. 2014 Feb 20;9(2):e88992. doi: 10.1371/journal.pone.0088992

Table 2. Sequences of AFLP markers showing homology to TE sequences.

TEs	AFLP marker	Marker size	Pos	Sim	Homologous region	Hybrid	Genbank reference
Baggins1^#	TGTCG21	377 bp	0.52	0.38	reverse transcriptase/RNAasa	SH	JX997206
BATUMI*	CACTC22	500 bp	0.60	0.60	polyprotein	SH	JX997209
Bel_1*	GGATT21	450 bp	0.93	0.93	internal region	BC1	JX997190
BS^#	TGTCG22	443 bp	0.71	0.62	internal region	SH	JX997207
CIRCE*	CACTC21	529 bp	0.62	0.55	internal region	SH	JX997212
DIVER*	TGTCG23	415 bp	0.63	0.33	endonuclease/integrase	SH	JX997208
Frogger*	CACAT21	153 bp	0.61	0.41	internal region	SH	not annotated
Galileo^▪	TGATT22	408 bp	0.99	0.1	internal region	BC3	JX997200
Galileo^▪	CGGGG22	172 bp	0.75	0.60	internal region	BC3	not annotated
Gypsy1*	CAGCA21	491 bp	0.83	0.70	internal region	BC1	JX997198
Gypsy1*	CCCCC22	540 bp	0.83	0.83	internal region	BC1	JX997192
Gypsy1*	CCGAT22	264 bp	0.72	0.64	internal region	BC3	JX997217
Gypsy1*	TGATT21	554 bp	0.52	0.34	LTR	BC3	JX997196
Gypsy3*	CGAGT21	707 bp	0.45	0.27	polyprotein	SH	JX997211
Gypsy8*	TGTCG21	377 bp	0.45	0.32	internal region	SH	JX997206
Gypsy8*	TGATT26	505 bp	0.70	0.70	poliprotein	BC3	JX997199
Gypsy9*	CCGAT23	303 bp	0.48	0.38	internal region	BC3	JX997204
Gypsy10*	TGTCG23	415 bp	0.71	0.64	internal region	SH	JX997208
Gypsy12*	CGGCA21	1231 bp	0.60	0.47	internal region	SH	JX997214
Helena^#	TGTCG22	443 bp	0.76	0.62	ORF2/endonuclease	SH	JX997207
Helena^#	TGTCG27	441 bp	0.80	0.76	reverse transcriptase/RNAasa	BC2	JX997216
Helena^#	TGTCG41	441pb	0.78	0.67	ORF2/endonuclease	DB	not annotated
Helitron-2^▪	TGCGG21	145 bp	0.77	0.46	internal region	BC3	not annotated
Helitron-2^▪	CGGCA21	1231 bp	0.62	0.51	5′region	SH	JX997214
Helitron-1N1^▪	CCGAT22	264 bp	0.92	0.92	internal region	BC3	JX997217
HETA^#	CACTC21	592 bp	0.41	0.31	internal region	SH	JX997212
Homo6^▪	TGATT25	442 bp	0.62	0.50	internal region	BC2	JX997193
Homo6^▪	TCAGT21	347 bp	0.88	0.88	internal region	BC2	JX997194
Homo6^▪	TGATT27	441 bp	0.68	0.58	internal region	BC3	JX997201
Homo6^▪	CCGAT24	320 bp	0.94	0.94	internal region	BC3	JX997205
LSU-rRNA_Hsa^Ø	CAGCG23	448 bp	0.42	0.31	HSU 13369 locus	BC2	not annotated
MAX*	CACTC22	500 bp	0.66	0.50	polyprotein	SH	JX997209
MINI-ME^#	GGCTC21	647 bp	0.58	0.46	internal region	BC1	JX997188
MINI-ME^#	CCCCC21	540 bp	0.71	0.71	internal region	BC1	JX997191
MINI-ME^#	TCAGT22	306 bp	0.71	0.62	internal region	BC2	JX997195
Osvaldo*	TGATT24	530 bp	0.63	0.51	internal region	BC3	JX997197
Osvaldo*	TGATT26	519 bp	0.56	0.46	internal region	SH	JX997213
Penelope^#	CCGAT21	309 bp	0.91	0.13	internal region	BC3	JX997203
TART^#	TGTCG23	415 bp	0.55	0.41	polyprotein	SH	JX997208
TART^#	TCTCG21	218 bp	0.55	0.29	polyprotein	BC3	JX997202
Transib1^▪	CAGCA22	359 bp	0.73	0.60	transposase	SH	JX997210
TRIM^#	TGTCG23	415 bp	0.58	0.41	internal region	SH	JX997208
UHU^▪	TGATT25	513 bp	0.66	0.52	internal region	BC3	JX997198
ZAM*	TGATT26	519 bp	0.58	0.35	internal region	SH	JX997213

Sim: similarity between 2 aligned fragments using the parameters of CENSOR tool referenced in material and methods section, * LTR retrotransposon, ^# non-LTR retrotransposon, ^▪ DNA transposon, ^Ø pseudogen, SH: segmental hybrid, BC1, BC2 and BC3:hybrids from backcrosses 1,2 and 3 respectively; DB: parental species D. buzzatii.