Locus 665

Sequence ID 3L_DroMel_CAF1
Location 1,980,177 – 1,980,276
Length 99
Max. P 0.912274
window1016 window1017

overview

Window 6

Location 1,980,177 – 1,980,276
Length 99
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 69.35
Mean single sequence MFE -21.70
Consensus MFE -5.73
Energy contribution -6.09
Covariance contribution 0.37
Combinations/Pair 1.43
Mean z-score -2.04
Structure conservation index 0.26
SVM decision value 0.06
SVM RNA-class probability 0.563858
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1980177 99 + 23771897
U----GUUGUUUCUUCUCCAACAGCAGUUUCCCUUUUAUUU-CUUCACUUGCUUGACACAAAAAAAAAUGCACACUAGCCG--------UGCUGCAGAAAGAAAUAGUAUCA
(----((((((........))))))).........((((((-((((..(((.......))).......(((((((.....)--------)).))))).)))))))))..... ( -16.90)
>DroSec_CAF1 31189 92 + 1
U----GUUGUUUCUUCUCCUGCAGCAGUUUCCCUUUUAUUU-CUUCACUCGCUGG-------AAGAAAUGCACACUAGCCG--------UGCUGCAGAAAGAAAUGGUAUCA
(----(..(((((((...(((((((((((.......(((((-((((.(.....))-------))))))))......)))..--------)))))))).)))))))..))... ( -28.22)
>DroSim_CAF1 45379 92 + 1
U----GUUGUUUCUUCUCCUGCAGCAGUUUCCCUUUUAUUU-CUUCACUUGCUGG-------AAGAAAUGCACACUGGCCG--------UGCUGCAGAAAGAAAUGGUAUCA
(----(..(((((((...(((((((((((.......(((((-((((.(.....))-------))))))))......)))..--------)))))))).)))))))..))... ( -28.12)
>DroEre_CAF1 36976 95 + 1
UGUCUGUUAUUUCUUCUCCACUAGCAGUUUCCCUUUUAUAUAGUAUACUUGCUGA---------AAAAUGCACACUAGCAG--------UGCUGCAAAAAGAAAUAGUAUCA
......(((((((((......(((((((....((.......))...)).))))).---------....(((((((.....)--------)).))))..)))))))))..... ( -16.60)
>DroYak_CAF1 31989 98 + 1
G----GUUAUUUCUUCUCCCCUAGCAGUUUCCCUUUUAUUU-CUUUACUUGCUGA---------AAAAUGCACACUUGCAGUGCUACAGUGCUGCAAAAAGAAAUAGUAUCA
(----(..(((.((........)).)))..))...((((((-((((...(((...---------.....)))...((((((..(....)..))))))))))))))))..... ( -23.40)
>DroAna_CAF1 29155 91 + 1
U----CCCGCCCCUCGCCUCUCGCCCAUCGCCCUCUGACUA-UUGCUAUUGCUAU---------CAGUUUCCCUUUCGCAG-------GAGUCGAAAAAACUAUGGGUAUCA
.----...((((.(((.(((..((..........((((...-..((....))..)---------)))..........))..-------))).))).........)))).... ( -16.95)
>consensus
U____GUUGUUUCUUCUCCACCAGCAGUUUCCCUUUUAUUU_CUUCACUUGCUGG_________AAAAUGCACACUAGCAG________UGCUGCAAAAAGAAAUAGUAUCA
......(((((((((......((((((.....................))))))..............((((((...............)).))))..)))))))))..... ( -5.73 =  -6.09 +   0.37)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,980,177 – 1,980,276
Length 99
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 69.35
Mean single sequence MFE -24.37
Consensus MFE -12.33
Energy contribution -12.62
Covariance contribution 0.28
Combinations/Pair 1.53
Mean z-score -1.81
Structure conservation index 0.51
SVM decision value 1.08
SVM RNA-class probability 0.912274
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1980177 99 - 23771897
UGAUACUAUUUCUUUCUGCAGCA--------CGGCUAGUGUGCAUUUUUUUUUGUGUCAAGCAAGUGAAG-AAAUAAAAGGGAAACUGCUGUUGGAGAAGAAACAAC----A
........(((((((..((((((--------.(((......)).(((((((((((.(((......)))..-..))))))))))).))))))).))))))).......----. ( -21.40)
>DroSec_CAF1 31189 92 - 1
UGAUACCAUUUCUUUCUGCAGCA--------CGGCUAGUGUGCAUUUCUU-------CCAGCGAGUGAAG-AAAUAAAAGGGAAACUGCUGCAGGAGAAGAAACAAC----A
........((((((.(((((((.--------..((......))(((((((-------((.....).))))-))))....((....))))))))))))))).......----. ( -28.20)
>DroSim_CAF1 45379 92 - 1
UGAUACCAUUUCUUUCUGCAGCA--------CGGCCAGUGUGCAUUUCUU-------CCAGCAAGUGAAG-AAAUAAAAGGGAAACUGCUGCAGGAGAAGAAACAAC----A
........((((((.((((((((--------.(.((..(....(((((((-------((.....).))))-))))..)..))...))))))))))))))).......----. ( -27.00)
>DroEre_CAF1 36976 95 - 1
UGAUACUAUUUCUUUUUGCAGCA--------CUGCUAGUGUGCAUUUU---------UCAGCAAGUAUACUAUAUAAAAGGGAAACUGCUAGUGGAGAAGAAAUAACAGACA
......(((((((((((....((--------((((((((((((.....---------.......)))))))).......((....)))).)))))))))))))))....... ( -22.70)
>DroYak_CAF1 31989 98 - 1
UGAUACUAUUUCUUUUUGCAGCACUGUAGCACUGCAAGUGUGCAUUUU---------UCAGCAAGUAAAG-AAAUAAAAGGGAAACUGCUAGGGGAGAAGAAAUAAC----C
......(((((((((.((((.(((((((....))).)))))))).((.---------.((((......(.-...)....((....))))).)..)))))))))))..----. ( -23.30)
>DroAna_CAF1 29155 91 - 1
UGAUACCCAUAGUUUUUUCGACUC-------CUGCGAAAGGGAAACUG---------AUAGCAAUAGCAA-UAGUCAGAGGGCGAUGGGCGAGAGGCGAGGGGCGGG----A
.....(((((.(((((((.((((.-------.(((....((....)).---------.((....))))).-.))))))))))).)))))(....)((.....))...----. ( -23.60)
>consensus
UGAUACCAUUUCUUUCUGCAGCA________CGGCUAGUGUGCAUUUU_________CCAGCAAGUGAAG_AAAUAAAAGGGAAACUGCUGCAGGAGAAGAAACAAC____A
........((((((.(((((((...........((......))....................................((....)))))))))))))))............ (-12.33 = -12.62 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:00 2006