Let us assume that you would like to filter a file with multiple fasta sequences with a defined sequence length. For eg. in a file with 2000 sequences (in fasta format), you would like to extract all sequences with 100 nt length.

Code: seqkit seq -M 100  test.fa-M option for maximum length

Now, let us assume that you are looking for all the 100 nt sequences with a G at
position 3 and C at position 12.

Code:

seqkit seq -M 100  test.fa | seqkit grep -s  -R 3:3 -p G | seqkit grep -s -R 12:12 -p C