Markers + reference

Herpetospermum

2 species · Cucurbitaceae · Cucurbitales

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Species 2
Genome length 156–156 kb
Candidate markers 267
Primer pairs 90

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 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 593 0.0517 0.98 74.8 yes View details
rps16-trnQ-UUG LSC 600 0.0918 1.00 88.2 yes View details
trnS-GCU-trnG-UCC LSC 1468 0.0316 0.99 68.7 yes View details
trnG-UCC-trnR-UCU LSC 252 0.1042 0.95 82.4 yes View details
trnR-UCU-atpA LSC 550 0.0523 0.97 74.8 yes View details
psbZ-trnG-GCC LSC 563 0.0538 0.96 78.1 yes View details
ndhC-trnV-UAC LSC 727 0.0472 0.99 77.4 yes View details
ycf1 IRb 1185 0.0142 0.89 55.2 no View details
ndhF-rpl32 SSC 613 0.0351 0.98 66.6 yes View details
rpl32-trnL-UAG SSC 1107 0.0669 0.96 79.6 yes View details
ycf1 SSC 5577 0.0281 0.98 58.3 yes View details
psaA-ycf3 LSC 727 0.0246 0.95 77.4 yes View details
trnH-GUG-psbA LSC 171 0.0435 0.94 73.5 yes View details
atpA-atpF LSC 65 0.0484 0.95 73.3 yes View details
trnC-GCA-petN LSC 897 0.0236 0.99 72.4 yes View details
trnT-UGU-trnL-UAA LSC 835 0.0263 1.00 71.3 yes View details
psbK-psbI LSC 399 0.0375 0.93 70.9 yes View details
atpB-rbcL LSC 772 0.0301 0.99 69.7 yes View details
ndhH-rps15 SSC 103 0.0680 1.00 69.7 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 GATCCACTTGGCTACATCCG AGCTGCTGTTGATGTTCCAT 220–227 1.000 83.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTGCTGTTGATGTTCCAT 234–241 1.000 83.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCTGTTGATGTTCCAT 233–240 1.000 83.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCTGTTGATGTTCCAT 235–242 1.000 82.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCTGCTGTTGATGTTCCATC 219–226 1.000 80.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 ACACATTTCCCTCTACCCCA CCCAATGAGCCGTTTATCGA 1282–1332 1.000 82.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACACATTTCCCTCTACCCCA TCCCAATGAGCCGTTTATCG 1283–1333 1.000 82.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACACATTTCCCTCTACCCCA ACAAGGCAGGGGTTTTTAGG 1102 0.500 59.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC ACAAGGCAGGGGTTTTTAGG 751 0.500 59.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT ACAAGGCAGGGGTTTTTAGG 750 0.500 59.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 673–893 1.000 84.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 684–904 1.000 83.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GACGACCAACCACTACCAAT 769–989 1.000 80.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GACGACCAACCACTACCAAT 780–1000 1.000 79.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 677–897 1.000 79.2
psbK-psbI_p1 psbK-psbI GCTGCCGTAAGCTTTCGATA TTACGTCCCGGGTCATTAGA 491–512 1.000 81.6
psbK-psbI_p2 psbK-psbI GCTGCCGTAAGCTTTCGATA ACGTCCCGGGTCATTAGATA 489–510 1.000 79.8
psbK-psbI_p3 psbK-psbI GCTGCCGTAAGCTTTCGATA TACGTCCCGGGTCATTAGAT 490–511 1.000 79.8
psbK-psbI_p4 psbK-psbI GCTGCCGTAAGCTTTCGATA TTCTTCACGTCCCGGATTAC 507–528 1.000 77.4
psbK-psbI_p5 psbK-psbI GCTGCCGTAAGCTTTCGATA CGTCCCGGGTCATTAGATAG 488–509 1.000 74.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CATCGTTAGCTTGGAAGGCT 1550–1581 1.000 82.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CATCGTTAGCTTGGAAGGCT 1549–1580 1.000 82.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CGTTAGCTTGGAAGGCTAGG 1547–1578 1.000 82.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CGTTAGCTTGGAAGGCTAGG 1546–1577 1.000 82.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA CATCGTTAGCTTGGAAGGCT 1604–1635 1.000 81.5
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 320–332 1.000 72.4
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 323–335 1.000 72.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 326–338 1.000 71.6
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 329–341 1.000 71.3
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 394–406 1.000 68.9

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
Herpetospermum darjeelingense PQ851716.1 156225 View on NCBI ↗
Herpetospermum pedunculosum NC_046858.1 156449 View on NCBI ↗