCCAU_______UGGCCACCGGACAGCACAA__CAAUGGCUGACCAG___CGUCAG
........(((((..(((((((.........)))))))...((((((......(((((........)))))..))))))...........)))))(((.......))).. (-23.23 = -24.40 +   1.17) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 2,013,476 – 2,013,574
Length 98
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 82.12
Mean single sequence MFE -34.38
Consensus MFE -23.82
Energy contribution -24.55
Covariance contribution 0.72
Combinations/Pair 1.16
Mean z-score -1.91
Structure conservation index 0.69
SVM decision value 0.39
SVM RNA-class probability 0.718177
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2013476 98 - 23771897
CUGACG---CUGGUCAGCCAUUG--UUGUGCUGUCCGUUGGCCA-------AUGGCCGAUAGCCAGACAUUUGCUAGUCAGGAAUUCAGACCAACUCUGGCUUUUCGCCC
.....(---(.((..(((((..(--(((..(((((((((((((.-------..))))))).....(((........))).)))...)))..))))..)))))..)))).. ( -33.00)
>DroSim_CAF1 79099 98 - 1
CUGACG---CUGGUCAGCCAUUG--UUGUGCUGUCCGGUGGCCA-------AUGGCCGAUAGCCAGACAUUUGCUAGUCAGGAAUUCAGACCAACUCUGGCUCUUCGCCC
.((.((---((((.((((((...--.)).)))).))))))..))-------..(((.((.(((((((...(((...(((.........)))))).))))))).)).))). ( -34.80)
>DroEre_CAF1 70169 98 - 1
CUGACG---CUGGUCAGCCAUUG--UUGUGCUGUCCGGUGGCCA-------AUGGCCGAUAGCCAGACAUUUGCUAGUCAGGAAUUCAGACCAACUGUGGCUUUUCGCCC
.((.((---((((.((((((...--.)).)))).))))))..))-------..(((.((.((((((((........))).((........)).....))))).)).))). ( -34.10)
>DroWil_CAF1 96867 87 - 1
CUGACACUACUGGUCAGCCAUUGUGUUGUGCUGUCCAGUGGC---------------------CAGACAUUUGCUAGUCAGGAAUUCAGCCCGAC--UGGCUUCUCUGCC
......(((((((.((((((......)).)))).))))))).---------------------((((.....(((((((.((.......)).)))--))))...)))).. ( -34.80)
>DroYak_CAF1 66149 105 - 1
CUGACG---CUGGUCAGCCAUUG--UUGUGCUGUCCGGUGGCCAAUGGCCAAUGGCCGAUAGCCAGACAUUUGCUAGUCAGGAAUUCAGACCAACUGUGGCUUUUCGCCC
((((((---((((.((((((...--.)).)))).)))))(((...(((((...)))))...)))............))))).....(((.....))).(((.....))). ( -37.70)
>DroAna_CAF1 61183 84 - 1
CUGACG---CUGGUCAGCCAUUG--UUGUGUUGUCCGGCGGC---------------------CAGACAUUUGCCAGUCAGGAAUUCAGAUCGGCUCUGGCUUUUGGCUC
....((---((((.((((((...--.)).)))).))))))((---------------------((((.....(((.(((.........))).)))))))))......... ( -31.90)
>consensus
CUGACG___CUGGUCAGCCAUUG__UUGUGCUGUCCGGUGGCCA_______AUGGCCGAUAGCCAGACAUUUGCUAGUCAGGAAUUCAGACCAACUCUGGCUUUUCGCCC
(((((....((((.((((((......)).)))).))))((((..........((((.....)))).......)))))))))(((...((.(((....))))).))).... (-23.82 = -24.55 +   0.72) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:17 2006