Markers + reference

Maclura

2 species · Moraceae · Rosales

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Species 2
Genome length 161–161 kb
Candidate markers 266
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 393 0.0138 0.92 57.9 yes View details
rps16-trnQ-UUG LSC 713 0.0112 1.00 58.1 yes View details
rpoB-trnC-GCA LSC 1207 0.0117 0.99 66.4 yes View details
psbM-trnD-GUC LSC 507 0.0118 1.00 56.6 yes View details
psbZ-trnG-GCC LSC 698 0.0102 0.98 66.4 yes View details
rpl32-trnL-UAG SSC 1891 0.0086 0.99 51.4 yes View details
ccsA SSC 972 0.0041 1.00 47.8 yes View details
ccsA-ndhD SSC 271 0.0332 1.00 67.8 yes View details
ycf1 SSC 5673 0.0044 1.00 40.2 yes View details
ndhE-ndhG SSC 279 0.0149 0.96 64.8 yes View details
psaI-ycf4 LSC 443 0.0092 0.98 62.5 yes View details
atpF-atpH LSC 488 0.0102 1.00 62.3 yes View details
ycf4-cemA LSC 939 0.0053 1.00 62.1 yes View details
petA-psbJ LSC 1113 0.0045 0.99 62.1 yes View details
rps4-trnT-UGU LSC 486 0.0043 0.97 62.0 yes View details
trnF-GAA-ndhJ LSC 712 0.0056 1.00 62.0 yes View details
ndhC-trnV-UAC LSC 434 0.0093 0.99 62.0 yes View details
rpl20-rps12 LSC 819 0.0049 1.00 61.7 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 95 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 CCTCTAGACCTAGCTGCTGT 437–466 1.000 83.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 440–469 1.000 83.2
trnH-GUG-psbA_p3 trnH-GUG-psbA TAATTATGGGCGAACGACGG CCTCTAGACCTAGCTGCTGT 491–520 1.000 83.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 438–467 1.000 83.1
trnH-GUG-psbA_p5 trnH-GUG-psbA TAATTATGGGCGAACGACGG TTCCCTCTAGACCTAGCTGC 494–523 1.000 83.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 793–799 1.000 80.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ACGTTGCCTTCTACCACATC GAGGTTCGAATCCTTCCGTC 779–785 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GTTGCCTTCTACCACATCGT GAGGTTCGAATCCTTCCGTC 777–783 1.000 79.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCGTGTCTTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 798–804 1.000 79.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CACGTTGCCTTCTACCACAT GAGGTTCGAATCCTTCCGTC 780–786 1.000 78.8
trnG-UCC_p1 trnG-UCC CGACTAAGTTTCTTGTTCGACA AGAAGACCTCTGTCCTATCCA 944–946 1.000 40.4
trnG-UCC_p2 trnG-UCC ACGACTAAGTTTCTTGTTCGAC AGAAGACCTCTGTCCTATCCA 945–947 1.000 40.4
trnG-UCC_p3 trnG-UCC ACGACTAAGTTTCTTGTTCGACA AGAAGACCTCTGTCCTATCCA 945–947 1.000 40.4
trnG-UCC_p4 trnG-UCC CGACTAAGTTTCTTGTTCGACA AGGTTTAGAAGACCTCTGTCCT 950–952 1.000 40.4
trnG-UCC_p5 trnG-UCC ACGACTAAGTTTCTTGTTCGAC AGGTTTAGAAGACCTCTGTCCT 951–953 1.000 40.4
atpF-atpH_p1 atpF-atpH GATGGCCAATAACCCAAGGA GAGGCAGAGGGGAAAATACG 652–674 1.000 76.6
atpF-atpH_p2 atpF-atpH GATGGCCAATAACCCAAGGA GCAGAGGGGAAAATACGAGG 649–671 1.000 76.6
atpF-atpH_p3 atpF-atpH GATGGCCAATAACCCAAGGA GGCAGAGGGGAAAATACGAG 650–672 1.000 76.6
atpF-atpH_p4 atpF-atpH GGATGGCCAATAACCCAAGG GCAGAGGGGAAAATACGAGG 650–672 1.000 75.5
atpF-atpH_p5 atpF-atpH GGATGGCCAATAACCCAAGG GGCAGAGGGGAAAATACGAG 651–673 1.000 75.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTTTCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 1287–1296 1.000 79.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTTTCCTCATTTCCACCCCC CCGGATTTGAACTGGGGAAA 1286–1295 1.000 79.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCTTTCCTCATTTCCACCCC TTGTTGATTAGGCGACACCC 1305–1314 1.000 78.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTTTCCTCATTTCCACCCCC TTGTTGATTAGGCGACACCC 1304–1313 1.000 78.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTTTCCTCATTTCCACCCCC AAAAGGATTTGCAGTCCCCC 1268–1277 1.000 77.6
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 618–620 1.000 59.1
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 619–621 1.000 55.0
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TCAATTGGTCAGAGCACCG 617–619 1.000 53.1
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC AGTTCAATTGGTCAGAGCACC 620–622 1.000 51.0
psbM-trnD-GUC_p5 psbM-trnD-GUC TAGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 619–621 1.000 50.7

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
Maclura cochinchinensis NC_066228.1 161295 View on NCBI ↗
Maclura tricuspidata NC_056295.1 161348 View on NCBI ↗