Markers + reference

Cannabis

2 species · Cannabaceae · Rosales

Back to catalogue

Species 2
Genome length 154–154 kb
Candidate markers 287
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 287 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 321 0.0031 1.00 54.7 yes View details
rps16 LSC 1151 0.0026 1.00 60.2 yes View details
trnS-GCU-trnG LSC 844 0.0024 1.00 60.2 yes View details
rpoC1 LSC 2864 0.0003 1.00 56.1 yes View details
accD LSC 1494 0.0000 1.00 33.0 yes View details
accD-psaI LSC 808 0.0025 1.00 60.2 yes View details
rpl16-rps3 LSC 1141 0.0009 1.00 59.3 yes View details
rpl32-trnL-UAG SSC 804 0.0087 1.00 63.8 yes View details
trnR-ACG SSC 74 0.0135 1.00 60.3 yes View details
matK LSC 1530 0.0007 1.00 59.4 yes View details
psbE-petL LSC 1119 0.0009 1.00 59.3 yes View details
ndhD SSC 1503 0.0007 1.00 59.1 yes View details
matK-trnK-UUU LSC 762 0.0000 1.00 58.9 yes View details
rps16-trnQ-UUG LSC 782 0.0000 1.00 58.9 yes View details
ndhF-rpl32 SSC 373 0.0000 0.95 58.8 yes View details
ycf3 LSC 2014 0.0000 1.00 57.7 yes View details
psaB LSC 2205 0.0005 1.00 57.5 yes View details
trnR-ACG SSC 74 0.0000 1.00 33.8 no 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 GATCCACTTGGCTACATCCG CCCTCTAGACTTAGCTGCTCT 389 1.000 70.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCCTCTAGACTTAGCTGCTCT 403 1.000 70.7
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCCCTCTAGACTTAGCTGCTC 390 1.000 70.7
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCCTCTAGACTTAGCTGCTCT 402 1.000 70.7
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCCTCTAGACTTAGCTGCTCT 404 1.000 70.7
trnK-UUU_p1 trnK-UUU AATGAAATGAGTTAACAAGTTCA TTTGTTAGGATTCCGATTGT 2747–2753 1.000 40.2
trnK-UUU_p2 trnK-UUU AATGAAATGAGTTAACAAGTTCA TGTTAGGATTCCGATTGTATCT 2745–2751 1.000 40.2
trnK-UUU_p3 trnK-UUU AATGAAATGAGTTAACAAGTTCA TTTTGTTAGGATTCCGATTGT 2748–2754 1.000 40.2
trnK-UUU_p4 trnK-UUU AAATGAAATGAGTTAACAAGTTCA TTTGTTAGGATTCCGATTGT 2748–2754 1.000 40.2
trnK-UUU_p5 trnK-UUU AATGAAATGAGTTAACAAGTTCA TTTTTGTTAGGATTCCGATTGT 2749–2755 1.000 40.2
matK_p1 matK TTCCACGGTCGAATAACCAA ACCTTGTTTGGACTGTATCGT 1629–1635 1.000 59.5
matK_p2 matK TTTCCACGGTCGAATAACCA ACCTTGTTTGGACTGTATCGT 1630–1636 1.000 59.5
matK_p3 matK TTTCCACGGTCGAATAACCAA ACCTTGTTTGGACTGTATCGT 1630–1636 1.000 57.2
matK_p4 matK ATTTCCACGGTCGAATAACCA ACCTTGTTTGGACTGTATCGT 1631–1637 1.000 55.5
matK_p5 matK TTCCACGGTCGAATAACCAA CCTTGTTTGGACTGTATCGT 1628–1634 1.000 52.8
matK-trnK-UUU_p1 matK-trnK-UUU GGAGGTCATGTTGCCAAGAT TCGGGTTGCTAACTCAATGG 856 1.000 78.2
matK-trnK-UUU_p2 matK-trnK-UUU GGAGGTCATGTTGCCAAGAT CGGGTTGCTAACTCAATGGT 855 1.000 77.6
matK-trnK-UUU_p3 matK-trnK-UUU TAGGAGGTCATGTTGCCAAG TCGGGTTGCTAACTCAATGG 858 1.000 72.9
matK-trnK-UUU_p4 matK-trnK-UUU TAGGAGGTCATGTTGCCAAG CGGGTTGCTAACTCAATGGT 857 1.000 72.4
matK-trnK-UUU_p5 matK-trnK-UUU AGGAGGTCATGTTGCCAAGA TCGGGTTGCTAACTCAATGG 857 1.000 71.8
rps16_p1 rps16 AGCAGAGAAAAGATTATAATCCGA AGTACTAACCGAACCAATGA 1271–1272 1.000 40.2
rps16_p2 rps16 AGCAGAGAAAAGATTATAATCCGA AAGTACTAACCGAACCAATGA 1272–1273 1.000 40.2
rps16_p3 rps16 AGCAGAGAAAAGATTATAATCCGAAC AGTACTAACCGAACCAATGA 1271–1272 1.000 40.2
rps16_p4 rps16 GCAGAGAAAAGATTATAATCCGAACT AGTACTAACCGAACCAATGA 1270–1271 1.000 40.2
rps16_p5 rps16 GCAGAGAAAAGATTATAATCCGAACT AAGTACTAACCGAACCAATGA 1271–1272 1.000 40.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 854–855 1.000 78.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 869–870 1.000 76.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 868–869 1.000 76.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 858–859 1.000 73.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 884–885 1.000 73.5

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
Cannabis sativa NC_026562.1 153871 View on NCBI ↗
Cannabis sativa subsp. sativa KR184827.1 153848 View on NCBI ↗