AlignACE ExampleMasking (old way)

5’- TCTCTCTCCACGGCTAATTAGGTGATCATGAAAAAATGAAAAATTCATGAGAAAAXAGTCAGACATCGAAACATACAT

5’- ATGGCAGAATCACTTTAAAACGTGGCCCCACCCGCTGCACCCTGTGCATTTTGTACGTTACTGCGAAATXACTCAACG

5’- CACATCCAACGAATCACCTCACCGTTATCGTGACTXACTTTCTTTCGCATCGCCGAAGTGCCATAAAAAATATTTTTT

5’- TGCGAACAAAAXAGTCATTACAACGAGGAAATAGAAGAAAATGAAAAATTTTCGACAAAATGTATAGTCATTTCTATC

5’- ACAAAGGTACCTTCCTGGCCAATCTCACAGATTTAATATAGTAAATTGTCATGCATATGACTXATCCCGAACATGAAA

5’- ATTGATTGACTXATTTTCCTCTGACTACTACCAGTTCAAAATGTTAGAGAAAAATAGAAAAGCAGAAAAAATAAATAA

5’- GGCGCCACAGTCCGCGTTTGGTTATCCGGCTGACTXATTCTGACTXTTTTTTGGAAAGTGTGGCATGTGCTTCACACA

AAAAGAGTCA

AAATGACTCA

AAGTGAGTCA

AAAAGAGTCA

GGATGAGTCA

AAATGAGTCA

GAATGAGTCA

AAAAGAGTCA

**********

…HIS7

…ARO4

…ILV6

…THR4

…ARO1

…HOM2

…PRO3

• Take the best motif found after a prescribed number of random seedings.

• Select the strongest position of the motif.

• Mark these sites in the input sequence, and do not allow future motifs to sample those sites.

• Continue sampling.

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