--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all stuff/Commonality and Difference finderMADE 7 TO 7.R	Wed Jan 16 13:55:22 2019 -0500
@@ -0,0 +1,1281 @@
+#I should make an SOP for this.  Problems we encountered: no x in the xY motif, and the kilodemon
+#the output files have both Y and xY, they shouldn't why is that happening?  make it not happen
+#make sure that accession numbers stay locked to each motif, somehow
+#output should look just like the KALIP input
+
+#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
+FullMotifsOnly_questionmark<-"NO"
+#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
+TruncatedMotifsOnly_questionmark<-"NO"
+#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps)
+Are_You_Looking_For_Commonality<-"YES"
+
+
+#put the names of your input files here
+FirstSubstrateSet<- read.csv("Galaxy63-BTK_PLUS-R1_Substrates.csv", stringsAsFactors=FALSE)
+Firstsubbackfreq<- read.csv("Galaxy64-BTK_PLUS-R1_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE)
+
+SecondSubstrateSet<- read.csv("Galaxy65-BTK_PLUS_R2_Substrates.csv", stringsAsFactors=FALSE)
+Secondsubbackfreq<- read.csv("Galaxy66-BTK_PLUS_R2_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE)
+
+ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE)
+Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE)
+
+#then put the names of your output files here
+Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv"
+Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv"
+
+# Shared_motifs_table<-"Shared motifs 7-27-17.csv"
+# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv"
+
+First_unshared_motifs_table<-"R1 substrates.csv"
+First_unshared_subbackfreq<-"R1 SBF.csv"
+
+Second_unshared_motifs_table<-"R2 subs.csv"
+Second_unshared_subbackfreq<-"R2 SBf.csv"
+
+Third_unshared_motifs_table<-"R3 subs.csv"
+Third_unshared_subbackfreq<-"R3 SBF.csv"
+
+#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles.  I think I'll poke around
+#other languages to see if any of them can do it.
+####################################################################################################################################
+
+
+
+
+
+FirstxY<-rep("xY",times=nrow(FirstSubstrateSet))
+FirstSubstrateSet[,11]<-FirstxY
+
+SecondxY<-rep("xY",times=nrow(SecondSubstrateSet))
+SecondSubstrateSet[,11]<-SecondxY
+
+ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet))
+ThirdSubstrateSet[,11]<-ThirdxY
+
+
+
+
+
+
+
+
+
+
+
+####################################################################################################################################
+####################################################################################################################################
+# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two 
+# separate proteins thus two separate accession numbers?
+# It should actually output the shared motif and BOTH accession numbers.  Right now it does not, it only maps out the second
+# accession number.  So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number
+####################################################################################################################################
+####################################################################################################################################
+####################################################################################################################################
+####################################################################################################################################
+
+#Create the motif sets, deciding wether or not you're looking for truncated or full here
+#full only
+if (Are_You_Looking_For_Commonality=="YES"){
+  if (FullMotifsOnly_questionmark=="YES"){
+    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+    leftspaces<-c()
+    rightspaces<-c()
+    for (i in 1:nrow(FirstSubstrateSet)){
+      FTLwtletters<-FirstSubstrateSet[i,4:18]
+      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
+      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
+      
+      
+      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
+        motif<-YYYmotif
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        FTLwtletters<-motif
+        FTLwtmotifs[i,1]<-FTLwtletters
+        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+        
+      }
+      
+    }
+    # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
+    # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
+    # 
+    
+    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
+    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
+    
+    for (i in 1:nrow(SecondSubstrateSet)){
+      D835letters<-SecondSubstrateSet[i,4:18]
+      D835letters<-D835letters[D835letters !="XXXXX"]
+      D835letters<-paste(D835letters, sep="", collapse="")
+      
+      
+      YYYmotif <- unlist(strsplit(D835letters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        D835letters<-motif
+        D835Ymotifs[i,1]<-D835letters
+        D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
+        
+      }
+    }
+    
+    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
+    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
+    
+    for (i in 1:nrow(ThirdSubstrateSet)){
+      ITDletters<-ThirdSubstrateSet[i,4:18]
+      ITDletters<-ITDletters[ITDletters !="XXXXX"]
+      ITDletters<-paste(ITDletters, sep="", collapse="")
+      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        ITDletters<-motif
+        ITDmotifs[i,1]<-ITDletters
+        ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
+        
+      }
+    }
+    
+  }
+  
+  ##############################################3
+  #Truncated only
+  if (TruncatedMotifsOnly_questionmark=="YES"){
+    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+    
+    for (i in 1:nrow(FirstSubstrateSet)){
+      FTLwtletters<-FirstSubstrateSet[i,4:18]
+      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
+      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
+      
+      
+      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        FTLwtletters<-motif
+        FTLwtmotifs[i,1]<-FTLwtletters
+        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+      
+    }
+    
+    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
+    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
+    
+    for (i in 1:nrow(SecondSubstrateSet)){
+      D835letters<-SecondSubstrateSet[i,4:18]
+      D835letters<-D835letters[D835letters !="XXXXX"]
+      D835letters<-paste(D835letters, sep="", collapse="")
+      
+      
+      YYYmotif <- unlist(strsplit(D835letters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        D835letters<-motif
+        D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
+        D835Ymotifs[i,1]<-D835letters
+      }
+    }
+    
+    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
+    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
+    
+    for (i in 1:nrow(ThirdSubstrateSet)){
+      ITDletters<-ThirdSubstrateSet[i,4:18]
+      ITDletters<-ITDletters[ITDletters !="XXXXX"]
+      ITDletters<-paste(ITDletters, sep="", collapse="")
+      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        ITDletters<-motif
+        ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
+        ITDmotifs[i,1]<-ITDletters
+      }
+    }
+    
+  }
+  
+  ###############################################
+  #ALL motifs, full and truncated
+  
+  if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
+    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+    
+    for (i in 1:nrow(FirstSubstrateSet)){
+      FTLwtletters<-FirstSubstrateSet[i,4:18]
+      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
+      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
+      leftspaces<-c()
+      rightspaces<-c()
+      
+      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        FTLwtletters<-motif
+        FTLwtmotifs[i,1]<-FTLwtletters
+        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+      
+      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        FTLwtletters<-motif
+        FTLwtmotifs[i,1]<-FTLwtletters
+        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+        
+        
+      }
+      
+    }
+    
+    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
+    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
+    
+    for (i in 1:nrow(SecondSubstrateSet)){
+      D835letters<-SecondSubstrateSet[i,4:18]
+      D835letters<-D835letters[D835letters !="XXXXX"]
+      D835letters<-paste(D835letters, sep="", collapse="")
+      leftspaces<-c()
+      rightspaces<-c()
+      
+      YYYmotif <- unlist(strsplit(D835letters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        D835letters<-motif
+        D835Ymotifs[i,1]<-D835letters
+        D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+      
+      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        D835letters<-motif
+        D835Ymotifs[i,1]<-D835letters
+        D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+    }
+    
+    
+    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
+    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
+    
+    for (i in 1:nrow(ThirdSubstrateSet)){
+      ITDletters<-ThirdSubstrateSet[i,4:18]
+      ITDletters<-ITDletters[ITDletters !="XXXXX"]
+      ITDletters<-paste(ITDletters, sep="", collapse="")
+      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
+      leftspaces<-c()
+      rightspaces<-c()
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        ITDletters<-motif
+        ITDmotifs[i,1]<-ITDletters
+        ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+      
+      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        ITDletters<-motif
+        ITDmotifs[i,1]<-ITDletters
+        ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+    }
+    
+  }
+  #############################################################################################################################
+  #############################################################################################################################
+  #############################################################################################################################
+  #############################################################################################################################
+  #############################################################################################################################
+  
+  #now look for either commonality or difference.  Actually could you look for both...
+  
+  if (Are_You_Looking_For_Commonality=="YES"){
+    
+    columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
+    columnalheader<-matrix(columnalheader,nrow = 1)
+    write.table(x=columnalheader,
+                file=Shared_subbackfreq_table,
+                quote=FALSE, sep=",",
+                row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+    
+    FirstOverlapmotifs<-c()
+    for (i in 1:nrow(ITDmotifs)){
+      for (j in 1:nrow(D835Ymotifs)){
+        if (is.na(ITDmotifs[i,1])!=TRUE&&is.na(D835Ymotifs[j,1])!=TRUE){
+          if (ITDmotifs[i,1]==D835Ymotifs[j,1]){
+            FirstOverlapmotifs<-c(FirstOverlapmotifs,D835Ymotifs[j,1])
+          }
+        }
+      }
+    }
+    
+    AllAccessionNumbers<-c()
+    columnalheader<-c(rep(NA,36))
+    FinalMatrix<-matrix(data =columnalheader,nrow = 1)
+    
+    FinalMotifs<-c(rep(NA,20))
+    FinalMotifsMatrix<-matrix(data = FinalMotifs,nrow = 1)
+    
+    
+    for (l in 1:length(FirstOverlapmotifs)) {
+      AccessionNumber<-00000000000
+      for (k in 1:nrow(FTLwtmotifs)) {
+        AccessionNumber<-0000000000000
+        if(is.na(FTLwtmotifs[k])!=TRUE){
+          #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
+          #destroyed immediately after use
+          if (FirstOverlapmotifs[l] == FTLwtmotifs[k]) {
+            substratematrix<-FirstSubstrateSet[k,1:20]
+            substratematrix<-as.matrix(substratematrix,nrow=1)
+            FinalMotifsMatrix<-rbind(FinalMotifsMatrix,substratematrix)
+            #when you find a match between the venn diagrams, save the substrate info you get into a matrix
+            
+            AccessionNumber <- as.character(FirstSubstrateSet[k, 3])
+            #then take the accession number 
+            
+            for (m in 1:ncol(Firstsubbackfreq)) {
+              AN <- as.character(Firstsubbackfreq[1, m])
+              if (grepl(pattern = AN,
+                        x = AccessionNumber,
+                        fixed = TRUE) == TRUE) {
+                outputmatrix <- as.character(Firstsubbackfreq[, m])
+                outputmatrix <- matrix(outputmatrix, nrow = 1)
+                #with that accession number, find a match in the subbackfreq file and save it here
+                FinalMatrix<-rbind(FinalMatrix,outputmatrix)
+              }
+            }
+          }
+        }
+      }
+    }
+    
+    
+    TrueMatrix<-FinalMatrix[!duplicated(FinalMatrix),]
+    TrueFinalMotifsMatrix<-FinalMotifsMatrix[!duplicated(FinalMotifsMatrix),]
+    
+    TrueFinalMotifsMatrix<-TrueFinalMotifsMatrix[2:nrow(TrueFinalMotifsMatrix),]
+    TrueMatrix<-TrueMatrix[2:nrow(TrueMatrix),]
+    
+    write.table(
+      x = TrueFinalMotifsMatrix,
+      file = Shared_motifs_table,
+      quote = FALSE,
+      sep = ",",
+      row.names = FALSE,
+      col.names = TRUE,
+      na = "",
+      append = TRUE
+    )
+    
+    
+    write.table(
+      x = TrueMatrix,
+      file = Shared_subbackfreq_table,
+      quote = FALSE,
+      sep = ",",
+      row.names = FALSE,
+      col.names = FALSE,
+      na = "",
+      append = TRUE
+    )
+  }
+}
+
+if (Are_You_Looking_For_Commonality=="NO"){
+  if (FullMotifsOnly_questionmark=="YES"){
+    FTLwtmotifs=rep(NA,times=nrow(FirstSubstrateSet))
+    FTLwtAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
+    leftspaces<-c()
+    rightspaces<-c()
+    for (i in 1:nrow(FirstSubstrateSet)){
+      FTLwtletters<-FirstSubstrateSet[i,4:18]
+      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
+      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
+      
+      
+      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
+        motif<-YYYmotif
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        FTLwtletters<-motif
+        FTLwtmotifs[i]<-FTLwtletters
+        FTLwtAccessionNumbers[i]<-FirstSubstrateSet[i,3]
+      }
+      
+    }
+    # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
+    # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
+    # 
+    
+    D835Ymotifs=rep(NA,times=nrow(FirstSubstrateSet))
+    D835YAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
+    
+    for (i in 1:nrow(SecondSubstrateSet)){
+      D835letters<-SecondSubstrateSet[i,4:18]
+      D835letters<-D835letters[D835letters !="XXXXX"]
+      D835letters<-paste(D835letters, sep="", collapse="")
+      
+      
+      YYYmotif <- unlist(strsplit(D835letters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        D835letters<-motif
+        D835Ymotifs[i]<-D835letters
+        D835YAccessionNumbers[i]<-SecondSubstrateSet[i,3]
+      }
+    }
+    
+    ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet))
+    ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
+    
+    for (i in 1:nrow(ThirdSubstrateSet)){
+      ITDletters<-ThirdSubstrateSet[i,4:18]
+      ITDletters<-ITDletters[ITDletters !="XXXXX"]
+      ITDletters<-paste(ITDletters, sep="", collapse="")
+      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        ITDletters<-motif
+        ITDmotifs[i]<-ITDletters
+        ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3]
+        
+      }
+    }
+    names(ITDmotifs)<-ITDAccessionNumbers
+    names(D835Ymotifs)<-D835YAccessionNumbers
+    names(FTLwtmotifs)<-FTLwtAccessionNumbers
+  }
+  
+  
+  ##############################################3
+  #Truncated only
+  if (TruncatedMotifsOnly_questionmark=="YES"){
+    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+    
+    for (i in 1:nrow(FirstSubstrateSet)){
+      FTLwtletters<-FirstSubstrateSet[i,4:18]
+      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
+      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
+      
+      
+      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        FTLwtletters<-motif
+        FTLwtmotifs[i,1]<-FTLwtletters
+        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+      
+    }
+    
+    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
+    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
+    i=2
+    for (i in 1:nrow(SecondSubstrateSet)){
+      D835letters<-SecondSubstrateSet[i,4:18]
+      D835letters<-D835letters[D835letters !="XXXXX"]
+      D835letters<-paste(D835letters, sep="", collapse="")
+      
+      
+      YYYmotif <- unlist(strsplit(D835letters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        D835letters<-motif
+        D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
+        D835Ymotifs[i,1]<-D835letters
+      }
+    }
+    
+    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
+    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
+    
+    for (i in 1:nrow(ThirdSubstrateSet)){
+      ITDletters<-ThirdSubstrateSet[i,4:18]
+      ITDletters<-ITDletters[ITDletters !="XXXXX"]
+      ITDletters<-paste(ITDletters, sep="", collapse="")
+      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        ITDletters<-motif
+        ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
+        ITDmotifs[i,1]<-ITDletters
+      }
+    }
+    names(FTLwtmotifs)<-FTLwtAccessionNumbers
+    names(D835Ymotifs)<-D835YAccessionNumbers
+    names(ITDmotifs)<-ITDAccessionNumbers
+  }
+  
+  ###############################################
+  #ALL motifs, full and truncated
+  
+  if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
+    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+    
+    for (i in 1:nrow(FirstSubstrateSet)){
+      FTLwtletters<-FirstSubstrateSet[i,4:18]
+      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
+      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
+      leftspaces<-c()
+      rightspaces<-c()
+      
+      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        FTLwtletters<-motif
+        FTLwtmotifs[i,1]<-FTLwtletters
+        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+      
+      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        FTLwtletters<-motif
+        FTLwtmotifs[i,1]<-FTLwtletters
+        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+        
+        
+      }
+      
+    }
+    
+    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
+    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
+    
+    for (i in 1:nrow(SecondSubstrateSet)){
+      D835letters<-SecondSubstrateSet[i,4:18]
+      D835letters<-D835letters[D835letters !="XXXXX"]
+      D835letters<-paste(D835letters, sep="", collapse="")
+      leftspaces<-c()
+      rightspaces<-c()
+      
+      YYYmotif <- unlist(strsplit(D835letters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        D835letters<-motif
+        D835Ymotifs[i,1]<-D835letters
+        D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+      
+      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        D835letters<-motif
+        D835Ymotifs[i,1]<-D835letters
+        D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+    }
+    
+    
+    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
+    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
+    
+    for (i in 1:nrow(ThirdSubstrateSet)){
+      ITDletters<-ThirdSubstrateSet[i,4:18]
+      ITDletters<-ITDletters[ITDletters !="XXXXX"]
+      ITDletters<-paste(ITDletters, sep="", collapse="")
+      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
+      leftspaces<-c()
+      rightspaces<-c()
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        ITDletters<-motif
+        ITDmotifs[i,1]<-ITDletters
+        ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+      
+      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        ITDletters<-motif
+        ITDmotifs[i,1]<-ITDletters
+        ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+    }
+    names(FTLwtmotifs)<-FTLwtAccessionNumbers
+    names(D835Ymotifs)<-D835YAccessionNumbers
+    names(ITDmotifs)<-ITDAccessionNumbers
+  }
+  
+  
+  FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
+  FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs]
+  FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
+  
+  
+  ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs]
+  ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs]
+  ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)]
+  
+  
+  D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
+  D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs]
+  D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
+  
+  
+  columnalheader<-c(rep(NA,35))
+  FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
+  
+  for (k in 1:length(FTLwtmotifsFINAL)) {
+    AN<-00000
+    #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
+    #destroyed immediately after use
+    for (m in 1:ncol(Firstsubbackfreq)) {
+      AN <- as.character(Firstsubbackfreq[1, m])
+      if (grepl(pattern = AN,
+                x = names(FTLwtmotifsFINAL[k]),
+                fixed = TRUE) == TRUE) {
+        outputmatrix <- as.character(Firstsubbackfreq[, m])
+        outputmatrix <- matrix(outputmatrix, nrow = 1)
+        #with that accession number, find a match in the subbackfreq file and save it here
+        FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix)
+      }
+    }
+  }
+  FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),]
+  
+  columnalheader<-c(rep(NA,35))
+  ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
+  
+  for (k in 1:length(ITDmotifsFINAL)) {
+    AN<-00000
+    #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
+    #destroyed immediately after use
+    for (m in 1:ncol(Thirdsubbackfreq)) {
+      AN <- as.character(Thirdsubbackfreq[1, m])
+      if (grepl(pattern = AN,
+                x = names(ITDmotifsFINAL[k]),
+                fixed = TRUE) == TRUE) {
+        outputmatrix <- as.character(Thirdsubbackfreq[, m])
+        outputmatrix <- matrix(outputmatrix, nrow = 1)
+        #with that accession number, find a match in the subbackfreq file and save it here
+        ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix)
+      }
+    }
+  }
+  ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),]
+  
+  columnalheader<-c(rep(NA,35))
+  D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
+  
+  for (k in 1:length(D835YmotifsFINAL)) {
+    #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
+    #destroyed immediately after use
+    for (m in 1:ncol(Secondsubbackfreq)) {
+      AN <- as.character(Secondsubbackfreq[1, m])
+      if (grepl(pattern = AN,
+                x = names(D835YmotifsFINAL[k]),
+                fixed = TRUE) == TRUE) {
+        outputmatrix <- as.character(Secondsubbackfreq[, m])
+        outputmatrix <- matrix(outputmatrix, nrow = 1)
+        #with that accession number, find a match in the subbackfreq file and save it here
+        D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix)
+      }
+    }
+  }
+  D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),]
+  
+  FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2)
+  
+  
+  write.table(x=FTLoutputmatrix,
+              file=First_unshared_motifs_table,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+  
+  columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1]))
+  columnalheader<-matrix(columnalheader,nrow = 1)
+  write.table(x=columnalheader,
+              file=First_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+  
+  write.table(x=FTLFinalMatrix,
+              file=First_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+  
+  ############################################################################################################
+  
+  D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2)
+  
+  write.table(x=D835Youtputmatrix,
+              file=Second_unshared_motifs_table,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+  
+  columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1]))
+  columnalheader<-matrix(columnalheader,nrow = 1)
+  write.table(x=columnalheader,
+              file=Second_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+  
+  write.table(x=D835YFinalMatrix,
+              file=Second_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+  
+  ############################################################################################################
+  
+  ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2)
+  
+  write.table(x=ITDoutputmatrix,
+              file=Third_unshared_motifs_table,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+  
+  columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1]))
+  columnalheader<-matrix(columnalheader,nrow = 1)
+  write.table(x=columnalheader,
+              file=Third_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+  
+  write.table(x=ITDFinalMatrix,
+              file=Third_unshared_subbackfreq,
+              quote=FALSE, sep=",",
+              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+  
+}
+
+# if (Are_You_Looking_For_Commonality=="NO"){
+#   
+#   
+#   FTLwtmotifsFULLMATRIX<-cbind(FTLwtmotifs,FTLwtAccessionNumbers)
+#   ITDmotifsFULLMATRIX<-cbind(ITDmotifs,ITDAccessionNumbers)
+#   D835YmotifsFULLMATRIX<-cbind(D835Ymotifs,D835YAccessionNumbers)
+#   # ?duplicated
+# 
+#   FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
+#   FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs]
+#   FTLwtmotifsFINAL<-matrix(data=FTLwtmotifsFINAL, ncol = 1)
+# 
+#   ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs]
+#   ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs]
+#   ITDmotifsFINAL<-matrix(data=ITDmotifsFINAL, ncol = 1)
+# 
+#   D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
+#   D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs]
+#   D835YmotifsFINAL<-matrix(data=D835YmotifsFINAL, ncol = 1)
+#   
+#   FTLnondupeAccessionNumbers<-c()
+#   
+#   for (z in 1:nrow(FTLwtmotifsFINAL)) {
+#     for (w in 1:nrow(FTLwtmotifsFULLMATRIX)) {
+#       if (is.na(FTLwtmotifsFULLMATRIX[w,1])!=TRUE)
+#         if (FTLwtmotifsFINAL[z]==FTLwtmotifsFULLMATRIX[w,1]){
+#           FTLnondupeAccessionNumbers<-c(FTLnondupeAccessionNumbers,FTLwtmotifsFULLMATRIX[w,2])
+#         }
+#     }  
+#   }
+# 
+#   
+#   #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them
+#   FTLnondupeAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)]
+#   
+#   columnalheader<-c(rep(NA,35))
+#   FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
+#   
+#   for (k in 1:length(FTLnondupeAccessionNumbers)) {
+#     #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
+#     #destroyed immediately after use
+#     for (m in 1:ncol(Firstsubbackfreq)) {
+#       AN <- as.character(Firstsubbackfreq[1, m])
+#       if (grepl(pattern = AN,
+#                 x = FTLnondupeAccessionNumbers[k],
+#                 fixed = TRUE) == TRUE) {
+#         outputmatrix <- as.character(Firstsubbackfreq[, m])
+#         outputmatrix <- matrix(outputmatrix, nrow = 1)
+#         #with that accession number, find a match in the subbackfreq file and save it here
+#         FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix)
+#       }
+#     }
+#   }
+#   ITDnondupeAccessionNumbers<-c()
+#   
+#   for (z in 1:nrow(ITDmotifsFINAL)) {
+#     for (w in 1:nrow(ITDmotifsFULLMATRIX)) {
+#       if (is.na(ITDmotifsFULLMATRIX[w,1])!=TRUE)
+#         if (ITDmotifsFINAL[z]==ITDmotifsFULLMATRIX[w,1]){
+#           ITDnondupeAccessionNumbers<-c(ITDnondupeAccessionNumbers,ITDmotifsFULLMATRIX[w,2])
+#         }
+#     }  
+#   }
+#   
+#   
+#   #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them
+#   ITDnondupeAccessionNumbers<-ITDnondupeAccessionNumbers[!duplicated(ITDnondupeAccessionNumbers)]
+#   
+#   columnalheader<-c(rep(NA,35))
+#   ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
+#   
+#   for (k in 1:length(ITDnondupeAccessionNumbers)) {
+#     #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
+#     #destroyed immediately after use
+#     for (m in 1:ncol(Thirdsubbackfreq)) {
+#       AN <- as.character(Thirdsubbackfreq[1, m])
+#       if (grepl(pattern = AN,
+#                 x = ITDnondupeAccessionNumbers[k],
+#                 fixed = TRUE) == TRUE) {
+#         outputmatrix <- as.character(Thirdsubbackfreq[, m])
+#         outputmatrix <- matrix(outputmatrix, nrow = 1)
+#         #with that accession number, find a match in the subbackfreq file and save it here
+#         ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix)
+#       }
+#     }
+#   }
+#   
+#   
+#   D835YnondupeAccessionNumbers<-c()
+#   
+#   for (z in 1:nrow(D835YmotifsFINAL)) {
+#     for (w in 1:nrow(D835YmotifsFULLMATRIX)) {
+#       if (is.na(D835YmotifsFULLMATRIX[w,1])!=TRUE)
+#         if (D835YmotifsFINAL[z]==D835YmotifsFULLMATRIX[w,1]){
+#           D835YnondupeAccessionNumbers<-c(D835YnondupeAccessionNumbers,D835YmotifsFULLMATRIX[w,2])
+#         }
+#     }  
+#   }
+#   
+#   
+#   #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them
+#   D835YnondupeAccessionNumbers<-D835YnondupeAccessionNumbers[!duplicated(D835YnondupeAccessionNumbers)]
+#   
+#   columnalheader<-c(rep(NA,35))
+#   D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
+#   
+#   for (k in 1:length(D835YnondupeAccessionNumbers)) {
+#     #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
+#     #destroyed immediately after use
+#     for (m in 1:ncol(Secondsubbackfreq)) {
+#       AN <- as.character(Secondsubbackfreq[1, m])
+#       if (grepl(pattern = AN,
+#                 x = D835YnondupeAccessionNumbers[k],
+#                 fixed = TRUE) == TRUE) {
+#         outputmatrix <- as.character(Secondsubbackfreq[, m])
+#         outputmatrix <- matrix(outputmatrix, nrow = 1)
+#         #with that accession number, find a match in the subbackfreq file and save it here
+#         D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix)
+#       }
+#     }
+#   }
+#   
+#   
+# 
+#   # FinalFTLmotifs<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
+#   # FinalFTLAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)]
+#   # necessaryNAs<-rep(NA,times=(length(FinalFTLmotifs)-length(FinalFTLAccessionNumbers)))
+#   # FinalFTLAccessionNumbers<-c(FinalFTLAccessionNumbers,necessaryNAs)
+#   # TRUEFTLoutputmatrix<-cbind(FinalFTLmotifs,FinalFTLAccessionNumbers)
+#   # TRUEFTLoutputmatrix
+# 
+#   write.table(x=FTLwtmotifsFINAL,
+#               file=First_unshared_motifs_table,
+#               quote=FALSE, sep=",",
+#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+#   
+#   columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1]))
+#   columnalheader<-matrix(columnalheader,nrow = 1)
+#   write.table(x=columnalheader,
+#               file=First_unshared_subbackfreq,
+#               quote=FALSE, sep=",",
+#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+#   
+#   write.table(x=FTLFinalMatrix,
+#               file=First_unshared_subbackfreq,
+#               quote=FALSE, sep=",",
+#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+#   
+# 
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   write.table(x=D835YmotifsFINAL,
+#               file=Second_unshared_motifs_table,
+#               quote=FALSE, sep=",",
+#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+#   
+#   columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1]))
+#   columnalheader<-matrix(columnalheader,nrow = 1)
+#   write.table(x=columnalheader,
+#               file=Second_unshared_subbackfreq,
+#               quote=FALSE, sep=",",
+#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+#   
+#   write.table(x=D835YFinalMatrix,
+#               file=Second_unshared_subbackfreq,
+#               quote=FALSE, sep=",",
+#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   
+#   write.table(x=ITDmotifsFINAL,
+#               file=Third_unshared_motifs_table,
+#               quote=FALSE, sep=",",
+#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+#   
+#   columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1]))
+#   columnalheader<-matrix(columnalheader,nrow = 1)
+#   write.table(x=columnalheader,
+#               file=Third_unshared_subbackfreq,
+#               quote=FALSE, sep=",",
+#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+#   
+#   write.table(x=ITDFinalMatrix,
+#               file=Third_unshared_subbackfreq,
+#               quote=FALSE, sep=",",
+#               row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+#   
+#   
+#   
+#   
+#   
+#   
+# }