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Table 4.

Percentage of Exons Correctly Aligned During the CHAOS-Based Anchoring Phase of LAGAN (Steps 1,2)

Alignment human vs.		90%–100%		50%–89%		10%–49%		0%–9%
Alignment human vs.		default	transl.	default	transl.	default	transl.	default	transl.
Chimpanzee	97	97	3	3	0	0	0	0
Baboon	77	77	21	21	3	3	0	0
Cow	21	21	43	43	36	36	0	0
Pig	19	19	33	30	47	50	1	1
Dog	20	20	37	37	41	42	2	1
Cat	20	20	41	41	39	39	0	0
Mouse	10	10	35	37	52	51	2	2
Rat	13	10	47	46	40	42	1	2
Chicken	9	9	26	41	62	47	3	3
Fugu	12	29	19	29	57	35	12	7
Zebrafish	27	33	29	42	38	25	4	0

[i] Percentage of human exons that have a given proportion of their lengths covered (90%–100%, 50%–89%, 10%–49%, and 0%–9%). Translated anchoring performs better at covering a greater proportion of exons. However, we do not have measurements on whether translated anchoring performs worse in covering biologically significant noncoding features.