Markers + reference

Centrosema

2 species · Fabaceae · Fabales

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Species 2
Genome length 154–155 kb
Candidate markers 260
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 8 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbZ-trnS-UGA LSC 408 0.0104 0.95 58.9 yes View details
trnS-UGA-psbC LSC 226 0.0442 1.00 70.4 yes View details
rpoC2 LSC 4164 0.0065 1.00 46.5 yes View details
psbK-trnQ-UUG LSC 526 0.0217 0.96 63.5 yes View details
trnQ-UUG-accD LSC 465 0.0272 0.87 67.0 yes View details
psaI-cemA LSC 1258 0.0245 0.97 69.2 yes View details
psbE-petL LSC 1039 0.0160 0.90 71.3 yes View details
trnP-UGG-psaJ LSC 445 0.0253 0.89 61.4 yes View details
rpl16 LSC 1834 0.0193 0.96 59.4 yes View details
ndhF-rpl32 SSC 774 0.0199 0.91 59.5 yes View details
rpl32-trnL-UAG SSC 548 0.0307 0.95 72.4 yes View details
rpl20-rps12 LSC 839 0.0085 0.98 65.3 yes View details
trnT-GGU-trnE-UUC LSC 817 0.0110 1.00 65.1 yes View details
petN-trnC-GCA LSC 889 0.0105 0.96 64.9 yes View details
ndhD-psaC SSC 133 0.0301 1.00 64.5 yes View details
accD-psaI LSC 566 0.0195 1.00 64.0 yes View details
trnR-ACG-trnN-GUU IRb 309 0.0194 1.00 63.9 yes View details
trnN-GUU-trnR-ACG IRa 309 0.0194 1.00 63.9 yes View details
trnL-UAA-trnT-UGU LSC 1014 0.0149 0.99 62.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGTCTTCTATGGATCGTTATGA GCGATTGGATATCCATACCCA 2862–2884 1.000 41.7
trnK-UUU_p2 trnK-UUU TGTCTTCTATGGATCGTTATGA TGCGATTGGATATCCATACCC 2863–2885 1.000 41.7
trnK-UUU_p3 trnK-UUU TTGTCTTCTATGGATCGTTATGA GCGATTGGATATCCATACCCA 2863–2885 1.000 41.7
trnK-UUU_p4 trnK-UUU TTGTCTTCTATGGATCGTTATGA TGCGATTGGATATCCATACCC 2864–2886 1.000 41.7
trnK-UUU_p5 trnK-UUU TGTCTTCTATGGATCGTTATGAT GCGATTGGATATCCATACCCA 2862–2884 1.000 41.7
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 1064–1066 1.000 80.5
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC AAAGCCAGCTATCGGAATCG 1109–1111 1.000 80.4
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC AAAGCCAGCTATCGGAATCG 1117–1119 1.000 79.9
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1072–1074 1.000 79.9
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC TCGAGAAAAGCCAGCTATCG 1115–1117 1.000 79.8
psbZ-trnS-UGA_p1 psbZ-trnS-UGA CGACCAACCATCAGGAGAAG CAACCACTCAGCCATCTCTC 511–531 1.000 83.7
psbZ-trnS-UGA_p2 psbZ-trnS-UGA CGACCAACCATCAGGAGAAG GTTTTCAAGACCGGGGCTAT 531–551 1.000 82.7
psbZ-trnS-UGA_p3 psbZ-trnS-UGA CCAACCATCAGGAGAAGCAA CAACCACTCAGCCATCTCTC 508–528 1.000 82.2
psbZ-trnS-UGA_p4 psbZ-trnS-UGA TACTCGACCAACCATCAGGA CAACCACTCAGCCATCTCTC 515–535 1.000 82.0
psbZ-trnS-UGA_p5 psbZ-trnS-UGA GACCAACCATCAGGAGAAGC CAACCACTCAGCCATCTCTC 510–530 1.000 81.8
trnS-UGA-psbC_p1 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG TAGGTCATTTATGGCACGCG 425–429 1.000 78.3
trnS-UGA-psbC_p2 trnS-UGA-psbC ATAGCCCCGGTCTTGAAAAC TAGGTCATTTATGGCACGCG 405–409 1.000 77.6
trnS-UGA-psbC_p3 trnS-UGA-psbC GCTTTTGGAGAGATGGCTGA TAGGTCATTTATGGCACGCG 432–436 1.000 77.5
trnS-UGA-psbC_p4 trnS-UGA-psbC GGGTTCGAATCCCTCTCTCT TAGGTCATTTATGGCACGCG 356–360 1.000 77.1
trnS-UGA-psbC_p5 trnS-UGA-psbC ATGGCTGAGTGGTTGATAGC TAGGTCATTTATGGCACGCG 420–424 1.000 75.8
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TTTCGTAGTACCCTACCCCC 958–973 1.000 79.4
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC TTTCGTAGTACCCTACCCCC 937–952 1.000 79.0
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC TGGCGTTACTCTACCACTGA TTTCGTAGTACCCTACCCCC 934–949 1.000 78.8
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT GCTGCCTCCTTGAAAGAGAG 920–935 1.000 78.6
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TGTCCTGAACCACTAGACGA 899–914 1.000 78.5
petN-trnC-GCA_p1 petN-trnC-GCA TTAAAGCAGCCCAAGCAAGA TGGTGGTGGGGTATTCTCAT 1029–1039 1.000 83.0
petN-trnC-GCA_p2 petN-trnC-GCA TTAAAGCAGCCCAAGCAAGA TTTCCCCAGTTCAAATCCGG 942–952 1.000 82.8
petN-trnC-GCA_p3 petN-trnC-GCA CAGCCCAAGCAAGACTTACT TGGTGGTGGGGTATTCTCAT 1023–1033 1.000 81.5
petN-trnC-GCA_p4 petN-trnC-GCA CAGCCCAAGCAAGACTTACT TTTCCCCAGTTCAAATCCGG 936–946 1.000 81.3
petN-trnC-GCA_p5 petN-trnC-GCA TTAAAGCAGCCCAAGCAAGA GGGGGACTGCAAATCCTTTT 960–970 1.000 80.5

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
Centrosema coriaceum NC_067530.1 154519 View on NCBI ↗
Centrosema pubescens NC_057278.1 154141 View on NCBI ↗