Markers + reference

Swertia

23 species · Gentianaceae · Gentianales

Back to catalogue

Species 23
Genome length 149–154 kb
Candidate markers 272
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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 350 0.0881 0.91 71.3 yes View details
rps16 LSC 1027 0.0394 0.99 69.5 yes View details
rps16-trnQ-UUG LSC 514 0.0430 0.99 72.1 yes View details
rpoB-trnC-GCA LSC 1188 0.0344 0.98 74.0 yes View details
ndhC-trnV-UAC LSC 995 0.0314 0.61 64.0 yes View details
psbE-petL LSC 1016 0.0327 0.98 70.2 yes View details
ycf1 IRb 989 0.0036 1.00 37.0 no View details
ndhF-rpl32 SSC 750 0.0456 0.99 78.4 yes View details
rpl32-trnL-UAG SSC 921 0.0459 0.99 85.0 yes View details
ycf1 SSC 5484 0.0270 0.99 65.7 yes View details
psbM-trnD-GUC LSC 862 0.0303 0.96 76.7 yes View details
petA-psbJ LSC 830 0.0287 1.00 74.9 yes View details
trnD-GUC-trnY-GUA LSC 114 0.0685 0.99 72.9 yes View details
trnS-GCU-trnG-UCC LSC 504 0.0357 0.99 71.8 yes View details
ycf3-trnS-GGA LSC 501 0.0334 0.99 71.0 yes View details
psbK-psbI LSC 399 0.0336 0.99 70.9 yes View details
trnC-GCA-petN LSC 816 0.0226 0.96 69.9 yes View details
atpA-atpF LSC 69 0.0458 1.00 69.4 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 CCACTTGGCTACATCCGC TTCCTCTAGACCTAGCTGCT 372–439 1.000 65.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CCACTTGGCTACATCCGC TTTCCTCTAGACCTAGCTGCT 373–440 1.000 63.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CCACTTGGCTACATCCGC ACCGTGCTAATCTTGGTATGG 423–490 0.957 63.2
trnH-GUG-psbA_p4 trnH-GUG-psbA CCACTTGGCTACATCCGC CCGTGCTAATCTTGGTATGGA 422–489 0.957 61.0
trnH-GUG-psbA_p5 trnH-GUG-psbA CCACTTGGCTACATCCGC CTTTCCTCTAGACCTAGCTGC 374–441 1.000 60.7
trnK-UUU_p1 trnK-UUU ATCGAAAACGGAAGGCTTGT ATGGCGGGTTTTTCGATACA 2920–2985 0.435 61.7
trnK-UUU_p2 trnK-UUU ATCGAAAACGGAAGGCTTGT TGGCGGGTTTTTCGATACAT 2919–2984 0.435 61.7
trnK-UUU_p3 trnK-UUU TCGAAAACGGAAGGCTTGTT TGGCGGGTTTTTCGATACAT 2918–2983 0.435 60.0
trnK-UUU_p4 trnK-UUU CCAAGCACACGCATTCTCTA ATGGCGGGTTTTTCGATACA 2943–2979 0.391 58.0
trnK-UUU_p5 trnK-UUU CCAAGCACACGCATTCTCTA TGGCGGGTTTTTCGATACAT 2942–2978 0.391 58.0
rps16_p1 rps16 GGTTGAGCTCCCCTTTCAAG AAATTCTAGAAGAACAAGGGA 974–1240 0.565 34.6
rps16_p2 rps16 GTTGAGCTCCCCTTTCAAGG AAATTCTAGAAGAACAAGGGA 973–1239 0.565 34.6
rps16_p3 rps16 ATATCCTGAACCGTTCCCGT AAATTCTAGAAGAACAAGGGA 995–1261 0.565 34.6
rps16_p4 rps16 AATATCCTGAACCGTTCCCG AAATTCTAGAAGAACAAGGGA 996–1262 0.565 34.6
rps16_p5 rps16 GTTGAGCTCCCCTTTCAAGG AAATTCTAGAAGAACAAGGGAT 973–1239 0.565 34.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCAAAGGGCGTTTCCTTGT TGAGTTGAGGGGTTCGTACT 1573–1995 0.652 77.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCAAAGGGCGTTTCCTTGT AGCAGCTTGCCAAACAAAAG 1447–1870 0.652 77.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCAAAGGGCGTTTCCTTGT CTTACAGCAGCTTGCCAAAC 1452–1875 0.652 76.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AATTTGCTCGACTGGGATCC TGAGTTGAGGGGTTCGTACT 1478–1794 0.609 74.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCAGCTGTAACCAGTCGTAC TGAGTTGAGGGGTTCGTACT 1915–2181 0.522 69.8
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT ACGAAGAGTTTGAGAGTAAGCA 432–515 1.000 70.9
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAGAGTTTGAGAGTAAGCA 427–510 1.000 70.9
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGAAGAGTTTGAGAGTAAGCA 424–507 1.000 68.8
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACGAAGAGTTTGAGAGTAAGCA 425–508 1.000 68.8
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACGAAGAGTTTGAGAGTAAGCA 426–509 1.000 68.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGTCGCTTTAGTCCA ACGAATCACACTTTTACCACT 557–701 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGTCGCTTTAGTCCAC ACGAATCACACTTTTACCACT 556–700 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGTCGCTTTAGTCCA AACGAATCACACTTTTACCACT 558–702 1.000 61.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGTCGCTTTAGTCCAC AACGAATCACACTTTTACCACT 557–701 1.000 61.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGTCGCTTTAGTC ACGAATCACACTTTTACCACT 559–703 1.000 60.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

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

Species Accession Length (bp) Link
Swertia bifolia MZ261897.1 153293 View on NCBI ↗
Swertia bimaculata PV365186.1 153495 View on NCBI ↗
Swertia cincta MZ261898.1 149089 View on NCBI ↗
Swertia dichotoma MW344297.1 153042 View on NCBI ↗
Swertia dilatata MW344298.1 150057 View on NCBI ↗
Swertia diluta NC_057681.1 153691 View on NCBI ↗
Swertia divaricata NC_073126.1 152073 View on NCBI ↗
Swertia erythrosticta NC_060388.1 153037 View on NCBI ↗
Swertia hispidicalyx NC_044474.1 149488 View on NCBI ↗
Swertia kouitchensis NC_064129.1 153484 View on NCBI ↗
Swertia leducii NC_045301.1 153015 View on NCBI ↗
Swertia macrosperma PV276231.1 153495 View on NCBI ↗
Swertia marginata NC_085251.1 152968 View on NCBI ↗
Swertia muliensis PZ182191.1 153511 View on NCBI ↗
Swertia multicaulis NC_050660.1 152190 View on NCBI ↗
Swertia nervosa NC_057596.1 153690 View on NCBI ↗
Swertia obtusa PP910654.1 153874 View on NCBI ↗
Swertia pubescens MZ261905.1 149036 View on NCBI ↗
Swertia punicea MZ261896.1 153448 View on NCBI ↗
Swertia souliei NC_052874.1 152804 View on NCBI ↗
Swertia speciosa OP837522.1 151600 View on NCBI ↗
Swertia verticillifolia MF795137.1 151682 View on NCBI ↗
Swertia wolfgangiana MW344307.1 153225 View on NCBI ↗