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

Prev [Page 11] Next

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
501	GI1478W02GXGZ7	1	SSR	FORWARD	148	20	60.14	50.00	2.00	0.00	ACATAGTTTCGCTTGCCCAC	GA	2	GAGAGAGAGAGAGAGA	231	379	379	5.00	1.00
502	GI1478W02GXGZ7	2	SSR	REVERSE	378	26	57.62	38.46	3.00	1.00	CGTAGTGTCTATTATGTTCTATTCGG	GA	2	GAGAGAGAGAGAGAGA
503	GI1478W02GGVHB	1	SSR	FORWARD	32	22	59.29	45.45	4.00	3.00	TCTTAACTTGCACACAAGGACC	AAATA	5	AAATAAAATAAAATA	255	371	371	5.00	0.00
504	GI1478W02GGVHB	2	SSR	REVERSE	286	21	60.14	42.86	3.00	0.00	GACCAAAAGTCAACAAGGCAA	AAATA	5	AAATAAAATAAAATA
505	GI1478W02GS5X3	1	SSR	FORWARD	46	20	60.03	55.00	2.00	2.00	CGTCCCTATCCTCCTCATCA	ATA	3	ATAATAATAATAATAATAATAATA	239	498	498	3.00	0.00
506	GI1478W02GS5X3	2	SSR	REVERSE	284	20	59.90	60.00	6.00	3.00	GGCCTACGTGGCACTCTAAG	ATA	3	ATAATAATAATAATAATAATAATA
507	GI1478W02GS5X3	1	SSR	FORWARD	46	20	60.03	55.00	2.00	2.00	CGTCCCTATCCTCCTCATCA	CTTTT	5	CTTTTCTTTTCTTTT	239	498	498	3.00	0.00
508	GI1478W02GS5X3	2	SSR	REVERSE	284	20	59.90	60.00	6.00	3.00	GGCCTACGTGGCACTCTAAG	CTTTT	5	CTTTTCTTTTCTTTT
509	GI1478W02JG1GW	1	SSR	FORWARD	67	21	59.00	42.86	4.00	3.00	TTACGAATTTACAACTGGCCC	ATT	3	ATTATTATTATTATTATT	250	383	383	6.00	2.00
510	GI1478W02JG1GW	2	SSR	REVERSE	316	20	60.45	45.00	4.00	2.00	CTGAAAATTAACCATCGCGG	ATT	3	ATTATTATTATTATTATT
511	GI1478W02H7ZYU	1	SSR	FORWARD	137	20	60.05	50.00	4.00	2.00	GGGTCCTTTCGTACCCAAAT	TTTTA	5	TTTTATTTTATTTTA	292	555	555	4.00	1.00
512	GI1478W02H7ZYU	2	SSR	REVERSE	428	20	60.07	45.00	4.00	2.00	TGTCCGATATGCTTTGTCCA	TTTTA	5	TTTTATTTTATTTTA
513	GI1478W02JWC0K	1	SSR	FORWARD	289	20	59.81	50.00	2.00	2.00	CAATCCACCCGACTACGAAT	TA	2	TATATATATATATATATA	191	482	482	4.00	3.00
514	GI1478W02JWC0K	2	SSR	REVERSE	479	24	57.76	37.50	4.00	0.00	AAGGAGGTGTAAATAGAATTGTGG	TA	2	TATATATATATATATATA
515	GI1478W02JZUHW	1	SSR	FORWARD	301	22	58.94	40.91	4.00	0.00	CGGCACCTACATATAAACCAAA	AAG	3	AAGAAGAAGAAGAAGAAGAAGAAG	130	431	431	4.00	2.00
516	GI1478W02JZUHW	2	SSR	REVERSE	430	24	59.29	41.67	4.00	2.00	CATGACCATACACGAGATAATGTG	AAG	3	AAGAAGAAGAAGAAGAAGAAGAAG
517	GI1478W02J1KPX	1	SSR	FORWARD	7	20	59.16	40.00	5.00	1.00	GGCCAAAATGCTGATTTCTT	TA	2	TATATATATATATATA	222	310	310	4.00	0.00
518	GI1478W02J1KPX	2	SSR	REVERSE	228	20	59.85	45.00	4.00	3.00	TCCAAAACCTAGCGAATGCT	TA	2	TATATATATATATATA
519	GI1478W02IIHNZ	1	SSR	FORWARD	21	20	60.39	45.00	2.00	1.00	GCTGACTTTTCGTTCGCATT	TA	2	TATATATATATATATATATATA	137	175	175	4.00	1.00
520	GI1478W02IIHNZ	2	SSR	REVERSE	157	20	59.21	45.00	6.00	2.00	CGCGATTCAAGCTTCAGTTA	TA	2	TATATATATATATATATATATA
521	GI1478W02JJ20A	1	SSR	FORWARD	224	20	60.17	55.00	4.00	0.00	ACTGCACCCGGAAAGTAGTG	TTTA	4	TTTATTTATTTATTTA	145	419	419	2.00	0.00
522	GI1478W02JJ20A	2	SSR	REVERSE	368	24	58.45	20.83	4.00	0.00	TGAAAATTGGAAGAAAAAGAAAAA	TTTA	4	TTTATTTATTTATTTA
523	GI1478W02IHTDJ	1	SSR	FORWARD	205	20	59.94	40.00	4.00	2.00	ACAATTTTGATTTCGTCGGC	TCT	3	TCTTCTTCTTCTTCT	181	477	477	5.00	1.00
524	GI1478W02IHTDJ	2	SSR	REVERSE	385	21	59.95	42.86	4.00	0.00	CAATGCAAACCATAGGAGGAA	TCT	3	TCTTCTTCTTCTTCT
525	GI1478W02HDTV6	1	SSR	FORWARD	242	20	60.07	45.00	4.00	0.00	AATCTCTGGCCGTTTGATTG	GGT	3	GGTGGTGGTGGTGGT	204	459	459	3.00	0.00
526	GI1478W02HDTV6	2	SSR	REVERSE	445	20	59.90	50.00	4.00	0.00	CAGCTTCGTCTTCGCTCTTT	GGT	3	GGTGGTGGTGGTGGT
527	GI1478W02I1J8R	1	SSR	FORWARD	31	20	59.31	55.00	4.00	1.00	CTTCTTCAGCTTCTCCAGCC	CATCTT	6	CATCTTCATCTTCATCTT	246	525	525	3.00	1.00
528	GI1478W02I1J8R	2	SSR	REVERSE	276	20	59.69	45.00	2.00	1.00	TTTGCTTATGTGATGCGGTC	CATCTT	6	CATCTTCATCTTCATCTT
529	GI1478W02G7KUK	1	SSR	FORWARD	35	20	59.97	50.00	2.00	1.00	GTGTTTTGCTACCCCCTTGA	TTGA	4	TTGATTGATTGATTGA	271	521	521	6.00	3.00
530	GI1478W02G7KUK	2	SSR	REVERSE	305	20	59.92	55.00	6.00	0.00	TGAGGGAGTAACCATGGGAG	TTGA	4	TTGATTGATTGATTGA
531	GI1478W02G7KUK	1	SSR	FORWARD	35	20	59.97	50.00	2.00	1.00	GTGTTTTGCTACCCCCTTGA	TCTCT	5	TCTCTTCTCTTCTCT	271	521	521	6.00	3.00
532	GI1478W02G7KUK	2	SSR	REVERSE	305	20	59.92	55.00	6.00	0.00	TGAGGGAGTAACCATGGGAG	TCTCT	5	TCTCTTCTCTTCTCT
533	GI1478W02GPH1G	1	SSR	FORWARD	234	20	59.98	45.00	5.00	1.00	TGCTGCATGGCTAATTTCTG	CAAAAG	6	CAAAAGCAAAAGCAAAAG	164	407	407	4.00	1.00
534	GI1478W02GPH1G	2	SSR	REVERSE	397	21	59.85	47.62	4.00	0.00	CGTATTTGCTCGATGAGAAGG	CAAAAG	6	CAAAAGCAAAAGCAAAAG
535	GI1478W02FO220	1	SSR	FORWARD	288	20	59.80	45.00	4.00	3.00	GATCACCATGCAAACCCTTT	ATT	3	ATTATTATTATTATT	172	509	509	6.00	0.00
536	GI1478W02FO220	2	SSR	REVERSE	459	20	59.35	45.00	4.00	2.00	TTGCTTGTGGTTATCGCACT	ATT	3	ATTATTATTATTATT
537	GI1478W02H4P0Z	1	SSR	FORWARD	53	21	59.25	47.62	6.00	0.00	TCAAGATCTGACCACTCACCA	GA	2	GAGAGAGAGAGAGAGA	228	450	450	6.00	0.00
538	GI1478W02H4P0Z	2	SSR	REVERSE	280	20	59.98	45.00	5.00	3.00	ATGGTGCAAAACTTTCGTCC	GA	2	GAGAGAGAGAGAGAGA
539	GI1478W02F68XA	1	SSR	FORWARD	287	20	59.90	45.00	2.00	0.00	TGAAGGGAAAATGGTGAAGG	AC	2	ACACACACACACACACACAC	203	501	501	3.00	1.00
540	GI1478W02F68XA	2	SSR	REVERSE	489	20	59.99	50.00	3.00	2.00	TGAATGAGAGTTGCCAGTGC	AC	2	ACACACACACACACACACAC
541	GI1478W02JCRGL	1	SSR	FORWARD	22	21	59.69	47.62	6.00	3.00	GGCAGTATTCCATTAAAGGGG	TTTTTC	6	TTTTTCTTTTTCTTTTTC	179	443	443	4.00	1.00
542	GI1478W02JCRGL	2	SSR	REVERSE	200	20	60.09	50.00	7.00	2.00	GCCATGTCATGCATCTTCAC	TTTTTC	6	TTTTTCTTTTTCTTTTTC
543	GI1478W02IHLI8	1	SSR	FORWARD	87	20	60.02	55.00	4.00	0.00	GGGCACTCGCACTAGAAAAG	ATA	3	ATAATAATAATAATAATA	299	544	544	4.00	0.00
544	GI1478W02IHLI8	2	SSR	REVERSE	385	20	59.95	50.00	4.00	2.00	CGAAGGATAACGGGTACGAA	ATA	3	ATAATAATAATAATAATA
545	GI1478W02F68Z6	1	SSR	FORWARD	138	20	59.89	55.00	5.00	2.00	GAGGATGGTGACCCGATCTA	ATCCG	5	ATCCGATCCGATCCG	268	518	518	3.00	2.00
546	GI1478W02F68Z6	2	SSR	REVERSE	405	20	59.89	45.00	6.00	2.00	CCGAATTCAACCCGAATCTA	ATCCG	5	ATCCGATCCGATCCG
547	GI1478W02HL945	1	SSR	FORWARD	76	22	59.59	36.36	7.00	1.00	TGAATTTCAGAAACAAGGACCA	ATAAAA	6	ATAAAAATAAAAATAAAA	140	344	344	4.00	2.00
548	GI1478W02HL945	2	SSR	REVERSE	215	21	58.95	33.33	5.00	3.00	TTCGATGATGAATGGTTTTCA	ATAAAA	6	ATAAAAATAAAAATAAAA
549	GI1478W02GUB2O	1	SSR	FORWARD	95	20	59.13	55.00	7.00	0.00	AACGTAACGTACCCAGCTCC	TAA	3	TAATAATAATAATAA	277	458	458	4.00	1.00
550	GI1478W02GUB2O	2	SSR	REVERSE	371	22	58.83	36.36	4.00	2.00	CGTGCGATAATTTGAATAAAGC	TAA	3	TAATAATAATAATAA

Prev [Page 11] Next

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