Table 1 Zebrafish tetra- and pentaSTR locus and primer information.

From: A 13-plex of tetra- and penta-STRs to identify zebrafish

locus	start	primer sequence	motif	SWS	perf rep	ref+tails	uni-dye	µM
chr23	1341696	F: AATATGTGACGTAGGTAGTAATGCAG	AATA	456	12	127	uni1-FAM	0.020
		R: TGCATTTGCTTATGTTTTTCttg						0.197
chr15	2218411	F: GAAGCCTGGGTCATTTTCAG	AAAC	534	11	147	uni2-PET	0.059
		R: GAAAATTCCTAAACTTTTATTCAGGTAGAA						0.592
chr17	2618753	F: gaggatgaaagcaGCACTTAAAA	ATTC	549	15	152	uni3-NED	0.040
		R: TGACAAATTGGAGAGTTGATTAAA						0.395
chr22	1488958	F: GAAGTCCTTACCAGCCACAAA	ATAG	594	16	167	uni4-VIC	0.010
		R: TTTAAAAGGTCAACAACGCATA						0.099
chr11	2435143	F: CGTGGCAGGAGCTGTGAA	TATTA	558	12	212	uni4-VIC	0.027
		R: CGCATTATGCCAGTCATGATAA						0.267
chr19	75036748	F: TTTGGTAATTTGATGATTTGGAA	TATAT	558	12	236	uni1-FAM	0.013
		R: TGTTAACGTCATAAAAATCTGATAAA						0.133
chr24	7379615	F: ACATTCTGGCTCCCATCAGA	ACTAC	561	11	238	uni3-NED	0.013
		R: CAGGCCTCTTGTGTTTGTGA						0.133
chr05	1147730	F: GCGGACATCTGACAACTGAA	ATAA	513	15	253	uni2-PET	0.053
		R: GGATGTGTGAAACGCAGATAA						0.533
chr14	2009429	F: AAGTGCAGCAGAGAATGTTGTTA	GATG	552	8	276	uni3-NED	0.020
		R: GCTGAGGCACGTATTTCCAA						0.200
chr21	2820816	F: GTCTCTCACCTCGTCTGTGAA	AAAC	537	11	319	uni1-FAM	0.020
		R: GGCTGTAAACATGAGCGAAG						0.200
chr04	1653932	F: GAGGATCGGAAAGCAGGTAAA	AATAC	522	11	375	uni1-FAM	0.013
		R: TGTTTGACTCAACTGTGGGTAA						0.133
chr09	2073768	F: tatataAAACACTATGTATTTGTATAATCAGAA	ATATA	522	11	419	uni4-VIC	0.027
		R: GACAAGACGGCTTCAGCAA						0.267
chr02	2168981	F: CCAACATCCGGCACAAATAA	TATTA	553	11	442	uni2-PET	0.040
		R: ATGTCTGAGGAAATATGAAATGATGAATAA						0.400

This table is sorted by increasing size of the amplicon. The locus name is given as the chromosome upon which it is located, followed by the genome position number of the simple tandem repeat (start; beginning position of the repeat from the zebrafish reference genome build Zv9). All F (forward) primers are labeled at the 5′ end with one of the universal primer tags/tails (sequence not shown), and all R (reverse) primers include a pigtail sequence (GTTTCTT; not shown) at the 5′ end to suppress the production of split peaks. Lower case letters within the primer sequences indicate repeats (e.g., SINEs or LINEs) over which the 3′ end of a primer may be partially designed. The motif for the tetra- and pentaSTRs is given in the next column and it is based upon the output of the Tandem Repeat Finder (TRF) in the UCSC Genome Browser. The Smith-Waterman score (SWS) provides an indication of the expected heterozygosity (discussed in the Materials and Methods section). The perfect repeat number (perf rep) is shown because it is correlated with the amount of stutter produced for a given STR²⁵. The reference genome size for the PCR product is given with the uni-primer and pigtail attached (ref+tails). The universal primer (uni-dye) information is given in the Methods and Materials section. The final concentration for each of the locus-specific primers is given in the last column. The final concentration of each universal primer is: uni-1, uni-3, and uni-4, 0.011 µM; and uni-2, 0.043 µM.

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Table 1 Zebrafish tetra- and pentaSTR locus and primer information.

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