Markers + reference

Coffea

11 species · Rubiaceae · Gentianales

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Species 11
Genome length 155–155 kb
Candidate markers 268
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0012 1.00 29.8 yes View details
trnK-UUU-rps16 LSC 868 0.0103 0.99 50.7 yes View details
atpH-atpI LSC 1047 0.0082 1.00 62.6 yes View details
psbM-trnD-GUC LSC 920 0.0111 1.00 57.2 yes View details
accD-psaI LSC 751 0.0149 1.00 55.4 yes View details
petA-psbJ LSC 876 0.0095 1.00 65.9 yes View details
psbE-petL LSC 1074 0.0089 1.00 56.5 yes View details
psaJ-rpl33 LSC 457 0.0082 1.00 42.4 yes View details
clpP1 LSC 2002 0.0055 1.00 45.8 yes View details
petD LSC 1200 0.0063 1.00 46.3 yes View details
rpl16 LSC 1407 0.0075 1.00 57.0 yes View details
rpl32-trnL-UAG SSC 849 0.0109 1.00 42.9 yes View details
trnH-GUG-psbA LSC 226 0.0363 1.00 69.1 yes View details
rpl20-rps12 LSC 770 0.0079 1.00 64.7 yes View details
trnT-GGU-psbD LSC 1162 0.0056 1.00 60.4 yes View details
atpB-rbcL LSC 770 0.0054 1.00 58.8 yes View details
petN-psbM LSC 1160 0.0067 1.00 58.4 yes View details
pafII-cemA LSC 846 0.0064 1.00 57.6 yes View details
rps18-rpl20 LSC 221 0.0200 1.00 56.4 yes View details
rpoC1 LSC 2801 0.0030 1.00 55.6 yes View details
rpoA LSC 1008 0.0032 1.00 54.9 yes View details
ndhC-trnV-UAC LSC 1180 0.0075 1.00 54.1 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 295–327 1.000 88.7
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 342–374 1.000 88.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 356–388 1.000 87.9
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 355–387 1.000 87.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 357–389 1.000 87.9
psbA_p1 psbA GATCCACTTGGCTACATCCG CCTCACGTCGGAAGAAGAAG 1942–1972 1.000 82.2
psbA_p2 psbA CAATCCACTGCCTTGATCCA CCTCACGTCGGAAGAAGAAG 1956–1986 1.000 82.1
psbA_p3 psbA AATCCACTGCCTTGATCCAC CCTCACGTCGGAAGAAGAAG 1955–1985 1.000 82.1
psbA_p4 psbA ACAATCCACTGCCTTGATCC CCTCACGTCGGAAGAAGAAG 1957–1987 1.000 82.1
psbA_p5 psbA CATCCGCCCCTCTACTCTAT CCTCACGTCGGAAGAAGAAG 1928–1958 1.000 81.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGCCCTAATCAAATGAAGTTCA 917–934 1.000 60.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGCCCTAATCAAATGAAGTTCA 916–933 1.000 60.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CGCCCTAATCAAATGAAGTTCA 926–943 1.000 59.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GAACTTCGCCCTAATCAAATGA 922–939 1.000 58.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGCCCTAATCAAATGAAGTTC 917–934 1.000 58.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1134–1143 1.000 78.7
atpH-atpI_p2 atpH-atpI CAGCAGTTCCTTGACCAACT TTTTTGCAACTTTAGCCGCG 1196–1205 1.000 78.6
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 1150–1159 1.000 77.8
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1135–1144 1.000 77.5
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 1149–1158 1.000 77.3
rpoC1_p1 rpoC1 AATCCTAGCTGAACCGGAGA CTCGTTCGAGAACTACGATCC 2957–2970 1.000 71.5
rpoC1_p2 rpoC1 AATCCTAGCTGAACCGGAGA TCGTTCGAGAACTACGATCC 2956–2969 1.000 70.9
rpoC1_p3 rpoC1 AATCCTAGCTGAACCGGAGA CGTTCGAGAACTACGATCCT 2955–2968 1.000 70.8
rpoC1_p4 rpoC1 ATCCTAGCTGAACCGGAGAG CTCGTTCGAGAACTACGATCC 2956–2969 1.000 70.4
rpoC1_p5 rpoC1 AATCCTAGCTGAACCGGAGA CCGGATTCATAGGAAGGAAGC 2892–2905 1.000 69.9
petN-psbM_p1 petN-psbM GTCTCGCTTGGGCTTCTTTA TCATTCTAGTTCCTACGGCCT 1240–1302 1.000 76.8
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TCATTCTAGTTCCTACGGCCT 1246–1308 1.000 76.3
petN-psbM_p3 petN-psbM GTCTCGCTTGGGCTTCTTTA TCTAGTTCCTACGGCCTTTCT 1236–1298 1.000 76.2
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TCTAGTTCCTACGGCCTTTCT 1242–1304 1.000 75.7
petN-psbM_p5 petN-psbM GTCTCGCTTGGGCTTCTTTA AGTTCCTACGGCCTTTCTACT 1233–1295 1.000 75.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Coffea ambongensis NC_079619.1 154826 View on NCBI ↗
Coffea arabica NC_008535.1 155189 View on NCBI ↗
Coffea arabica x Coffea canephora NC_083905.1 155188 View on NCBI ↗
Coffea arabica x Coffea liberica NC_083908.1 155011 View on NCBI ↗
Coffea bissetiae NC_079620.1 154781 View on NCBI ↗
Coffea boinensis NC_079618.1 154879 View on NCBI ↗
Coffea canephora NC_030053.1 154751 View on NCBI ↗
Coffea eugenioides NC_083907.1 155123 View on NCBI ↗
Coffea liberica MW970411.1 154799 View on NCBI ↗
Coffea liberica var. dewevrei OQ946698.1 154814 View on NCBI ↗
Coffea racemosa NC_083906.1 154942 View on NCBI ↗