Markers + reference

Campylotropis

20 species · Fabaceae · Fabales

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Species 20
Genome length 149–153 kb
Candidate markers 268
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 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
ndhK LSC 642 0.0050 1.00 44.8 yes View details
trnF-GAA-trnL-UAA LSC 403 0.0119 1.00 61.6 yes View details
trnL-UAA-trnT-UGU LSC 955 0.0116 1.00 67.7 yes View details
psbD-trnT-GGU LSC 1398 0.0099 0.98 74.7 yes View details
psbM-petN LSC 773 0.0149 0.98 73.0 yes View details
rps2-atpI LSC 346 0.0335 0.92 75.3 yes View details
atpA-trnR-UCU LSC 342 0.0155 1.00 64.6 yes View details
trnG-UCC-trnS-GCU LSC 415 0.0213 1.00 68.3 yes View details
accD LSC 1527 0.0040 1.00 43.2 yes View details
accD-psaI LSC 332 0.0246 0.92 71.0 yes View details
petA-psbJ LSC 853 0.0113 0.99 68.9 yes View details
psaJ-rpl33 LSC 494 0.0128 0.99 59.3 yes View details
rps3-rps19 LSC 484 0.0213 1.00 84.2 yes View details
trnT-GGU-trnD-GUC LSC 265 0.0202 1.00 75.5 yes View details
rps8-rpl14 LSC 345 0.0194 1.00 75.5 yes View details
atpH-atpF LSC 590 0.0130 0.98 74.6 yes View details
rpl32-trnL-UAG SSC 583 0.0119 0.99 70.1 yes View details
ycf3-psaA LSC 674 0.0116 1.00 68.9 yes View details
trnG-GCC-psbZ LSC 578 0.0111 1.00 68.2 yes View details
trnH-GUG-psbA LSC 289 0.0154 0.97 68.1 yes View details
trnQ-UUG-rps16 LSC 414 0.0130 1.00 66.8 yes View details
ndhA SSC 2373 0.0061 1.00 66.5 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 CTGCCTTAATCCACTTGGCT CCCTCTAGATCTAGCTGCGA 355–376 1.000 86.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TCCCTCTAGATCTAGCTGCG 356–377 1.000 86.7
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCCTCTAGATCTAGCTGCGA 356–377 1.000 86.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TCCCTCTAGATCTAGCTGCG 357–378 1.000 86.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GCGAATGACGGGAATTGAAC CCCTCTAGATCTAGCTGCGA 400–421 1.000 85.5
ndhK_p1 ndhK AGGGGGCATTAGAATGGTCT CAGTTCACTGCTTCATGGGA 744–759 0.900 76.6
ndhK_p2 ndhK GGTTCAGTTTATGCATGGCG CAGTTCACTGCTTCATGGGA 766–781 0.900 75.7
ndhK_p3 ndhK GTTTATGCATGGCGAAAGGG CAGTTCACTGCTTCATGGGA 760–775 0.900 75.5
ndhK_p4 ndhK GCGAAAGGGGGCATTAGAAT CAGTTCACTGCTTCATGGGA 749–764 0.900 74.8
ndhK_p5 ndhK AGGGGGCATTAGAATGGTCT TCACTGCTTCATGGGAGGAT 740–755 0.900 74.8
trnF-GAA-trnL-UAA_p1 trnF-GAA-trnL-UAA TTTGAACTGGTGACACGAGG AATCGTGAGGGTTCAAGTCC 485–522 1.000 82.3
trnF-GAA-trnL-UAA_p2 trnF-GAA-trnL-UAA TACCAACTGAGCTATCCCGA AATCGTGAGGGTTCAAGTCC 447–484 1.000 79.7
trnF-GAA-trnL-UAA_p3 trnF-GAA-trnL-UAA GAACTGGTGACACGAGGATT AATCGTGAGGGTTCAAGTCC 482–519 1.000 79.1
trnF-GAA-trnL-UAA_p4 trnF-GAA-trnL-UAA TTTGAACTGGTGACACGAGG TTCAAGTCCCTCTATCCCCA 474–511 1.000 78.6
trnF-GAA-trnL-UAA_p5 trnF-GAA-trnL-UAA TCCTCTGCTCTACCAACTGA AATCGTGAGGGTTCAAGTCC 457–494 1.000 78.3
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT GCGATGCTCTAACCTCTGAG 957–1045 1.000 86.6
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT ATCGAGAAAAGCCGGCTATC 1009–1097 1.000 86.1
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT GGATTCGAACCGATGACCAT 989–1077 1.000 85.6
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU CCCATTGTGAATTCCAGGGT GCGATGCTCTAACCTCTGAG 1044–1132 0.950 83.5
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU CCCATTGTGAATTCCAGGGT ATCGAGAAAAGCCGGCTATC 1096–1184 0.950 83.1
ycf3-psaA_p1 ycf3-psaA AAGTTGCGGAGTCTTGGTTT TTTCACTTCTGGTTCCGGTG 826–857 1.000 88.0
ycf3-psaA_p2 ycf3-psaA TGGTTTAATCAAGCCGCTGA TTTCACTTCTGGTTCCGGTG 812–843 1.000 87.0
ycf3-psaA_p3 ycf3-psaA AAGCTATAGCCCTTACCCCC TTTCACTTCTGGTTCCGGTG 781–812 1.000 86.6
ycf3-psaA_p4 ycf3-psaA GAAGTTGCGGAGTCTTGGTT TTTCACTTCTGGTTCCGGTG 827–858 1.000 85.2
ycf3-psaA_p5 ycf3-psaA CCCTTACCCCCGGGAATTAT TTTCACTTCTGGTTCCGGTG 772–803 1.000 84.4
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTCCTGAAGGTTGGTCAAGT 729–785 1.000 78.4
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CCCGTTGTATTTGCTTCTCC 745–801 1.000 76.1
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCCTGAAGGTTGGTCA 732–788 1.000 76.0
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TCTCCTGAAGGTTGGTCAAG 730–786 1.000 76.0
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CCCGTTGTATTTGCTTCTCCT 745–801 1.000 75.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (20)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Campylotropis bonii NC_064525.1 153122 View on NCBI ↗
Campylotropis brevifolia NC_064509.1 148855 View on NCBI ↗
Campylotropis capillipes NC_064510.1 152978 View on NCBI ↗
Campylotropis delavayi NC_064511.1 149088 View on NCBI ↗
Campylotropis grandifolia NC_064512.1 149165 View on NCBI ↗
Campylotropis harmsii NC_064513.1 149291 View on NCBI ↗
Campylotropis henryi NC_064515.1 149153 View on NCBI ↗
Campylotropis howellii NC_064514.1 149312 View on NCBI ↗
Campylotropis latifolia NC_064516.1 149176 View on NCBI ↗
Campylotropis macrocarpa NC_044100.1 148814 View on NCBI ↗
Campylotropis parviflora NC_064517.1 148932 View on NCBI ↗
Campylotropis pinetorum NC_064518.1 149227 View on NCBI ↗
Campylotropis polyantha NC_064519.1 149001 View on NCBI ↗
Campylotropis sulcata NC_064520.1 148981 View on NCBI ↗
Campylotropis teretiracemosa NC_064521.1 149169 View on NCBI ↗
Campylotropis thomsonii NC_064522.1 148963 View on NCBI ↗
Campylotropis trigonoclada NC_064523.1 149227 View on NCBI ↗
Campylotropis wilsonii NC_064524.1 149113 View on NCBI ↗
Campylotropis xinfeniae OR506464.1 149073 View on NCBI ↗
Campylotropis yunnanensis subsp. filipes OM775453.1 149122 View on NCBI ↗