Sequence signature analysis of chromosome identity in three Drosophila species

BMC Bioinformatics

Table 1 The length, number of N and A/T content of all chromosomes used in this study.

	Original sequence length	% N	% A/T	% removed by Tandem Repeats Finder	% A/T after Tandem Repeats Finder masking	% Removed by RepeatMasker	% A/T after RepeatMasker masking
Dm
X	21780003	0.10	57.42	2.12	57.34	8.80	56.55
2L	22217931	0.01	58.08	0.81	58.07	6.59	57.54
2R	20302755	0.02	56.55	0.91	56.54	7.88	56.05
3L	23352213	0.05	57.92	0.87	57.93	6.77	57.36
3R	27890790	0.00	57.08	0.68	57.07	5.33	56.60
4(F)	1237870	0.08	64.71	1.17	64.53	26.70	64.58
Dy
X	21591847	3.28	56.73	3.45	56.58
2L	22678881	1.31	57.19	1.56	57.18
2R	21288905	1.39	56.74	1.33	56.75
3L	24977971	2.19	57.57	1.57	57.57
3R	29717196	1.88	56.81	1.47	56.82
4(F)	1395135	2.16	64.53	3.38	64.51
Dp
XL	24630256	4.10	54.22	2.86	54.33
4	26108043	3.64	55.99	2.31	56.02
3	19738113	3.41	53.52	1.50	53.61
XR	24186629	3.87	53.76	3.63	53.96
2	25998849	3.13	55.10	1.86	55.15
5(F)	849497	25.81	61.45	1.02	61.42

The percentages of base pairs removed by Tandem Repeats Finder and RepeatMasker as well as the A/T content of the remaining sequences are also given. The Dp chromosomes are listed in the same order as the corresponding Dm chromosomes.

ISSN: 1471-2105