Markers + reference

Corynonema

2 species · Rutaceae · Sapindales

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Species 2
Genome length 155–156 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 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
rps16-trnQ-UUG LSC 791 0.0499 0.99 75.2 yes View details
trnS-GCU-trnG-UCC LSC 882 0.0631 0.79 76.2 yes View details
rpoB-trnC-GCA LSC 1244 0.0495 0.94 83.4 yes View details
trnE-UUC-trnT-GGU LSC 730 0.0528 0.99 74.4 yes View details
trnS-GGA-rps4 LSC 275 0.0595 0.98 69.4 yes View details
petA-psbJ LSC 1071 0.0495 1.00 74.2 yes View details
rpl32-trnL-UAG SSC 606 0.0475 0.90 75.2 yes View details
ndhD SSC 1479 0.0270 1.00 60.7 yes View details
ycf1 SSC 5472 0.0386 0.99 65.2 yes View details
ndhE-ndhG SSC 220 0.0463 0.98 79.7 yes View details
trnH-GUG-psbA LSC 308 0.0779 1.00 79.0 yes View details
trnF-GAA-ndhJ LSC 475 0.0582 0.83 77.5 yes View details
trnT-UGU-trnL-UAA LSC 777 0.0442 0.87 76.4 yes View details
psaC-ndhE SSC 240 0.0500 1.00 75.2 yes View details
rpl36-rps8 LSC 356 0.0408 0.96 73.1 yes View details
trnL-UAA-trnF-GAA LSC 364 0.0470 0.99 72.8 yes View details
trnD-GUC-trnY-GUA LSC 462 0.0355 0.92 71.5 yes View details
trnW-CCA-trnP-UGG LSC 185 0.0486 1.00 71.5 yes View details
atpF-atpH LSC 474 0.0486 1.00 70.7 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 95 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 CGTGCTAACCTTGGTATGGA 426–516 1.000 77.6
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGTGCTAACCTTGGTATGG 427–517 1.000 77.6
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CGTGCTAACCTTGGTATGGA 440–530 1.000 77.4
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGTGCTAACCTTGGTATGG 441–531 1.000 77.4
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CGTGCTAACCTTGGTATGGA 439–529 1.000 77.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA CTTACAGCAGCTTGCCAAAC 1393–1456 1.000 86.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGGATACGCTTTTGATGGA CTTACAGCAGCTTGCCAAAC 1713–1776 1.000 86.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 882–888 1.000 83.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAAATTGAAATGGGGCGTCG 940–946 1.000 83.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGGGATACGCTTTTGATGGA GAGGTTCGAATCCTTCCGTC 1202–1208 1.000 83.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TGAACGAATCACACTTTTACCAC 786–950 1.000 60.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA ACGAATCACACTTTTACCACT 783–947 1.000 59.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAACGAATCACACTTTTACCAC 844–1008 1.000 59.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA GAACGAATCACACTTTTACCACT 785–949 1.000 58.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC TGAACGAATCACACTTTTACCAC 783–947 1.000 58.7
atpF-atpH_p1 atpF-atpH TGGGTCCAGCCTATTCTTGA GTTGTGGCATTAGCGCTTTT 697–701 1.000 82.2
atpF-atpH_p2 atpF-atpH TGGGTCCAGCCTATTCTTGA ATTTCTGCCGCTTCCGTTAT 889–893 1.000 81.9
atpF-atpH_p3 atpF-atpH GGTGCTTTGTCTGGACTTCA GTTGTGGCATTAGCGCTTTT 910–915 1.000 81.9
atpF-atpH_p4 atpF-atpH GGTGCTTTGTCTGGACTTCA ATTTCTGCCGCTTCCGTTAT 1102–1107 1.000 81.8
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG ATTTCTGCCGCTTCCGTTAT 777–781 1.000 81.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC ATCGTTTGTTGATCAGGCGA 1306–1355 1.000 86.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC GTTTGTTGATCAGGCGACAC 1303–1352 1.000 84.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC AAAAGGATTTGCAGTCCCCC 1265–1314 1.000 84.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC GCGACACCCAGATTTGAACT 1290–1339 1.000 83.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCATTTCCATCTCCGAGCAT ATCGTTTGTTGATCAGGCGA 1300–1349 1.000 83.6
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 502–532 1.000 80.6
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 501–531 1.000 80.6
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 523–553 1.000 79.6
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 522–552 1.000 79.4
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GATTCTTCCTGGGTCGATGC 556–586 1.000 79.0

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
Corynonema fitzgeraldii NC_081895.1 156096 View on NCBI ↗
Corynonema pungens NC_081897.1 155376 View on NCBI ↗