MAST hit_list strand meaning

[Liam]

I ran MAST with the -hit_list option and am confused by the strand column output.

What do the numbers associated with the strand value mean? I understand +/- refer to the sense/antisense strands, but what does "-4", "+3", "-2", etc. mean?

Thanks for your help.

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Command

mast -bfile /genome/mm10.order1.bfile -ev 1000 -hit_list /motifs/CTCF.meme /fasta/myseqs.fa

First few lines of output

# All non-overlapping hits in all sequences from "/fasta/myseqs.fa".
# sequence_name (strand+/-)motif id alt_id hit_start hit_end score hit_p-value
chr1:4142496-4142913 -4 MA1930.1 CTCF 217 251  1655.04 6.22e-07
chr1:4173310-4173681 +3 MA1929.1 CTCF 180 213  1866.64 2.16e-07
chr1:4228149-4228530 -2 MA0139.1 CTCF 177 195  1897.43 2.69e-07
chr1:4228149-4228530 +2 MA0139.1 CTCF 331 349   773.70 9.16e-05

Program info: MEME suite version 5.5.7 (Apptainer image built from the MEME Docker image)

[cegrant]

The columns in the hit list output are described in the documentation for the MAST command line in the section near the bottom titled "Hit List". The number after (+/-) strand indicator is the motif number. Each motif in the input file is numbered along the id and alt-id. For example, motif 2 has the id MA0139.1 and the alt-id CTCF.