library (Biostrings)

## Loading required package: BiocGenerics

## Loading required package: parallel

## 
## Attaching package: 'BiocGenerics'

## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
##     parLapplyLB, parRapply, parSapply, parSapplyLB

## The following objects are masked from 'package:stats':
## 
##     IQR, mad, xtabs

## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, as.vector, cbind,
##     colnames, do.call, duplicated, eval, evalq, Filter, Find, get,
##     grep, grepl, intersect, is.unsorted, lapply, lengths, Map,
##     mapply, match, mget, order, paste, pmax, pmax.int, pmin,
##     pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
##     setdiff, sort, table, tapply, union, unique, unlist, unsplit

## Loading required package: S4Vectors

## Loading required package: stats4

## Loading required package: IRanges

## Loading required package: XVector

SEQs<-readDNAStringSet(file="C-C.fa", format="fasta");SEQs

##   A DNAStringSet instance of length 3
##     width seq                                          names               
## [1]   448 CTTCTTGACGGACCACGACGA...TTTTTTTTTTTTTTTTTTTT 151222-48_K21_78_...
## [2]   509 TCTTAGTTCTGACTCGCCTGA...ACAAATTTTTATAATTTCTT 151222-48_L21_81_...
## [3]   471 TGGTTAGTCAGTTTTACCGTA...TTTTTTTTTTTTTTTTTTTT 151222-48_M21_91_...

width(SEQs);length(SEQs)

## [1] 448 509 471

## [1] 3

CviAII_selC<-readDNAStringSet(file="CviAII_selC.fa", format="fasta");CviAII_selC

##   A DNAStringSet instance of length 1
##     width seq                                          names               
## [1]    15 GACTGCGTACCATGC                              CviAII_selprimerC

CviAII_selCcomp<-complement(CviAII_selC);CviAII_selCcomp

##   A DNAStringSet instance of length 1
##     width seq                                          names               
## [1]    15 CTGACGCATGGTACG                              CviAII_selprimerC

Pos<-regexpr(CviAII_selCcomp,SEQs);Pos

## [1] -1 -1 -1
## attr(,"match.length")
## [1] -1 -1 -1
## attr(,"useBytes")
## [1] TRUE

MseI_selC<-readDNAStringSet(file="MseI_selC.fa", format="fasta");MseI_selC

##   A DNAStringSet instance of length 1
##     width seq                                          names               
## [1]    17 GATGAGTCCTGAGTAAC                            MseI_selprimerC

MseI_selCRC<-reverseComplement(MseI_selC);MseI_selCRC

##   A DNAStringSet instance of length 1
##     width seq                                          names               
## [1]    17 GTTACTCAGGACTCATC                            MseI_selprimerC

length(MseI_selCRC);width(MseI_selCRC)

## [1] 1

## [1] 17

Pos1<-gregexpr("N",SEQs);Pos1

## [[1]]
## [1] -1
## attr(,"match.length")
## [1] -1
## attr(,"useBytes")
## [1] TRUE
## 
## [[2]]
## [1] -1
## attr(,"match.length")
## [1] -1
## attr(,"useBytes")
## [1] TRUE
## 
## [[3]]
## [1] -1
## attr(,"match.length")
## [1] -1
## attr(,"useBytes")
## [1] TRUE

#cambiar la letra según la base selectiva de CviAII (poner la complementaria a la de analisis)
Pos2<-regexpr("G",SEQs);Pos2

## [1] 7 6 2
## attr(,"match.length")
## [1] 1 1 1
## attr(,"useBytes")
## [1] TRUE

Pos3<-regexpr(MseI_selCRC,SEQs);Pos3

## [1]  -1  -1 263
## attr(,"match.length")
## [1] -1 -1 17
## attr(,"useBytes")
## [1] TRUE

K<-Pos2+1;L<-Pos3-1
seqslimpias<-subseq(SEQs, start =K, end =L);seqslimpias

##   A DNAStringSet instance of length 3
##     width seq                                          names               
## [1]   440 ACGGACCACGACGATCAATTG...TTTTTTTTTTTTTTTTTTTT 151222-48_K21_78_...
## [2]   502 TTCTGACTCGCCTGAGCGGGG...TACAAATTTTTATAATTTCT 151222-48_L21_81_...
## [3]   260 GTTAGTCAGTTTTACCGTAAG...TCACAAGGGAGCCGGGTCCA 151222-48_M21_91_...

width(seqslimpias);width(SEQs)

## [1] 440 502 260

## [1] 448 509 471

writeXStringSet(seqslimpias,file="seqslimpC-C.fa",format="fasta")