Markers + reference

Halenia

2 species · Gentianaceae · Gentianales

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Species 2
Genome length 153–153 kb
Candidate markers 275
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 342 0.0830 0.67 71.8 yes View details
rps16-trnQ-UUG LSC 1328 0.0205 0.99 62.5 yes View details
atpH-atpI LSC 963 0.0198 0.99 69.8 yes View details
petN-psbM LSC 1091 0.0129 1.00 60.6 yes View details
accD LSC 1902 0.0101 0.94 68.1 yes View details
ndhF-rpl32 SSC 754 0.0193 0.96 61.3 yes View details
ndhA SSC 2254 0.0145 0.98 55.6 yes View details
rps15-ycf1 SSC 4952 0.0186 1.00 48.9 yes View details
rps19-trnH-GUG IRa 1 0.0000 0.99 71.0 no View details
ndhD-psaC SSC 89 0.0562 1.00 70.6 yes View details
psbT-psbN LSC 60 0.0333 1.00 70.0 yes View details
rpl22-rps19 LSC 63 0.0172 0.92 66.3 yes View details
trnG-GCC-trnfM-CAU LSC 237 0.0306 0.97 65.0 yes View details
trnT-GGU-psbD LSC 1265 0.0095 1.00 64.6 yes View details
psaI-ycf4 LSC 448 0.0156 1.00 64.6 yes View details
ycf3-trnS-GGA LSC 506 0.0179 0.99 64.1 yes View details
ndhH-rps15 SSC 130 0.0234 0.98 63.4 yes View details
trnG-UCC-trnR-UCU LSC 181 0.0331 1.00 63.3 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 CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 315–416 1.000 86.6
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 316–417 1.000 86.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 308–409 1.000 85.1
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TCCTCTAGACCTAGCTGCTG 316–417 1.000 84.2
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TCCTCTAGACCTAGCTGCTG 317–418 1.000 84.0
trnK-UUU_p1 trnK-UUU ATCGAAAACGGAAGGCTTGT AGAGCGTTCGCCTAGAAAAG 2872–2879 1.000 80.3
trnK-UUU_p2 trnK-UUU ATCGAAAACGGAAGGCTTGT GAGCGTTCGCCTAGAAAAGA 2871–2878 1.000 80.3
trnK-UUU_p3 trnK-UUU ATCGAAAACGGAAGGCTTGT TGGCGGGTTTTTCGATACAT 2937–2944 1.000 79.4
trnK-UUU_p4 trnK-UUU ATCGAAAACGGAAGGCTTGT GAGAGCGTTCGCCTAGAAAA 2880 0.500 59.1
trnK-UUU_p5 trnK-UUU ATCGAAAACGGAAGGCTTGT TAAGAGAGCGTTCGCCTAGA 2883 0.500 58.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GGTTGAGCTCCCCTTTCAAG GAGGTTCGAATCCTTCCGTC 1406–1621 1.000 78.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTTGAGCTCCCCTTTCAAGG GAGGTTCGAATCCTTCCGTC 1405–1620 1.000 78.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATATCCTGAACCGTTCCCGT GAGGTTCGAATCCTTCCGTC 1427–1642 1.000 77.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AATATCCTGAACCGTTCCCG GAGGTTCGAATCCTTCCGTC 1428–1643 1.000 76.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACAGGTGCAACGATTAACGA GAGGTTCGAATCCTTCCGTC 1373 0.500 58.1
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG GGAAAGAATTTGCGTCCAAT 307–317 1.000 56.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG GGAAAGAATTTGCGTCCAAT 310–320 1.000 55.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAATTTGCGTCCAATAGGA 303–313 1.000 55.2
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU GACGCTCAAAACGCTGAATC GGAAAGAATTTGCGTCCAAT 346–356 1.000 55.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAATTTGCGTCCAATAGGA 306–316 1.000 55.0
atpH-atpI_p1 atpH-atpI AAGCAAGTCCTACAGCCAAC AGGTGAATCTATGGAGGGCC 1049–1052 1.000 76.5
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC AGGTGAATCTATGGAGGGCC 1103–1106 1.000 76.2
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG AGGTGAATCTATGGAGGGCC 1107–1110 1.000 76.1
atpH-atpI_p4 atpH-atpI CAGCAGCAATAACAGAAGCG AGGTGAATCTATGGAGGGCC 1028–1031 1.000 76.0
atpH-atpI_p5 atpH-atpI GAAGCAAGTCCTACAGCCAA AGGTGAATCTATGGAGGGCC 1050–1053 1.000 75.9
petN-psbM_p1 petN-psbM AGTAAGTCTTGCTTGGGCTG TCATTCTAGTTCCTACCGCCT 1238–1248 1.000 71.3
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGGTTTAA TCATTCTAGTTCCTACCGCCT 1232–1242 1.000 69.8
petN-psbM_p3 petN-psbM GGGGGCATAATTCACATGGA TCATTCTAGTTCCTACCGCCT 1261–1271 1.000 69.7
petN-psbM_p4 petN-psbM GTCTTGCTTGGGCTGGTTTA TCATTCTAGTTCCTACCGCCT 1233–1243 1.000 69.7
petN-psbM_p5 petN-psbM AGGGGGCATAATTCACATGG TCATTCTAGTTCCTACCGCCT 1262–1272 1.000 69.7

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
Halenia coreana NC_042674.1 153198 View on NCBI ↗
Halenia elliptica NC_050657.1 153305 View on NCBI ↗