Markers + reference

Beilschmiedia

19 species · Lauraceae · Laurales

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Species 19
Genome length 158–159 kb
Candidate markers 258
Primer pairs 90

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 10 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 388 0.0104 1.00 47.3 yes View details
atpH-atpI LSC 919 0.0071 1.00 61.7 yes View details
petA-psbJ LSC 1160 0.0092 0.99 73.2 yes View details
rps19 LSC 279 0.0022 1.00 25.3 yes View details
ycf1 IRb 1362 0.0008 1.00 50.2 no View details
ndhF SSC 2229 0.0055 1.00 50.1 yes View details
ndhF-rpl32 SSC 1196 0.0106 0.99 61.5 yes View details
ndhD SSC 1506 0.0032 1.00 48.8 yes View details
ycf1 SSC 5505 0.0086 1.00 52.5 yes View details
accD-psaI LSC 672 0.0070 0.95 68.9 yes View details
rps8-rpl14 LSC 197 0.0111 0.98 67.3 yes View details
rps15-ycf1 SSC 376 0.0092 1.00 66.6 yes View details
clpP LSC 2065 0.0022 1.00 64.9 yes View details
matK LSC 1524 0.0039 1.00 64.5 yes View details
trnC-GCA-petN LSC 1084 0.0061 0.99 64.3 yes View details
rpoB-trnC-GCA LSC 1171 0.0033 1.00 63.6 yes View details
rps16-trnQ-UUG LSC 997 0.0034 0.99 63.2 yes View details
rpl32-trnL-UAG SSC 1365 0.0069 1.00 62.2 yes View details
ndhG-ndhI SSC 397 0.0136 0.99 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA ATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 445–454 1.000 68.0
trnH-GUG-psbA_p2 trnH-GUG-psbA ATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 448–457 1.000 67.9
trnH-GUG-psbA_p3 trnH-GUG-psbA ATCCACTTGGCTACATCCG TAGACCTAGCTGCTGTCGAA 441–450 1.000 67.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ATCCACTTGGCTACATCCGC CCTCTAGACCTAGCTGCTGT 445–454 1.000 67.3
trnH-GUG-psbA_p5 trnH-GUG-psbA CCACTTGGCTACATCCGC CCTCTAGACCTAGCTGCTGT 443–452 1.000 67.3
matK_p1 matK CCACTACACTACTGCATGAGC CTTGTTCTGACCGTATCGCA 1709–1724 0.947 68.6
matK_p2 matK TCAACCACTACACTACTGCA CTTGTTCTGACCGTATCGCA 1713–1728 1.000 67.4
matK_p3 matK CCACTACACTACTGCATGAGC TTGTTCTGACCGTATCGCAC 1708–1723 0.947 66.3
matK_p4 matK ACCACTACACTACTGCATGAG CTTGTTCTGACCGTATCGCA 1710–1725 0.947 65.2
matK_p5 matK CACTACACTACTGCATGAGC CTTGTTCTGACCGTATCGCA 1708–1723 0.947 64.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCAAGAATCCACAGCCGATA GAGGTTCGAATCCTTCCGTC 1055–1116 1.000 85.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1026–1087 1.000 84.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCAAGAATCCACAGCCGATA CTCGGAGGTTCGAATCCTTC 1059–1120 1.000 84.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1030–1091 1.000 83.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCCGATAATGTCCTT GAGGTTCGAATCCTTCCGTC 1047–1108 1.000 82.8
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTGCAACTTTAGCCGCAG 814–1022 0.947 82.3
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCAG 872–1080 0.947 82.1
atpH-atpI_p3 atpH-atpI AACGGAAGCAGCAGAAATCA CGAATCCATGGAGGGTCATC 784–992 0.947 82.0
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCCGCAG 832–1040 0.947 81.9
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 842–1050 0.947 81.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCGTCAAACCTTGGTCAATGA CCGGATTTGAACTGGGGAAA 1289–1306 1.000 72.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCTTTCGTCAAACCTTGGTCA CCGGATTTGAACTGGGGAAA 1293–1310 1.000 72.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCGTCAAACCTTGGTCAATGA TTGTTAATCAGGCGACACCC 1307–1324 1.000 72.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCTTTCGTCAAACCTTGGTCA TTGTTAATCAGGCGACACCC 1311–1328 1.000 71.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCGTCAAACCTTGGTCAATGA AAAAGGATTTGCAGTCCCCC 1271–1288 1.000 70.8
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 1107–1206 1.000 85.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1051–1150 1.000 85.3
trnC-GCA-petN_p3 trnC-GCA-petN GGGTGTCGCCTGATTAACAA AGCCCAAGCGAGACTTACTA 1033–1132 1.000 84.5
trnC-GCA-petN_p4 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGAGTCCACTTCTTCCCCAT 1168–1267 1.000 83.7
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 1112–1211 1.000 83.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (19)

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

Species Accession Length (bp) Link
Beilschmiedia appendiculata NC_051896.1 158639 View on NCBI ↗
Beilschmiedia brachythyrsa NC_051895.1 158546 View on NCBI ↗
Beilschmiedia brenesii NC_051897.1 158671 View on NCBI ↗
Beilschmiedia brevipaniculata NC_051898.1 158475 View on NCBI ↗
Beilschmiedia brunnea NC_051899.1 158323 View on NCBI ↗
Beilschmiedia delicata NC_051900.1 158518 View on NCBI ↗
Beilschmiedia fasciata NC_051901.1 158414 View on NCBI ↗
Beilschmiedia fordii PQ899492.1 158400 View on NCBI ↗
Beilschmiedia glauca NC_051902.1 158566 View on NCBI ↗
Beilschmiedia immersinervis NC_051903.1 158564 View on NCBI ↗
Beilschmiedia kunstleri PQ899493.1 158621 View on NCBI ↗
Beilschmiedia obtusifolia NC_051904.1 158233 View on NCBI ↗
Beilschmiedia pergamentacea NC_051905.1 158438 View on NCBI ↗
Beilschmiedia pierreana NC_051906.1 158553 View on NCBI ↗
Beilschmiedia purpurascens NC_051917.1 158416 View on NCBI ↗
Beilschmiedia robusta PQ899495.1 158411 View on NCBI ↗
Beilschmiedia rufohirtella NC_051907.1 158496 View on NCBI ↗
Beilschmiedia tungfangensis PQ899496.1 158536 View on NCBI ↗
Beilschmiedia yunnanensis NC_051909.1 158443 View on NCBI ↗