../fixtures/ex10_hg38_alugedon.align.format
2	91	14685	MER33#DNA/hAT-Charlie
92	230	10983	FLAM_C#SINE/Alu
231	517	9749	AluSq2#SINE/Alu
518	816	8515	AluSq#SINE/Alu
850	1142	6047	AluSx#SINE/Alu
1143	1166	4813	AluYf1#SINE/Alu
1167	1459	3579	AluSx#SINE/Alu
1460	1619	2345	AluJb#SINE/Alu
1620	1720	14685	MER33#DNA/hAT-Charlie
-------------------------------------------------------------
../fixtures/ex1_hg38_nesting.align.format
361	499	35663	L2#LINE/L2
712	951	44301	HAL1#LINE/L1
983	1095	40599	Charlie12#DNA/hAT-Charlie
1096	1403	29493	AluY#SINE/Alu
1404	1518	40599	MER30#DNA/hAT-Charlie


1550	1942	25791	LTR16C#LTR/ERVL
1943	2628	44301	HAL1#LINE/L1
2663	2730	44301	HAL1#LINE/L1
2974	3102	19621	FLAM_A#SINE/Alu
3110	3204	17153	L1MB7_3end#LINE/L1
3210	3462	43067	HAL1#LINE/L1
3463	3696	13451	HAL1ME#LINE/L1
3830	4081	43067	HAL1#LINE/L1
4118	4369	8515	AluSz#SINE/Alu
4372	4902	43067	HAL1#LINE/L1
4948	5092	3579	L2c_3end#LINE/L2
5201	5252	1111	L2d2_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex2_hg38_nesting.align.format
2589	2952	49237	L1ME4b_3end#LINE/L1
2958	3027	46769	L2b_3end#LINE/L2
3259	3714	44301	L1MA3_3end#LINE/L1
3919	4231	41833	AluSq#SINE/Alu
4387	4522	68981	L4_A_Mam#LINE/RTE-X
4538	4769	61577	L1M5_orf2#LINE/L1
4770	4897	35663	MLT2C2#LTR/ERVL
4994	5077	33195	HY1#scRNA
5078	5195	31961	MLT1E3#LTR/ERVL-MaLR
5205	5359	29493	MLT2F#LTR/ERVL
5363	5585	61577	L1M5_orf2#LINE/L1
5586	5741	61577	L1ME3B_3end#LINE/L1
5747	6292	23323	MLT1F1#LTR/ERVL-MaLR
6293	6393	60343	L1ME3_3end#LINE/L1
6394	6718	59109	L1ME3B_3end#LINE/L1
6719	6784	59109	L1ME3_3end#LINE/L1
6846	6956	59109	L1ME3B_3end#LINE/L1
7124	7263	66513	L4_B_Mam#LINE/RTE-X
7269	7314	55407	MSTC#LTR/ERVL-MaLR
7315	7620	10983	AluSx1#SINE/Alu
7621	8015	55407	MSTC#LTR/ERVL-MaLR
8048	8353	66513	L4_B_Mam#LINE/RTE-X
8355	8401	52939	L4_A_Mam#LINE/RTE-X
8731	8921	2345	L1MB8_3end#LINE/L1
-------------------------------------------------------------
../fixtures/ex3_hg38_nesting.align.format
650	883	25791	L2c_3end#LINE/L2
884	1229	23323	LTR40a#LTR/ERVL
1231	1270	9749	LTR40b#LTR/ERVL
1276	1448	18387	MSTB1#LTR/ERVL-MaLR
1449	1577	6047	AluJr4#SINE/Alu
1578	1700	18387	MSTA1#LTR/ERVL-MaLR
1701	1822	18387	MSTB1#LTR/ERVL-MaLR
1823	1879	23323	LTR40a#LTR/ERVL
1880	2099	25791	L2c_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex4_hg38_badoverlap.align.format
7	146	3579	MIR#SINE/MIR
150	296	1111	L2a_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex5_hg38_composite.align.format
2	219	29493	AluYg6#SINE/Alu
605	1292	33195	Tigger1#DNA/TcMar-Tigger
1293	1596	25791	AluYa5#SINE/Alu
1598	2176	33195	Tigger1#DNA/TcMar-Tigger
2177	2328	22089	AluSg#SINE/Alu
2329	2627	20855	AluSx3#SINE/Alu
2632	2680	18387	AluYa8#SINE/Alu
2681	2781	17153	AluSz6#SINE/Alu
2783	3092	33195	Tigger1#DNA/TcMar-Tigger
3093	3925	13451	SVA_B#Retroposon/SVA
3926	3952	12217	SVA_A#Retroposon/SVA
3953	4625	10983	SVA_B#Retroposon/SVA
4651	5032	33195	Tigger1#DNA/TcMar-Tigger
5033	5328	7281	AluSg7#SINE/Alu
5329	5778	33195	Tigger1#DNA/TcMar-Tigger
6059	6172	31961	LTR38A1#LTR/ERV1
6173	6315	2345	L1PA15_3end#LINE/L1
6316	6669	31961	LTR38A1#LTR/ERV1
-------------------------------------------------------------
../fixtures/ex6_hg38_ambiguous.align.format
2	155	10983	AluSp#SINE/Alu
156	192	9749	AluSz6#SINE/Alu
200	278	13451	LTR5B#LTR/ERVK
280	537	4813	AluYb10#SINE/Alu
538	986	3579	LTR5A#LTR/ERVK
987	1479	13451	LTR5B#LTR/ERVK
1480	1759	1111	AluYj4#SINE/Alu
-------------------------------------------------------------
../fixtures/ex7_hg38_ambiguous.align.format
104	216	31961	L2#LINE/L2
308	462	29493	L2c_3end#LINE/L2
632	995	27025	L1MB2_3end#LINE/L1
1107	1315	36897	L2#LINE/L2
1357	1437	22089	MER106A#DNA/hAT-Charlie
1438	1577	20855	MER106B#DNA/hAT-Charlie
1578	1962	36897	L2#LINE/L2
1981	2139	17153	MER58A#DNA/hAT-Charlie
2140	2489	15919	L2a_3end#LINE/L2
2716	2835	13451	L3#LINE/CR1
2906	3023	10983	MIRc#SINE/MIR
3181	3308	8515	AluJr4#SINE/Alu
3309	3341	7281	AluSp#SINE/Alu
3436	3509	35663	MIR3#SINE/MIR
3510	3685	3579	MER20#DNA/hAT-Charlie
3686	3735	2345	MIR1_Amn#SINE/MIR
3736	3786	34429	MIR3#SINE/MIR
-------------------------------------------------------------
../fixtures/ex8_hg38_alugedon.align.format
99	401	12217	AluSx1#SINE/Alu
403	702	9749	AluSc#SINE/Alu
703	898	8515	AluSx4#SINE/Alu
900	1032	6047	AluJo#SINE/Alu
1033	1202	14685	AluSq4#SINE/Alu
1203	1502	3579	AluY#SINE/Alu
1503	1793	2345	AluSg#SINE/Alu
1794	1932	14685	AluSg#SINE/Alu
-------------------------------------------------------------
../fixtures/ex9_hg38_alugedon.align.format
15	87	8515	L1MB5_3end#LINE/L1
88	383	7281	AluSx#SINE/Alu
384	534	10983	AluJb#SINE/Alu
535	698	4813	AluYb10#SINE/Alu
699	999	3579	AluY#SINE/Alu
1000	1149	10983	AluJo#SINE/Alu
1150	1201	1111	L1M4_orf2#LINE/L1
-------------------------------------------------------------
../fixtures/ex10_hg38_alugedon.align.format
2	91	14685	MER33#DNA/hAT-Charlie
92	230	10983	FLAM_C#SINE/Alu
231	517	9749	AluSq2#SINE/Alu
518	816	8515	AluSq#SINE/Alu
850	1142	6047	AluSx#SINE/Alu
1143	1166	4813	AluYf1#SINE/Alu
1167	1459	3579	AluSx#SINE/Alu
1460	1619	2345	AluJb#SINE/Alu
1620	1720	14685	MER33#DNA/hAT-Charlie
-------------------------------------------------------------
../fixtures/ex1_hg38_nesting.align.format
361	499	35663	L2#LINE/L2
712	951	44301	HAL1#LINE/L1
983	1095	40599	Charlie12#DNA/hAT-Charlie
1096	1403	29493	AluY#SINE/Alu
1404	1518	40599	MER30#DNA/hAT-Charlie
1550	1942	25791	LTR16C#LTR/ERVL
1943	2628	44301	HAL1#LINE/L1
2663	2730	44301	HAL1#LINE/L1
2974	3102	19621	FLAM_A#SINE/Alu
3110	3204	17153	L1MB7_3end#LINE/L1
3210	3462	43067	HAL1#LINE/L1
3463	3696	13451	HAL1ME#LINE/L1
3830	4081	43067	HAL1#LINE/L1
4118	4369	8515	AluSz#SINE/Alu
4372	4902	43067	HAL1#LINE/L1
4948	5092	3579	L2c_3end#LINE/L2
5201	5252	1111	L2d2_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex2_hg38_nesting.align.format
2589	2952	49237	L1ME4b_3end#LINE/L1
2958	3027	46769	L2b_3end#LINE/L2
3259	3714	44301	L1MA3_3end#LINE/L1
3919	4231	41833	AluSq#SINE/Alu
4387	4522	68981	L4_A_Mam#LINE/RTE-X
4538	4769	61577	L1M5_orf2#LINE/L1
4770	4897	35663	MLT2C2#LTR/ERVL
4994	5077	33195	HY1#scRNA
5078	5195	31961	MLT1E3#LTR/ERVL-MaLR
5205	5359	29493	MLT2F#LTR/ERVL
5363	5585	61577	L1M5_orf2#LINE/L1
5586	5741	61577	L1ME3B_3end#LINE/L1
5747	6292	23323	MLT1F1#LTR/ERVL-MaLR
6293	6393	60343	L1ME3_3end#LINE/L1
6394	6718	59109	L1ME3B_3end#LINE/L1
6719	6784	59109	L1ME3_3end#LINE/L1
6846	6956	59109	L1ME3B_3end#LINE/L1
7124	7263	66513	L4_B_Mam#LINE/RTE-X
7269	7314	55407	MSTC#LTR/ERVL-MaLR
7315	7620	10983	AluSx1#SINE/Alu
7621	8015	55407	MSTC#LTR/ERVL-MaLR
8048	8353	66513	L4_B_Mam#LINE/RTE-X
8355	8401	52939	L4_A_Mam#LINE/RTE-X
8731	8921	2345	L1MB8_3end#LINE/L1
-------------------------------------------------------------
../fixtures/ex3_hg38_nesting.align.format
650	883	25791	L2c_3end#LINE/L2
884	1229	23323	LTR40a#LTR/ERVL
1231	1270	9749	LTR40b#LTR/ERVL
1276	1448	18387	MSTB1#LTR/ERVL-MaLR
1449	1577	6047	AluJr4#SINE/Alu
1578	1700	18387	MSTA1#LTR/ERVL-MaLR
1701	1822	18387	MSTB1#LTR/ERVL-MaLR
1823	1879	23323	LTR40a#LTR/ERVL
1880	2099	25791	L2c_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex4_hg38_badoverlap.align.format
7	146	3579	MIR#SINE/MIR
150	296	1111	L2a_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex5_hg38_composite.align.format
2	219	29493	AluYg6#SINE/Alu
605	1292	33195	Tigger1#DNA/TcMar-Tigger
1293	1596	25791	AluYa5#SINE/Alu
1598	2176	33195	Tigger1#DNA/TcMar-Tigger
2177	2328	22089	AluSg#SINE/Alu
2329	2627	20855	AluSx3#SINE/Alu
2632	2680	18387	AluYa8#SINE/Alu
2681	2781	17153	AluSz6#SINE/Alu
2783	3092	33195	Tigger1#DNA/TcMar-Tigger
3093	3925	13451	SVA_B#Retroposon/SVA
3926	3952	12217	SVA_A#Retroposon/SVA
3953	4625	10983	SVA_B#Retroposon/SVA
4651	5032	33195	Tigger1#DNA/TcMar-Tigger
5033	5328	7281	AluSg7#SINE/Alu
5329	5778	33195	Tigger1#DNA/TcMar-Tigger
6059	6172	31961	LTR38A1#LTR/ERV1
6173	6315	2345	L1PA15_3end#LINE/L1
6316	6669	31961	LTR38A1#LTR/ERV1
-------------------------------------------------------------
../fixtures/ex6_hg38_ambiguous.align.format
2	155	10983	AluSp#SINE/Alu
156	192	9749	AluSz6#SINE/Alu
200	278	13451	LTR5B#LTR/ERVK
280	537	4813	AluYb10#SINE/Alu
538	986	3579	LTR5A#LTR/ERVK
987	1479	13451	LTR5B#LTR/ERVK
1480	1759	1111	AluYj4#SINE/Alu
-------------------------------------------------------------
../fixtures/ex7_hg38_ambiguous.align.format
104	216	31961	L2#LINE/L2
308	462	29493	L2c_3end#LINE/L2
632	995	27025	L1MB2_3end#LINE/L1
1107	1315	36897	L2#LINE/L2
1357	1437	22089	MER106A#DNA/hAT-Charlie
1438	1577	20855	MER106B#DNA/hAT-Charlie
1578	1962	36897	L2#LINE/L2
1981	2139	17153	MER58A#DNA/hAT-Charlie
2140	2489	15919	L2a_3end#LINE/L2
2716	2835	13451	L3#LINE/CR1
2906	3023	10983	MIRc#SINE/MIR
3181	3308	8515	AluJr4#SINE/Alu
3309	3341	7281	AluSp#SINE/Alu
3436	3509	35663	MIR3#SINE/MIR
3510	3685	3579	MER20#DNA/hAT-Charlie
3686	3735	2345	MIR1_Amn#SINE/MIR
3736	3786	34429	MIR3#SINE/MIR
-------------------------------------------------------------
../fixtures/ex8_hg38_alugedon.align.format
99	401	12217	AluSx1#SINE/Alu
403	702	9749	AluSc#SINE/Alu
703	898	8515	AluSx4#SINE/Alu
900	1032	6047	AluJo#SINE/Alu
1033	1202	14685	AluSq4#SINE/Alu
1203	1502	3579	AluY#SINE/Alu
1503	1793	2345	AluSg#SINE/Alu
1794	1932	14685	AluSg#SINE/Alu
-------------------------------------------------------------
../fixtures/ex9_hg38_alugedon.align.format
15	87	8515	L1MB5_3end#LINE/L1
88	383	7281	AluSx#SINE/Alu
384	534	10983	AluJb#SINE/Alu
535	698	4813	AluYb10#SINE/Alu
699	999	3579	AluY#SINE/Alu
1000	1149	10983	AluJo#SINE/Alu
1150	1201	1111	L1M4_orf2#LINE/L1
-------------------------------------------------------------
../fixtures/ex10_hg38_alugedon.align.format
2	91	18387	MER33#DNA/hAT-Charlie
92	230	10983	AluJb#SINE/Alu
231	517	9749	AluSz#SINE/Alu
518	816	8515	AluSx1#SINE/Alu
850	1148	6047	AluSx#SINE/Alu
1149	1159	15919	AluY#SINE/Alu
1160	1459	3579	AluSx#SINE/Alu
1460	1619	15919	AluJb#SINE/Alu
1620	1720	18387	MER33#DNA/hAT-Charlie
-------------------------------------------------------------
../fixtures/ex1_hg38_nesting.align.format
361	499	36897	L2#LINE/L2
712	951	45535	HAL1#LINE/L1
983	1103	41833	MER30#DNA/hAT-Charlie
1104	1403	30727	AluY#SINE/Alu
1404	1518	41833	MER30#DNA/hAT-Charlie
1550	1943	27025	LTR16C#LTR/ERVL
1944	2628	45535	HAL1#LINE/L1
2663	2730	45535	HAL1#LINE/L1
2974	3043	20855	AluJr#SINE/Alu
3044	3102	19621	AluJr#SINE/Alu
3110	3204	17153	L1MB7_3end#LINE/L1
3210	3663	44301	HAL1#LINE/L1
3664	3696	13451	HAL1ME#LINE/L1
3830	4081	44301	HAL1#LINE/L1
4118	4369	8515	AluSz#SINE/Alu
4372	4902	44301	HAL1#LINE/L1
4948	5092	3579	L2c_3end#LINE/L2
5201	5252	1111	L2d2_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex2_hg38_nesting.align.format
2564	2588	50471	L1MC5_3end#LINE/L1
2589	2952	49237	L1ME4b_3end#LINE/L1
2958	3027	46769	L2b_3end#LINE/L2
3259	3713	44301	L1MA3_3end#LINE/L1
3714	3732	43067	L1MB3_3end#LINE/L1
3919	4231	40599	AluSx1#SINE/Alu
4387	4522	72683	L4_A_Mam#LINE/RTE-X
4538	4766	64045	L1M5_orf2#LINE/L1
4767	4897	34429	MLT2C1#LTR/ERVL
4994	5077	31961	HY1#scRNA
5078	5195	30727	MLT1E3#LTR/ERVL-MaLR
5205	5359	28259	MLT2F#LTR/ERVL
5363	5705	64045	L1M5_orf2#LINE/L1
5706	5741	70215	L1ME3B_3end#LINE/L1
5747	5948	61577	MLT1F1#LTR/ERVL-MaLR
5949	6185	20855	MLT1F#LTR/ERVL-MaLR
6186	6292	60343	MLT1F2#LTR/ERVL-MaLR
6293	6784	70215	L1ME3A_3end#LINE/L1
6846	6956	68981	L1ME3B_3end#LINE/L1
7124	7263	67747	L4_B_Mam#LINE/RTE-X
7269	7314	55407	MSTC#LTR/ERVL-MaLR
7315	7620	9749	AluSx1#SINE/Alu
7621	8015	55407	MSTC#LTR/ERVL-MaLR
8048	8310	67747	L4_B_Mam#LINE/RTE-X
8311	8401	72683	L4_A_Mam#LINE/RTE-X
8731	8921	2345	L1MB7_3end#LINE/L1
-------------------------------------------------------------
../fixtures/ex3_hg38_nesting.align.format
650	883	24557	L2c_3end#LINE/L2
884	1229	22089	LTR40a#LTR/ERVL
1230	1270	9749	LTR40b#LTR/ERVL
1274	1442	17153	MSTB#LTR/ERVL-MaLR
1443	1577	6047	AluJr#SINE/Alu
1578	1820	17153	MSTB#LTR/ERVL-MaLR
1823	1879	22089	LTR40a#LTR/ERVL
1880	2099	24557	L2c_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex4_hg38_badoverlap.align.format
7	146	3579	MIR#SINE/MIR
150	296	1111	L2a_3end#LINE/L2
-------------------------------------------------------------
../fixtures/ex5_hg38_composite.align.format
2	219	30727	AluY#SINE/Alu
605	1292	61577	Tigger1#DNA/TcMar-Tigger
1293	1596	27025	AluY#SINE/Alu
1598	2176	61577	Tigger1#DNA/TcMar-Tigger
2177	2328	43067	AluSx#SINE/Alu
2329	2627	22089	AluSx#SINE/Alu
2628	2781	43067	AluSz#SINE/Alu
2783	3092	61577	Tigger1#DNA/TcMar-Tigger
3093	3587	60343	SVA_B#Retroposon/SVA
3588	3925	59109	SVA_D#Retroposon/SVA
3926	3952	57875	SVA_D#Retroposon/SVA
3953	4266	56641	SVA_D#Retroposon/SVA
4267	4625	55407	SVA_B#Retroposon/SVA
4651	5032	54173	Tigger1#DNA/TcMar-Tigger
5033	5328	8515	AluSx1#SINE/Alu
5329	5778	54173	Tigger1#DNA/TcMar-Tigger
6059	6172	33195	LTR38A1#LTR/ERV1
6173	6268	3579	L1PA15_3end#LINE/L1
6269	6320	2345	L1PA16_3end#LINE/L1
6321	6669	33195	LTR38A1#LTR/ERV1
-------------------------------------------------------------
../fixtures/ex6_hg38_ambiguous.align.format
2	156	10983	AluSp#SINE/Alu
157	192	9749	AluSz6#SINE/Alu
200	278	13451	LTR5B#LTR/ERVK
280	537	4813	AluY#SINE/Alu
538	624	3579	LTR5A#LTR/ERVK
625	1479	13451	LTR5B#LTR/ERVK
1480	1759	1111	AluY#SINE/Alu
-------------------------------------------------------------
../fixtures/ex7_hg38_ambiguous.align.format
104	216	33195	L2#LINE/L2
308	462	30727	L2c_3end#LINE/L2
617	635	28259	L1MA3_3end#LINE/L1
636	995	27025	L1MB2_3end#LINE/L1
1107	1315	36897	L2#LINE/L2
1357	1437	22089	MER106A#DNA/hAT-Charlie
1438	1577	20855	MER106B#DNA/hAT-Charlie
1578	1962	36897	L2#LINE/L2
1981	2139	17153	MER58A#DNA/hAT-Charlie
2140	2489	15919	L2a_3end#LINE/L2
2716	2835	13451	L3#LINE/CR1
2906	3023	10983	MIRc#SINE/MIR
3181	3308	8515	AluJr#SINE/Alu
3309	3341	7281	AluSp#SINE/Alu
3436	3509	35663	MIR3#SINE/MIR
3510	3685	3579	MER20#DNA/hAT-Charlie
3686	3736	2345	MIR#SINE/MIR
3737	3786	35663	MIR3#SINE/MIR
-------------------------------------------------------------
../fixtures/ex8_hg38_alugedon.align.format
99	401	13451	AluSx1#SINE/Alu
403	580	10983	AluY#SINE/Alu
581	702	9749	AluSx#SINE/Alu
703	898	8515	AluSx#SINE/Alu
900	1032	6047	AluJr#SINE/Alu
1033	1202	15919	AluSx1#SINE/Alu
1203	1502	3579	AluY#SINE/Alu
1503	1798	2345	AluSx#SINE/Alu
1799	1932	15919	AluSx#SINE/Alu
-------------------------------------------------------------
../fixtures/ex9_hg38_alugedon.align.format
15	87	8515	L1MB5_3end#LINE/L1
88	383	7281	AluSx#SINE/Alu
384	534	10983	AluJb#SINE/Alu
535	704	4813	AluY#SINE/Alu
705	999	3579	AluY#SINE/Alu
1000	1149	10983	AluJr#SINE/Alu
1150	1201	1111	L1M4_orf2#LINE/L1
-------------------------------------------------------------
