Markers + reference

Maerua

2 species · Capparaceae · Brassicales

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Species 2
Genome length 155–156 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

14 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
trnH-GUG-psbA LSC 409 0.0645 0.91 74.2 yes View details
trnR-UCU-atpA LSC 268 0.1051 0.96 78.0 yes View details
trnC-GCA-petN LSC 706 0.0370 0.96 76.0 yes View details
psbM-trnD-GUC LSC 1020 0.0278 0.49 62.0 yes View details
rps8 LSC 405 0.0198 1.00 54.0 yes View details
rpl22 LSC 483 0.0352 1.00 63.4 yes View details
ycf1 IRb 1032 0.0039 1.00 47.1 no View details
ndhF-rpl32 SSC 920 0.0272 0.96 66.9 yes View details
rpl32-trnL-UAG SSC 1116 0.0529 0.98 80.8 yes View details
ccsA SSC 981 0.0173 1.00 55.9 yes View details
ccsA-ndhD SSC 330 0.0925 0.85 77.5 yes View details
ndhA SSC 2143 0.0235 0.99 64.9 yes View details
rps15-ycf1 SSC 393 0.0256 0.99 56.1 yes View details
ycf1 SSC 5424 0.0223 1.00 52.8 yes View details
trnL-UAG-ccsA SSC 121 0.0526 0.94 76.3 yes View details
infA-rps8 LSC 127 0.0750 0.94 74.8 yes View details
trnG-UCC-trnfM-CAU LSC 139 0.0511 0.99 74.0 yes View details
rps4-trnT-UGU LSC 385 0.0247 0.95 69.3 yes View details
trnE-UUC-trnT-GGU LSC 756 0.0294 0.99 68.9 yes View details
trnM-CAU-psbD LSC 1385 0.0256 0.96 67.7 yes View details
trnS-UGA-psbZ LSC 344 0.0267 0.98 66.9 yes View details
petN-psbM LSC 634 0.0221 1.00 66.0 yes View details
trnL-UAA-trnF-GAA LSC 359 0.0288 0.97 65.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGTGTAGCTGGTGTATTCGG 866–893 1.000 84.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GGTGTAGCTGGTGTATTCGG 880–907 1.000 84.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GGTGTAGCTGGTGTATTCGG 879–906 1.000 84.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GGTGTAGCTGGTGTATTCGG 881–908 1.000 84.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCAGCTGT 476 0.500 58.4
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CCTCTACCAAGGCATTCACC 673–686 1.000 84.4
trnR-UCU-atpA_p2 trnR-UCU-atpA TTCTGTGAAAGCACCCAGAC CCTCTACCAAGGCATTCACC 879–892 1.000 83.3
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CCCTGGTCGTGAAGCTTATC 1260–1273 1.000 82.1
trnR-UCU-atpA_p4 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CCTGGTCGTGAAGCTTATCC 1259–1272 1.000 82.1
trnR-UCU-atpA_p5 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GGTCGTGAAGCTTATCCAGG 1256–1269 1.000 82.1
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCATGCGAGACTTACTA 736–762 1.000 83.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 797–823 1.000 82.1
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTTCCCCATACTACGAGGG 787–813 1.000 81.9
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCATGCGAGACTTACTA 754–780 1.000 81.2
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 815–841 1.000 79.8
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCATGGGCT GCACTCTTCATTCTCGTTCCT 789–795 1.000 71.4
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCATGGGCT ACTGCACTCTTCATTCTCGT 792–798 1.000 70.7
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT GCACTCTTCATTCTCGTTCCT 728–734 1.000 70.5
petN-psbM_p4 petN-psbM CCCTCGTAGTATGGGGAAGA GCACTCTTCATTCTCGTTCCT 738–744 1.000 70.2
petN-psbM_p5 petN-psbM TCCCTCGTAGTATGGGGAAG GCACTCTTCATTCTCGTTCCT 739–745 1.000 70.2
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 624–1138 1.000 73.2
psbM-trnD-GUC_p2 psbM-trnD-GUC ACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 620–1134 1.000 72.5
psbM-trnD-GUC_p3 psbM-trnD-GUC GGAACGAGAATGAAGAGTGCA TTCAATTGGTCAGAGCACCG 623–1137 1.000 71.0
psbM-trnD-GUC_p4 psbM-trnD-GUC AACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 621–1135 1.000 70.3
psbM-trnD-GUC_p5 psbM-trnD-GUC GGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 623–1137 1.000 69.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 897–902 1.000 81.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 859–864 1.000 80.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 838–843 1.000 80.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 894–899 1.000 80.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCGATGACTTACGCCTTACC 856–861 1.000 79.4

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
Maerua crassifolia NC_058239.1 155685 View on NCBI ↗
Maerua oblongifolia NC_058240.1 155436 View on NCBI ↗