Large-scale identification of polymorphic microsatellites using an in silico approach

BMC Bioinformatics

Table 3 Motif length and position of polymorphic SSRs in EST sequences of chicken, rice, Arabidopsis, Brassica, potato and tomato

species		Di^a-	Tri-^a	Penta^a	Others^b	total	Density^c
chicken	all	846 (49%)	378 (22%)	386 (22%)	114 (7%)	1724 (100%)	71.51
	coding	95	70	38	9	212	55.13
	5'UTR¹	19	33	24	10	86	137.66
	3'UTR²	155	54	77	24	310	74.81
	TSS³	1	3	3	1	8
rice	all	1070 (40%)	1113 (42%)	320 (12%)	143 (5%)	2646 (100%)	93.47
	coding	154	372	86	26	638	57.33
	5'UTR¹	294	285	69	32	680	227.16
	3'UTR²	342	121	70	36	569	92.66
	TSS³	5	0	1	1	7
Arabidopsis	all	668 (53%)	410 (33%)	133(11%)	37 (3%)	1248 (100%)	102.63
	coding	196	222	34	13	465	72.84
	5'UTR¹	193	73	34	7	307	215.96
	3'UTR²	136	42	40	10	228	112.02
	TSS³	6	2	1	1	10
Brassica	all	468 (47%)	350 (35%)	139 (14%)	40 (4%)	997 (100%)	119.45
	coding	55	203	43	13	314	63.09
	5'UTR¹	205	55	27	13	300	378.62
	3'UTR²	126	44	47	9	226	169.90
	TSS³	1	2	3	2	8
potato	all	379 (35%)	358 (33%)	248 (23%)	95 (9%)	1080 (100%)	89.78
	coding	61	155	87	44	347	62.66
	5'UTR¹	64	38	29	8	139	160.21
	3'UTR²	129	40	59	24	252	134.75
	TSS³	0	1	3	1	5
tomato	all	124 (47%)	79 (30%)	54 (20%)	8 (3%)	265 (100%)	98.52
	coding	42	35	19	2	98	67.06
	5'UTR¹	50	18	19	1	88	265.74
	3'UTR²	12	7	5	0	24	70.79
	TSS³	1	1	1	1	4

^aDi- is dinucleotide SSR, and so on for others; ^bothers means tetranucleotide and hexanucleotides repeats or higher
^cDensity of number of SSR per 100 kb of EST sequences (See Materials & Methods).
¹ 5' UTR is the portion of an mRNA from the 5' end to the position of the first codon used in translation.
²The 3' UTR is the portion of an mRNA from the last codon used in translation to the 3' end of the mRNA.
³ TSS is the position of the first codon (translation start) and the last codon (translation stop) used in translation. SSR contain the first codon or the last codon.

ISSN: 1471-2105