RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes

Table 2 Target and source locus for the 3' transduced flank in the main (human) and comparative genomes (chimpanzee) for loci annotated as INDEL_PTS

GENOME	LOCUS	L1HS	CHR	CONTIG	ORIENT	QFC	QLC	SFC	SLC	Source-Genic/Intergenic (based on CDS)
human	Target	L1HS_4_19c	4	NC_000004	Minus	1	91	88487299	88487209
human	Source	L1HS_4_19c	4	NC_000004	Plus	16	91	88496516	88496591	HSD17B11, INTRON 5
Chimp	Source	L1HS_4_19c	4	NC_006471	Plus	16	91	90265309	90265384	DHRS8, INTRONS 4,5
human	Target	L1HS_7_7	7	NC_000007	Plus	1	619	69306280	69306898
human	Source	L1HS_7_7	5	NC_000005	Minus	3	606	140466972	140466369	Intergenic
Chimp	Source	L1HS_7_7	5	NC_006472	Minus	3	606	142876752	142876149	Intergenic

RISCI confirmation of 3' flank transduction concurrent with insertion mediated deletion (INDEL_PTS) by unambiguous identification of the source locus in main and comparative genomes. As expected, no hit is found for the target locus in the comparative genome, and one to one chromosomal correspondence for the source locus in main and comparative genome is noticed. Also the source locus hit both in the main genome and in the comparative genome is shorter than the target hit since no match is found for the poly A tail at the source locus. CHR - chromosome, ORIENT - orientation, QFC - Query first coordinate, QLC - Query last coordinate, SFC - Subject first coordinate, SLC - Subject last coordinate. Source loci found within genes (and within exons or introns if CDS coordinates are available are also reported). HSD17B11 and DHRS8 are aliases of eachother.