Markers + reference

Maytenus

3 species · Celastraceae · Celastrales

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Species 3
Genome length 157–159 kb
Candidate markers 276
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0006 1.00 45.5 yes View details
trnK-UUU-rps16 LSC 577 0.0058 1.00 51.9 yes View details
psbK-psbI LSC 463 0.0058 1.00 37.2 yes View details
rpoB-trnC-GCA LSC 973 0.0041 1.00 61.4 yes View details
psbZ-trnG-GCC LSC 691 0.0048 1.00 63.0 yes View details
psbE-petL LSC 1134 0.0041 1.00 61.5 yes View details
rpl20-rps12 LSC 765 0.0026 1.00 47.9 yes View details
petD LSC 1264 0.0032 1.00 60.9 yes View details
rpl22 LSC 561 0.0065 1.00 53.3 yes View details
trnR-ACG-trnN-GUU IRb 603 0.0077 1.00 63.7 yes View details
trnN-GUU-ndhF IRb 2130 0.0044 1.00 52.1 yes View details
ycf1 SSC 5766 0.0030 1.00 43.7 yes View details
trnN-GUU-trnR-ACG IRa 603 0.0077 1.00 63.7 yes View details
trnT-UGU-trnL-UAA LSC 1095 0.0018 1.00 62.1 yes View details
trnH-GUG-psbA LSC 559 0.0070 0.93 61.3 no View details
trnC-GCA-petN LSC 878 0.0023 1.00 60.3 yes View details
rpl16-rps3 LSC 166 0.0120 1.00 60.2 yes View details
ndhF SSC 1491 0.0022 1.00 60.2 yes View details
atpB-rbcL LSC 752 0.0018 1.00 59.9 yes View details
rbcL LSC 1428 0.0019 1.00 59.9 yes View details
psaI-ycf4 LSC 484 0.0055 1.00 59.8 yes View details
psbC LSC 1422 0.0014 1.00 59.6 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA GGGTTGCTATTGCTCCTTCA TGCTTGGGAGTCCCTGATAA 1167 1.000 78.8
psbA_p2 psbA GGGTTGCTATTGCTCCTTCA TAGAGAATGCGTGTGCTTGG 1180 1.000 76.8
psbA_p3 psbA AGGGTTGCTATTGCTCCTTC TGCTTGGGAGTCCCTGATAA 1168 1.000 76.4
psbA_p4 psbA TCTCAAAAACCCGAACTCGT TGCTTGGGAGTCCCTGATAA 1146 1.000 74.9
psbA_p5 psbA AGGGTTGCTATTGCTCCTTC TAGAGAATGCGTGTGCTTGG 1181 1.000 74.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGCGATCTTCCCAACTCTAC ACACAAAAAGGGGGTTGGAT 713–729 1.000 75.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ACACAAAAAGGGGGTTGGAT 633–649 1.000 75.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ACACAAAAAGGGGGTTGGAT 632–648 1.000 75.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCGCGATCTTCCCAACTCTA ACACAAAAAGGGGGTTGGAT 714–730 1.000 74.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTACAGATAGCGTGGACGA ACACAAAAAGGGGGTTGGAT 698–714 1.000 74.1
psbK-psbI_p1 psbK-psbI CAAGCTGCTGTCAGTTTTCG CCGAAGATGAAGAGCGAAAC 552 1.000 71.9
psbK-psbI_p2 psbK-psbI AAGCTGCTGTCAGTTTTCGA CCGAAGATGAAGAGCGAAAC 551 1.000 71.8
psbK-psbI_p3 psbK-psbI AGCTGCTGTCAGTTTTCGAT CCGAAGATGAAGAGCGAAAC 550 1.000 70.7
psbK-psbI_p4 psbK-psbI GCAAGCTGCTGTCAGTTTTC CCGAAGATGAAGAGCGAAAC 553 1.000 70.2
psbK-psbI_p5 psbK-psbI CAGTCATCCCTGTGCTCTTT CCGAAGATGAAGAGCGAAAC 593 1.000 68.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTTCCCTCATTTCCATCCCC GCTTTTGTTGATCAGGCGAC 1083 1.000 79.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1061 1.000 79.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTTCCCTCATTTCCATCCCC AGCTTTTGTTGATCAGGCGA 1084 1.000 79.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGTTCCCTCATTTCCATCCC GCTTTTGTTGATCAGGCGAC 1084 1.000 77.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGTTCCCTCATTTCCATCCC CCGGATTTGAACTGGGGAAA 1062 1.000 77.2
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 933–952 1.000 78.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 994–1013 1.000 76.9
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 951–970 1.000 76.3
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 1012–1031 1.000 74.7
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 932–951 1.000 72.5
psbC_p1 psbC TTCTCAGGAAATCCGTGCAG AGCCATGGTGGAAGTAAATGA 1583 1.000 65.5
psbC_p2 psbC TTCTCAGGAAATCCGTGCAG TCAAGTAGTGGATCTCTTGCC 1553 1.000 64.2
psbC_p3 psbC AGGTATTCGTGCTTGGATGG AGCCATGGTGGAAGTAAATGA 1511 1.000 63.6
psbC_p4 psbC TTCTCAGGAAATCCGTGCAG AGCCATGGTGGAAGTAAATGAA 1583 1.000 63.0
psbC_p5 psbC TTCTCAGGAAATCCGTGCAG TGACCCAATCTACCCAACTAGA 1618 1.000 62.8

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
Maytenus confertiflora NC_065706.1 158787 View on NCBI ↗
Maytenus guangxiensis NC_047301.1 157102 View on NCBI ↗
Maytenus hookeri NC_065707.1 158807 View on NCBI ↗