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go through each block column

go through each block column. Column location in block added to list. Go through list of ambiguous positions. is there a single SSE assignment or multiple SSE assignment?. is there a single SSE assignment or multiple assignment with weight above threshold?.

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go through each block column

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  1. go through each block column Column location in block added to list Go through list of ambiguous positions is there a single SSE assignment or multiple SSE assignment? is there a single SSE assignment or multiple assignment with weight above threshold? Does the ambiguous columns contain flanking SSE? does the ambiguous columns contains only SSE appearing in the flanking positions? Are both flanks of ambiguous regions identical? Are there <=2 consecutive columns with ambiguous SSE assignment Go to next column Were all blocks columns analyzed? single assignment Multiple assignment SSE assigned to consensus 'compressing' consecutive repeats (e.g a single H is assigned for HHH) single Multiple assignment Consensus assigned end yes no yes no yes yes yes no no No consensus is assigned end no

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