Markers + reference

Psittacanthus

5 species · Loranthaceae · Santalales

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Species 5
Genome length 120–125 kb
Candidate markers 231
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 231 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 660 0.1054 0.34 70.5 yes View details
rps12-trnV-GAC IRb 1577 0.0792 0.86 80.2 yes View details
trnI-GAU-trnA-UGC IRb 266 0.3246 0.68 68.5 yes View details
ccsA-psaC SSC 546 0.1214 0.91 78.2 yes View details
trnA-UGC-trnI-GAU IRa 266 0.3368 0.68 68.5 yes View details
trnV-GAC-rps12 IRa 1577 0.0893 0.89 80.7 yes View details
psaC-ycf1 SSC 593 0.0877 0.99 84.8 yes View details
trnT-GGU-psbD LSC 568 0.0759 0.99 83.4 yes View details
petN-psbM LSC 788 0.0570 0.98 83.3 yes View details
psbE-petL LSC 927 0.0535 0.98 83.3 yes View details
rpoB-trnC-GCA LSC 801 0.0592 0.97 82.6 yes View details
psaA-ycf3 LSC 610 0.0450 0.96 82.0 yes View details
petA-psbJ LSC 522 0.0466 1.00 81.8 yes View details
trnR-ACG-trnN-GUU IRb 476 0.0956 0.99 81.7 yes View details
trnN-GUU-trnR-ACG IRa 476 0.1012 0.99 81.7 yes View details
ycf3-trnS-GGA LSC 655 0.0488 0.94 80.9 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG ACGAGTACTCTACCGTCGAG AGACAGGTATGACCGGCATA 1227 0.200 46.7
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AGACGAGTACTCTACCGTCG AGACAGGTATGACCGGCATA 1229 0.200 46.7
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG CGAGTACTCTACCGTCGAGT AGACAGGTATGACCGGCATA 1226 0.200 46.7
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG GACGAGTACTCTACCGTCGA AGACAGGTATGACCGGCATA 1228 0.200 46.7
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG CGAGTACTCTACCGTCGAGT GCTATTCGGAGGTTCGAGTC 721 0.200 46.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCGGGGCTTTGCAATATTTG TATAGTTATAGCCCGGCCCC 1286–1490 0.800 79.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CACGAGCCCATATCCTTTCC TATAGTTATAGCCCGGCCCC 1408–1612 0.800 79.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AAGACTAGAGCCCCGCTTAT TATAGTTATAGCCCGGCCCC 1616–1820 0.800 78.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATGCGAACCCATAGCTGATG TATAGTTATAGCCCGGCCCC 1464–1668 0.800 78.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAAGACTAGAGCCCCGCTTA TATAGTTATAGCCCGGCCCC 1617–1821 0.800 78.5
petN-psbM_p1 petN-psbM GTATCATTTTGGCGGCATGG TCCACCCCGAACTTTTGAAA 1994–2066 0.400 59.0
petN-psbM_p2 petN-psbM AGGGGGAGGGTTCAAGATAC TCCACCCCGAACTTTTGAAA 2082 0.200 43.6
petN-psbM_p3 petN-psbM AGGGGGAGGGTTCAAGATAC TTCCACCCCGAACTTTTGAA 2083 0.200 43.6
petN-psbM_p4 petN-psbM GGGGCCGGGCTATAACTATA TCCACCCCGAACTTTTGAAA 1764 0.200 43.5
petN-psbM_p5 petN-psbM GGGGCCGGGCTATAACTATA TTCCACCCCGAACTTTTGAA 1765 0.200 43.5
trnT-GGU-psbD_p1 trnT-GGU-psbD CGGATTTGAACCAGCGTAGA TCAGGGCCCCATAGTAACAA 1543–1975 1.000 89.8
trnT-GGU-psbD_p2 trnT-GGU-psbD CGGATTTGAACCAGCGTAGA TTCAGGGCCCCATAGTAACA 1544–1976 1.000 89.8
trnT-GGU-psbD_p3 trnT-GGU-psbD CGGATTTGAACCAGCGTAGA AGCTTGGGTGGGGTTAAAAG 1976–2408 1.000 89.2
trnT-GGU-psbD_p4 trnT-GGU-psbD CGGATTTGAACCAGCGTAGA AGTTTCTTCAGCTTGGGTGG 1985–2417 1.000 89.1
trnT-GGU-psbD_p5 trnT-GGU-psbD CGACCCAGAAGGAATCCTTG AGCTTGGGTGGGGTTAAAAG 1908–2262 0.600 68.6
psaA-ycf3_p1 psaA-ycf3 CTGGCCCATTCTTCGAAAGA TGGTTGAAGATCACGAGACG 717–798 1.000 86.4
psaA-ycf3_p2 psaA-ycf3 TCTGGCCCATTCTTCGAAAG TGGTTGAAGATCACGAGACG 718–799 1.000 86.3
psaA-ycf3_p3 psaA-ycf3 CTGGCCCATTCTTCGAAAGA GGTTGAAGATCACGAGACGT 716–797 1.000 86.3
psaA-ycf3_p4 psaA-ycf3 TCTGGCCCATTCTTCGAAAG GGTTGAAGATCACGAGACGT 717–798 1.000 86.3
psaA-ycf3_p5 psaA-ycf3 GTCTGGCCCATTCTTCGAAA TGGTTGAAGATCACGAGACG 719–800 1.000 85.8
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CTTCAACAAGCGCGGATTTT GGAGCCCGCCAATTAGTTAA 1406–1483 1.000 89.3
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TGAGCGGGGCTAATGTTTTT GGAGCCCGCCAATTAGTTAA 1927–1985 1.000 88.5
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CTTCAACAAGCGCGGATTTT TTTTCATTTCTTGTCCGCGC 1068–1121 0.800 79.7
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TGAGCGGGGCTAATGTTTTT TTTTCATTTCTTGTCCGCGC 1563–1622 0.800 78.9
ycf3-trnS-GGA_p5 ycf3-trnS-GGA ACAGAAGGGGTTGTGCAATT TTTTCATTTCTTGTCCGCGC 1145 0.200 46.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Psittacanthus auriculatus PP236145.1 121238 View on NCBI ↗
Psittacanthus palmeri PP236144.1 122407 View on NCBI ↗
Psittacanthus rhynchanthus PP579889.1 120345 View on NCBI ↗
Psittacanthus schiedeanus NC_084374.1 122586 View on NCBI ↗
Psittacanthus sonorae PP313080.1 125427 View on NCBI ↗