Markers + reference

Coulteria

2 species · Fabaceae · Fabales

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Species 2
Genome length 161–161 kb
Candidate markers 268
Primer pairs 115

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1139 0.0009 1.00 59.3 yes View details
rps16-trnQ-UUG LSC 667 0.0030 1.00 60.5 yes View details
rpoC1 LSC 2836 0.0011 1.00 56.6 yes View details
rpoB-trnC-GCA LSC 1186 0.0009 0.98 60.5 yes View details
trnC-GCA-petN LSC 1178 0.0008 1.00 59.2 yes View details
psbM-trnD-GUC LSC 949 0.0011 0.99 59.9 yes View details
trnT-GGU-psbD LSC 1498 0.0013 1.00 59.5 yes View details
ycf3 LSC 2025 0.0010 1.00 58.2 yes View details
accD-psaI LSC 356 0.0056 1.00 56.9 yes View details
rps11-rpl36 LSC 378 0.0028 0.96 60.1 yes View details
rps8-rpl14 LSC 400 0.0025 1.00 51.8 yes View details
ccsA SSC 972 0.0021 1.00 59.9 yes View details
ndhG-ndhI SSC 425 0.0047 1.00 57.8 yes View details
ndhA SSC 2366 0.0013 0.99 58.4 yes View details
rps3-rps19 LSC 785 0.0000 0.98 61.0 yes View details
cemA LSC 690 0.0014 1.00 59.6 yes View details
rps3 LSC 657 0.0015 1.00 59.6 yes View details
trnK-UUU-rps16 LSC 1125 0.0000 1.00 59.2 yes View details
trnQ-UUG-psbK LSC 565 0.0018 1.00 59.2 yes View details
atpH-atpI LSC 1266 0.0008 1.00 59.2 yes View details
petN-psbM LSC 1222 0.0008 1.00 59.2 yes View details
petA-psbJ LSC 1184 0.0008 1.00 59.2 yes View details
psbE-petL LSC 1294 0.0008 1.00 59.2 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC CCTTGAAAAAGGCGCTCAAC 1317–1322 1.000 77.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC CTTGAAAAAGGCGCTCAACC 1316–1321 1.000 77.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAGGCCGGTGTTTTTATGGA 1268–1273 1.000 77.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGGCCGGTGTTTTTATGGAA 1267–1272 1.000 77.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TCCTTGAAAAAGGCGCTCAA 1318–1323 1.000 77.2
rps16_p1 rps16 GAATAGAGCAAGAGAGCGGG GGCCCCAAACTAGAGGAATG 1261–1266 1.000 78.7
rps16_p2 rps16 ACAAGTCATCCACACCCTCT GGCCCCAAACTAGAGGAATG 1202 1.000 77.5
rps16_p3 rps16 GAATAGAGCAAGAGAGCGGG TGGCCCCAAACTAGAGGAAT 1262–1267 1.000 76.6
rps16_p4 rps16 GAATAGAGCAAGAGAGCGGG TACTGGCCCCAAACTAGAGG 1265–1270 1.000 75.8
rps16_p5 rps16 ACAAGTCATCCACACCCTCT TGGCCCCAAACTAGAGGAAT 1203 1.000 75.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 747 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 749 1.000 78.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 735 1.000 78.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 750 1.000 77.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 748 1.000 76.8
trnQ-UUG-psbK_p1 trnQ-UUG-psbK TACTCTGGGACGGAAGGATT GCGTAGGCTTCCGGTAATTT 732–733 1.000 73.1
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GCGTAGGCTTCCGGTAATTT 694–695 1.000 72.1
trnQ-UUG-psbK_p3 trnQ-UUG-psbK ATACTCTGGGACGGAAGGAT GCGTAGGCTTCCGGTAATTT 733–734 1.000 71.3
trnQ-UUG-psbK_p4 trnQ-UUG-psbK ACTCTGGGACGGAAGGATTC GCGTAGGCTTCCGGTAATTT 731–732 1.000 71.1
trnQ-UUG-psbK_p5 trnQ-UUG-psbK TACTCTGGGACGGAAGGATT GCTTCCGGTAATTTTGCGAA 726–727 1.000 70.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1353 1.000 78.7
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1354 1.000 77.5
atpH-atpI_p3 atpH-atpI CCTTCTACAGCTTGACCTGC TTTTGCAACTTTAGCTGCGG 1434 1.000 76.8
atpH-atpI_p4 atpH-atpI TCCCTTCTACAGCTTGACCT TTTTGCAACTTTAGCTGCGG 1436 1.000 76.4
atpH-atpI_p5 atpH-atpI CCCTTCTACAGCTTGACCTG TTTTGCAACTTTAGCTGCGG 1435 1.000 75.8
rpoC1_p1 rpoC1 CCGAATTCACACCGGTATCA ACGATCTTTGGCTCTGGAAC 2991 1.000 76.9
rpoC1_p2 rpoC1 CCCGAATTCACACCGGTATC ACGATCTTTGGCTCTGGAAC 2992 1.000 75.9
rpoC1_p3 rpoC1 AGAAACCCGAATTCACACCG ACGATCTTTGGCTCTGGAAC 2997 1.000 75.4
rpoC1_p4 rpoC1 CCGAATTCACACCGGTATCA CGATCTTTGGCTCTGGAACT 2990 1.000 74.5
rpoC1_p5 rpoC1 CCCGAATTCACACCGGTATC CGATCTTTGGCTCTGGAACT 2991 1.000 73.6

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
Coulteria mollis MZ441394.1 160553 View on NCBI ↗
Coulteria platyloba NC_047340.1 160677 View on NCBI ↗