Markers + reference

Macrosolen

4 species · Loranthaceae · Santalales

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Species 4
Genome length 123–128 kb
Candidate markers 233
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 233 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnR-UCU LSC 396 0.0932 0.87 78.1 yes View details
rpoB-trnC-GCA LSC 668 0.1176 0.84 78.8 yes View details
trnE-UUC-trnT-GGU LSC 486 0.0950 1.00 81.4 yes View details
trnT-GGU-psbD LSC 674 0.0902 1.00 89.2 yes View details
rpl36-rps8 LSC 257 0.1680 1.00 77.6 yes View details
ccsA-psaC SSC 855 0.1032 0.65 74.9 yes View details
psaC-ycf1 SSC 561 0.1710 0.76 75.7 yes View details
ycf1 SSC 5244 0.0715 1.00 78.4 yes View details
rpl20-rps12 LSC 689 0.0535 1.00 84.6 yes View details
atpB-rbcL LSC 613 0.0636 0.99 84.3 yes View details
petN-psbM LSC 567 0.0750 0.99 83.7 yes View details
rbcL-accD LSC 617 0.1002 1.00 83.7 yes View details
psbE-petL LSC 956 0.0758 0.96 83.7 yes View details
psaA-ycf3 LSC 549 0.0692 0.96 82.4 yes View details
clpP-psbB LSC 419 0.0569 1.00 82.2 yes View details
trnD-GUC-trnY-GUA LSC 420 0.0774 1.00 81.7 yes View details
matK-trnK-UUU LSC 709 0.0503 1.00 81.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TTATCTACCCGGACCCCTTC ACCGGTCGTCTGATTCTTTG 2976 0.250 48.6
trnK-UUU_p2 trnK-UUU TTATCTACCCGGACCCCTTC CAACCGGTCGTCTGATTCTT 2978 0.250 48.6
trnK-UUU_p3 trnK-UUU TTATCTACCCGGACCCCTTC CCATAGGAATCAACCGGTCG 2988 0.250 48.2
trnK-UUU_p4 trnK-UUU TTATCTACCCGGACCCCTTC TAGGAATCAACCGGTCGTCT 2985 0.250 48.0
trnK-UUU_p5 trnK-UUU CTACCCGGACCCCTTCATAA ACCGGTCGTCTGATTCTTTG 2972 0.250 47.7
matK-trnK-UUU_p1 matK-trnK-UUU AGTCCTGTTTCCGAGCTAGA ACGGTAGAGTACTCGGCTTT 779–789 0.750 70.4
matK-trnK-UUU_p2 matK-trnK-UUU AGTCCTGTTTCCGAGCTAGA ACCGGTCGTCTGATTCTTTG 1122–1334 0.500 58.5
matK-trnK-UUU_p3 matK-trnK-UUU AGTCCTGTTTCCGAGCTAGA CAACCGGTCGTCTGATTCTT 1124–1336 0.500 58.5
matK-trnK-UUU_p4 matK-trnK-UUU AGTCCTGTTTCCGAGCTAGA CCATAGGAATCAACCGGTCG 1134–1346 0.500 58.1
matK-trnK-UUU_p5 matK-trnK-UUU AGTCCTGTTTCCGAGCTAGA TAGGAATCAACCGGTCGTCT 1131–1343 0.500 57.9
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA ACCTCTGTCCTATCCATTAGACA 467–611 1.000 66.5
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU CTTTAGCCCACTCAGCCATC ACCTCTGTCCTATCCATTAGACA 452–596 1.000 64.2
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU TTAGCAATCCGCCGCTTTAG ACCTCTGTCCTATCCATTAGACA 466–610 1.000 61.2
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU TTTAGCCCACTCAGCCATCT ACCTCTGTCCTATCCATTAGACA 451–595 1.000 61.2
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA CCTCTGTCCTATCCATTAGACA 466–610 1.000 61.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTCATTTCCATCCCAGAGC CTTACCACTCGGCCATGC 366–900 1.000 74.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCTCATTTCCATCCCAGAGC CCTTACCACTCGGCCATG 367–901 1.000 71.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CTCATTTCCATCCCAGAGCA CTTACCACTCGGCCATGC 365–899 1.000 68.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCATTTCCATCCCAGAGCA CCTTACCACTCGGCCATG 366–900 1.000 65.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTCATTTCCATCCCAGAGCAT CTTACCACTCGGCCATGC 365–899 1.000 64.7
petN-psbM_p1 petN-psbM GATTCGGGAAAGGGGGATTC TGATTGTACAAGGACAGCGG 1571–1617 0.500 60.8
petN-psbM_p2 petN-psbM GATTCGGGAAAGGGGGATTC GATTGTACAAGGACAGCGGT 1570–1616 0.500 60.8
petN-psbM_p3 petN-psbM TTTCCCCAGTTCAAATCCGG TGATTGTACAAGGACAGCGG 1424–1472 0.500 60.2
petN-psbM_p4 petN-psbM GCATAACTGACGAAGGGAGG TGATTGTACAAGGACAGCGG 1694 0.250 48.8
petN-psbM_p5 petN-psbM GCATAACTGACGAAGGGAGG GATTGTACAAGGACAGCGGT 1693 0.250 48.8
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GTGCTCTAACCAGTTGAACT TCTACGCTGGTTCAAATCCG 446–479 1.000 70.5
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA TGCTCTAACCAGTTGAACTACA TCTACGCTGGTTCAAATCCG 445–478 1.000 68.4
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA ACCAGTTGAACTACAATCCC TCTACGCTGGTTCAAATCCG 438–471 1.000 67.6
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA AACCAGTTGAACTACAATCCC TCTACGCTGGTTCAAATCCG 439–472 1.000 66.2
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA GTGCTCTAACCAGTTGAACTAC TCTACGCTGGTTCAAATCCG 446–479 1.000 65.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Macrosolen bibracteolatus NC_088734.1 127059 View on NCBI ↗
Macrosolen cochinchinensis NC_039376.1 122986 View on NCBI ↗
Macrosolen parasiticus NC_088733.1 127769 View on NCBI ↗
Macrosolen tricolor MH161425.1 126621 View on NCBI ↗