Markers + reference

Maranthes

3 species · Chrysobalanaceae · Malpighiales

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Species 3
Genome length 162–163 kb
Candidate markers 266
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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpF LSC 1359 0.0052 1.00 51.6 yes View details
trnC-GCA-petN LSC 1004 0.0046 1.00 58.8 yes View details
trnG-UCC-trnfM-CAU LSC 196 0.0374 1.00 79.6 yes View details
ndhC-trnV-UAC LSC 1146 0.0058 1.00 62.7 yes View details
psaJ-rpl33 LSC 560 0.0145 0.98 72.0 yes View details
psbB LSC 1527 0.0013 1.00 36.8 yes View details
ycf1 IRb 1105 0.0006 1.00 36.3 no View details
ndhF-rpl32 SSC 1089 0.0056 0.98 52.1 yes View details
rpl32-trnL-UAG SSC 1304 0.0072 1.00 58.4 yes View details
psaC SSC 246 0.0027 1.00 29.1 yes View details
ycf1 SSC 5517 0.0035 1.00 40.4 yes View details
trnT-GGU-psbD LSC 1585 0.0025 1.00 64.9 yes View details
atpI-rps2 LSC 341 0.0098 1.00 64.5 yes View details
rps2-rpoC2 LSC 268 0.0106 0.94 63.3 yes View details
trnG-GCC-trnR-UCU LSC 723 0.0028 0.97 63.1 yes View details
trnE-UUC-trnT-GGU LSC 660 0.0035 1.00 63.0 yes View details
rbcL-accD LSC 799 0.0042 1.00 61.9 yes View details
psbT-psbN LSC 79 0.0338 1.00 61.5 yes View details
petN-psbM LSC 1116 0.0012 0.98 61.2 yes View details
trnQ-UUG-psbK LSC 417 0.0033 0.96 60.6 yes View details
petA-psbJ LSC 797 0.0017 1.00 60.1 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
trnQ-UUG-psbK_p1 trnQ-UUG-psbK ATAGGTATACGCTGGGACGG TAGGCTTCGGGCAATTTTGT 573–589 1.000 78.2
trnQ-UUG-psbK_p2 trnQ-UUG-psbK ATAGGTATACGCTGGGACGG GCTTCGGGCAATTTTGTGAA 570–586 1.000 77.7
trnQ-UUG-psbK_p3 trnQ-UUG-psbK ATAGGTATACGCTGGGACGG GTAGGCTTCGGGCAATTTTG 574–590 1.000 76.6
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA TAGGCTTCGGGCAATTTTGT 528–544 1.000 76.6
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GCTTCGGGCAATTTTGTGAA 525–541 1.000 76.1
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 757–807 1.000 67.7
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 760–810 1.000 67.4
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 763–813 1.000 67.0
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 766–816 1.000 66.8
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 761–811 1.000 65.2
atpF_p1 atpF TGCCTACAATTACACTAGAAGGA ATCTATAAAATAAGAGGAGATCCA 1387–1407 1.000 41.8
atpF_p2 atpF TGCCTACAATTACACTAGAAGGA TCTATAAAATAAGAGGAGATCCAT 1386–1406 1.000 41.8
atpF_p3 atpF TGCCTACAATTACACTAGAAGGA ATCTATAAAATAAGAGGAGATCCAT 1387–1407 1.000 41.8
atpF_p4 atpF TGCCTACAATTACACTAGAAGG ATCTATAAAATAAGAGGAGATCCA 1387–1407 1.000 41.8
atpF_p5 atpF TGCCTACAATTACACTAGAAGG TCTATAAAATAAGAGGAGATCCAT 1386–1406 1.000 41.8
atpI-rps2_p1 atpI-rps2 TGAGCATGGACTTGAAACCC ACGCTATTGCTTCAATCCGA 439–485 1.000 81.7
atpI-rps2_p2 atpI-rps2 TGAGCATGGACTTGAAACCC TGCAATTTGTGAGGGTCGTT 396–442 1.000 81.7
atpI-rps2_p3 atpI-rps2 TGAGCATGGACTTGAAACCC TTGCAATTTGTGAGGGTCGT 397–443 1.000 81.7
atpI-rps2_p4 atpI-rps2 TGAGCATGGACTTGAAACCC GCAATTTGTGAGGGTCGTTC 395–441 1.000 81.6
atpI-rps2_p5 atpI-rps2 GAAATGCTGGCCTACTTCCA ACGCTATTGCTTCAATCCGA 404–450 1.000 81.4
rps2-rpoC2_p1 rps2-rpoC2 GTGCCATTCTTGGATCCCAT CTTGTTCCACCACCGAGAAT 424–441 1.000 81.8
rps2-rpoC2_p2 rps2-rpoC2 AATGAACTCCTGCTTCCAGC CTTGTTCCACCACCGAGAAT 385–402 1.000 81.5
rps2-rpoC2_p3 rps2-rpoC2 AAGGTGCCATTCTTGGATCC CTTGTTCCACCACCGAGAAT 427–444 1.000 81.2
rps2-rpoC2_p4 rps2-rpoC2 GTGCCATTCTTGGATCCCAT CGAGGGGGAAAGGAGAGATA 445–462 1.000 80.0
rps2-rpoC2_p5 rps2-rpoC2 AAGGTGCCATTCTTGGATCC CGAGGGGGAAAGGAGAGATA 448–465 1.000 79.4
trnC-GCA-petN_p1 trnC-GCA-petN GGGTGTCGCCTGATTAACAA AGCCCAAGCGAGACTTACTA 1052 1.000 77.9
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1088 1.000 76.5
trnC-GCA-petN_p3 trnC-GCA-petN CTGCAAATCCTTTTTCCCCG AGCCCAAGCGAGACTTACTA 1082 1.000 76.4
trnC-GCA-petN_p4 trnC-GCA-petN GGGTGTCGCCTGATTAACAA AGAGTCCACTTCTTCCCCAT 1113 1.000 76.2
trnC-GCA-petN_p5 trnC-GCA-petN TCCTTTTTCCCCGGTTCAAA AGCCCAAGCGAGACTTACTA 1075 1.000 75.7

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
Maranthes gabunensis NC_030577.1 162659 View on NCBI ↗
Maranthes glabra NC_030578.1 162185 View on NCBI ↗
Maranthes kerstingii NC_030579.1 162391 View on NCBI ↗