Markers + reference

Humulus

2 species · Cannabaceae · Rosales

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Species 2
Genome length 154–154 kb
Candidate markers 268
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 289 0.0346 1.00 72.4 yes View details
trnK-UUU-rps16 LSC 903 0.0089 1.00 57.2 yes View details
rps16-trnQ-UUG LSC 396 0.0153 0.99 61.3 yes View details
atpF LSC 1304 0.0054 1.00 54.5 yes View details
rpoC2 LSC 4197 0.0024 1.00 55.1 yes View details
rpoB-trnC-GCA LSC 1221 0.0049 1.00 62.0 yes View details
trnC-GCA-petN LSC 934 0.0064 1.00 61.8 yes View details
psbC-trnS-UGA LSC 232 0.0302 1.00 56.3 yes View details
ycf4-cemA LSC 703 0.0100 1.00 64.5 yes View details
psbE-petL LSC 1117 0.0072 1.00 63.0 yes View details
rpl32-trnL-UAG SSC 804 0.0118 0.95 62.6 yes View details
ycf1 SSC 5583 0.0034 1.00 54.6 yes View details
accD-psaI LSC 890 0.0046 0.98 63.0 yes View details
atpH-atpI LSC 722 0.0028 0.98 62.7 yes View details
petA-psbJ LSC 899 0.0034 0.99 61.3 yes View details
trnE-UUC-trnT-GGU LSC 640 0.0016 0.98 61.2 yes View details
rpl16 LSC 1449 0.0028 0.99 60.9 yes View details
trnS-GCU-trnG-UCC LSC 817 0.0049 1.00 60.8 yes View details
petN-psbM LSC 938 0.0021 0.99 60.5 yes View details
trnT-GGU-psbD LSC 1133 0.0027 1.00 60.4 yes View details
psbI-trnS-GCU LSC 147 0.0136 1.00 60.3 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 115 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 CCTCTAGACCTAGCTGCTGT 355 1.000 80.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 369 1.000 80.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 368 1.000 80.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 370 1.000 80.6
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 358 1.000 80.6
trnK-UUU_p1 trnK-UUU ACTGAAATGAGTTAACAAGTTCAGA TCTCTTTATTAGGATTCCGATTGT 2730–2745 1.000 40.7
trnK-UUU_p2 trnK-UUU ACTGAAATGAGTTAACAAGTTCAGA AGGATTCCGATTGTATCTATACA 2720–2735 1.000 40.7
trnK-UUU_p3 trnK-UUU ACTGAAATGAGTTAACAAGTTCAGA TCAATCTCTTTATTAGGATTCCGA 2734–2749 1.000 40.7
trnK-UUU_p4 trnK-UUU TGGTTGAATAACTGAAATGAGT TCTCTTTATTAGGATTCCGATTGT 2740–2755 1.000 40.7
trnK-UUU_p5 trnK-UUU ACTGAAATGAGTTAACAAGTTCAG TCTCTTTATTAGGATTCCGATTGT 2730–2745 1.000 40.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TTCCTTGAAAAAGGCGCTCA 1053–1067 1.000 73.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TCAAAGAAGGCTGGGGTTTT 1008–1022 1.000 72.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TTCAAAGAAGGCTGGGGTTT 1009–1023 1.000 72.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TTTCAAAGAAGGCTGGGGTT 1010–1024 1.000 72.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA TTCCTTGAAAAAGGCGCTCA 1051–1065 1.000 72.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 466–469 1.000 79.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 481–484 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 480–483 1.000 77.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 470–473 1.000 75.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 496–499 1.000 74.9
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TGGACTAAAGCGTCGGATTG 260 1.000 80.0
psbI-trnS-GCU_p2 psbI-trnS-GCU TATCTAATGATCCGGGGCGT TGGACTAAAGCGTCGGATTG 261 1.000 80.0
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA GTGGACTAAAGCGTCGGATT 261 1.000 80.0
psbI-trnS-GCU_p4 psbI-trnS-GCU TATCTAATGATCCGGGGCGT GTGGACTAAAGCGTCGGATT 262 1.000 80.0
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TTTTTCGTACCGAGGGTTCG 223 1.000 78.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATTCATCAAACCGAGGGACC 932–935 1.000 77.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATTCATCAAACCGAGGGACC 931–934 1.000 77.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATTCATCAAACCGAGGGACC 986–989 1.000 75.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGAAAACGGAAAGAGAGGG ATTCATCAAACCGAGGGACC 992–995 1.000 75.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC ATTCATCAAACCGAGGGACC 934–937 1.000 74.3

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
Humulus scandens NC_039730.1 153776 View on NCBI ↗
Humulus yunnanensis MK423880.1 153612 View on NCBI ↗