../fixtures/ex10_hg38_alugedon.align.format
1	90	12217	MER33#DNA/hAT-Charlie
91	229	9749	FLAM_C#SINE/Alu
230	516	8515	AluSq2#SINE/Alu
517	815	7281	AluSq#SINE/Alu
849	1141	6047	AluSx#SINE/Alu
1142	1165	4813	AluYf1#SINE/Alu
1166	1458	3579	AluSx#SINE/Alu
1459	1618	2345	AluJb#SINE/Alu
1619	1719	12217	MER33#DNA/hAT-Charlie
-------------------------------------------------------------
../fixtures/ex1_hg38_nesting.align.format
360	498	22089	L2#LINE/L2
711	950	29493	HAL1#LINE/L1
982	1094	25791	Charlie12#DNA/hAT-Charlie
1096	1402	17153	AluY_short_#SINE/Alu
1403	1517	25791	MER30#DNA/hAT-Charlie
1549	1941	14685	LTR16C#LTR/ERVL
1942	2729	29493	HAL1#LINE/L1
2973	3101	12217	FLAM_A#SINE/Alu
3109	3203	10983	L1MB7_3end#LINE/L1
3209	3461	28259	HAL1#LINE/L1
3462	3695	8515	HAL1ME#LINE/L1
3829	4080	28259	HAL1#LINE/L1
4117	4368	4813	AluSz#SINE/Alu
4371	4901	28259	HAL1#LINE/L1
4947	5091	2345	L2c_3end#LINE/L2
5200	5251	1111	L2d2_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex2_hg38_nesting.align.format
2563	2587	34429	L1MC5_3end#LINE/L1
2588	2951	33195	L1ME4b_3end#LINE/L1
2957	3026	31961	L2b_3end#LINE/L2
3258	3713	29493	L1MA3_3end#LINE/L1
3918	4230	27025	AluSq#SINE/Alu
4386	4521	49237	L4_A_Mam#LINE/RTE-X
4537	4768	43067	L1M5_orf2#LINE/L1
4769	4896	23323	MLT2C2#LTR/ERVL
4993	5076	22089	HY1#scRNA
5077	5194	20855	MLT1E3#LTR/ERVL-MaLR
5204	5358	19621	MLT2F#LTR/ERVL
5362	5584	43067	L1M5_orf2#LINE/L1
5585	5740	41833	L1ME3B_3end#LINE/L1
5746	6291	15919	MLT1F1#LTR/ERVL-MaLR
6292	6392	14685	L1ME3_3end#LINE/L1
6393	6955	41833	L1ME3B_3end#LINE/L1
7123	7262	48003	L4_B_Mam#LINE/RTE-X
7268	7313	39365	MSTC#LTR/ERVL-MaLR
7314	7619	9749	AluSx1#SINE/Alu
7620	8014	39365	MSTC#LTR/ERVL-MaLR
8047	8352	48003	L4_B_Mam#LINE/RTE-X
8354	8400	36897	L4_A_Mam#LINE/RTE-X
8730	8920	2345	L1MB8_3end#LINE/L1
8921	8932	1111	L1MA5_3end#LINE/L1
-------------------------------------------------------------
../fixtures/ex3_hg38_nesting.align.format
649	882	24557	L2c_3end#LINE/L2
883	1228	22089	LTR40a#LTR/ERVL
1230	1269	9749	LTR40b#LTR/ERVL
1275	1447	17153	MSTB1#LTR/ERVL-MaLR
1448	1576	6047	AluJr4#SINE/Alu
1577	1699	17153	MSTA1#LTR/ERVL-MaLR
1700	1821	17153	MSTB1#LTR/ERVL-MaLR
1822	1878	22089	LTR40a#LTR/ERVL
1879	2098	24557	L2c_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex4_hg38_badoverlap.align.format
6	145	3579	MIR#SINE/MIR
149	295	1111	L2a_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex5_hg38_composite.align.format
1	218	24557	AluYg6#SINE/Alu
604	1291	30727	Tigger1#DNA/TcMar-Tigger
1292	1595	22089	AluYa5#SINE/Alu
1597	2175	30727	Tigger1#DNA/TcMar-Tigger
2176	2327	28259	AluSx_short_#SINE/Alu
2328	2626	18387	AluSx3#SINE/Alu
2631	2679	15919	AluYa8#SINE/Alu
2680	2780	28259	AluSz6#SINE/Alu
2782	3091	30727	Tigger1#DNA/TcMar-Tigger
3092	3924	10983	SVA_B#Retroposon/SVA
3925	3951	9749	SVA_A#Retroposon/SVA
3952	4624	8515	SVA_B#Retroposon/SVA
4650	5031	30727	Tigger1#DNA/TcMar-Tigger
5032	5327	6047	AluSg7#SINE/Alu
5328	5777	30727	Tigger1#DNA/TcMar-Tigger
6058	6171	25791	LTR38A1#LTR/ERV1
6172	6314	2345	L1PA15_3end#LINE/L1
6315	6668	25791	LTR38A1#LTR/ERV1
-------------------------------------------------------------
../fixtures/ex6_hg38_ambiguous.align.format
1	155	10983	AluSp#SINE/Alu
157	198	8515	AluY_short_#SINE/Alu
199	277	12217	LTR5B#LTR/ERVK
279	536	4813	AluYb10#SINE/Alu
537	985	3579	LTR5A#LTR/ERVK
986	1478	12217	LTR5B#LTR/ERVK
1479	1758	1111	AluYj4#SINE/Alu
-------------------------------------------------------------
../fixtures/ex7_hg38_ambiguous.align.format
103	215	27025	L2#LINE/L2
307	461	25791	L2c_3end#LINE/L2
616	633	24557	L1MA2_3end#LINE/L1
634	994	23323	L1MB2_3end#LINE/L1
1106	1314	29493	L2#LINE/L2
1356	1436	19621	MER106A#DNA/hAT-Charlie
1437	1576	18387	MER106B#DNA/hAT-Charlie
1577	1961	29493	L2#LINE/L2
1980	2138	15919	MER58A#DNA/hAT-Charlie
2139	2488	14685	L2a_3end#LINE/L2
2715	2834	12217	L3#LINE/CR1
2905	3022	10983	MIRc#SINE/MIR
3180	3307	8515	AluJr4#SINE/Alu
3308	3340	7281	AluSp#SINE/Alu
3435	3508	28259	MIR3#SINE/MIR
3509	3684	4813	MER20#DNA/hAT-Charlie
3685	3734	3579	MIR1_Amn#SINE/MIR
3735	3785	28259	MIR3#SINE/MIR
4034	4092	1111	AluSx_short_#SINE/Alu
-------------------------------------------------------------
../fixtures/ex8_hg38_alugedon.align.format
98	400	12217	AluSx1#SINE/Alu
402	701	9749	AluSc#SINE/Alu
702	897	8515	AluSx4#SINE/Alu
899	1031	6047	AluJo#SINE/Alu
1032	1201	13451	AluSq4#SINE/Alu
1202	1501	3579	AluY#SINE/Alu
1502	1792	2345	AluSg#SINE/Alu
1793	1931	13451	AluSg#SINE/Alu
-------------------------------------------------------------
../fixtures/ex9_hg38_alugedon.align.format
14	86	8515	L1MB5_3end#LINE/L1
87	382	7281	AluSx#SINE/Alu
383	533	10983	AluJb#SINE/Alu
534	697	4813	AluYb10#SINE/Alu
698	998	3579	AluY#SINE/Alu
999	1148	10983	AluJo#SINE/Alu
1149	1200	1111	L1M4_orf2#LINE/L1
-------------------------------------------------------------
../fixtures/ex10_hg38_alugedon.align.format
1	90	12217	MER33#DNA/hAT-Charlie
91	229	9749	FLAM_C#SINE/Alu
230	516	8515	AluSq2#SINE/Alu
517	815	7281	AluSq#SINE/Alu
849	1141	6047	AluSx#SINE/Alu
1142	1165	4813	AluYf1#SINE/Alu
1166	1458	3579	AluSx#SINE/Alu
1459	1618	2345	AluJb#SINE/Alu
1619	1719	12217	MER33#DNA/hAT-Charlie
-------------------------------------------------------------
../fixtures/ex1_hg38_nesting.align.format
360	498	22089	L2#LINE/L2
711	950	29493	HAL1#LINE/L1
982	1094	25791	Charlie12#DNA/hAT-Charlie
1096	1402	17153	AluY_short_#SINE/Alu
1403	1517	25791	MER30#DNA/hAT-Charlie
1549	1941	14685	LTR16C#LTR/ERVL
1942	2729	29493	HAL1#LINE/L1
2973	3101	12217	FLAM_A#SINE/Alu
3109	3203	10983	L1MB7_3end#LINE/L1
3209	3461	28259	HAL1#LINE/L1
3462	3695	8515	HAL1ME#LINE/L1
3829	4080	28259	HAL1#LINE/L1
4117	4368	4813	AluSz#SINE/Alu
4371	4901	28259	HAL1#LINE/L1
4947	5091	2345	L2c_3end#LINE/L2
5200	5251	1111	L2d2_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex2_hg38_nesting.align.format
2563	2587	34429	L1MC5_3end#LINE/L1
2588	2951	33195	L1ME4b_3end#LINE/L1
2957	3026	31961	L2b_3end#LINE/L2
3258	3713	29493	L1MA3_3end#LINE/L1
3918	4230	27025	AluSq#SINE/Alu
4386	4521	49237	L4_A_Mam#LINE/RTE-X
4537	4768	43067	L1M5_orf2#LINE/L1
4769	4896	23323	MLT2C2#LTR/ERVL
4993	5076	22089	HY1#scRNA
5077	5194	20855	MLT1E3#LTR/ERVL-MaLR
5204	5358	19621	MLT2F#LTR/ERVL
5362	5584	43067	L1M5_orf2#LINE/L1
5585	5740	41833	L1ME3B_3end#LINE/L1
5746	6291	15919	MLT1F1#LTR/ERVL-MaLR
6292	6392	14685	L1ME3_3end#LINE/L1
6393	6955	41833	L1ME3B_3end#LINE/L1
7123	7262	48003	L4_B_Mam#LINE/RTE-X
7268	7313	39365	MSTC#LTR/ERVL-MaLR
7314	7619	9749	AluSx1#SINE/Alu
7620	8014	39365	MSTC#LTR/ERVL-MaLR
8047	8352	48003	L4_B_Mam#LINE/RTE-X
8354	8400	36897	L4_A_Mam#LINE/RTE-X
8730	8920	2345	L1MB8_3end#LINE/L1
8921	8932	1111	L1MA5_3end#LINE/L1
-------------------------------------------------------------
../fixtures/ex3_hg38_nesting.align.format
649	882	24557	L2c_3end#LINE/L2
883	1228	22089	LTR40a#LTR/ERVL
1230	1269	9749	LTR40b#LTR/ERVL
1275	1447	17153	MSTB1#LTR/ERVL-MaLR
1448	1576	6047	AluJr4#SINE/Alu
1577	1699	17153	MSTA1#LTR/ERVL-MaLR
1700	1821	17153	MSTB1#LTR/ERVL-MaLR
1822	1878	22089	LTR40a#LTR/ERVL
1879	2098	24557	L2c_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex4_hg38_badoverlap.align.format
6	145	3579	MIR#SINE/MIR
149	295	1111	L2a_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex5_hg38_composite.align.format
1	218	24557	AluYg6#SINE/Alu
604	1291	30727	Tigger1#DNA/TcMar-Tigger
1292	1595	22089	AluYa5#SINE/Alu
1597	2175	30727	Tigger1#DNA/TcMar-Tigger
2176	2327	28259	AluSx_short_#SINE/Alu
2328	2626	18387	AluSx3#SINE/Alu
2631	2679	15919	AluYa8#SINE/Alu
2680	2780	28259	AluSz6#SINE/Alu
2782	3091	30727	Tigger1#DNA/TcMar-Tigger
3092	3924	10983	SVA_B#Retroposon/SVA
3925	3951	9749	SVA_A#Retroposon/SVA
3952	4624	8515	SVA_B#Retroposon/SVA
4650	5031	30727	Tigger1#DNA/TcMar-Tigger
5032	5327	6047	AluSg7#SINE/Alu
5328	5777	30727	Tigger1#DNA/TcMar-Tigger
6058	6171	25791	LTR38A1#LTR/ERV1
6172	6314	2345	L1PA15_3end#LINE/L1
6315	6668	25791	LTR38A1#LTR/ERV1
-------------------------------------------------------------
../fixtures/ex6_hg38_ambiguous.align.format
1	155	10983	AluSp#SINE/Alu
157	198	8515	AluY_short_#SINE/Alu
199	277	12217	LTR5B#LTR/ERVK
279	536	4813	AluYb10#SINE/Alu
537	985	3579	LTR5A#LTR/ERVK
986	1478	12217	LTR5B#LTR/ERVK
1479	1758	1111	AluYj4#SINE/Alu
-------------------------------------------------------------
../fixtures/ex7_hg38_ambiguous.align.format
103	215	27025	L2#LINE/L2
307	461	25791	L2c_3end#LINE/L2
616	633	24557	L1MA2_3end#LINE/L1
634	994	23323	L1MB2_3end#LINE/L1
1106	1314	29493	L2#LINE/L2
1356	1436	19621	MER106A#DNA/hAT-Charlie
1437	1576	18387	MER106B#DNA/hAT-Charlie
1577	1961	29493	L2#LINE/L2
1980	2138	15919	MER58A#DNA/hAT-Charlie
2139	2488	14685	L2a_3end#LINE/L2
2715	2834	12217	L3#LINE/CR1
2905	3022	10983	MIRc#SINE/MIR
3180	3307	8515	AluJr4#SINE/Alu
3308	3340	7281	AluSp#SINE/Alu
3435	3508	28259	MIR3#SINE/MIR
3509	3684	4813	MER20#DNA/hAT-Charlie
3685	3734	3579	MIR1_Amn#SINE/MIR
3735	3785	28259	MIR3#SINE/MIR
4034	4092	1111	AluSx_short_#SINE/Alu
-------------------------------------------------------------
../fixtures/ex8_hg38_alugedon.align.format
98	400	12217	AluSx1#SINE/Alu
402	701	9749	AluSc#SINE/Alu
702	897	8515	AluSx4#SINE/Alu
899	1031	6047	AluJo#SINE/Alu
1032	1201	13451	AluSq4#SINE/Alu
1202	1501	3579	AluY#SINE/Alu
1502	1792	2345	AluSg#SINE/Alu
1793	1931	13451	AluSg#SINE/Alu
-------------------------------------------------------------
../fixtures/ex9_hg38_alugedon.align.format
14	86	8515	L1MB5_3end#LINE/L1
87	382	7281	AluSx#SINE/Alu
383	533	10983	AluJb#SINE/Alu
534	697	4813	AluYb10#SINE/Alu
698	998	3579	AluY#SINE/Alu
999	1148	10983	AluJo#SINE/Alu
1149	1200	1111	L1M4_orf2#LINE/L1
-------------------------------------------------------------
