Markers + reference

Meliosma

2 species · Sabiaceae · Proteales

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Species 2
Genome length 160–160 kb
Candidate markers 269
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 884 0.3342 0.89 81.8 yes View details
rps16-trnQ-UUG LSC 1731 0.3347 0.56 74.8 yes View details
trnS-GCU-trnG-UCC LSC 1099 0.3026 0.82 81.3 yes View details
petN-psbM LSC 1212 0.2570 0.70 77.2 yes View details
trnE-UUC-trnT-GGU LSC 828 0.2705 0.90 83.2 yes View details
trnT-UGU-trnL-UAA LSC 962 0.2777 0.82 80.1 yes View details
ndhC-trnV-UAC LSC 749 0.3597 0.93 83.9 yes View details
ycf1 IRb 1384 0.0679 0.99 75.8 no View details
ndhF-rpl32 SSC 1333 0.3165 0.67 76.0 yes View details
ycf1 SSC 5685 0.1949 0.97 75.7 yes View details
psaA-ycf3 LSC 660 0.1697 0.93 83.7 yes View details
ycf3-trnS-GGA LSC 880 0.2002 0.94 83.7 yes View details
atpB-rbcL LSC 765 0.1389 0.94 83.6 yes View details
rpl16 LSC 1459 0.1664 0.94 83.4 yes View details
psbE-petL LSC 1403 0.1930 0.90 83.2 yes View details
rpl20-rps12 LSC 780 0.1602 0.96 83.0 yes View details
atpH-atpI LSC 1178 0.2055 0.89 82.5 yes View details
petA-psbJ LSC 1092 0.2495 0.90 82.4 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GCCGTACGAGGAGAAAACTT 1311–1347 1.000 91.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1310–1346 1.000 91.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG ACCGAGAAAGGATCCTGGAA 1646 0.500 59.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG ACCGAGAAAGGATCCTGGAA 1645 0.500 59.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCCTTTCAGGATCAGTCGT ACCGAGAAAGGATCCTGGAA 1647 0.500 59.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1075–1804 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1086–1815 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1087–1816 1.000 85.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1067–1796 1.000 85.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 1074–1803 1.000 84.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 1118–1152 1.000 55.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC GAACGAATCACACTTTTACCACT 1120–1154 1.000 53.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC AACGAATCACACTTTTACCACT 1119–1153 1.000 53.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TACCACTAAACTATACCCGC 1104–1138 1.000 52.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC GAACGAATCACACTTTTACCAC 1120–1154 1.000 52.0
trnG-UCC_p1 trnG-UCC TAGCCGGGCCTTTTCTTTTT CATCGGATTGGGTGTGAGAG 1557 0.500 59.5
trnG-UCC_p2 trnG-UCC TAGCCGGGCCTTTTCTTTTT CTCTCACGGTGGAAGAACAG 2037 0.500 59.4
trnG-UCC_p3 trnG-UCC TAGCCGGGCCTTTTCTTTTT AAAAGCATCGGATTGGGTGT 1562 0.500 59.4
trnG-UCC_p4 trnG-UCC TAGCCGGGCCTTTTCTTTTT CATTCACCGAGGAAGCAGAA 1878 0.500 59.2
trnG-UCC_p5 trnG-UCC TAGCCGGGCCTTTTCTTTTT AAGACATTCACCGAGGAAGC 1882 0.500 59.2
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TATGGTCCTTGGGTTCCCTT 1684 1.000 91.1
atpH-atpI_p2 atpH-atpI GCCACGACCAGTCCATAAAT TATGGTCCTTGGGTTCCCTT 1864 0.500 59.1
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT ACAAACCATTCCTACCGACG 1772 0.500 59.0
atpH-atpI_p4 atpH-atpI GCCACGACCAGTCCATAAAT ACAAACCATTCCTACCGACG 1952 0.500 59.0
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT CTGGTCAGGGGCTCTTTTAC 1628 0.500 58.8
petN-psbM_p1 petN-psbM ACGAATGTGTCTCCCGATTG CGTCATCAGATGGGTGTGTT 2189 0.500 59.1
petN-psbM_p2 petN-psbM CACGAATGTGTCTCCCGATT CGTCATCAGATGGGTGTGTT 2190 0.500 59.1
petN-psbM_p3 petN-psbM CGAATGTGTCTCCCGATTGT CGTCATCAGATGGGTGTGTT 2188 0.500 59.1
petN-psbM_p4 petN-psbM CTAACCCCCAGTCACGAATG CGTCATCAGATGGGTGTGTT 2202 0.500 59.0
petN-psbM_p5 petN-psbM AGTAAATCTCGCTTGGGCTG CGTCATCAGATGGGTGTGTT 1757 0.500 59.0

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
Meliosma aff. cuneifolia Moore 333 NC_029430.1 160357 View on NCBI ↗
Meliosma oldhamii NC_058700.1 159950 View on NCBI ↗