Markers + reference

Lecanorchis

2 species · Orchidaceae · Asparagales

Back to catalogue

Species 2
Genome length 70–74 kb
Candidate markers 86
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 86 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnD-GUC-trnfM-CAU LSC 1380 0.0933 0.98 85.2 yes View details
accD-rps18 LSC 3319 0.0563 0.86 71.4 yes View details
rrn16-rrn23 SSC 1762 0.0882 0.94 86.8 yes View details
rrn5-trnN-GUU SSC 1476 0.0834 0.94 83.0 yes View details
trnN-GUU-ycf1 SSC 879 0.1296 0.90 85.1 yes View details
rps19-rpl2 LSC 613 0.1039 0.93 92.6 yes View details
matK-trnQ-UUG LSC 604 0.1122 0.97 83.3 yes View details
rps12 IRb 1715 0.0362 0.92 82.7 yes View details
rps12 IRa 1715 0.0362 0.92 82.7 yes View details
rpl2-rpl23 IRb 504 0.0876 0.70 78.7 yes View details
rpl14-rpl16 LSC 369 0.1276 0.91 78.6 yes View details
rpl23-matK IRa 635 0.0680 0.76 78.5 no View details
trnQ-UUG-rps2 LSC 564 0.0412 0.90 77.6 yes View details
rrn4.5-rrn5 SSC 183 0.0575 0.95 76.8 yes View details
rpl20-rps12 LSC 992 0.0384 0.97 74.7 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnQ-UUG_p1 matK-trnQ-UUG TTGAAATTCCGACGTTGACG TAAGGCAACGGGTTTTGGTC 683–2027 1.000 71.9
matK-trnQ-UUG_p2 matK-trnQ-UUG TTGAAATTCCGACGTTGACG GTAAGGCAACGGGTTTTGGT 684–2028 1.000 69.6
matK-trnQ-UUG_p3 matK-trnQ-UUG TTTGAAATTCCGACGTTGACG TAAGGCAACGGGTTTTGGTC 684–2028 1.000 69.5
matK-trnQ-UUG_p4 matK-trnQ-UUG TTGAAATTCCGACGTTGACG AAGGTTCGAATCCTTCCGC 653–1997 1.000 68.2
matK-trnQ-UUG_p5 matK-trnQ-UUG TTGAAATTCCGACGTTGACG TATAAAGAGATGGGGCGTGG 711–2055 1.000 67.5
trnQ-UUG-rps2_p1 trnQ-UUG-rps2 GACCAAAACCCGTTGCCTTA AGATTTTTCGATTCCGGCCA 659–711 1.000 80.0
trnQ-UUG-rps2_p2 trnQ-UUG-rps2 ATGAAGACAAAACTGGGGCG AGATTTTTCGATTCCGGCCA 705–757 1.000 79.3
trnQ-UUG-rps2_p3 trnQ-UUG-rps2 GACCAAAACCCGTTGCCTTA GCAATTTGTGAGGGTCGTTC 589–641 1.000 78.6
trnQ-UUG-rps2_p4 trnQ-UUG-rps2 GACCAAAACCCGTTGCCTTA TTGTGAGGGTCGTTCTAGCT 584–636 1.000 78.4
trnQ-UUG-rps2_p5 trnQ-UUG-rps2 ATGAAGACAAAACTGGGGCG GCAATTTGTGAGGGTCGTTC 635–687 1.000 77.9
trnD-GUC-trnfM-CAU_p1 trnD-GUC-trnfM-CAU CGCTCTGACCGATTGAACTA AAATCCCGGTTTTTCAACGC 1498–2354 1.000 80.8
trnD-GUC-trnfM-CAU_p2 trnD-GUC-trnfM-CAU CGCTCTGACCGATTGAACTA GTAGCTCGCAAGGCTCATAA 1462–2318 1.000 80.3
trnD-GUC-trnfM-CAU_p3 trnD-GUC-trnfM-CAU CGCTCTGACCGATTGAACTA TAGCTCGCAAGGCTCATAAC 1461–2317 1.000 80.3
trnD-GUC-trnfM-CAU_p4 trnD-GUC-trnfM-CAU CGCTCTGACCGATTGAACTA TTTTCAACGCGGAGTAGAGC 1488–2344 1.000 77.4
trnD-GUC-trnfM-CAU_p5 trnD-GUC-trnfM-CAU CGCTCTGACCGATTGAACTA GGTTTTTCAACGCGGAGTAG 1491–2347 1.000 77.3
accD-rps18_p1 accD-rps18 AAATACAGGATCGCGGAACC ATGCGCAGTTACGAAGGATT 1243–1508 1.000 91.1
accD-rps18_p2 accD-rps18 AAATACAGGATCGCGGAACC CCCCGACCCCCTATAAGTAG 891–1174 1.000 91.1
accD-rps18_p3 accD-rps18 AAATACAGGATCGCGGAACC CCCGACCCCCTATAAGTAGG 890–1173 1.000 91.1
accD-rps18_p4 accD-rps18 AAATACAGGATCGCGGAACC CGATGTCGTAGGTTCGAGTC 1044–1315 1.000 90.9
accD-rps18_p5 accD-rps18 AAATACAGGATCGCGGAACC CAAAAAGCCCCTTGAGGTCT 1441 0.500 59.6
rpl20-rps12_p1 rpl20-rps12 GCCCCTATAAAGGTTGAGGC TGTCACTAAATCTCCTGCGC 1136–1187 1.000 84.3
rpl20-rps12_p2 rpl20-rps12 GCCCCTATAAAGGTTGAGGC ACTAAATCTCCTGCGCTTCG 1132–1183 1.000 83.8
rpl20-rps12_p3 rpl20-rps12 GCCCCTATAAAGGTTGAGGC CTAAATCTCCTGCGCTTCGA 1131–1182 1.000 82.7
rpl20-rps12_p4 rpl20-rps12 GCCCCTATAAAGGTTGAGGC TAAATCTCCTGCGCTTCGAG 1130–1181 1.000 82.7
rpl20-rps12_p5 rpl20-rps12 TTCTTTTTCGACGTCTCCGG TGTCACTAAATCTCCTGCGC 1105–1156 1.000 82.7
rpl14-rpl16_p1 rpl14-rpl16 CAACTCTTTAGCTCCGCTGT ATACGCTCTTCAGGCACTTG 737–754 1.000 87.8
rpl14-rpl16_p2 rpl14-rpl16 GGGTTTCCTGCTTGATCGAT ATACGCTCTTCAGGCACTTG 958–975 1.000 86.2
rpl14-rpl16_p3 rpl14-rpl16 GGGTTTCCTGCTTGATCGAT CCTGCTTGGATCACTGCTAG 936–953 1.000 86.1
rpl14-rpl16_p4 rpl14-rpl16 ACTTCGGGCGCTAATGAAAT ATACGCTCTTCAGGCACTTG 1042–1059 1.000 85.7
rpl14-rpl16_p5 rpl14-rpl16 ACTTCGGGCGCTAATGAAAT CCTGCTTGGATCACTGCTAG 1020–1037 1.000 85.6

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
Lecanorchis japonica NC_046799.1 70498 View on NCBI ↗
Lecanorchis kiusiana NC_046798.1 74084 View on NCBI ↗