Markers + reference

Melicope

2 species · Rutaceae · Sapindales

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Species 2
Genome length 159–159 kb
Candidate markers 273
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 359 0.0407 0.96 74.5 yes View details
psbA LSC 1062 0.0085 1.00 49.7 yes View details
trnK-UUU-rps16 LSC 546 0.0307 0.95 68.1 yes View details
rps16 LSC 1166 0.0155 1.00 53.9 yes View details
rps16-trnQ-UUG LSC 823 0.0140 0.95 71.3 yes View details
trnS-GCU-trnG-UCC LSC 995 0.0145 0.97 56.5 yes View details
trnT-GGU-psbD LSC 1245 0.0113 1.00 61.7 yes View details
psbE-petL LSC 1346 0.0126 1.00 54.9 yes View details
rpl16 LSC 1381 0.0101 1.00 50.2 yes View details
trnN-GUU-rpl32 SSC 4597 0.0076 1.00 58.0 yes View details
rpl32-trnL-UAG SSC 1014 0.0169 0.99 69.0 yes View details
ndhG SSC 537 0.0223 1.00 57.9 yes View details
ycf1 SSC 5469 0.0103 1.00 56.4 yes View details
atpA-atpF LSC 60 0.0333 1.00 71.7 yes View details
psbC-trnS-UGA LSC 249 0.0321 1.00 71.0 yes View details
rpl16-rps3 LSC 161 0.0437 0.99 65.5 yes View details
atpH-atpI LSC 1020 0.0079 1.00 63.7 yes View details
rpoB-trnC-GCA LSC 1216 0.0111 0.96 63.5 yes View details
psaJ-rpl33 LSC 482 0.0089 0.94 63.5 yes View details
atpF-atpH LSC 466 0.0108 0.99 63.2 yes View details
petB LSC 1395 0.0072 1.00 62.9 yes View details
psaA-ycf3 LSC 734 0.0068 1.00 62.7 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CGTGCTAACCTTGGTATGGA 484–501 1.000 78.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TCGTGCTAACCTTGGTATGG 485–502 1.000 78.2
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CGTGCTAACCTTGGTATGGA 485–502 1.000 77.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TCGTGCTAACCTTGGTATGG 486–503 1.000 77.9
trnH-GUG-psbA_p5 trnH-GUG-psbA CAACCCACTGCCTTAATCCA CGTGCTAACCTTGGTATGGA 491–508 1.000 77.5
psbA_p1 psbA CTGCCTTAATCCACTTGGCT ACATAGGGAAAGCTGTGTGC 1821–1846 1.000 79.4
psbA_p2 psbA CTGCCTTAATCCACTTGGCT CATAGGGAAAGCTGTGTGCA 1820–1845 1.000 79.4
psbA_p3 psbA CTGCCTTAATCCACTTGGCT TATGCTTGGGAGTCCCTGAT 1494–1511 1.000 79.4
psbA_p4 psbA ACTGCCTTAATCCACTTGGC ACATAGGGAAAGCTGTGTGC 1822–1847 1.000 79.2
psbA_p5 psbA ACTGCCTTAATCCACTTGGC CATAGGGAAAGCTGTGTGCA 1821–1846 1.000 79.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG ATTTCAAAGAAAGCGGGGGT 651–652 1.000 84.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCAAAGAAAGCGGGGGT 640–641 1.000 83.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAAGCGGGGGT 639–640 1.000 83.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TCAAAGAAAGCGGGGGTTTT 648–649 1.000 83.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TTCAAAGAAAGCGGGGGTTT 649–650 1.000 83.3
rps16_p1 rps16 AGCCGTACTTAAAAGCCGAG CAATTGAGACGGGGGTGATT 2220–2227 1.000 82.0
rps16_p2 rps16 CCTTTCAGGATCAGTCGTGG CAATTGAGACGGGGGTGATT 2304–2311 1.000 81.8
rps16_p3 rps16 AGCCGTACTTAAAAGCCGAG TGAGACGGGGGTGATTCATA 2216–2223 1.000 81.7
rps16_p4 rps16 CCTTTCAGGATCAGTCGTGG TGAGACGGGGGTGATTCATA 2300–2307 1.000 81.5
rps16_p5 rps16 CTCTCCCGAAGATTTGGACG CAATTGAGACGGGGGTGATT 2275–2282 1.000 81.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 882–917 1.000 79.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 891–926 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GGGTTTTGGTCCCGGTATTC 897–932 1.000 77.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GGGTTTTGGTCCCGGTATTC 896–931 1.000 77.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAATAGAAATGGGGCGTGGC 918–953 1.000 76.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TACCACTAAACTATACCCGC 1033–1046 1.000 51.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TTACCACTAAACTATACCCGC 1034–1047 1.000 50.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC TACCACTAAACTATACCCGC 1030–1043 1.000 49.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGCTTTAATCCACTCAGCCA TACCACTAAACTATACCCGC 1029–1042 1.000 49.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCCGACGCTTTAATCCACTC TACCACTAAACTATACCCGC 1034–1047 1.000 48.8

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
Melicope hayesii NC_081882.1 158901 View on NCBI ↗
Melicope pteleifolia NC_050882.1 159012 View on NCBI ↗