Markers + reference

Loranthus

6 species · Loranthaceae · Santalales

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Species 6
Genome length 122–125 kb
Candidate markers 238
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 238 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0065 1.00 35.8 yes View details
petN-psbM LSC 852 0.0180 0.98 69.3 yes View details
psbM-trnD-GUC LSC 635 0.0227 1.00 64.1 yes View details
ycf3-trnS-GGA LSC 584 0.0304 1.00 71.7 yes View details
trnT-UGU-trnL-UAA LSC 692 0.0241 1.00 65.2 yes View details
rpl16-rps3 LSC 592 0.0255 1.00 64.2 yes View details
ycf1 IRb 864 0.0044 1.00 47.8 no View details
ycf1 SSC 5019 0.0190 1.00 56.7 yes View details
trnH-psbA LSC 233 0.0569 0.95 76.6 yes View details
ycf4-cemA LSC 135 0.0486 0.96 75.9 yes View details
psbT-psbN LSC 67 0.0557 1.00 74.9 yes View details
psbC-trnS-UGA LSC 167 0.0311 1.00 68.5 yes View details
trnP-UGG-psaJ LSC 244 0.0287 1.00 64.6 yes View details
trnL-CAA-ndhB IRb 756 0.0067 1.00 64.5 yes View details
ndhB-trnL-CAA IRa 756 0.0067 1.00 64.5 yes View details
atpB-rbcL LSC 817 0.0126 0.99 63.9 yes View details
petL-petG LSC 186 0.0262 0.98 62.6 yes View details
atpI-rps2 LSC 216 0.0170 1.00 61.9 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CAATCCACTGCCTTGATCCA GCCCGTAGTAGGTATCTGGT 480–497 0.833 79.9
trnH-psbA_p2 trnH-psbA AATCCACTGCCTTGATCCAC GCCCGTAGTAGGTATCTGGT 479–496 0.833 79.9
trnH-psbA_p3 trnH-psbA CAATCCACTGCCTTGATCCA TGGCCCGTAGTAGGTATCTG 482–499 0.833 79.8
trnH-psbA_p4 trnH-psbA ACAATCCACTGCCTTGATCC GCCCGTAGTAGGTATCTGGT 481–498 0.833 79.8
trnH-psbA_p5 trnH-psbA CAATCCACTGCCTTGATCCA GTTGATAGTCAAGGTCGCGT 408–412 0.500 63.2
psbA_p1 psbA AGAACTCGTATACACTAGTAAAGA CGTGCTTGGGAGTCTTTGAT 1132 1.000 41.3
psbA_p2 psbA AGAACTCGTATACACTAGTAAAGA AGAGAGTTTTCGTGCTTGGG 1142 0.833 34.5
psbA_p3 psbA AGAACTCGTATACACTAGTAAAGA AGAGTTTTCGTGCTTGGGAG 1140 0.833 34.5
psbA_p4 psbA AGAACTCGTATACACTAGTAAAGA GAGAGTTTTCGTGCTTGGGA 1141 0.833 34.5
psbA_p5 psbA AGAACTCGTATACACTAGTAAAGA TTTCGTGCTTGGGAGTCTTT 1135 0.833 34.5
atpI-rps2_p1 atpI-rps2 TGAGCATGGACTTGGAAACC ATTTCGATTCCGGCGAATGA 426–437 1.000 83.1
atpI-rps2_p2 atpI-rps2 TGAGCATGGACTTGGAAACC TTTCGATTCCGGCGAATGAT 425–436 1.000 83.1
atpI-rps2_p3 atpI-rps2 TGAGCATGGACTTGGAAACC GGATATTTCGATTCCGGCGA 430–441 1.000 82.9
atpI-rps2_p4 atpI-rps2 GAGCATGGACTTGGAAACCT ATTTCGATTCCGGCGAATGA 425–436 1.000 82.2
atpI-rps2_p5 atpI-rps2 GAGCATGGACTTGGAAACCT TTTCGATTCCGGCGAATGAT 424–435 1.000 82.2
petN-psbM_p1 petN-psbM GTATGGGGGAGAAGTGGACT ACGTAAAAACGGCTAGTCAA 595–915 1.000 64.8
petN-psbM_p2 petN-psbM AGTATGGGGGAGAAGTGGAC ACGTAAAAACGGCTAGTCAA 596–916 1.000 64.7
petN-psbM_p3 petN-psbM AGTATGGGGGAGAAGTGGAC TCCTTTACGTAAAAACGGCT 602–922 1.000 64.5
petN-psbM_p4 petN-psbM GTATGGGGGAGAAGTGGACT TCCTTTACGTAAAAACGGCT 601–921 1.000 64.5
petN-psbM_p5 petN-psbM TATGGGGGAGAAGTGGACTC ACGTAAAAACGGCTAGTCAA 594–914 1.000 64.3
psbM-trnD-GUC_p1 psbM-trnD-GUC TTGACTAGCCGTTTTTACGT TTCAACTGGTTAGAGCACCG 691–835 1.000 64.7
psbM-trnD-GUC_p2 psbM-trnD-GUC AGCCGTTTTTACGTAAAGGA TTCAACTGGTTAGAGCACCG 685–829 1.000 64.4
psbM-trnD-GUC_p3 psbM-trnD-GUC TTTGACTAGCCGTTTTTACGT TTCAACTGGTTAGAGCACCG 692–836 1.000 63.0
psbM-trnD-GUC_p4 psbM-trnD-GUC AGCCGTTTTTACGTAAAGGAT TTCAACTGGTTAGAGCACCG 685–829 1.000 61.0
psbM-trnD-GUC_p5 psbM-trnD-GUC ACTAGCCGTTTTTACGTAAAGGA TTCAACTGGTTAGAGCACCG 688–832 1.000 60.9
psbC-trnS-UGA_p1 psbC-trnS-UGA TCGTAGGTCATTTGTGGCAC GGTTGATAGCTCCGGTCTTG 354–355 1.000 80.4
psbC-trnS-UGA_p2 psbC-trnS-UGA TCGTAGGTCATTTGTGGCAC GGGTTCGAATCCCTCTCTCT 300–301 1.000 79.6
psbC-trnS-UGA_p3 psbC-trnS-UGA GCAGCAGGATTTGAAAAGGG GGTTGATAGCTCCGGTCTTG 313–314 1.000 79.3
psbC-trnS-UGA_p4 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGTTGATAGCTCCGGTCTTG 317–318 1.000 79.3
psbC-trnS-UGA_p5 psbC-trnS-UGA GCTGCAGCAGGATTTGAAAA GGTTGATAGCTCCGGTCTTG 316–317 1.000 78.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Loranthus delavayi NC_058858.1 124326 View on NCBI ↗
Loranthus grewingkii NC_058861.1 122216 View on NCBI ↗
Loranthus kaoi NC_058863.1 124322 View on NCBI ↗
Loranthus lambertianus NC_058864.1 125032 View on NCBI ↗
Loranthus pseudo-odoratus NC_058865.1 124474 View on NCBI ↗
Loranthus tanakae NC_058867.1 121709 View on NCBI ↗