Markers + reference

Capsicum

15 species · Solanaceae · Solanales

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Species 15
Genome length 157–157 kb
Candidate markers 265
Primer pairs 90

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ LSC 1272 0.0067 1.00 57.9 yes View details
atpH-atpI LSC 1184 0.0060 1.00 51.4 yes View details
psaA-ycf3 LSC 840 0.0082 0.96 57.3 yes View details
rps4-trnT LSC 376 0.0137 1.00 56.2 yes View details
accD LSC 1656 0.0034 1.00 55.7 yes View details
rpl20 LSC 465 0.0184 1.00 57.9 yes View details
ycf1 IRb 1161 0.0017 1.00 51.5 yes View details
ndhF-rpl32 SSC 253 0.0100 1.00 41.5 yes View details
rpl32-trnL SSC 870 0.0089 1.00 51.4 yes View details
ycf1 SSC 5721 0.0048 1.00 41.7 yes View details
trnL-trnF LSC 593 0.0063 1.00 58.8 yes View details
rps19-rpl2 IRb 76 0.0103 0.96 55.7 yes View details
ndhC-trnV LSC 1136 0.0038 1.00 52.6 yes View details
accD-psaI LSC 760 0.0020 0.98 52.5 yes View details
trnF-ndhJ LSC 671 0.0059 1.00 50.7 yes View details
psaJ-rpl33 LSC 436 0.0055 1.00 49.9 yes View details
trnH-psbA LSC 468 0.0073 0.99 49.0 yes View details
trnE-trnT LSC 705 0.0025 1.00 48.9 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 580–595 1.000 79.6
trnH-psbA_p2 trnH-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 594–609 1.000 79.4
trnH-psbA_p3 trnH-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 593–608 1.000 79.4
trnH-psbA_p4 trnH-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 595–610 1.000 79.4
trnH-psbA_p5 trnH-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 581–596 1.000 79.1
rps16-trnQ_p1 rps16-trnQ AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1305–1429 1.000 85.1
rps16-trnQ_p2 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1288–1412 1.000 84.7
rps16-trnQ_p3 rps16-trnQ CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1306–1430 1.000 84.1
rps16-trnQ_p4 rps16-trnQ CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1303–1427 1.000 82.8
rps16-trnQ_p5 rps16-trnQ GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1302–1426 1.000 82.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TACCTGTCATGCTCCTTGGA 1320–1328 1.000 82.1
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TACCTGTCATGCTCCTTGGA 1403–1411 1.000 81.2
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TACCTGTCATGCTCCTTGGA 1407–1415 1.000 81.2
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TACCTGTCATGCTCCTTGGA 1321–1329 1.000 81.0
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TACCTGTCATGCTCCTTGGA 1335–1343 1.000 80.7
trnE-trnT_p1 trnE-trnT TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 836–861 1.000 80.9
trnE-trnT_p2 trnE-trnT TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 815–840 1.000 80.5
trnE-trnT_p3 trnE-trnT TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 812–837 1.000 80.4
trnE-trnT_p4 trnE-trnT GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 798–823 1.000 80.2
trnE-trnT_p5 trnE-trnT TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 833–858 1.000 79.8
psaA-ycf3_p1 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCAAGCCGCTGAGTATTGG 926–1032 1.000 84.9
psaA-ycf3_p2 psaA-ycf3 GCCCATTCCTCGAAAGAAGT GGAAACAGGCTATAGCGCTT 908–1014 1.000 84.9
psaA-ycf3_p3 psaA-ycf3 GCCCATTCCTCGAAAGAAGT CAGAGGCTTGGTTCGATCAA 941–1047 1.000 84.4
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGAAGT CGATCAAGCCGCTGAGTATT 928–1034 1.000 84.1
psaA-ycf3_p5 psaA-ycf3 GCCCATTCCTCGAAAGAAGT AGCCGCTGAGTATTGGAAAC 922–1028 1.000 83.2
rps4-trnT_p1 rps4-trnT GATCATTTCCGGTCCTAGGC CTCAGAGGTTAGAGCATCGC 533–538 1.000 83.1
rps4-trnT_p2 rps4-trnT ATCATTTCCGGTCCTAGGCT CTCAGAGGTTAGAGCATCGC 532–537 1.000 83.0
rps4-trnT_p3 rps4-trnT GATCATTTCCGGTCCTAGGC AGATTTCTGTGATGTGGGCC 560–565 1.000 82.8
rps4-trnT_p4 rps4-trnT ATCATTTCCGGTCCTAGGCT AGATTTCTGTGATGTGGGCC 559–564 1.000 82.7
rps4-trnT_p5 rps4-trnT GATCATTTCCGGTCCTAGGC ATGGTCATCGGTTCGATTCC 501–506 1.000 82.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Capsicum annuum NC_018552.1 156781 View on NCBI ↗
Capsicum annuum var. annuum OR038714.1 156817 View on NCBI ↗
Capsicum annuum var. glabriusculum KR078311.1 156817 View on NCBI ↗
Capsicum baccatum NC_072696.1 157475 View on NCBI ↗
Capsicum baccatum var. baccatum NC_039693.1 157053 View on NCBI ↗
Capsicum baccatum var. pendulum NC_039692.1 157144 View on NCBI ↗
Capsicum baccatum var. praetermissum NC_039695.1 157056 View on NCBI ↗
Capsicum chacoense NC_033525.1 156995 View on NCBI ↗
Capsicum chinense NC_030543.1 156807 View on NCBI ↗
Capsicum eximium NC_033527.1 156947 View on NCBI ↗
Capsicum frutescens NC_028007.1 156817 View on NCBI ↗
Capsicum galapagoense NC_033524.1 156959 View on NCBI ↗
Capsicum lycianthoides NC_026551.1 156583 View on NCBI ↗
Capsicum pubescens NC_039694.1 157390 View on NCBI ↗
Capsicum tovarii NC_033526.1 156816 View on NCBI ↗