Table 4.

fasta36 output formats (-m)

- m	Output options
0	Default, conventional 3 line alignment, identities indicated with ’:’, conservative replacements ’.’ :
MWRTCGPPYT
::..:: :::
MWKSCGYPYT
1	Similar to -m 0, but conservative replacements indicated with ’x’, non-conservative replacements ’X’ (good for highly identical alignments)
MWRTCGPPYT
xx  X
MWKSCGYPYT
2	Similar to -m 0, but 2-line alignment:
MWRTCGPPYT
..KS..Y...
3	One line alignment:
	MWKSCGYPYT
6	-m 0 using HTML output with links
B	BLAST alignment style:
Query     1    MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRIL 60
M+ WGY HNGP+HWH+ FP AKGE QSPV++ T ++DPSL+P SVSYD ++ IL
Sbjct      1    MAKEWGYASHNGPDHWHELFPNAKGENQSPVELHTKDIRHDPSLQPWSVSYDGGSAKTIL 60
BB	BLAST alignment style with BLAST-like beginning, end
8	BLAST tabular output
8C	BLAST tabular output with comments
8CC	BLAST tabular output with comments and CIGAR string, annotations (Figure 3.9.2B)
8CB	BLAST tabular output with comments and Blast BTOP alignment encoding, annotations.
9	FASTA tabular output
9i	FASTA -m 1 output with identity, alignment length
9C	-m 9 output with CIGAR string, annotations
9B	-m 9 output with BTOP string, annotations
10	Parse-able alignments with label:value output