Table 1.

Number of sequences with palindromic (P) segments of 2–8 bp in length downstream/upstream of the V_H, diversity (D) and J_H gene segments. The P segments were found using JointMLa, which allows P nucleotides to start at the end of the gene segment irrespective of the amount of trimming. P-values are calculated using Fisher's exact test. Similar results were obtained using JointHMMa (data not shown)

	Sequences			Permutated sequences*
Distance from heptamer to gene end†	No. of sequences	No. with P	% with P	No. of sequences	No. with P	% with P	P-value
VH gene
1	1448	474	32·7	1635	103	6·3	< 10−5
2	1027	48	4·7	1068	65	6·1	0·091
3	762	53	7·0	612	36	5·9	0·245
JH gene
1	324	60	18·5	350	23	6·6	< 10−5
2	184	2	1·0	209	3	1·4	0·560
3	219	8	3·7	250	14	5·6	0·220
5′ end of D gene
1	519	128	24·7	619	54	8·7	< 10−5
2	343	31	9·0	347	26	7·5	0·275
3	474	25	5·3	454	17	3·7	0·168
3′ end of D gene
1	616	86	14·0	684	58	8·5	0·001
2	266	30	11·3	276	24	8·7	0·195
3	460	5	1·1	485	9	1·9	0·241

^*See the Materials and methods section.

^†All positions up to 10 bp from the heptamer were analysed. No statistically significant differences were found except for at untrimmed ends.