Markers + reference

Garuga

3 species · Burseraceae · Sapindales

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Species 3
Genome length 159–159 kb
Candidate markers 268
Primer pairs 85

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 8 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1153 0.0012 1.00 47.1 yes View details
trnE-UUC-trnT-GGU LSC 783 0.0000 1.00 37.4 yes View details
trnT-GGU-psbD LSC 1504 0.0027 1.00 47.9 yes View details
petA-psbJ LSC 1098 0.0012 1.00 47.0 yes View details
ccsA SSC 969 0.0007 1.00 46.7 yes View details
ccsA-ndhD SSC 313 0.0000 1.00 34.0 yes View details
ndhD SSC 1500 0.0004 1.00 46.5 yes View details
rps15 SSC 273 0.0000 1.00 29.6 yes View details
ycf1 SSC 5190 0.0004 1.00 40.2 yes View details
cemA LSC 699 0.0010 1.00 46.9 yes View details
petN-psbM LSC 726 0.0009 1.00 46.8 yes View details
pafI-trnS-GGA LSC 753 0.0009 1.00 46.8 yes View details
rpl32-trnL-UAG SSC 1238 0.0005 1.00 46.6 yes View details
matK LSC 1518 0.0004 1.00 46.5 yes View details
accD LSC 1500 0.0004 1.00 46.5 yes View details
rpoA-rps11 LSC 65 0.0103 1.00 46.5 yes View details
psaA-pafI LSC 701 0.0000 1.00 46.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK TTCGTATTGCCTGAACATTT CCTTGTTTTGACTGTATCGCA 1714 1.000 40.0
matK_p2 matK TTCGTATTGCCTGAACATTT ACCTTGTTTTGACTGTATCGC 1715 1.000 40.0
matK_p3 matK TTCGTATTGCCTGAACATTT CCTTGTTTTGACTGTATCGCAC 1714 1.000 40.0
matK_p4 matK TTCGTATTGCCTGAACATTT CCCATGCATCATTTGATAACCC 1674 1.000 40.0
matK_p5 matK TTCGTATTGCCTGAACATTT CCCCATGCATCATTTGATAACC 1675 1.000 40.0
rps16_p1 rps16 GGAGTCATCCACACCCTCTT CTGTGTATCGACCGAAGCAA 1270–1271 1.000 74.4
rps16_p2 rps16 GGAGTCATCCACACCCTCT CTGTGTATCGACCGAAGCAA 1270–1271 1.000 72.1
rps16_p3 rps16 GAGTCATCCACACCCTCTTT CTGTGTATCGACCGAAGCAA 1269–1270 1.000 70.8
rps16_p4 rps16 GGAGTCATCCACACCCTCTT TGTGTATCGACCGAAGCAAT 1269–1270 1.000 69.1
rps16_p5 rps16 GAGTCATCCACACCCTCTTTT CTGTGTATCGACCGAAGCAA 1269–1270 1.000 68.7
petN-psbM_p1 petN-psbM TAGTTAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 888 1.000 67.6
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 827 1.000 66.0
petN-psbM_p3 petN-psbM TAGTTAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 888 1.000 63.4
petN-psbM_p4 petN-psbM TAGTTAGTCTCGCTTGGGCT ACGTAAAAACGGTTAGCCAA 838 1.000 62.2
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTC 827 1.000 61.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 886 1.000 77.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 865 1.000 77.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 865 1.000 77.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 844 1.000 77.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 862 1.000 77.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GAAACGATCCCTCCGTAACC 1646 1.000 79.2
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GAAACGATCCCTCCGTAACC 1649 1.000 79.1
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ATCCCTCCGTAACCAGTCAT 1640 1.000 78.4
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ATCCCTCCGTAACCAGTCAT 1643 1.000 78.2
trnT-GGU-psbD_p5 trnT-GGU-psbD TCCTATCTGCCCAGTGACTC GAAACGATCCCTCCGTAACC 1701 1.000 78.0
psaA-pafI_p1 psaA-pafI GCCCATTCCTCGAAAGAAGT TATCGCGCTTACTCCTGGTA 850–851 1.000 78.9
psaA-pafI_p2 psaA-pafI GCCCATTCCTCGAAAGAAGT CGCGCTTACTCCTGGTAATT 847–848 1.000 78.7
psaA-pafI_p3 psaA-pafI GCCCATTCCTCGAAAGAAGT AGCGCAGAATTGGTTGAAGA 820–821 1.000 78.3
psaA-pafI_p4 psaA-pafI GCCCATTCCTCGAAAGAAGT ATTGGTTGAAGATCACGGGG 812–813 1.000 78.1
psaA-pafI_p5 psaA-pafI TTGAGAAATGACCGGGTCTG TATCGCGCTTACTCCTGGTA 870–871 1.000 76.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Garuga floribunda var. gamblei PP337695.1 159421 View on NCBI ↗
Garuga forrestii NC_069621.1 159421 View on NCBI ↗
Garuga pinnata NC_071194.1 159422 View on NCBI ↗