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Table 4.

Performance of CAP3 and PHRAP

Program	Data set[i]	Length of longest contig	No. of large contigs	Total length of gaps	Total no. of internal errors[ii]
CAP3	3XA	6189	57	52,885	443
PHRAP	3XA	6396	54	38,146	529
CAP3	3XB	12,368	44	71,761	71
PHRAP	3XB	13,116	47	60,436	228
CAP3	3XC	10,709	49	54,229	227
PHRAP	3XC	11,406	45	34,727	332
CAP3	3XD	11,408	43	67,586	115
PHRAP	3XD	11,350	49	60,312	240
CAP3	5XA	10,582	42	27,965	249
PHRAP	5XA	18,268	31	14,396	252
CAP3	5XB	26,034	17	10,405	100
PHRAP	5XB	33,693	18	7,322	115
CAP3	5XC	20,939	29	20,520	172
PHRAP	5XC	20,912	27	16,617	261
CAP3	5XD	14,219	35	23,635	46
PHRAP	5XD	14,696	33	17,113	129
CAP3	8XA	71,025	12	4,681	83
PHRAP	8XA	71,395	8	1,061	80
CAP3	8XB	53,127	8	883	59
PHRAP	8XB	53,078	7	542	36
CAP3	8XC	52,134	8	752	4
PHRAP	8XC	76,922	6	774	6
CAP3	8XD	72,690	7	1,241	35
PHRAP	8XD	102,523	6	648	60
CAP3	10XA	91,380	4	0	28
PHRAP	10XA	91,329	3	0	11
CAP3	10XB	167,655	1	0	5
PHRAP	10XB	138,551	2	0	7
CAP3	10XC	106,631	5	321	44
PHRAP	10XC	77,747	4	330	12
CAP3	10XD	79,900	4	468	2
PHRAP	10XD	79,978	3	346	2

[i] The number in the name of a data set is the estimated depth of coverage for the data set.

[ii] An error in a consensus sequence is internal if it is not within 500 bases of either sequence end.