Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers

Table 2 Repeat families in the YE-IGS of Equisetum ramosissimum and E. arvense 1 sequence identified by VMATCH

Repeat family^a	Consensus^b	Size	Copy Number
*Equisetum ramosissimum*			54
A	YTATGGACWWDAAATCCATAR	21	13
B	WCTGRACTCAAAATTCAGAATW	22	4
C	AAGACCTATGGACATGAAATCCATAGGTTGA	31	4
D	TAGCTRTGGACATAAAATCCATAGCT	26	4
E	TTAATTAGTTCTTGACACAAAATCAAGAACT	31	3
F	CTATGAACGTTGATAAGAACAC	22	3
G	ATTAGYTCTTGACACAAAATCRAGAA	26	3
H	ASCTMTGGACAATAAATCCATAGSTTG	27	3
I	GAATTATGGACAAGAAATCYATA	23	3
J	AGCTCTGGACATAAAATCCAGAGCTTTACGGTAG	34	2
K	ACGATCTCTGGACAAAAAATCCATAGAT	28	2
L	TTGGTGGTAAAAGCTATAGACAAGAAATCTATAGCTTG	38	2
M	TGGACTCAAAATCCATAGGTTG	22	2
N	TTTAGGTTCTTTACTTGCACTCTATA	26	2
O	TAATTAGTTCTGGACTTAAAAT	22	2
P	ATTGATTACTATATAATAAAT	21	2
*E. arvense* 1			84
A	YTATGGACAAGAAATCCATARVT	23	19
B	YTMTGGACTTAAAATCCATAGDTTK	25	17
C	TAKAWCTCTGGACTTAAAATCCATAGDTT	29	7
D	GTTTTATTTATGGACAAGAAATCCATAA	28	4
E	TTATGGACTGTAAATCCATAR	21	3
F	TTATGGACAAGAAATCCGTAACTATAGAACTAT	33	3
G	GGGTTTTATTTATGGACAAGAAATCCATAGATTG	34	3
H	TATAGTTATAGGTCTGGTGGTARA	24	3
I	TTMTGGACAASAAATCYATAAGT	23	3
J	TTGACAACAAATCCAKAATATCT	23	3
K	TAAYTTCTAGACTCAAAATCTA	22	3
L	TTTCTGGACAAGAAATCCRGAA	22	3
M	GGTACGAYTTCTGGACAATAAATCCAGAATATATGT	36	3
N	AATATCTATAGACTCCAAATCTATAGATATAGTTATAGGTTAGGT	45	2
O	TTATGGACAAGAAATCCATAAATATAGGCT	30	2
P	TTGGTGATATAACTCTGGACTTAAAATCCATAG	33	2
Q	ATATCTATAGACTCCAAATCTATA	24	2
R	ATATATGTATGGACCTGTTGACAACAAATCCATA	34	2

a - Families of non-overlapping repeats sharing ≥ 85% sequence identities;
b - The underlined DNA strings are mutually complementary and have potential to form a paired double helix. The putative secondary structures of the repeat families are provided in Additional file 3-4.

ISSN: 1471-2229