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Marcel Costa 1 year ago
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  1. +205
    -0
      ONATRY-CIT/app.R
  2. +19
    -0
      Scripts/Human.Codon.Usage
  3. +60
    -0
      Scripts/pca_HAdV5_EGFP_MONO_EMM_BH_VCN_APIS_MOD_PDT_ADAPT_Tox.txt
  4. +17
    -0
      Scripts/tabla_cai_early_proteins.txt
  5. +55
    -0
      Scripts/tabla_cai_human_proteins.txt
  6. +18
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      Scripts/tabla_cai_late_proteins.txt
  7. +37
    -0
      Scripts/tabla_cai_viral_proteins.txt
  8. +36
    -0
      example.fasta

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ONATRY-CIT/app.R
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library(shiny)
library(coRdon)
library(Biostrings)
library(tidyverse)
library(pcaMethods)
library(ggpubr)
# Define UI for application that draws a histogram
ui <- fluidPage(
verticalLayout(
titlePanel("ONATRY-CIT"),
wellPanel(
textAreaInput("query", "Text in fasta format", width = "100%", height = "300px"),
actionButton("submit", label = "Submit")
),
plotOutput("result", width = "1200px", height = "800px")
)
)
# Define server logic required to draw a histogram
server <- function(input, output) {
process<-eventReactive(input$submit, {
fa=input$query
fasplit<-strsplit(gsub("^>","",fa), ">")[[1]]
txtQuery<-c()
names<-c()
for (i in 1:length(fasplit)){
query_split<-strsplit(fasplit[[i]], "\n|\r")[[1]]
names<-c(names, strsplit(query_split[1], " ")[[1]][1])
txtQuery<-c(txtQuery, paste0(query_split[2:length(query_split)], collapse = ""))
}
names(txtQuery)<-names
txtQuery<-gsub("\n","",txtQuery)
dnaQuery<-DNAStringSet(txtQuery)
Query<-codonTable(dnaQuery)
CodRef<-list(
Ala=c("GCG","GCA","GCT","GCC"),
Cys=c("TGT","TGC"),
Asp=c("GAT","GAC"),
Glu=c("GAG","GAA"),
Phe=c("TTT","TTC"),
Gly=c("GGG","GGA","GGT","GGC"),
His=c("CAT","CAC"),
Ile=c("ATA","ATT","ATC"),
Lys=c("AAG","AAA"),
Leu=c("TTG","TTA","CTG","CTA","CTT","CTC"),
Met=c("ATG"),
Asn=c("AAT","AAC"),
Pro=c("CCG","CCA","CCT","CCC"),
Gln=c("CAG","CAA"),
Arg=c("AGG","AGA","CGG","CGA","CGT","CGC"),
Ser=c("AGT","AGC","TCG","TCA","TCT","TCC"),
Thr=c("ACG","ACA","ACT","ACC"),
Val=c("GTG","GTA","GTT","GTC"),
Trp=c("TGG"),
Tyr=c("TAT","TAC"),
End=c("TGA","TAG","TAA")
)
UsedCodons<-unlist(CodRef[sapply(CodRef,length) > 1 & names(CodRef) != "End"])
list2data<-function(x, var.column="Names", val.column="Values"){
names<-c()
for (name in names(x)){
names<-c(names, rep(name, length(x[[name]])))
}
df<-data.frame(names, unlist(x), row.names = NULL)
colnames(df)<-c(var.column, val.column)
return(df)
}
Query_CU<-t(codonCounts(Query)) %>%
as.data.frame() %>%
setNames(names(txtQuery)) %>%
rownames_to_column("codon") %>%
# mutate(across(all_of(names(txtQuery)), function(x) x=1000*x/sum(x))) %>%
merge(list2data(CodRef, "AA","codon")) %>%
group_by(AA) %>%
mutate(across(all_of(names(txtQuery)), function(x) x=x/sum(x))) %>%
ungroup()
pca_ref<-read.table("../Scripts/pca_HAdV5_EGFP_MONO_EMM_BH_VCN_APIS_MOD_PDT_ADAPT_Tox.txt",sep="\t", dec = ",", header = T)
pca_ref$codon<-gsub(" ","",pca_ref$codon)
pca_tab<-merge(pca_ref,
Query_CU %>% select(-AA)
)
pcares<-pca(pca_tab %>% column_to_rownames("codon") %>% as.matrix %>% t(),
method="svd", nPCs=10) #comando para hacer el PCA
g_PCA<-pcares@scores %>%
as.data.frame %>%
rownames_to_column("NAME") %>%
add_column("TYPE"=c(rep("Structural", 20),rep("Early",16), rep("References", 6),
rep("Query",length(names(txtQuery))))) %>%
ggplot(aes(PC1,PC2, color=TYPE))+
geom_point(size=15, alpha=0.25)+
geom_point(data=function(x){filter(x, TYPE %in% c("References","Query"))},size=2, alpha=0.5)+
geom_text(aes(label=NAME),show.legend=FALSE)+
scale_color_manual(values=c("Early"="cornflowerblue","Structural"="darkgrey","References"="brown","Query"="black"))+
theme_gray(base_size = 15)+
ggtitle("PCA Codon Usage")+
theme(aspect.ratio = 1)
hcu<-read.table("../Scripts/Human.Codon.Usage", header = F, sep=" ")
hcu<-rbind(
hcu[,c("V1","V2")] %>% rename(Codon=V1, Usage=V2),
hcu[,c("V3","V4")] %>% rename(Codon=V3, Usage=V4),
hcu[,c("V5","V6")] %>% rename(Codon=V5, Usage=V6),
hcu[,c("V7","V8")] %>% rename(Codon=V7, Usage=V8)
) %>%
mutate(Usage=as.numeric(gsub("\\([0-9]*\\)","",Usage)))
w<-merge(
list2data(CodRef, "AA","Codon"),
hcu
) %>%
group_by(AA) %>%
mutate(Weight=Usage/max(Usage))
Query_codons<-sapply(txtQuery, function(x) substring(x,seq(1,(nchar(x)-2),3), seq(3,nchar(x),3)))
Query_CAI<-do.call(rbind, lapply(names(Query_codons), function(x){
merge(
data.frame(Position=1:length(Query_codons[[x]]),
Codon=Query_codons[[x]],
Name=x),
w[,c("Codon","AA","Weight")]
) %>% arrange(Position)
}))
Query_CAI[Query_CAI$AA %in% c("Met","End","Trp"),"Weight"]<-0
#CAI
CAI<-Query_CAI %>% group_by(Name) %>%
summarise(mean=round(mean(Weight),digits = 2))
lengths<-Query_CAI %>% group_by(Name) %>% summarise(lengths=length(Weight))
lowess<-Query_CAI %>% group_by(Name) %>%
summarise(Weight=tail(lowess(Weight, f=0.15)$y,1))
g_CAI<-ggplot(Query_CAI, aes(Position, Weight, color=Name))+
geom_line(color=rgb(1,1,1,0.0))+
geom_smooth(se=F)+
geom_text(data=data.frame(Position=lengths$lengths+3,
Weight=lowess$Weight,
CAI=CAI$mean,
Name=CAI$Name),
aes(label=CAI), hjust=0, vjust=0.5, show.legend = F)+
ggtitle("CAI along sequence")+
theme_gray(base_size = 15)
AApos3<-sapply(txtQuery, function(x) strsplit(x, "")[[1]][seq(3, nchar(x), 3)])
GC3<-sapply(AApos3, function(x) 100*length(x[x %in% c("G","C")])/length(x))
table<-rbind(
read.table("../Scripts/tabla_cai_human_proteins.txt",header=TRUE,sep="\t",dec=".") %>% add_column(Type="Human"),
read.table("../Scripts/tabla_cai_early_proteins.txt",header=TRUE,sep="\t",dec=".") %>% add_column(Type="Early"),
read.table("../Scripts/tabla_cai_late_proteins.txt",header=TRUE,sep="\t",dec=".") %>% add_column(Type="Late")
)
dtGC3<-data.frame(
Name=c("LGFP", "EGFP","BWT","BHU",names(GC3)),
X.G.C.3.=c(44.8,96.7,70.8,84.9,GC3),
Type=factor(c("Low Expression","High Expression","High Expression","High Expression",rep("Query",length(GC3))),
levels = c("Early","Late","Human","High Expression","Low Expression","Query"))
)
table$Type<-factor(table$Type, levels=c("Early","Late","Human","High Expression","Low Expression","Query"))
g_GC3<-ggplot(table, aes(`X.G.C.3.`, fill=Type))+
geom_density(alpha=0.5)+
geom_density(fill=NA, aes(color=Type))+
scale_fill_manual(values=c("Early"="grey80","Late"="grey30", "Human"="#FFFF99",
"Low Expression"="red","High Expression"="green","Query"="purple"),drop=F)+
scale_color_manual(values=c("Early"="grey30","Late"="grey30", "Human"="#FFFF99",
"Low Expression"="red","High Expression"="green","Query"="purple"),drop=F)+
geom_segment(data=dtGC3, aes(x = X.G.C.3.,xend = X.G.C.3., y=0, yend=0.025, color=Type), linetype=2, linewidth=1, show.legend = F)+
geom_text(data=dtGC3, aes(x = X.G.C.3., y=0.026, label=Name, color=Type), angle=90, vjust=0.5, hjust=0, size=6, show.legend = F)+
xlim(0,100)+
labs(x="%GC3",y="Density")+
theme_classic(base_size = 15)+
ggtitle("%GC3")+
theme(panel.border = element_rect(fill=NA), aspect.ratio = 1)
ggarrange(
ggarrange(g_PCA, g_GC3),
g_CAI, ncol = 1, heights = c(0.6, 0.4)
)
})
output$result <- renderPlot({
observeEvent(input$submit, {})
if(input$query != ""){
process()
}
})
}
# Run the application
shinyApp(ui = ui, server = server)

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Scripts/Human.Codon.Usage
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TTT 17.1(189379) TCT 15.4(171196) TAT 12.0(132715) TGT 10.6(117458)
TTC 19.5(216388) TCC 17.7(196012) TAC 14.6(161579) TGC 12.2(135489)
TTA 7.8(86682) TCA 12.5(139095) TAA 0.5(5404) TGA 0.9(9518)
TTG 12.9(143507) TCG 4.5(50249) TAG 0.4(4328) TGG 12.1(134648)
CTT 13.3(147569) CCT 17.9(198345) CAT 11.1(123609) CGT 4.5(49921)
CTC 19.2(212802) CCC 20.3(225420) CAC 15.2(168062) CGC 10.5(115976)
CTA 7.2(79488) CCA 17.3(192119) CAA 12.7(140427) CGA 6.2(68859)
CTG 39.4(437308) CCG 7.3(81354) CAG 34.9(387120) CGG 11.7(129331)
ATT 15.8(175259) ACT 13.3(147134) AAT 17.1(190114) AGT 12.6(139465)
ATC 19.9(220634) ACC 18.4(203602) AAC 18.6(206688) AGC 19.9(220505)
ATA 7.5(82922) ACA 15.1(167136) AAA 25.1(278169) AGA 12.0(133268)
ATG 21.3(236510) ACG 6.0(66200) AAG 31.9(353825) AGG 11.9(131616)
GTT 10.9(121302) GCT 18.4(204091) GAT 22.3(246943) GGT 10.6(117456)
GTC 14.0(155761) GCC 28.1(311996) GAC 25.1(278549) GGC 22.3(247607)
GTA 7.1(78882) GCA 16.1(178106) GAA 30.4(336665) GGA 16.5(183190)
GTG 27.6(305878) GCG 7.6(84501) GAG 40.7(451726) GGG 16.5(182999)

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Scripts/pca_HAdV5_EGFP_MONO_EMM_BH_VCN_APIS_MOD_PDT_ADAPT_Tox.txt
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codon IV2a pol U_exon pTP 52K pIIIa III fiber pVII V X pVI hexon protease DBP 100K 33K IX 22K pVIII E3_12_5K E3_CR1_alpha0 E3_gp19K 10_5K E3_RID_alpha E3_RID_beta E3_14_7K E4_ORF6_7 E4_34K E4_ORF4 E4_ORF3 E4_ORFB E1B55K E1A E1B19K E4_ORF1 GFP_DEopt APIS_BH OPT_BH GFP_opt PH20 Tox
GCG "0,24" "0,26" "0,33" "0,14" "0,4" "0,47" "0,36" "0,05" "0,36" "0,44" "0,45" "0,18" "0,15" "0,07" "0,62" "0,19" "0,35" "0,05" "0,17" "0,37" "0,17" 0 "0,1" "0,29" "0,38" "0,2" "0,25" "0,2" "0,14" "0,36" 0 "0,13" "0,11" "0,29" "0,29" "0,1" 0 "0,57" 0 0 0 "0,32"
GCA "0,18" "0,12" "0,33" "0,08" "0,2" "0,18" "0,2" "0,2" "0,12" "0,09" "0,09" "0,12" "0,11" 0 "0,06" "0,15" "0,41" "0,27" "0,33" "0,05" "0,17" 0 "0,1" 0 "0,13" "0,1" "0,25" 0 0 "0,09" 0 "0,13" "0,28" "0,07" "0,07" "0,1" "0,88" "0,04" "0,04" 0 "0,26" "0,21"
GCT "0,12" "0,06" 0 "0,03" "0,13" "0,1" "0,13" "0,32" "0,09" "0,09" 0 "0,06" "0,31" "0,07" "0,13" "0,12" "0,15" "0,27" "0,22" "0,26" "0,17" 0 "0,6" "0,14" "0,25" "0,2" 0 "0,6" "0,29" "0,36" "0,38" "0,5" "0,33" "0,29" "0,43" "0,5" "0,13" "0,04" "0,22" 0 "0,48" "0,25"
GCC "0,45" "0,56" "0,33" "0,75" "0,27" "0,25" "0,31" "0,43" "0,42" "0,38" "0,45" "0,65" "0,44" "0,86" "0,19" "0,54" "0,09" "0,41" "0,28" "0,32" "0,5" 1 "0,2" "0,57" "0,25" "0,5" "0,5" "0,2" "0,57" "0,18" "0,63" "0,25" "0,28" "0,36" "0,21" "0,3" 0 "0,35" "0,74" 1 "0,26" "0,22"
TGT "0,14" "0,08" 0 "0,29" 0 0 0 1 0 0 0 0 "0,29" "0,5" "0,15" "0,14" 0 0 "0,33" 0 "0,56" "0,5" "0,38" 0 "0,33" "0,2" "0,33" 1 "0,63" "0,75" "0,33" "0,5" "0,52" "0,5" "0,67" 1 1 0 0 0 "0,64" "0,83"
TGC "0,86" "0,92" 0 "0,71" 1 0 1 0 0 0 1 1 "0,71" "0,5" "0,85" "0,86" 1 0 "0,67" 0 "0,44" "0,5" "0,63" 1 "0,67" "0,8" "0,67" 0 "0,38" "0,25" "0,67" "0,5" "0,48" "0,5" "0,33" 0 0 1 1 1 "0,36" "0,17"
GAT "0,31" "0,21" "0,5" "0,31" "0,31" "0,17" "0,23" "0,48" "0,17" "0,47" 0 "0,4" "0,39" "0,4" "0,33" "0,23" "0,17" "0,71" 0 "0,11" "0,5" 0 "0,33" "0,67" 0 "0,6" "0,43" "0,67" "0,89" "0,33" "0,71" "0,57" "0,73" "0,44" "0,86" "0,5" "0,72" "0,36" "0,05" "0,11" "0,67" "0,82"
GAC "0,69" "0,79" "0,5" "0,69" "0,69" "0,83" "0,77" "0,52" "0,83" "0,53" 0 "0,6" "0,61" "0,6" "0,67" "0,78" "0,83" "0,29" 1 "0,89" "0,5" 0 "0,67" "0,33" 1 "0,4" "0,57" "0,33" "0,11" "0,67" "0,29" "0,43" "0,27" "0,56" "0,14" "0,5" "0,28" "0,64" "0,95" "0,89" "0,33" "0,18"
GAG "0,26" "0,66" "0,67" "0,59" "0,95" "0,84" "0,75" "0,26" 1 "0,61" 0 "0,67" "0,35" "0,67" "0,6" "0,68" "0,63" "0,67" "0,68" "0,5" "0,9" 0 "0,4" 0 "0,5" 0 "0,44" "0,6" "0,79" "0,33" "0,67" "0,63" "0,81" "0,63" "0,56" "0,86" "0,5" "0,67" "0,96" "0,94" "0,4" "0,5"
GAA "0,74" "0,34" "0,33" "0,41" "0,05" "0,16" "0,25" "0,74" 0 "0,39" 0 "0,33" "0,65" "0,33" "0,4" "0,32" "0,38" "0,33" "0,32" "0,5" "0,1" 0 "0,6" 0 "0,5" 1 "0,56" "0,4" "0,21" "0,67" "0,33" "0,38" "0,19" "0,38" "0,44" "0,14" "0,5" "0,33" "0,04" "0,06" "0,6" "0,5"
TTT "0,55" "0,46" 1 "0,48" "0,64" "0,42" "0,5" "0,89" "0,5" 1 0 "0,17" "0,6" "0,79" "0,47" "0,56" "0,5" "0,67" "0,25" "0,78" 1 "0,67" "0,63" "0,6" "0,83" "0,63" 1 1 1 "0,5" 1 1 "0,72" 1 "0,9" "0,82" "0,5" "0,25" "0,75" 0 "0,54" "0,67"
TTC "0,45" "0,54" 0 "0,52" "0,36" "0,58" "0,5" "0,11" "0,5" 0 1 "0,83" "0,4" "0,21" "0,53" "0,44" "0,5" "0,33" "0,75" "0,22" 0 "0,33" "0,38" "0,4" "0,17" "0,38" 0 0 0 "0,5" 0 0 "0,28" 0 "0,1" "0,18" "0,5" "0,75" "0,25" 1 "0,46" "0,33"
GGG "0,23" "0,19" 0 "0,22" "0,23" "0,32" "0,27" "0,1" "0,2" "0,1" 0 "0,13" "0,1" "0,33" "0,2" "0,11" 0 "0,33" "0,14" "0,18" 0 "0,4" 0 0 0 0 0 "0,13" "0,14" "0,25" "0,25" "0,4" "0,36" "0,33" "0,43" "0,11" 0 "0,26" 0 "0,14" "0,08" "0,15"
GGA "0,19" "0,29" "0,33" "0,35" "0,19" "0,12" "0,11" "0,35" "0,07" "0,19" "0,27" "0,09" "0,21" "0,08" "0,2" "0,34" "0,67" "0,33" "0,14" "0,32" "0,57" 0 0 "0,75" 1 "0,4" "0,57" "0,38" "0,14" "0,25" "0,38" 0 "0,21" "0,07" 0 0 "0,45" "0,17" "0,35" 0 "0,6" "0,13"
GGT "0,23" "0,16" "0,33" "0,05" "0,04" "0,15" "0,16" "0,19" "0,13" "0,19" "0,09" "0,17" "0,28" "0,17" "0,2" "0,21" "0,17" "0,17" "0,14" "0,14" "0,14" "0,4" "0,67" 0 0 0 "0,29" "0,13" "0,36" "0,5" "0,13" "0,4" "0,21" "0,47" "0,29" "0,67" "0,41" "0,13" 0 0 "0,24" "0,48"
GGC "0,35" "0,35" "0,33" "0,38" "0,54" "0,41" "0,46" "0,35" "0,6" "0,52" "0,64" "0,61" "0,41" "0,42" "0,4" "0,34" "0,17" "0,17" "0,57" "0,36" "0,29" "0,2" "0,33" "0,25" 0 "0,6" "0,14" "0,38" "0,36" 0 "0,25" "0,2" "0,23" "0,13" "0,29" "0,22" "0,14" "0,43" "0,65" "0,86" "0,08" "0,25"
CAT "0,21" "0,16" 0 "0,25" "0,36" "0,3" "0,3" "0,43" 0 "0,5" 0 0 "0,19" 0 "0,19" "0,25" "0,5" 0 "0,5" 0 "0,43" 0 "0,5" "0,33" "0,33" "0,5" 0 "0,67" "0,25" "0,5" "0,33" "0,75" "0,38" "0,27" "0,5" 0 "0,22" "0,75" 0 0 "0,33" "0,82"
CAC "0,79" "0,84" 0 "0,75" "0,64" "0,7" "0,7" "0,57" 1 "0,5" 1 1 "0,81" 1 "0,81" "0,75" "0,5" 0 "0,5" 1 "0,57" 1 "0,5" "0,67" "0,67" "0,5" 1 "0,33" "0,75" "0,5" "0,67" "0,25" "0,62" "0,73" "0,5" 1 "0,78" "0,25" 1 1 "0,67" "0,18"
ATA "0,27" "0,19" "0,5" "0,09" "0,54" "0,36" "0,13" "0,38" "0,17" "0,11" 0 "0,13" "0,26" "0,33" "0,19" "0,17" "0,67" 0 "0,33" "0,21" 0 "0,14" "0,18" "0,13" "0,18" "0,33" "0,13" "0,5" "0,19" "0,4" "0,3" "0,57" "0,24" "0,08" "0,6" "0,33" 0 "0,25" 0 0 "0,48" "0,03"
ATT "0,23" "0,14" "0,5" "0,27" "0,15" "0,21" "0,26" "0,58" "0,5" "0,33" "0,6" "0,38" "0,5" "0,67" "0,25" "0,33" "0,33" 1 0 "0,5" "0,67" "0,71" "0,73" "0,38" "0,36" "0,33" "0,75" "0,25" "0,31" "0,2" "0,6" "0,14" "0,48" "0,5" "0,2" "0,67" "0,92" "0,19" "0,25" 0 "0,35" "0,49"
ATC "0,5" "0,67" 0 "0,64" "0,31" "0,43" "0,61" "0,04" "0,33" "0,56" "0,4" "0,5" "0,24" 0 "0,56" "0,5" 0 0 "0,67" "0,29" "0,33" "0,14" "0,09" "0,5" "0,45" "0,33" "0,13" "0,25" "0,5" "0,4" "0,1" "0,29" "0,29" "0,42" "0,2" 0 "0,08" "0,56" "0,75" 1 "0,16" "0,49"
AAG "0,4" "0,56" "0,8" "0,75" "0,91" "0,71" "0,63" "0,27" "0,67" "0,69" 0 "0,75" "0,61" "0,5" "0,85" "0,61" "0,5" 1 "0,75" 1 "0,33" 0 "0,4" "0,33" 0 "0,25" "0,56" 1 "0,5" "0,5" 1 0 "0,76" 0 "0,78" 0 "0,75" "0,41" 1 "0,95" "0,26" "0,21"
AAA "0,6" "0,44" "0,2" "0,25" "0,09" "0,29" "0,37" "0,73" "0,33" "0,31" 0 "0,25" "0,39" "0,5" "0,15" "0,39" "0,5" 0 "0,25" 0 "0,67" 1 "0,6" "0,67" 0 "0,75" "0,44" 0 "0,5" "0,5" 0 1 "0,24" 1 "0,22" 0 "0,25" "0,59" 0 "0,05" "0,74" "0,79"
TTG "0,1" "0,08" "0,29" "0,14" "0,13" "0,18" "0,25" "0,2" 0 "0,14" "0,13" "0,11" "0,12" "0,12" "0,18" "0,17" "0,05" "0,5" "0,18" "0,07" "0,07" 0 "0,15" "0,2" "0,14" 0 "0,2" "0,29" "0,24" "0,2" "0,47" "0,33" "0,19" "0,26" "0,3" "0,17" 0 "0,24" 0 0 "0,21" "0,31"
TTA 0 "0,02" 0 "0,05" 0 "0,01" 0 "0,03" 0 0 0 0 "0,01" 0 0 "0,01" 0 0 "0,09" 0 "0,13" 0 "0,08" 0 "0,07" "0,18" 0 "0,07" "0,07" 0 "0,05" 0 "0,03" "0,13" "0,04" "0,08" 0 "0,08" 0 0 "0,04" "0,22"
CTG "0,4" "0,29" "0,57" "0,22" "0,65" "0,54" "0,5" "0,06" "0,67" "0,52" "0,38" "0,79" "0,28" "0,29" "0,56" "0,24" "0,63" "0,31" "0,36" "0,29" "0,33" 0 "0,08" "0,1" "0,07" "0,27" "0,2" "0,43" "0,45" "0,4" "0,11" "0,33" "0,46" "0,22" "0,52" "0,42" "0,76" "0,26" "0,97" "0,86" "0,15" "0,2"
CTA "0,08" "0,14" "0,14" "0,09" "0,05" "0,16" "0,09" "0,34" 0 "0,17" 0 "0,05" "0,18" "0,06" "0,21" "0,21" "0,05" 0 "0,09" "0,07" "0,07" "0,2" "0,23" "0,2" 0 "0,27" "0,2" "0,14" "0,1" 0 0 "0,06" "0,14" 0 "0,04" "0,08" 0 "0,16" 0 0 "0,13" "0,09"
CTT "0,22" "0,14" 0 "0,09" "0,1" "0,07" "0,11" "0,23" "0,33" "0,1" "0,13" "0,05" "0,31" "0,12" "0,05" "0,22" "0,16" "0,19" "0,09" "0,36" "0,27" "0,4" "0,23" "0,4" "0,43" "0,27" "0,2" "0,07" "0,1" "0,4" "0,37" "0,28" "0,16" "0,35" "0,09" "0,25" 0 "0,08" "0,03" 0 "0,3" "0,11"
CTC "0,2" "0,34" 0 "0,41" "0,07" "0,03" "0,05" "0,14" 0 "0,07" "0,38" 0 "0,09" "0,41" 0 "0,14" "0,11" 0 "0,18" "0,21" "0,13" "0,4" "0,23" "0,1" "0,29" 0 "0,2" 0 "0,03" 0 0 0 "0,03" "0,04" 0 0 "0,24" "0,18" 0 "0,14" "0,17" "0,07"
AAT "0,17" "0,15" 1 "0,07" "0,14" "0,06" "0,21" "0,43" "0,17" 0 0 "0,33" "0,37" "0,1" "0,17" "0,12" 0 "0,6" 0 "0,2" "0,5" "0,5" "0,67" "0,38" 0 "0,8" "0,5" "0,57" "0,38" 0 1 1 "0,52" "0,43" "0,4" 1 "0,62" "0,29" 0 0 "0,72" "0,47"
AAC "0,83" "0,85" 0 "0,93" "0,86" "0,94" "0,79" "0,57" "0,83" 1 0 "0,67" "0,63" "0,9" "0,83" "0,88" 1 "0,4" 1 "0,8" "0,5" "0,5" "0,33" "0,63" 0 "0,2" "0,5" "0,43" "0,63" 1 0 0 "0,48" "0,57" "0,6" 0 "0,38" "0,71" 1 1 "0,28" "0,53"
CCG "0,31" "0,28" 0 "0,47" "0,15" "0,46" "0,24" "0,08" "0,14" "0,27" "0,4" "0,23" "0,07" "0,07" "0,31" "0,31" "0,38" "0,25" "0,45" "0,14" "0,2" 0 0 0 0 "0,08" 0 "0,29" "0,14" 0 0 "0,5" "0,09" "0,24" "0,67" "0,22" 0 "0,55" 0 0 "0,11" "0,64"
CCA "0,1" "0,17" 1 "0,09" "0,15" "0,12" "0,14" "0,28" "0,29" "0,09" "0,2" "0,12" "0,21" "0,21" "0,22" "0,15" "0,05" "0,13" "0,1" "0,1" 0 1 "0,67" "0,4" "0,33" "0,31" "0,2" "0,14" "0,21" "0,2" 0 0 "0,23" "0,17" "0,17" 0 "0,6" "0,05" 0 0 "0,32" "0,18"
CCT "0,23" "0,16" 0 "0,13" "0,31" "0,07" "0,24" "0,38" 0 "0,12" 0 "0,23" "0,32" 0 "0,16" "0,15" "0,05" "0,13" "0,05" "0,24" "0,2" 0 "0,17" 0 "0,33" "0,15" "0,4" "0,36" "0,21" "0,2" 1 "0,38" "0,27" "0,37" "0,17" "0,67" "0,4" "0,25" "0,35" 0 "0,36" "0,14"
CCC "0,36" "0,4" 0 "0,32" "0,38" "0,34" "0,38" "0,26" "0,57" "0,52" "0,4" "0,42" "0,39" "0,71" "0,31" "0,39" "0,52" "0,5" "0,4" "0,52" "0,6" 0 "0,17" "0,6" "0,33" "0,46" "0,4" "0,21" "0,43" "0,6" 0 "0,13" "0,41" "0,22" 0 "0,11" 0 "0,15" "0,65" 1 "0,21" "0,05"
CAG "0,79" "0,76" "0,75" "0,78" "0,72" "0,84" "0,77" "0,16" "0,5" "0,87" 1 "0,36" "0,54" "0,83" "0,81" "0,61" "0,64" "0,83" "0,55" "0,73" "0,5" 1 "0,6" 0 1 "0,25" "0,6" "0,71" 1 1 "0,5" "0,4" "0,75" "0,88" "0,91" "0,75" "0,63" "0,65" 1 1 "0,32" "0,3"
CAA "0,21" "0,24" "0,25" "0,22" "0,28" "0,16" "0,23" "0,84" "0,5" "0,13" 0 "0,64" "0,46" "0,17" "0,19" "0,39" "0,36" "0,17" "0,45" "0,27" "0,5" 0 "0,4" 1 0 "0,75" "0,4" "0,29" 0 0 "0,5" "0,6" "0,25" "0,13" "0,09" "0,25" "0,38" "0,35" 0 0 "0,68" "0,7"
AGG "0,2" "0,09" "0,4" "0,12" "0,11" "0,09" "0,03" "0,1" "0,12" "0,09" "0,12" "0,11" "0,14" "0,09" "0,08" "0,07" "0,29" 0 "0,08" "0,06" "0,09" "0,2" "0,25" 0 "0,33" 0 "0,25" "0,29" "0,29" "0,2" "0,33" "0,13" "0,49" "0,22" "0,14" "0,25" "0,43" "0,36" 0 0 "0,12" 0
AGA "0,14" "0,03" "0,6" "0,05" "0,02" "0,06" "0,11" "0,6" "0,02" "0,04" "0,12" 0 "0,2" 0 "0,03" "0,08" "0,12" 0 "0,08" "0,12" "0,09" "0,4" "0,25" "0,25" "0,33" "0,4" "0,13" 0 0 "0,2" "0,22" "0,13" "0,14" "0,33" "0,29" "0,13" "0,43" "0,14" "0,36" 0 "0,41" "0,05"
CGG "0,09" "0,1" 0 "0,05" "0,3" "0,26" "0,2" 0 "0,12" "0,11" "0,18" "0,06" "0,09" 0 "0,32" "0,1" "0,06" "0,13" 0 "0,12" "0,27" 0 0 0 0 0 0 "0,21" "0,29" "0,2" "0,11" "0,13" "0,11" "0,11" "0,29" "0,25" 0 "0,21" 0 0 "0,12" 0
CGA "0,2" "0,09" 0 "0,05" "0,07" "0,02" "0,03" 0 "0,12" "0,17" "0,06" "0,22" "0,05" "0,09" "0,08" "0,16" "0,18" 0 "0,08" "0,24" 0 0 0 "0,25" "0,17" "0,2" 0 "0,21" "0,13" "0,13" "0,11" "0,13" "0,03" 0 0 0 0 "0,18" 0 0 "0,18" "0,11"
CGT "0,09" "0,19" 0 "0,1" "0,07" "0,09" "0,06" 0 "0,05" "0,09" "0,29" "0,22" "0,11" "0,18" "0,08" "0,05" "0,12" "0,25" "0,25" "0,35" "0,09" 0 0 0 0 "0,2" "0,13" "0,14" "0,03" "0,07" 0 "0,25" "0,05" "0,11" "0,07" "0,13" 0 "0,04" 0 0 "0,06" "0,55"
CGC "0,29" "0,5" 0 "0,62" "0,43" "0,47" "0,57" "0,3" "0,57" "0,5" "0,24" "0,39" "0,41" "0,64" "0,41" "0,54" "0,24" "0,63" "0,5" "0,12" "0,45" "0,4" "0,5" "0,5" "0,17" "0,2" "0,5" "0,14" "0,26" "0,2" "0,22" "0,25" "0,19" "0,22" "0,21" "0,25" "0,14" "0,07" "0,64" 1 "0,12" "0,29"
AGT "0,08" "0,03" 0 0 "0,05" "0,19" "0,1" "0,19" "0,1" "0,11" 0 "0,08" "0,07" "0,15" "0,1" "0,1" "0,1" "0,05" "0,05" "0,14" "0,33" 0 "0,2" "0,2" 0 "0,18" "0,25" "0,18" "0,29" 0 0 "0,18" "0,03" "0,25" "0,13" 0 0 "0,12" 0 0 "0,26" "0,32"
AGC "0,21" "0,26" 1 "0,29" "0,68" "0,46" "0,48" "0,12" "0,3" "0,22" 0 "0,5" "0,18" "0,25" "0,34" "0,29" "0,3" "0,27" "0,4" "0,14" "0,33" "0,17" "0,6" 0 "0,33" "0,18" "0,25" "0,18" "0,24" 0 "0,5" "0,27" "0,42" "0,15" "0,25" 0 "0,22" "0,35" 1 "0,7" "0,24" "0,25"
TCG "0,08" "0,16" 0 "0,23" 0 "0,1" "0,14" 0 "0,2" "0,06" "0,5" "0,17" "0,12" "0,1" "0,17" "0,12" "0,2" "0,05" "0,15" "0,33" 0 0 0 0 0 0 "0,25" "0,09" 0 "0,38" 0 "0,09" "0,1" "0,1" 0 "0,17" 0 "0,24" 0 0 0 "0,14"
TCA 0 "0,14" 0 "0,03" "0,05" "0,04" "0,05" "0,31" 0 "0,11" 0 0 "0,15" "0,1" "0,1" "0,14" "0,1" "0,14" "0,15" "0,14" 0 "0,33" "0,2" 0 0 "0,09" "0,25" 0 0 0 0 "0,09" "0,03" "0,05" "0,06" "0,17" 0 0 0 0 "0,12" "0,1"
TCT "0,25" "0,05" 0 "0,1" "0,05" "0,06" "0,07" "0,21" 0 "0,11" 0 "0,13" "0,22" "0,2" "0,12" "0,07" "0,05" "0,23" 0 "0,1" 0 "0,5" 0 "0,6" "0,33" "0,27" 0 "0,45" "0,19" "0,38" "0,5" "0,36" "0,26" "0,35" "0,31" "0,67" "0,67" "0,06" 0 0 "0,24" "0,08"
TCC "0,38" "0,36" 0 "0,35" "0,18" "0,15" "0,17" "0,17" "0,4" "0,39" "0,5" "0,13" "0,27" "0,2" "0,17" "0,29" "0,25" "0,27" "0,25" "0,14" "0,33" 0 0 "0,2" "0,33" "0,27" 0 "0,09" "0,29" "0,25" 0 0 "0,16" "0,1" "0,25" 0 "0,11" "0,24" 0 "0,3" "0,15" "0,11"
ACG "0,11" "0,12" 0 "0,18" "0,36" "0,24" "0,12" "0,02" "0,15" "0,13" "0,5" "0,13" "0,14" "0,18" "0,24" "0,14" "0,11" "0,23" "0,09" "0,13" 0 1 0 0 "0,14" 0 0 "0,06" "0,28" "0,33" 0 "0,33" "0,07" "0,27" "0,2" 0 0 "0,53" 0 0 0 "0,23"
ACA 0 "0,07" 0 "0,06" "0,18" "0,18" "0,12" "0,36" "0,15" "0,16" 0 "0,27" "0,18" "0,09" "0,1" "0,14" "0,32" "0,08" "0,27" "0,2" 0 0 "0,26" "0,56" "0,29" "0,09" "0,08" "0,29" "0,28" "0,17" "0,67" 0 "0,19" "0,18" "0,2" 0 "0,38" 0 0 0 "0,41" "0,26"
ACT "0,21" "0,1" 1 "0,09" 0 "0,12" "0,12" "0,36" "0,31" "0,1" 0 "0,07" "0,26" "0,27" "0,1" "0,06" "0,26" "0,23" "0,09" "0,33" "0,33" 0 "0,37" 0 "0,29" "0,55" "0,17" "0,41" "0,22" "0,17" 0 0 "0,19" "0,09" "0,2" "0,25" "0,44" "0,06" "0,29" "0,06" "0,41" "0,07"
ACC "0,68" "0,71" 0 "0,68" "0,45" "0,45" "0,65" "0,26" "0,38" "0,61" "0,5" "0,53" "0,42" "0,45" "0,57" "0,66" "0,32" "0,46" "0,55" "0,33" "0,67" 0 "0,37" "0,44" "0,29" "0,36" "0,75" "0,24" "0,22" "0,33" "0,33" "0,67" "0,56" "0,45" "0,4" "0,75" "0,19" "0,41" "0,71" "0,94" "0,19" "0,44"
GTG "0,32" "0,36" 1 "0,37" "0,68" "0,74" "0,6" "0,26" "0,76" "0,52" 1 "0,58" "0,45" 0 "0,91" "0,4" "0,17" "0,5" "0,29" "0,5" "0,2" "0,5" "0,38" "0,2" "0,2" "0,33" "0,29" "0,44" "0,65" "0,31" "0,33" "0,38" "0,59" "0,5" "0,29" "0,32" "0,35" "0,54" "0,93" "0,72" "0,23" "0,44"
GTA "0,32" "0,18" 0 "0,1" "0,16" "0,09" "0,07" "0,26" "0,06" "0,15" 0 "0,26" "0,17" "0,5" "0,06" "0,16" "0,17" 0 0 "0,2" 0 0 0 "0,4" "0,1" 0 "0,29" 0 "0,09" "0,15" "0,11" 0 "0,26" "0,15" 0 "0,21" 0 "0,18" 0 "0,06" "0,29" "0,11"
GTT "0,16" "0,09" 0 "0,1" "0,12" "0,03" "0,07" "0,39" "0,06" "0,15" 0 "0,16" "0,25" "0,25" "0,03" "0,14" "0,33" "0,3" "0,43" "0,1" "0,4" "0,5" "0,5" "0,2" "0,3" "0,5" "0,14" "0,56" "0,22" "0,38" "0,44" "0,38" "0,13" "0,25" "0,29" "0,42" "0,47" "0,18" "0,07" 0 "0,43" "0,18"
GTC "0,21" "0,37" 0 "0,43" "0,04" "0,15" "0,25" "0,1" "0,12" "0,18" 0 0 "0,13" "0,25" 0 "0,3" "0,33" "0,2" "0,29" "0,2" "0,4" 0 "0,13" "0,2" "0,4" "0,17" "0,29" 0 "0,04" "0,15" "0,11" "0,25" "0,03" "0,1" "0,43" "0,05" "0,18" "0,11" 0 "0,22" "0,06" "0,27"
TAT "0,21" "0,14" 0 "0,1" "0,2" "0,2" "0,09" "0,47" "0,5" "0,33" 0 "0,5" "0,23" "0,29" "0,5" "0,1" "0,5" "0,5" 0 "0,13" "0,33" 1 "0,7" 1 "0,5" "0,4" 0 0 "0,27" "0,25" "0,5" "0,5" "0,4" "0,8" 0 "0,6" "0,55" "0,24" 0 "0,09" "0,59" "0,63"
TAC "0,79" "0,86" 1 "0,9" "0,8" "0,8" "0,91" "0,53" "0,5" "0,67" 0 "0,5" "0,77" "0,71" "0,5" "0,9" "0,5" "0,5" 1 "0,88" "0,67" 0 "0,3" 0 "0,5" "0,6" 1 1 "0,73" "0,75" "0,5" "0,5" "0,6" "0,2" 1 "0,4" "0,45" "0,76" 1 "0,91" "0,41" "0,38"

+ 17
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Scripts/tabla_cai_early_proteins.txt
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Name Length CAI %G+C %G+C(1) %G+C(2) %G+C(3) Nc
E1A 870 0.760 54.8 64.1 46.9 53.4 51.9
E1B19K 531 0.789 52.5 54.8 41.8 61.0 52.8
E1B55K 1491 0.798 52.6 52.7 45.5 59.6 48.5
E3_12.5K 324 0.783 54.0 63.9 40.7 57.4 60.1
E3_CR1-alpha0 192 0.691 44.3 42.2 45.3 45.3 40.4
E3_gp19K 483 0.753 40.0 39.8 37.3 42.9 53.1
10.5K 282 0.743 46.5 41.5 44.7 53.2 52.0
E3_RID-alpha 276 0.704 46.7 48.9 38.0 53.3 61.0
E3_RID-beta 399 0.739 46.1 45.1 48.1 45.1 58.5
E3_14.7K 387 0.749 48.8 54.3 35.7 56.6 51.5
E4_ORF6/7 453 0.755 51.7 53.6 49.7 51.7 52.9
E4_34K_(reversa_complementaria) 885 0.805 53.4 50.5 45.4 64.4 46.9
E4_ORF4_(reversa_complementaria) 345 0.714 54.5 55.7 49.6 58.3 60.6
E4_ORF3_(reversa_complementaria) 351 0.771 45.0 56.4 29.9 48.7 47.4
E4_ORFB_(reversa_complementaria) 393 0.698 48.3 60.3 35.1 49.6 55.6
E4_ORF1_(reversa_complementaria) 387 0.708 47.3 60.5 36.4 45.0 43.0

+ 55
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Scripts/tabla_cai_human_proteins.txt
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+ 18
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Scripts/tabla_cai_late_proteins.txt
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@ -0,0 +1,18 @@
Name Length CAI %G+C %G+C(1) %G+C(2) %G+C(3) Nc
pol 3597 0.760 60.9 63.2 46.1 73.4 43.6
pTP 2016 0.772 62.9 66.2 45.2 77.2 41.3
52K 1248 0.798 63.3 70.7 43.3 76.0 40.8
pIIIa 1758 0.764 62.5 64.2 45.4 78.0 42.7
III 1716 0.804 58.7 57.0 44.4 74.8 42.1
pVII 597 0.767 70.4 68.8 65.3 76.9 41.7
V 1107 0.759 62.3 67.2 49.6 70.2 44.5
X 243 0.734 70.0 71.6 61.7 76.5 39.8
pVI 753 0.773 61.1 62.2 51.8 69.3 41.5
hexon 2859 0.767 49.0 51.6 38.7 56.7 52.4
protease 615 0.788 54.8 52.2 45.4 66.8 42.8
DBP(reversa_complementaria) 1590 0.769 59.7 60.8 44.3 74.2 42.1
100K 2424 0.751 58.5 65.2 42.6 67.6 46.7
33K 690 0.708 59.4 62.6 53.0 62.6 49.1
22K 591 0.758 61.9 61.9 51.8 72.1 49.8
pVIII 684 0.716 57.3 59.6 51.8 60.5 52.5
fiber 1746 0.702 44.2 49.7 45.5 37.3 46.6

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Scripts/tabla_cai_viral_proteins.txt
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Name Length CAI %G+C %G+C(1) %G+C(2) %G+C(3) Nc
E1A 870 0.760 54.8 64.1 46.9 53.4 51.9
E1B19K 531 0.789 52.5 54.8 41.8 61.0 52.8
E1B55K 1491 0.798 52.6 52.7 45.5 59.6 48.5
IX 423 0.783 57.7 55.3 56.7 61.0 49.4
IVa2 1350 0.758 56.3 61.3 41.8 65.8 50.0
pol 3597 0.760 60.9 63.2 46.1 73.4 43.6
pTP 2016 0.772 62.9 66.2 45.2 77.2 41.3
52K 1248 0.798 63.3 70.7 43.3 76.0 40.8
pIIIa 1758 0.764 62.5 64.2 45.4 78.0 42.7
III 1716 0.804 58.7 57.0 44.4 74.8 42.1
pVII 597 0.767 70.4 68.8 65.3 76.9 41.7
V 1107 0.759 62.3 67.2 49.6 70.2 44.5
X 243 0.734 70.0 71.6 61.7 76.5 39.8
pVI 753 0.773 61.1 62.2 51.8 69.3 41.5
hexon 2859 0.767 49.0 51.6 38.7 56.7 52.4
protease 615 0.788 54.8 52.2 45.4 66.8 42.8
DBP(reversa_complementaria) 1590 0.769 59.7 60.8 44.3 74.2 42.1
100K 2424 0.751 58.5 65.2 42.6 67.6 46.7
33K 690 0.708 59.4 62.6 53.0 62.6 49.1
22K 591 0.758 61.9 61.9 51.8 72.1 49.8
pVIII 684 0.716 57.3 59.6 51.8 60.5 52.5
E3_12.5K 324 0.783 54.0 63.9 40.7 57.4 60.1
E3_CR1-alpha0 192 0.691 44.3 42.2 45.3 45.3 40.4
E3_gp19K 483 0.753 40.0 39.8 37.3 42.9 53.1
10.5K 282 0.743 46.5 41.5 44.7 53.2 52.0
E3_RID-alpha 276 0.704 46.7 48.9 38.0 53.3 61.0
E3_RID-beta 399 0.739 46.1 45.1 48.1 45.1 58.5
E3_14.7K 387 0.749 48.8 54.3 35.7 56.6 51.5
U_exon(reversa_complementaria) 168 0.830 45.8 50.0 30.4 57.1 30.1
fiber 1746 0.702 44.2 49.7 45.5 37.3 46.6
E4_ORF6/7 453 0.755 51.7 53.6 49.7 51.7 52.9
E4_34K_(reversa_complementaria) 885 0.805 53.4 50.5 45.4 64.4 46.9
E4_ORF4_(reversa_complementaria) 345 0.714 54.5 55.7 49.6 58.3 60.6
E4_ORF3_(reversa_complementaria) 351 0.771 45.0 56.4 29.9 48.7 47.4
E4_ORFB_(reversa_complementaria) 393 0.698 48.3 60.3 35.1 49.6 55.6
E4_ORF1_(reversa_complementaria) 387 0.708 47.3 60.5 36.4 45.0 43.0

+ 36
- 0
example.fasta
View File

@ -0,0 +1,36 @@
>GFP (WT)
ATGAGTAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATG *
GGCACAAATTCTCTGTCAGTGGAGAGGGTGAAGGTGATGCAACATACGGAAAACTTACCCTTAAATTTAT
TTGCACTACTGGAAAGCTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGC
TTTTCAAGATACCCAGATCATATGAAACAGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTAC
AGGAAAGAACTATATTTTACAAAGATGACGGGAACTACAAATCACGTGCTGAAGTCAAGTTTGAAGGTGA
TACCCTCGTTAATAGAATTGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTTGGACACAAA
ATGGAATACAACTATAACTCACACAATGTATACATCATGGCAGACAAACAAAAGAATGGAATCAAAGTTA
ACTTCAAAATTAGACACAACATTGAAGATGGAAGCGTTCAACTAGCAGACCATTATCAACAAAATACTCC
AATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCCAAAGAT
CCCAACGAAAAGAGAGATCACATGATCCTTCTTGAGTTTGTAACAGCTGCTGGGATTACACATGGCATGG
ATGAACTATACAAATAA
>TOX (human protein)
ATGGACGTAAGATTTTATCCACCTCCAGCCCAGCCCGCCGCTGCGCCCGACGCTCCCTGTCTGGGACCTT
CTCCCTGCCTGGACCCCTACTATTGCAACAAGTTTGACGGTGAGAACATGTATATGAGCATGACAGAGCC
GAGCCAGGACTATGTGCCAGCCAGCCAGTCCTACCCTGGTCCAAGCCTGGAAAGTGAAGACTTCAACATT
CCACCAATTACTCCTCCTTCCCTCCCAGACCACTCGCTGGTGCACCTGAATGAAGTTGAGTCTGGTTACC
ATTCTCTGTGTCACCCCATGAACCATAATGGCCTGCTACCATTTCATCCACAAAACATGGACCTCCCTGA
AATCACAGTCTCCAATATGCTGGGCCAGGATGGAACACTGCTTTCTAATTCCATTTCTGTGATGCCAGAT
ATACGAAACCCAGAAGGAACTCAGTACAGTTCCCATCCTCAGATGGCAGCCATGAGACCAAGGGGCCAGC
CTGCAGACATCAGGCAGCAGCCAGGAATGATGCCACATGGCCAGCTGACTACCATTAACCAGTCACAGCT
AAGTGCTCAACTTGGTTTGAATATGGGAGGAAGCAATGTTCCCCACAACTCACCATCTCCACCTGGAAGC
AAGTCTGCAACTCCTTCACCATCCAGTTCAGTGCATGAAGATGAAGGCGATGATACCTCTAAGATCAATG
GTGGAGAGAAGCGGCCTGCCTCTGATATGGGGAAAAAACCAAAAACTCCCAAAAAGAAGAAGAAGAAGGA
TCCCAATGAGCCCCAGAAGCCTGTGTCTGCCTATGCGTTATTCTTTCGTGATACTCAGGCCGCCATCAAG
GGCCAAAATCCAAACGCTACCTTTGGCGAAGTCTCTAAAATTGTGGCTTCAATGTGGGACGGTTTAGGAG
AAGAGCAAAAACAGGTCTATAAAAAGAAAACCGAGGCTGCGAAGAAGGAGTACCTGAAGCAACTCGCAGC
ATACAGAGCCAGCCTTGTATCCAAGAGCTACAGTGAACCTGTTGACGTGAAGACATCTCAACCTCCTCAG
CTGATCAATTCGAAGCCGTCGGTGTTCCATGGGCCCAGCCAGGCCCACTCGGCCCTGTACCTAAGTTCCC
ACTATCACCAACAACCGGGAATGAATCCTCACCTAACTGCCATGCATCCTAGTCTCCCCAGGAACATAGC
CCCCAAGCCGAATAACCAAATGCCAGTGACTGTCTCTATAGCAAACATGGCTGTGTCCCCTCCTCCTCCC
CTCCAGATCAGCCCGCCTCTTCACCAGCATCTCAACATGCAGCAGCACCAGCCGCTCACCATGCAGCAGC
CCCTTGGGAACCAGCTCCCCATGCAGGTCCAGTCTGCCTTACACTCACCCACCATGCAGCAAGGATTTAC
TCTTCAACCCGACTATCAGACTATTATCAATCCTACATCTACAGCTGCACAAGTTGTCACCCAGGCAATG
GAGTATGTGCGTTCGGGGTGCAGAAATCCTCCCCCACAACCGGTGGACTGGAATAACGACTACTGCAGTA
GTGGGGGCATGCAGAGGGACAAAGCACTGTACCTTACTTGA

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