Markers + reference

Byrsonima

2 species · Malpighiaceae · Malpighiales

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Species 2
Genome length 160–160 kb
Candidate markers 281
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 281 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 276 0.0145 1.00 60.8 yes View details
rps16 LSC 1133 0.0018 1.00 52.0 yes View details
rps16-trnQ LSC 1550 0.0052 1.00 61.9 yes View details
atpA LSC 1512 0.0020 1.00 46.7 yes View details
psbZ-trnG LSC 549 0.0111 0.99 61.4 yes View details
rbcL LSC 1449 0.0048 1.00 47.4 yes View details
psaI-ycf4 LSC 470 0.0107 1.00 62.6 yes View details
rps11 LSC 417 0.0096 1.00 46.5 yes View details
rpl32-trnL SSC 426 0.0094 1.00 56.3 yes View details
ndhD SSC 1491 0.0013 1.00 50.4 yes View details
atpA-atpF LSC 58 0.0690 1.00 83.6 yes View details
ccsA-ndhD SSC 238 0.0420 1.00 71.8 yes View details
matK-trnK-UUU LSC 716 0.0056 1.00 62.0 yes View details
psaA-ycf3 LSC 829 0.0012 0.97 62.0 yes View details
petN-psbM LSC 1360 0.0030 0.97 61.9 yes View details
psbT-psbN LSC 65 0.0154 1.00 61.3 yes View details
psaJ-rpl33 LSC 519 0.0058 1.00 60.8 yes View details
trnS-trnG-GCC LSC 894 0.0035 0.97 60.7 yes View details
atpH-atpI LSC 1096 0.0027 1.00 60.3 yes View details
psbM-trnD LSC 1079 0.0019 0.99 60.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA TGGTTAGTTATGGGCGAACG CCTCTAGACCTAGCTGCTGT 408 1.000 80.2
trnH-GUG-psbA_p2 trnH-GUG-psbA TGGTTAGTTATGGGCGAACG TTCCCTCTAGACCTAGCTGC 411 1.000 80.1
trnH-GUG-psbA_p3 trnH-GUG-psbA TTAGTTATGGGCGAACGACG CCTCTAGACCTAGCTGCTGT 405 1.000 79.6
trnH-GUG-psbA_p4 trnH-GUG-psbA TTAGTTATGGGCGAACGACG TTCCCTCTAGACCTAGCTGC 408 1.000 79.5
trnH-GUG-psbA_p5 trnH-GUG-psbA TGGTTAGTTATGGGCGAACG TGGAAGTTATGCACGAACGT 443 1.000 79.4
trnK-UUU_p1 trnK-UUU AGTTGAAGTGAGTTAAAAATCGCA TGTGTCCTGCGATTCAATCT 2726–2732 1.000 40.4
trnK-UUU_p2 trnK-UUU AGTTGAAGTGAGTTAAAAATCGCA TTGTGTCCTGCGATTCAATCT 2727–2733 1.000 40.4
trnK-UUU_p3 trnK-UUU GTTGAAGTGAGTTAAAAATCGCA TGTGTCCTGCGATTCAATCT 2725–2731 1.000 40.4
trnK-UUU_p4 trnK-UUU AGTTGAAGTGAGTTAAAAATCGCA GTGTCCTGCGATTCAATCTCT 2725–2731 1.000 40.4
trnK-UUU_p5 trnK-UUU TGAAGTGAGTTAAAAATCGCA TGTGTCCTGCGATTCAATCT 2723–2729 1.000 40.4
matK-trnK-UUU_p1 matK-trnK-UUU ACCATGATCATGAGCAAGTGT TGAGGGTTGCTAACTCAACG 858–864 1.000 68.7
matK-trnK-UUU_p2 matK-trnK-UUU ACCATGATCATGAGCAAGTGT AACGGTAGAGTACTCGGCTT 842–848 1.000 68.7
matK-trnK-UUU_p3 matK-trnK-UUU ACCATGATCATGAGCAAGTGT ACGGTAGAGTACTCGGCTTT 841–847 1.000 68.7
matK-trnK-UUU_p4 matK-trnK-UUU ACTCCCGAAAGATAAGTGGG TGAGGGTTGCTAACTCAACG 829–835 1.000 68.7
matK-trnK-UUU_p5 matK-trnK-UUU CTCCCGAAAGATAAGTGGGT TGAGGGTTGCTAACTCAACG 828–834 1.000 68.7
rps16_p1 rps16 TGAGTTATCCACACCCTCGT TCCGTGAACCAATGACTATTCA 1244–1248 1.000 59.2
rps16_p2 rps16 CCACACCCTCGTAGTGTACT TCCGTGAACCAATGACTATTCA 1236–1240 1.000 56.1
rps16_p3 rps16 TCCACACCCTCGTAGTGTAC TCCGTGAACCAATGACTATTCA 1237–1241 1.000 56.1
rps16_p4 rps16 ATCCACACCCTCGTAGTGTA TCCGTGAACCAATGACTATTCA 1238–1242 1.000 55.6
rps16_p5 rps16 TGAGTTATCCACACCCTCGT CCGTGAACCAATGACTATTCA 1243–1247 1.000 55.4
rps16-trnQ_p1 rps16-trnQ GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1636–1656 1.000 79.8
rps16-trnQ_p2 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1620–1640 1.000 78.9
rps16-trnQ_p3 rps16-trnQ TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1631–1651 1.000 78.4
rps16-trnQ_p4 rps16-trnQ AGCCGATCATGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1637–1657 1.000 77.4
rps16-trnQ_p5 rps16-trnQ CCGAGAGCAACTTCATTCCT GAGGTTCGAATCCTTCCGTC 1692–1712 1.000 76.9
trnS-trnG-GCC_p1 trnS-trnG-GCC CAATCCGACGCTTTAGTCCA GAATATGAGCCGAGGGATCC 1006–1027 1.000 76.7
trnS-trnG-GCC_p2 trnS-trnG-GCC CAATCCGACGCTTTAGTCCA GGAATATGAGCCGAGGGATC 1007–1028 1.000 76.7
trnS-trnG-GCC_p3 trnS-trnG-GCC AATCCGACGCTTTAGTCCAC GAATATGAGCCGAGGGATCC 1005–1026 1.000 76.7
trnS-trnG-GCC_p4 trnS-trnG-GCC AATCCGACGCTTTAGTCCAC GGAATATGAGCCGAGGGATC 1006–1027 1.000 76.7
trnS-trnG-GCC_p5 trnS-trnG-GCC CAATCCGACGCTTTAGTCCA AATATGAGCCGAGGGATCCC 1005–1026 1.000 76.4

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
Byrsonima coccolobifolia NC_037191.1 160329 View on NCBI ↗
Byrsonima crassifolia NC_037192.1 160212 View on NCBI ↗