Input  sequence  file         Or paste sequences

Blank,tab and digit sequence-character options               Check if digit characters exist?                                Yes No               Check if blank or tab characters exist?                    Yes No

Valid sequence-character options               Check for specific characters?                                Yes No               If Yes,                             Select a valid character set to use                                    1.User-defined 2.prot. primary (20): ACDEFGHIKLMNPQRSTVWY 3.prot. primary (23): ACDEFGHIKLMNPQRSTVWYBXZ 4.prot. secondary: (3-state): CEH 5.prot. secondary: (DSSP states): CEHBGIST 6.DNA (4): ACGT 7.DNA (6): ACGTRY 8.DNA (extended): ACGTBDHKMNRSVWY 9.RNA: ACGUI                             If User-defined type,                                    Enter the name of file containing valid characters:                                                                       Or directly enter valid characters:                                                                Are letters case sensitive?                        Yes No

Compostional analysis options                Perform special DNA analysis?                            Yes No               Treat upper and lowercase letters as different?       Yes No

Definition line format options               Maximum length of definition line                                           Add the sequence length to each definition line?      Yes No               Add CG percentage to each definition line?            Yes No               Add uppercase ATCG percent to definition line?    Yes No

Sequence line format options               Maximum length of sequence line                                           Change the letter cases?        No change   to uppercase   to lowercase               Insert position count at start of each line?                 Yes No               Insert blank after every   characters?          Yes No

Sequence filter options               Delete sequences with < characters?                             Yes No               Delete sequences with > characters?                             Yes No               Delete sequences with < % ATCG?                               Yes No