Large tandem repeats of grass frog (Rana temporaria) in silico and in situ

BMC Genomics

Table 2 First 12 families of TRs in the R. temporaria genome assembly

N	TR	Number of arrays	Mean GC, %	Max_array length, bp	Chromosome	Dfam TE	% in genome
1	1149A	62	37.21	24,814	All but 9, Unpl		0.022
2	138A	35	46.36	62,988	1, 2, 3, 4, 5, 8, 9, Unpl	U5 snRNA, U4 snRNA	0.018
3	27A	29	48.4	100,622	All but 1, 3, 5, 9, Unpl		0.015
4	35A	27	38.04	62,152	2, 4, 11, 13, Unpl		0.014
5	494A	21	46.83	57,784	1, 2, 3, 4, 5, 8, 9, Unpl		0.012
6	219A	20	50.75	57,710	8, 13, Unpl	5S rRNA	0.013
7	44A	13	47.2	38,448	1, 2, 3, 5, 8, 10, 13, Unpl		0.006
8	31A	10	47.36	17,669	1, 2, 4, 8, 12, Unpl		0.004
9	140A	9	56.47	19,368	1, 2, 3, 4, 5, 12, 13		0.003
10	44B	9	41.74	44,868	1, 4, 5, 6, 8, 9, 10		0.004
11	1099A	7	48.83	32,032	3, 4, Unpl	tRNA	0.003
12	32A	7	44.55	77,222	1, 3, 4, 6, Unpl		0.004

GC% - average GC content in TRs in percent; TR similarity by Dfam database; TR chromosome positions predicted in silico. TRs for which FISH was performed on metaphase plates (Fig. 1) are shown in bold italic. Unpl – unplaced scaffolds

ISSN: 1471-2164