SSR Screening and Primers in Carrizo citrange genome shotgun Sequences

SSR is a simple sequence repeat, which is a useful genetic marker. SSR primers are picked from the SSR-flanking regions.
A citrus SSR and SSR primers database was constructed using BatchPrimer3.

ID Primer Seq SSR SSR Motif

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Index	ID	Count	Primer_type	Orientation	Start	Len	tm	GC%	Any compl	3' compl	Primer Seq	SSR Motif	Motif Len	SSR	Prod Size	Seq Length	Included Length	Pair any compl	Pair 3' compl
451	GI1478W02FO3XT	1	SSR	FORWARD	56	22	60.32	45.45	5.00	2.00	CCTTAAAGCCACCTATGATCCA	TTTGGT	6	TTTGGTTTTGGTTTTGGT	252	530	530	7.00	3.00
452	GI1478W02FO3XT	2	SSR	REVERSE	307	20	59.97	45.00	4.00	1.00	TGGCTTTGGGGTTAAAGTTG	TTTGGT	6	TTTGGTTTTGGTTTTGGT
453	GI1478W02HTUEB	1	SSR	FORWARD	118	23	59.14	39.13	3.00	2.00	CGACAAGAGTTGGTATTTGATGA	AAAAAT	6	AAAAATAAAAATAAAAATAAAAATAAAAAT	192	389	389	5.00	0.00
454	GI1478W02HTUEB	2	SSR	REVERSE	309	20	59.86	55.00	7.00	1.00	ACAACAGTTGACCCCCTGAC	AAAAAT	6	AAAAATAAAAATAAAAATAAAAATAAAAAT
455	GI1478W02HRFD2	1	SSR	FORWARD	152	20	59.92	50.00	6.00	2.00	TCTTCAGAGGTCCGGAAAGA	AAT	3	AATAATAATAATAATAAT	179	465	465	3.00	0.00
456	GI1478W02HRFD2	2	SSR	REVERSE	330	20	59.73	45.00	4.00	0.00	CACTTGTCAGCCCAAAACAA	AAT	3	AATAATAATAATAATAAT
457	GI1478W02GZFJQ	1	SSR	FORWARD	128	20	60.18	50.00	6.00	2.00	ATTCAGTACTCTGCGCGCTT	TATT	4	TATTTATTTATTTATT	114	317	317	4.00	0.00
458	GI1478W02GZFJQ	2	SSR	REVERSE	241	20	60.13	60.00	4.00	3.00	TAGCACCTCCCCTACGTGAC	TATT	4	TATTTATTTATTTATT
459	GI1478W02GWVR4	1	SSR	FORWARD	371	20	59.98	55.00	8.00	1.00	GGAGCTCCATTTAGCGACTG	TTTTA	5	TTTTATTTTATTTTA	132	569	569	3.00	2.00
460	GI1478W02GWVR4	2	SSR	REVERSE	502	24	58.18	25.00	2.00	0.00	AAAAACAACAATACCCAAAAGAAA	TTTTA	5	TTTTATTTTATTTTA
461	GI1478W02FKZS3	1	SSR	FORWARD	196	22	58.68	31.82	4.00	1.00	AAATCATGCGACTGTTGTTTTT	GTC	3	GTCGTCGTCGTCGTC	171	411	411	3.00	0.00
462	GI1478W02FKZS3	2	SSR	REVERSE	366	20	59.17	50.00	4.00	1.00	TCTCTCTTATTCCGGCTGCT	GTC	3	GTCGTCGTCGTCGTC
463	GI1478W02GLFUF	1	SSR	FORWARD	55	20	59.82	50.00	5.00	2.00	GAGTTACCATTGGACCGCAT	AAAAT	5	AAAATAAAATAAAAT	270	551	551	4.00	2.00
464	GI1478W02GLFUF	2	SSR	REVERSE	324	20	60.08	45.00	4.00	2.00	ATTGAGTTTTGAGCATGGGC	AAAAT	5	AAAATAAAATAAAAT
465	GI1478W02GDOPQ	1	SSR	FORWARD	94	20	60.02	50.00	5.00	0.00	GTAGAATTTCGGGGATGGGT	AAG	3	AAGAAGAAGAAGAAG	251	511	511	4.00	3.00
466	GI1478W02GDOPQ	2	SSR	REVERSE	344	20	58.54	50.00	6.00	2.00	CGTGCACACACACACACATA	AAG	3	AAGAAGAAGAAGAAG
467	GI1478W02ITMCA	1	SSR	FORWARD	375	20	60.26	50.00	3.00	2.00	TATCACTGGAAGGTGCGACA	CCCGTG	6	CCCGTGCCCGTGCCCGTG	105	492	492	4.00	1.00
468	GI1478W02ITMCA	2	SSR	REVERSE	479	20	60.29	55.00	4.00	0.00	TGCATCAGCAGAGAGACTGG	CCCGTG	6	CCCGTGCCCGTGCCCGTG
469	GI1478W02HI20Y	1	SSR	FORWARD	222	20	60.87	45.00	7.00	3.00	TGCAACTTGCTGAGCTTCAA	AT	2	ATATATATATATATATAT	123	504	504	5.00	2.00
470	GI1478W02HI20Y	2	SSR	REVERSE	344	20	59.82	45.00	6.00	2.00	CATTGTTCCCAATGTTGTGC	AT	2	ATATATATATATATATAT
471	GI1478W02F4B50	1	SSR	FORWARD	138	22	59.39	31.82	4.00	2.00	TCATTCCCTTCATCAATTCAAA	ATTT	4	ATTTATTTATTTATTTATTT	164	580	580	4.00	3.00
472	GI1478W02F4B50	2	SSR	REVERSE	301	22	57.95	31.82	2.00	0.00	AACCACCCCACTTTTTATTTTT	ATTT	4	ATTTATTTATTTATTTATTT
473	GI1478W02I43ZP	1	SSR	FORWARD	303	20	60.89	50.00	6.00	2.00	CGATCGACAGACCCATGATT	TTTTTA	6	TTTTTATTTTTATTTTTA	207	540	540	3.00	1.00
474	GI1478W02I43ZP	2	SSR	REVERSE	509	21	57.76	42.86	5.00	1.00	TCTAAATTAACCCCCTGCACT	TTTTTA	6	TTTTTATTTTTATTTTTA
475	GI1478W02HA7YF	1	SSR	FORWARD	59	20	59.74	50.00	7.00	0.00	TGGGACCCAGAGGATTATTG	GT	2	GTGTGTGTGTGTGTGTGTGT	264	420	420	4.00	2.00
476	GI1478W02HA7YF	2	SSR	REVERSE	322	22	59.60	31.82	6.00	0.00	TGATTAATTTTCCGCATTAGCA	GT	2	GTGTGTGTGTGTGTGTGTGT
477	GI1478W02IKQY4	1	SSR	FORWARD	46	24	58.19	29.17	7.00	0.00	AACATAAGTTTTGTGGTTTCGTTT	TTA	3	TTATTATTATTATTA	120	360	360	6.00	0.00
478	GI1478W02IKQY4	2	SSR	REVERSE	165	20	58.86	45.00	5.00	3.00	AGCATTGACCACCAATGTGT	TTA	3	TTATTATTATTATTA
479	GI1478W02JTZ8Z	1	SSR	FORWARD	393	20	60.34	50.00	4.00	2.00	CTTGGCAGAGAAATAGGCCA	AAAAAG	6	AAAAAGAAAAAGAAAAAG	107	528	528	4.00	3.00
480	GI1478W02JTZ8Z	2	SSR	REVERSE	499	20	58.44	55.00	3.00	0.00	CAGTTGGACTTGTGGCTCTC	AAAAAG	6	AAAAAGAAAAAGAAAAAG
481	GI1478W02JWXL2	1	SSR	FORWARD	65	20	59.85	45.00	4.00	1.00	GCAAGTGGACAATGCTTTCA	TTA	3	TTATTATTATTATTATTATTATTATTATTATTA	276	350	350	4.00	1.00
482	GI1478W02JWXL2	2	SSR	REVERSE	340	20	60.23	55.00	6.00	3.00	CGGGTCCGGTACCTAAAGTT	TTA	3	TTATTATTATTATTATTATTATTATTATTATTA
483	GI1478W02GWKEL	1	SSR	FORWARD	210	23	59.85	39.13	3.00	2.00	TCGGTCCCTCTAATAAACATTCA	ATT	3	ATTATTATTATTATT	269	480	480	4.00	1.00
484	GI1478W02GWKEL	2	SSR	REVERSE	478	20	59.53	55.00	2.00	2.00	CCTCTCCCTCTCTCGCATTA	ATT	3	ATTATTATTATTATT
485	GI1478W02IPFTR	1	SSR	FORWARD	93	20	60.43	45.00	5.00	2.00	TGGACTCAGTTTTTCGCACA	AT	2	ATATATATATATATATAT	273	369	369	4.00	1.00
486	GI1478W02IPFTR	2	SSR	REVERSE	365	20	60.47	45.00	8.00	2.00	TTGGTATTCCAAGCCAGCAT	AT	2	ATATATATATATATATAT
487	GI1478W02GLXSK	1	SSR	FORWARD	47	26	58.99	26.92	6.00	1.00	CCAAAGATTGCATATTTATTTTAGGA	ATT	3	ATTATTATTATTATTATT	293	397	397	3.00	1.00
488	GI1478W02GLXSK	2	SSR	REVERSE	339	20	58.53	55.00	6.00	2.00	ATGACGTGTACCACGCTACC	ATT	3	ATTATTATTATTATTATT
489	GI1478W02GJT5D	1	SSR	FORWARD	289	20	60.41	55.00	2.00	0.00	CAAACAGGCACTAACCCCAC	AAAT	4	AAATAAATAAATAAAT	127	496	496	7.00	0.00
490	GI1478W02GJT5D	2	SSR	REVERSE	415	20	60.22	40.00	5.00	1.00	TAGTGCCGATTCAATGCAAA	AAAT	4	AAATAAATAAATAAAT
491	GI1478W02ISS6Y	1	SSR	FORWARD	144	20	60.12	45.00	5.00	2.00	CGTCAACGAATTGAATGCAC	AGGAG	5	AGGAGAGGAGAGGAG	284	490	490	5.00	1.00
492	GI1478W02ISS6Y	2	SSR	REVERSE	427	20	60.05	55.00	2.00	0.00	TCACCACCTCTCCATTCCTC	AGGAG	5	AGGAGAGGAGAGGAG
493	GI1478W02GAGTV	1	SSR	FORWARD	13	20	60.34	55.00	4.00	1.00	CCTCTCGATCCAAGTCCTCA	GAC	3	GACGACGACGACGAC	272	320	320	4.00	2.00
494	GI1478W02GAGTV	2	SSR	REVERSE	284	20	60.02	50.00	5.00	3.00	AGGCTGACCGTAGCTTTGAA	GAC	3	GACGACGACGACGAC
495	GI1478W02JGFGH	1	SSR	FORWARD	279	20	59.52	50.00	2.00	0.00	CCACAACACTCTCAATCCCA	ATCC	4	ATCCATCCATCCATCC	201	541	541	5.00	3.00
496	GI1478W02JGFGH	2	SSR	REVERSE	479	20	59.96	50.00	3.00	0.00	ACCTCGCATTGGTATTCTGG	ATCC	4	ATCCATCCATCCATCC
497	GI1478W02HWW6T	1	SSR	FORWARD	27	25	59.87	32.00	7.00	3.00	TGATGGGAATAAATACCATATTGCT	AG	2	AGAGAGAGAGAGAGAGAGAG	273	302	302	7.00	3.00
498	GI1478W02HWW6T	2	SSR	REVERSE	299	27	59.05	33.33	4.00	2.00	CCTTACCTTCACATACACTTTTATTCA	AG	2	AGAGAGAGAGAGAGAGAGAG
499	GI1478W02JSXUG	1	SSR	FORWARD	236	20	60.02	50.00	5.00	1.00	GATGTTGCTGCTAACGACGA	ATT	3	ATTATTATTATTATT	207	541	541	6.00	3.00
500	GI1478W02JSXUG	2	SSR	REVERSE	442	21	59.96	38.10	4.00	0.00	TGGATTCATCAACGTCAACAA	ATT	3	ATTATTATTATTATT

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Check here for the sequence database, sample table of citrus candidate genes, and other data.