cleaned up readme

README.md

@@ -41,16 +41,16 @@ Next, a fasta-file (with protein sequences) should be basted against the newly c
 element proteins.
 
     detector blast species_peptides.fasta known_te_db species_blast_output
-    
- This command will blast a protein fasta-file species_peptides.fasta against known_te_db (created in the previous step).
- The output will be stored in species_blast_output
+
+This command will blast a protein fasta-file species_peptides.fasta against known_te_db (created in the previous step).
+The output will be stored in species_blast_output
 
- Finally, from the output, sequences similar to known transposable element proteins can be extracted using the analyze 
- command below.
+Finally, from the output, sequences similar to known transposable element proteins can be extracted using the analyze
+command below.
 
-     detector analyze species_blast_output species_putative_te.lst
+    detector analyze species_blast_output species_putative_te.lst
      
- The file species_putative_te.lst will be created if putative transposable element proteins are found.
+The file species_putative_te.lst will be created if putative transposable element proteins are found.
 
 
 Finally, detector can be used to remove the putative TEs from a fasta file.