data<-readLines(textConnection("Aleiodes_bicolor_MRS1008 TATTTTATATTTTTTATTT                                      
Aleiodes_praetor_UK_MRS67_                       XXXXXXXXXGTTTTATAT
Aleiodes_rugulosus_CollHH1599_Norway      xxxxxxxxxATTTTGTATTTTTT
Aleiodes_seriatus_MRS252_France      xxxxxxxxxxxxxxxxxxxxxxxxx
Aleiodes_seriatus_MRS254_France        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Aleiodes_seriatus_MRS263_France    xxxxxxxxxATTTTATACTTTTTATTTGG
Aleiodes_seriatus_MRS264_France      xxxxxxxxxATTTTATACTTTTTATTTGG
Aleiodes_seriatus_MRS136_France         GATATTGGAATTTTATATTT
MRS239_Aleiodes_seriatus_Russia     xxxxxxxxxGTTTTATACTTCTTATTT
Aleiodes_seriatus_MRS222_Germany    xxxxxxxxxATTTtaTaCTTTTTATT
Aleiodes_sibiricus_MRS313_Sweden      xxxxxxxxxxTTTTGTATTTTTTATT
Aleiodes_signatus_MRS378_Sweden       xxxxxxxxxxxTTTATATTTTTTATT 
Aleiodes_signatus_MRS712_Sweden       GATATTGGTATTTTATATTTTTTA
Aleiodes_unipunctator_CollHH1603_Norway   xxxxxxxATTTTATATTTTTTATG"))
startwithMRS<-function(b){
mrs<-unlist(regmatches(x = b, gregexpr("MRS[0-9]+",text = b)))
if(length(mrs)>0) { # the MRS string occurs on the line
z<-gsub(mrs,"",b) # remove the original MRS number occurrence
z<-paste(mrs,"_",z,sep="") # paste the MRS number at the beginning 
}
else z<-b # the MRS string does not occur on the line
z
}
MRSatstart<-unlist(lapply(data, function(x) startwithMRS(x)))
sort(MRSatstart)