Markers + reference

Tongoloa

14 species · Apiaceae · Apiales

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Species 14
Genome length 158–172 kb
Candidate markers 282
Primer pairs 90

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 8 remaining regions by MarkerSeek score (out of 282 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 329 0.0622 0.95 82.6 yes View details
trnE-UUC-trnT-GGU LSC 944 0.0258 0.96 68.8 yes View details
rps4-trnT-UGU LSC 422 0.0382 0.94 68.0 yes View details
petA-psbJ LSC 971 0.0237 0.97 78.2 yes View details
psaJ-rpl33 LSC 452 0.0123 1.00 54.9 yes View details
rpl33-rps18 LSC 248 0.0670 0.93 76.9 yes View details
trnN-GUU-ndhF IRb 2227 0.0073 0.99 52.1 yes View details
ndhF-rpl32 SSC 1192 0.0231 0.96 74.3 yes View details
rpl32-trnL-UAG SSC 726 0.0295 0.91 79.4 yes View details
ndhG-ndhI SSC 442 0.0447 0.88 70.1 yes View details
rpl36-trnH-GUG IRa 388 0.1200 0.46 67.3 no View details
trnW-CCA-trnP-UGG LSC 177 0.0543 0.88 80.4 yes View details
ndhC-trnV-UAC LSC 746 0.0146 1.00 74.5 yes View details
rps2-rpoC2 LSC 238 0.0258 0.95 71.3 yes View details
trnS-UGA-psbZ LSC 347 0.0220 0.99 70.9 yes View details
psbM-trnD-GUC LSC 708 0.0115 0.99 68.9 yes View details
psbZ-trnG-GCC LSC 294 0.0169 1.00 68.8 yes View details
rps15-ycf1 SSC 371 0.0383 0.97 68.4 yes View details
rpoB-trnC-GCA LSC 1240 0.0127 1.00 67.5 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-GUG-psbA_p1 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TGGAAGTTATGCACGAACGT 438–489 1.000 89.7
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TGGAAGTTATGCACGAACGT 437–488 1.000 89.7
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TGGAAGTTATGCACGAACGT 439–490 1.000 89.7
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGGAAGTTATGCACGAACGT 424–475 0.929 86.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGCACGAACGTAATGCTCAT 415–466 0.929 85.9
rps2-rpoC2_p1 rps2-rpoC2 AATGAACTCCGGCCTTCATC TTTGAGGGGGAAATGAGAGA 393–409 1.000 70.6
rps2-rpoC2_p2 rps2-rpoC2 CCGGCCTTCATCATCTCTTC TTTGAGGGGGAAATGAGAGA 385–401 1.000 70.1
rps2-rpoC2_p3 rps2-rpoC2 CGGCCTTCATCATCTCTTCC TTTGAGGGGGAAATGAGAGA 384–400 1.000 70.1
rps2-rpoC2_p4 rps2-rpoC2 AATGAACTCCGGCCTTCATC TTGAGGGGGAAATGAGAGAT 392–408 1.000 68.7
rps2-rpoC2_p5 rps2-rpoC2 AAAATGAACTCCGGCCTTCA TTTGAGGGGGAAATGAGAGA 395–411 1.000 68.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CTTACCACTCGGCCATATCG 1135–1335 1.000 86.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CCGGATTTGAACTGGGGAAA 1175–1375 1.000 86.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA TTATTGATCAGGCGACACCC 1193–1393 1.000 84.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA AAGGGATTGGATTTCGAGCC 1366 0.071 41.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA GGGATTGGATTTCGAGCCTT 1364 0.071 41.0
psbM-trnD-GUC_p1 psbM-trnD-GUC AGCAGAAAAGCAGTAGGAACT TTCAATTGGTCAGAGCACCG 822–846 1.000 68.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AAGCAGAAAAGCAGTAGGAACT TTCAATTGGTCAGAGCACCG 823–847 1.000 65.9
psbM-trnD-GUC_p3 psbM-trnD-GUC AGCAGAAAAGCAGTAGGAACT GTTCAATTGGTCAGAGCACC 823–847 1.000 64.3
psbM-trnD-GUC_p4 psbM-trnD-GUC AGCAGAAAAGCAGTAGGAAC TTCAATTGGTCAGAGCACCG 822–846 1.000 64.1
psbM-trnD-GUC_p5 psbM-trnD-GUC GCAGAAAAGCAGTAGGAACT TTCAATTGGTCAGAGCACCG 821–845 1.000 64.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CAAGAAGAGACCATTCCGGG GAACCGATGACTTACGCCTT 469–1224 0.714 78.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CCAAGAAGAGACCATTCCGG GAACCGATGACTTACGCCTT 470–1225 0.714 78.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CCCAAGAAGAGACCATTCCG GAACCGATGACTTACGCCTT 471–1226 0.714 78.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CAAGAAGAGACCATTCCGGG AAAGTCAAAGCCCCTTACCG 494–1249 0.714 77.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CCAAGAAGAGACCATTCCGG AAAGTCAAAGCCCCTTACCG 495–1250 0.714 77.6
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC CCAACCATCAGGAGAAGCAA 464–499 1.000 83.8
trnS-UGA-psbZ_p2 trnS-UGA-psbZ GAGCTATCAACCACTCAGCC CCAACCATCAGGAGAAGCAA 471–506 1.000 83.4
trnS-UGA-psbZ_p3 trnS-UGA-psbZ GGAGCTATCAACCACTCAGC CCAACCATCAGGAGAAGCAA 472–507 1.000 83.4
trnS-UGA-psbZ_p4 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC CCAACCATCAGGAGAAGCAA 479–514 1.000 83.3
trnS-UGA-psbZ_p5 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC GACCAACCATCAGGAGAAGC 466–501 1.000 83.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Tongoloa arguta NC_083206.1 161099 View on NCBI ↗
Tongoloa dunnii NC_083192.1 161186 View on NCBI ↗
Tongoloa elata NC_083208.1 158624 View on NCBI ↗
Tongoloa filicaudicis NC_083193.1 159842 View on NCBI ↗
Tongoloa gracilis NC_083198.1 172450 View on NCBI ↗
Tongoloa loloensis NC_083210.1 161702 View on NCBI ↗
Tongoloa napifera NC_083194.1 159803 View on NCBI ↗
Tongoloa rubronervis NC_083209.1 161273 View on NCBI ↗
Tongoloa silaifolia NC_049062.1 161122 View on NCBI ↗
Tongoloa spathulata OP477474.1 167356 View on NCBI ↗
Tongoloa stewardii NC_083201.1 161591 View on NCBI ↗
Tongoloa taeniophylla NC_083204.1 157959 View on NCBI ↗
Tongoloa tagongensis NC_083202.1 163061 View on NCBI ↗
Tongoloa xinlongensis OP477475.1 159336 View on NCBI ↗