Frameshift and wild-type proteins are often highly similar because the genetic code and genomes were optimized for frameshift tolerance

Table 3 The similarities of proteins and their frameshifts (aligned by FrameAlign)

Type	Species	Number of CDSs	Average Similarity						Number of Gaps
Type	Species	Number of CDSs	δ₁₂	δ₁₃	δ₂₃	δ	MAX	MIN	Number of Gaps
Real CDSs (FrameAlign)	H. sapiens	71,853	0.492 ± 0.043	0.472 ± 0.044	0.434 ± 0.040	0.466 ± 0.029	0.713	0.194	2
	P. troglodytes	15,781	0.491 ± 0.046	0.468 ± 0.046	0.431 ± 0.042	0.463 ± 0.030	0.625	0.311	2
	M. musculus	27,208	0.484 ± 0.046	0.469 ± 0.042	0.426 ± 0.040	0.460 ± 0.029	0.739	0.286	2
	X. tropicalis	7706	0.481 ± 0.042	0.481 ± 0.041	0.439 ± 0.037	0.467 ± 0.028	0.644	0.353	2
	D. rerio	14,151	0.471 ± 0.044	0.468 ± 0.040	0.408 ± 0.040	0.449 ± 0.030	0.614	0.314	2
	D. melanogaster	23,936	0.475 ± 0.046	0.457 ± 0.044	0.362 ± 0.047	0.431 ± 0.030	0.689	0.236	2
	C. elegans	29,227	0.450 ± 0.047	0.475 ± 0.045	0.421 ± 0.043	0.449 ± 0.032	0.634	0.224	2
	A. thaliana	35,378	0.442 ± 0.045	0.477 ± 0.044	0.412 ± 0.041	0.444 ± 0.031	0.882	0.244	2
	S. cerevisiae	5889	0.461 ± 0.041	0.510 ± 0.042	0.423 ± 0.038	0.465 ± 0.029	0.692	0.259	2
	E.coli	4140	0.435 ± 0.046	0.426 ± 0.047	0.372 ± 0.043	0.411 ± 0.030	0.571	0.237	2
	Average	235,269	0.468 ± 0.045	0.470 ± 0.043	0.413 ± 0.041	0.450 ± 0.030	0.882^a	0.194^a	2
Random CDSs (FrameAlign)	Three frames	100,000	0.394 ± 0.028	0.394 ± 0.028	0.395 ± 0.028	0.394 ± 0.016	0.477	0.330	2
Random CDSs (FrameAlign)	Three random CDSs	100000 × 3	0.383 ± 0.028	0.383 ± 0.028	0.383 ± 0.028	0.383 ± 0.018	0.458	0.304	0

^aVery large/small similarity values were observed in a few very short or repetitive peptides

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