RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

In alpha testing (2022/Oct)

Changed the notation of position on the opposite strand in DNA data to cx-cy, where x and y are counted from the 5' end of the strand where the similar region is found (2022/Oct/9).

Fixed a bug in calculating coverage when the reference consists of two or more sequences (2022/Nov/4).

Changed the conditions to concatanate multiple hits (Maximum separation and Maximum overlap in the setting panel below) to use length relative to the reference. (2022/Dec/19).

Fixed a problem when reference sequence is shorter than the "Maximum overlap" parameter (2022/Dec/22).

Extract a specific region using LAST.

Specific region to be used as reference (FASTA format):
Protein example: single sequence with single domain, or Pfam-seed
Nucleotide example: RNA gene

or upload a plain text file:     Clear

Full-length sequences from which the specific region above will be extracted: 
Protein example: a set of full-length genes
Nucleotide example: a set of genomic sequences
Gaps (-) will be reset, if any, and extra regions will be removed.

or upload a plain text file:     Clear
Zipped file is acceptable.

Output order:

Sequence title:

Title length in Clustal format (only first word is used as title):

Job name (optional):
(basic Latin alphabet, number and space only)

Notify when finished (optional; recommended when submitting large data):
Email address:

Advanced settings

Minimum coverage:
Include sequences that cover at least (0.0 – 1.0) of the reference.

Maximum separation:
Concatenate multiple hits (not regard them as duplication) if the hits are separated by less than (0 – 10,000) bases/residues.

Maximum overlap:
Concatenate multiple hits (not regard them as duplication) if the hits overlap by less than (0 – 100) bases/residues.