Table S2 . Detailed analysis of loci 13, 17, 19 42, 18 and 50 in sequenced strains (AmoebaDB).

 S2 Contigs shaded in yellow represent poor assembly (having gaps). SINE elements of <100 bp are considered to be negative (-) occupancy. NA-not applied. As mentioned in the text and figure 5 assembly of Rahman sequence at the SINE region is erroneous in the database. In fact the entire EhSINE1 sequence is missing in Rahman. 


	Eh strain	locus	ID	SINE	start	End	Remarks
				occupancy			
	DS4	13	EHDS4_4213	+	84933	85542	
		17	EHDS4_2840	+	84936	85541	
		19	EHDS4_3346	+	26367	26920	
		42	EHDS4_3522	+	21707	21978	Truncated (271 bp of EhSINE1)
		SINE2					
		18	EHDS4_4206	+	1601	2278	
		50	EHDS4_3252	+	145133	145728	Eh SINE2 slightly truncated from both sides
	HM1:CA	13	EHHM1_CA_4213	+	79360	79884	100 bp deletion within EhSINE1
		17	EHHM1_CA_2840	+	13367	13921	
		19	EHHM1_CA_3346	+	22600	23100	
		42	EHHM1_CA_3522	+	25911	26448	30 bp deletion within EhSINE1at 3' end
		SINE2					
		18	EHHM1_CA_4206	+	1570	2251	
		50	EHHM1_CA_3252	+	136204	136749	Deletion from within EhSINE2 (414-532)
	KU27	13	EHKU27_4213	+	84501	85105	
		17	EHKU27_2840	+	14648	14878	Truncated from 5' end (230 bp of EhSINE1)
		19	EHKU27_3346	+	26048	26601	
		42	EHKU27_3522	+	20600	21115	EhSINE1 slightly truncated from 5' end
		SINE2					
		18	EHKU27_4206	+	1588	2240	Small (20bp) deletion within EhSINE2 (3 IR instead
							of 4 IR)
		50	EHKU27_3252	+	145081	145650	Truncation from 5' end and 13 bp deletion within
							EhSINE2
	KU48	13	EHKU48_4213	+	72608	73198	40 bp deletion within EhSINE1
		17	EHKU48_2840	+	13293	13847	
		19	EHKU48_3346	+	17941	18501	
		42	EHKU48_3522	+	21600	22120	
		SINE2					
		18	EHKU48_4206	-	NA	NA	
		50	EHKU48_3252	+	125979	126087	Only 109 bp of EhSINE2 present
	KU50	13	EHKU50_4213	+	47531	48136	Slightly truncated from 5' end and 10 bp deletion
							within EhSINE1
		17	EHKU50_2840	+	4860	5439	Truncation from 3' end of EhSINE1
		19	EHKU50_3346	-	7929	7885	Only 40 bp of EhSINE1present
		42	EHKU50_3522	+	11229	11469	EhSINE1truncated from both side (240 bp of
							EhSINE1 present)
		SINE2					
		18	EHKU50_4206	-	NA	NA	
		50	EHKU50_3252	+	145787	146189	Truncated from 5' end of EhSINE1
	MS96	13	EHMS96_4213	-	82910	82990	Only 80 bp of EhSINE1present
		17	EHMS96_2840	+	14705	14308	Truncated from both side (397 bp of EhSINE1
							present)
		19	EHMS96_3346	+	26383	26937	
		42	EHMS96_3522	+	24410	24950	EhSINE1 slightly truncated at 5' end
		SINE2					
		18	EHMS96_4206	+	1615	2236	Slight (37 bp) deletion within EhSINE2
		50	EHMS96_3252	-	NA	NA	
	Rahman	13	EhRm_Scaffold01127	-	NA	NA	
		17	EhRm_scaffold00561	-	29831	29913	Only 90 bp EhSINE1 present
		19	EhRm_scaffold00536	-	NA	NA	
			EhRm_contig21711				
		42	EhRm_scaffold00892	-	NA	NA	
		SINE2					
		18	EhRm_scaffold00754	-	NA	NA	
		50	EhRm_scaffold00159	-	NA	NA	
	Scaffolds/