Rice transposable elements are characterized by various methylation environments in the genome

BMC Genomics

Table 1 Copy numbers and conservation degrees of 12 transposable elements based on the BLAST analyses

TE	Accession or reference (1)	Size (Pb)	Total count of Blast (A) (2)	Highest score (bit) (3)	Count over 80% of the highest score (B) (4)	80% of highest score	Conservation degree (B/A%) (5)
noaCRR1	AY827986	794	479	1467	29	1173	6.05
RIRE5	AB105803LTR	995	270	1674	14	1339	5.19
RIRE7	AB033234LTR	858	119	1541	30	1232	25.21
p-SINE1	Mochizuki et al. (1992) p-SINE1 consensus	123	207	209	66	167	31.88
Akan	AB077838	486	110	784	47	627	42.73
Kiddo	AF484680	269	42	459	37	367	88.1
Kiserul	AB077834	259	835	453	390	362	46.71
mPing	BK000588	430	50	795	48	636	96
Mashu	AB077839	263	563	457	441	360	78.33
Tabitoll	AB077831	146	563	226	339	180	60.21
Toya	AB077842	176	11	287	8	229	72.73
Basho	Inukai and Sano (2002) MS399	201	396	359	29	287	7.32

1: Representatives of the 12 TEs were selected from these accessions or references, which were used as the queries for the BLAST analyses.
2: These correspond to numbers of the sequences hit by the rice BLAST analyses at NCBI as described in Materials and Methods.
3: The scores are those of the most homologous sequences hit by the BLAST analyses.
4: The numbers of the sequences with more than 80% of the highest scores.
5: Conservation degrees of the TEs are estimated by percentages of the counts with more than 80% of the highest scores(B) in the total counts (A).

ISSN: 1471-2164