Markers + reference

Gambeya

4 species · Sapotaceae · Ericales

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Species 4
Genome length 159–159 kb
Candidate markers 269
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 529 0.0107 1.00 57.8 yes View details
petN-psbM LSC 1212 0.0080 1.00 54.7 yes View details
atpB-rbcL LSC 795 0.0067 0.99 57.3 yes View details
petA-psbJ LSC 1086 0.0054 0.99 58.8 yes View details
ycf2-trnL-CAA IRb 709 0.0078 1.00 55.8 yes View details
ycf1 IRb 1068 0.0000 1.00 34.7 no View details
rpl32-trnL-UAG SSC 907 0.0075 1.00 60.7 yes View details
ndhD SSC 1512 0.0029 1.00 37.2 yes View details
ndhA SSC 2220 0.0049 1.00 51.2 yes View details
rps15-ycf1 SSC 389 0.0146 0.99 61.7 yes View details
ycf1 SSC 5661 0.0030 1.00 44.0 yes View details
ccsA-ndhD SSC 196 0.0255 0.99 69.4 yes View details
rps16-trnQ-UUG LSC 895 0.0041 1.00 63.3 yes View details
ycf3-trnS-GCU LSC 856 0.0037 1.00 62.2 yes View details
psbK-psbI LSC 421 0.0059 1.00 59.7 yes View details
trnG-GCC-trnfM-CAU LSC 170 0.0109 0.99 58.9 yes View details
rbcL-accD LSC 592 0.0017 1.00 58.4 yes View details
ycf4-cemA LSC 932 0.0034 1.00 58.1 yes View details
psaC-ndhE SSC 247 0.0061 1.00 56.8 yes View details
petD-rpoA LSC 250 0.0147 1.00 56.5 yes View details
trnL-CAA-ycf2 IRa 709 0.0078 1.00 55.8 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA TTAGTTATGGGCGAACGACG CCTCTAGACCTCGCTGCTAT 657–689 1.000 80.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTCGCTGCTAT 602–634 1.000 80.5
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTCGCTGCTAT 603–635 1.000 80.3
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCTCTAGACCTCGCTGCTAT 595–627 1.000 78.9
trnH-GUG-psbA_p5 trnH-GUG-psbA TTAGTTATGGGCGAACGACG AACTTCCCTCTAGACCTCGC 663–695 1.000 77.2
trnK-UUU_p1 trnK-UUU GCCCGTGTCAACCAATATCT ATGATGGGTTCGCTGGATTC 2975–2981 1.000 80.4
trnK-UUU_p2 trnK-UUU GCCCGTGTCAACCAATATCT GATGGGTTCGCTGGATTCAT 2973–2979 1.000 80.4
trnK-UUU_p3 trnK-UUU TGAATCCAGTGGGTTGCAAA ATGATGGGTTCGCTGGATTC 2928–2934 1.000 80.1
trnK-UUU_p4 trnK-UUU TGAATCCAGTGGGTTGCAAA GATGGGTTCGCTGGATTCAT 2926–2932 1.000 80.1
trnK-UUU_p5 trnK-UUU GCCCGTGTCAACCAATATCT TGGGTTCGCTGGATTCATTT 2971–2977 1.000 78.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 972–981 1.000 81.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCTGTCTTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 976–985 1.000 80.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 965–974 1.000 80.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACGGATCCTGTCTTT GAGGTTCGAATCCTTCCGTC 986–995 1.000 79.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG AAATTTAAATGGGGCGTGGC 1029–1038 1.000 78.9
psbK-psbI_p1 psbK-psbI CAAGCTGCCGTAAGTTTTCG TCTTCACGTCCAGGATTACG 550–552 1.000 73.2
psbK-psbI_p2 psbK-psbI AGCTGCCGTAAGTTTTCGAT TCTTCACGTCCAGGATTACG 548–550 1.000 72.8
psbK-psbI_p3 psbK-psbI AAGCTGCCGTAAGTTTTCGA TCTTCACGTCCAGGATTACG 549–551 1.000 72.5
psbK-psbI_p4 psbK-psbI GCTGCCGTAAGTTTTCGATG TCTTCACGTCCAGGATTACG 547–549 1.000 72.3
psbK-psbI_p5 psbK-psbI GCCAGTCATACCTGTGCTTT TCTTCACGTCCAGGATTACG 593–595 1.000 72.1
petN-psbM_p1 petN-psbM TAGTTAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1374–1395 1.000 68.5
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1313–1334 1.000 67.0
petN-psbM_p3 petN-psbM TAGTTAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 1374–1395 1.000 64.3
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTC 1313–1334 1.000 62.8
petN-psbM_p5 petN-psbM ATAGTTAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTCT 1375–1396 1.000 62.6
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU TTCTCTTTGCCACGGAGAAG CTTGAGGTCACGGGTTCAAA 249–251 1.000 79.9
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU TTCTCTTTGCCACGGAGAAG TCAGTTCTTCTCTTCAGCGC 306–308 1.000 79.4
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU TTCTCTTTGCCACGGAGAAG GTCACGGGTTCAAATCCTGT 243–245 1.000 79.4
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU TTCTCTTTGCCACGGAGAAG TCACGGGTTCAAATCCTGTC 242–244 1.000 78.9
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU TTCTCTTTGCCACGGAGAAG TGAGGTCACGGGTTCAAATC 247–249 1.000 78.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Gambeya africana MZ274138.1 158899 View on NCBI ↗
Gambeya gigantea MZ274139.1 158929 View on NCBI ↗
Gambeya lacourtiana MZ274140.1 158891 View on NCBI ↗
Gambeya subnuda MZ274141.1 159269 View on NCBI ↗