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Illustration of the GLASS alignment of human and mouse orthologs, Human Comparative Indicator Sequence (HCIS), and base scores for local windows of length 5. HCIS is essentially the output of the global alignment system. It is defined as a binary sequence with 1 indicating a match and 0 a mismatch/gap in the alignment. LBS/RBS at position i is the number of matches in the local window of length k (5 in the example, 20–30 in the study) that ends/starts at position i.
