Markers + reference

Fockea

2 species · Apocynaceae · Gentianales

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Species 2
Genome length 160–161 kb
Candidate markers 265
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 275 0.0836 1.00 78.8 yes View details
rps16-trnQ-UUG LSC 1231 0.0163 1.00 58.7 yes View details
rps2-rpoC2 LSC 5479 0.0097 0.99 43.8 yes View details
accD LSC 2202 0.0154 0.74 49.9 yes View details
clpP LSC 2016 0.0165 0.99 57.4 yes View details
ycf1 SSC 5814 0.0327 0.91 63.5 yes View details
ndhG-ndhI SSC 171 0.0491 0.95 75.7 yes View details
rpl32-trnL-UAG SSC 821 0.0183 1.00 69.4 yes View details
petA-psbJ LSC 680 0.0150 0.98 69.0 yes View details
ndhC-trnV-UAC LSC 1476 0.0107 0.95 67.6 yes View details
ccsA-ndhD SSC 253 0.0356 1.00 67.6 yes View details
psaA-ycf3 LSC 877 0.0094 0.97 67.2 yes View details
ycf4-cemA LSC 678 0.0134 0.99 66.4 yes View details
trnN-GUU-ndhF IRb 1567 0.0063 0.92 66.0 yes View details
trnG-UCC-trnR-UCU LSC 179 0.0173 0.97 65.6 yes View details
petN-psbM LSC 1194 0.0075 1.00 63.1 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 80 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 344 1.000 83.7
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 391 1.000 83.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 405 1.000 83.2
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 404 1.000 83.2
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 406 1.000 83.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1304–1327 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1315–1338 1.000 79.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1308–1331 1.000 74.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1334–1357 1.000 74.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1316–1339 1.000 74.5
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 254–259 1.000 66.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 257–262 1.000 65.9
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 260–265 1.000 65.4
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 263–268 1.000 65.2
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 258–263 1.000 63.7
rps2-rpoC2_p1 rps2-rpoC2 GCCTTCGATGGTTACGTCTT CGGCATTCTGTTCTACAGCT 674–699 1.000 84.6
rps2-rpoC2_p2 rps2-rpoC2 GCCTTCGATGGTTACGTCTT AAAGGTGAACGGCATTCTGT 683–708 1.000 84.5
rps2-rpoC2_p3 rps2-rpoC2 GCCTTCGATGGTTACGTCTT AAGGTGAACGGCATTCTGTT 682–707 1.000 84.5
rps2-rpoC2_p4 rps2-rpoC2 GCCTTCGATGGTTACGTCTT CTGAGGAAGCCCTTTACGAC 770–795 1.000 84.1
rps2-rpoC2_p5 rps2-rpoC2 GCCTTCGATGGTTACGTCTT ATCACCATCTTGACCGCTTC 1317–1342 1.000 82.5
petN-psbM_p1 petN-psbM TCGTAGTGTGGGGAAGAAGT TCATTCTAGTTCCTACCGCCT 1288 1.000 72.3
petN-psbM_p2 petN-psbM TTTCCCTTTCGCTCGTAGTG TCATTCTAGTTCCTACCGCCT 1300 1.000 71.7
petN-psbM_p3 petN-psbM TCGTAGTGTGGGGAAGAAGT TCTAGTTCCTACCGCCTTTCT 1284 1.000 71.7
petN-psbM_p4 petN-psbM CGTAGTGTGGGGAAGAAGTG TCATTCTAGTTCCTACCGCCT 1287 1.000 71.7
petN-psbM_p5 petN-psbM ACATTTTCCCTTTCGCTCGT TCATTCTAGTTCCTACCGCCT 1304 1.000 71.5
psaA-ycf3_p1 psaA-ycf3 GCCCATTCCTCGAAAGATGT ATCAAGCTGCCGAGTATTGG 1027–1055 1.000 82.1
psaA-ycf3_p2 psaA-ycf3 TGAGAAATGACCCGGTTTGG ATCAAGCTGCCGAGTATTGG 1046–1074 1.000 81.6
psaA-ycf3_p3 psaA-ycf3 GCCCATTCCTCGAAAGATGT CGATCAAGCTGCCGAGTATT 1029–1057 1.000 81.3
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGATGT TTGAAGATCACGAGGCGTTT 956–984 1.000 81.3
psaA-ycf3_p5 psaA-ycf3 GCCCATTCCTCGAAAGATGT TTGGTTGAAGATCACGAGGC 960–988 1.000 81.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Fockea edulis NC_079594.1 161450 View on NCBI ↗
Fockea multiflora NC_079595.1 160246 View on NCBI ↗