Markers + reference

Gentianopsis

3 species · Gentianaceae · Gentianales

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Species 3
Genome length 151–151 kb
Candidate markers 274
Primer pairs 100

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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 369 0.0054 1.00 46.6 yes View details
atpH-atpI LSC 1094 0.0043 1.00 61.6 yes View details
psbM-trnD-GUC LSC 855 0.0039 1.00 47.3 yes View details
ycf3 LSC 2033 0.0003 1.00 32.6 yes View details
ndhC-trnV-UAC LSC 1083 0.0138 0.93 66.4 yes View details
ycf4-cemA LSC 540 0.0049 1.00 39.8 yes View details
psaJ-rpl33 LSC 405 0.0049 1.00 44.0 yes View details
rpl16 LSC 1185 0.0058 0.96 52.5 yes View details
ycf1 IRb 981 0.0000 1.00 30.1 no View details
ndhF-rpl32 SSC 764 0.0052 1.00 59.2 yes View details
ycf1 SSC 5478 0.0043 1.00 55.4 yes View details
psbE-petL LSC 1210 0.0033 1.00 60.9 yes View details
accD-psaI LSC 604 0.0011 1.00 59.6 yes View details
trnH-GUG-psbA LSC 409 0.0058 0.84 59.2 yes View details
ycf4 LSC 555 0.0024 1.00 58.9 yes View details
ccsA SSC 975 0.0034 1.00 58.0 yes View details
trnT-UGU-trnL-UAA LSC 896 0.0045 0.98 57.0 yes View details
trnT-GGU-psbD LSC 1267 0.0021 1.00 56.8 yes View details
rpoC1 LSC 2789 0.0007 1.00 56.6 yes View details
trnE-UUC-trnT-GGU LSC 794 0.0038 0.99 55.9 yes View details
trnS-UGA-psbZ LSC 334 0.0040 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 100 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 TTCCTCTAGACCTAGCTGCT 436–485 1.000 74.4
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCCTCTAGACCTAGCTGCT 437–486 1.000 74.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAATCTTGGTATGG 487–536 1.000 73.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC ACCGTGCTAATCTTGGTATGG 488–537 1.000 73.6
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG TTCCTCTAGACCTAGCTGCT 429–478 1.000 72.8
psbK-psbI_p1 psbK-psbI TGGAAAATTGCCTGAAGCCT ACGAAGAGTTTGAGAGTAAGCA 510–573 1.000 59.6
psbK-psbI_p2 psbK-psbI CTTTTGTTTGGCAAGCTGCT ACGAAGAGTTTGAGAGTAAGCA 427–490 1.000 59.4
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAGAGTTTGAGAGTAAGCA 422–485 1.000 59.4
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGAAGAGTTTGAGAGTAAGCA 419–482 1.000 57.4
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACGAAGAGTTTGAGAGTAAGCA 420–483 1.000 57.4
atpH-atpI_p1 atpH-atpI AAGCAAGTCCTACAGCCAAC GCTGCGGCTTATATAGGTGA 1196–1197 1.000 73.8
atpH-atpI_p2 atpH-atpI AAGCAAGTCCTACAGCCAAC ATTTTTGCAACCCTAGCTGC 1211–1212 1.000 73.7
atpH-atpI_p3 atpH-atpI TACCCTCTACAGCTTGACCC GCTGCGGCTTATATAGGTGA 1250–1251 1.000 73.5
atpH-atpI_p4 atpH-atpI GCGATACCCTCTACAGCTTG GCTGCGGCTTATATAGGTGA 1254–1255 1.000 73.4
atpH-atpI_p5 atpH-atpI TACCCTCTACAGCTTGACCC ATTTTTGCAACCCTAGCTGC 1265–1266 1.000 73.4
rpoC1_p1 rpoC1 GAGAGGCCTGAATTTGCACT AGGAAGGAAGCTTAATCGCA 2875–2879 1.000 70.1
rpoC1_p2 rpoC1 GAGAGGCCTGAATTTGCACT GAGGAAGGAAGCTTAATCGCA 2876–2880 1.000 70.0
rpoC1_p3 rpoC1 TTTGCGGAAAACCTCCCTTT AGGAAGGAAGCTTAATCGCA 2946–2950 1.000 69.7
rpoC1_p4 rpoC1 TTTGCGGAAAACCTCCCTTT GAGGAAGGAAGCTTAATCGCA 2947–2951 1.000 69.6
rpoC1_p5 rpoC1 GAGAGGCCTGAATTTGCACT AGAGGAAGGAAGCTTAATCGC 2877–2881 1.000 69.3
psbM-trnD-GUC_p1 psbM-trnD-GUC AATGCCCGCAAAACTACTCA CACCTATTCAATTCCCGGGG 1559–1574 1.000 79.5
psbM-trnD-GUC_p2 psbM-trnD-GUC ATGCCCGCAAAACTACTCAA CACCTATTCAATTCCCGGGG 1558–1573 1.000 79.5
psbM-trnD-GUC_p3 psbM-trnD-GUC TGCCCGCAAAACTACTCAAT CACCTATTCAATTCCCGGGG 1557–1572 1.000 79.5
psbM-trnD-GUC_p4 psbM-trnD-GUC AAAAATCGGCGAGGCTTACT CACCTATTCAATTCCCGGGG 1606–1621 1.000 79.4
psbM-trnD-GUC_p5 psbM-trnD-GUC TGCCCGCAAAACTACTCAAT ACCTATTCAATTCCCGGGGA 1556–1571 1.000 78.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 870–897 1.000 80.6
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 849–876 1.000 80.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCGATGACTTACGCCTTACC 867–894 1.000 79.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG AAACCAAAGCCCCTTATCGG 894–921 1.000 79.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCGATGACTTACGCCTTACC 846–873 1.000 79.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Gentianopsis barbata OP837515.1 151179 View on NCBI ↗
Gentianopsis grandis NC_049879.1 151271 View on NCBI ↗
Gentianopsis paludosa NC_050656.1 151308 View on NCBI ↗