Markers + reference

Cenostigma

2 species · Fabaceae · Fabales

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Species 2
Genome length 159–160 kb
Candidate markers 268
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 360 0.0253 0.99 63.6 yes View details
trnK-UUU-rps16 LSC 1225 0.0091 0.99 65.4 yes View details
trnQ-UUG-psbK LSC 543 0.0173 0.96 62.7 yes View details
psbK-psbI LSC 404 0.0075 0.99 52.8 yes View details
trnR-UCU-atpA LSC 343 0.0488 0.96 70.5 yes View details
psbZ-trnG-GCC LSC 522 0.0140 0.96 69.0 yes View details
ndhC-trnV-UAC LSC 623 0.0202 0.96 60.0 yes View details
rpoA LSC 996 0.0020 1.00 45.4 yes View details
rps11-rpl36 LSC 345 0.0339 0.86 73.0 yes View details
rps3-rps19 LSC 649 0.0109 0.99 65.4 yes View details
rpl32-trnL-UAG SSC 391 0.0256 1.00 66.6 yes View details
ndhA SSC 2341 0.0056 0.99 58.6 yes View details
petD-rpoA LSC 205 0.0390 1.00 74.9 yes View details
rps16-trnQ-UUG LSC 640 0.0095 0.98 65.9 yes View details
ndhF-rpl32 SSC 911 0.0077 0.99 63.9 yes View details
trnT-UGU-trnL-UAA LSC 1479 0.0061 0.99 63.3 yes View details
rps7-rps12 IRb 53 0.0189 1.00 63.3 yes View details
rps12-rps7 IRa 53 0.0189 1.00 63.3 yes View details
psaJ-rpl33 LSC 494 0.0101 1.00 62.6 yes View details
petA-psbJ LSC 1207 0.0058 1.00 62.3 yes View details
ycf1 IRb 753 0.0040 0.99 62.2 yes View details
ycf1 SSC 5388 0.0030 1.00 54.2 no 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 105 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 TTCCCTCTAGACCTAGCTGC 428–430 1.000 80.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 442–444 1.000 80.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 441–443 1.000 80.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 443–445 1.000 80.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGAGCTAACCTTGGTATGG 477–479 1.000 79.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAAAAGGCGCTCAACCTACA 1413–1417 1.000 80.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC CCTTGAAAAAGGCGCTCAAC 1418–1422 1.000 79.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC CTTGAAAAAGGCGCTCAACC 1417–1421 1.000 79.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TGAAAAAGGCGCTCAACCTA 1415–1419 1.000 78.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGGCCGGTGTTTTTATGGAA 1368–1372 1.000 78.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 720–756 1.000 81.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 722–758 1.000 80.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 708–744 1.000 79.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 723–759 1.000 79.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 721–757 1.000 78.4
trnQ-UUG-psbK_p1 trnQ-UUG-psbK TACTCTGGGACGGAAGGATT ACTTGAATAAAGGGCGGAGT 676–683 1.000 70.1
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA ACTTGAATAAAGGGCGGAGT 638–645 1.000 69.3
trnQ-UUG-psbK_p3 trnQ-UUG-psbK ATACTCTGGGACGGAAGGAT ACTTGAATAAAGGGCGGAGT 677–684 1.000 68.3
trnQ-UUG-psbK_p4 trnQ-UUG-psbK ACTCTGGGACGGAAGGATTC ACTTGAATAAAGGGCGGAGT 675–682 1.000 68.1
trnQ-UUG-psbK_p5 trnQ-UUG-psbK TACTCTGGGACGGAAGGATT ACTTGAATAAAGGGCGGAGTT 676–683 1.000 68.0
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT TTCTTCACGTCCCGGATTAC 543–547 1.000 75.3
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGTCCCGGATTAC 538–542 1.000 75.3
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT GGATTACGTCCTGGATCGTT 530–534 1.000 73.5
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGTCCTGGATCGTT 525–529 1.000 73.5
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTCTTCACGTCCCGGATTAC 535–539 1.000 73.3
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GCGAGTTGCTCAAACAATCC 1112–1190 1.000 81.9
trnR-UCU-atpA_p2 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG GCGAGTTGCTCAAACAATCC 1115–1193 1.000 81.7
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CGAAGCTTATCCGGGAGATG 1513–1591 1.000 81.1
trnR-UCU-atpA_p4 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG ATCCCTCCAAACAAGCACAG 1577–1655 1.000 80.9
trnR-UCU-atpA_p5 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GATCCCTCCAAACAAGCACA 1578–1656 1.000 80.9

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
Cenostigma microphyllum MZ441392.1 159456 View on NCBI ↗
Cenostigma pyramidale NC_047360.1 159795 View on NCBI ↗