Markers + reference

Toxicodendron

5 species · Anacardiaceae · Sapindales

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Species 5
Genome length 160–160 kb
Candidate markers 273
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

14 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 557 0.0430 1.00 86.1 yes View details
trnK-UUU-rps16 LSC 998 0.0176 0.99 72.4 yes View details
trnT-UGU-trnL-UAA LSC 1023 0.0120 0.99 62.8 yes View details
petG-trnW-CCA LSC 157 0.0293 1.00 64.3 yes View details
trnW-CCA-trnP-UGG LSC 172 0.0355 1.00 73.0 yes View details
petD LSC 525 0.0050 1.00 43.9 yes View details
rps19-rpl2 IRb 170 0.0271 1.00 61.8 yes View details
rpl2 IRb 1490 0.0011 1.00 49.1 no View details
ycf1 IRb 1101 0.0022 1.00 46.7 no View details
ndhF-rpl32 SSC 1052 0.0117 0.99 58.3 yes View details
rpl32-trnL-UAG SSC 953 0.0134 1.00 62.7 yes View details
ccsA-ndhD SSC 324 0.0262 0.99 62.3 yes View details
ycf1 SSC 5652 0.0076 1.00 45.1 yes View details
rpl2 IRa 1490 0.0011 1.00 50.3 yes View details
rpl2-trnH-GUG IRa 154 0.1418 0.60 69.3 no View details
petD-rpoA LSC 257 0.0416 0.99 67.0 yes View details
ndhD-psaC SSC 524 0.0112 0.99 66.9 yes View details
trnE-UUC-trnT-GGU LSC 830 0.0072 1.00 65.5 yes View details
petA-psbJ LSC 782 0.0083 1.00 65.3 yes View details
atpA-atpF LSC 56 0.0232 1.00 64.3 yes View details
trnC-GCA-petN LSC 678 0.0089 1.00 63.8 yes View details
pafI-trnS-GGA LSC 405 0.0081 0.99 63.6 yes View details
petN-psbM LSC 716 0.0114 1.00 63.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 582–653 1.000 89.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 596–667 1.000 89.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 595–666 1.000 89.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 597–668 1.000 89.2
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 611–682 1.000 86.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCGATGGTATGGACGAATC TATTTCAAAGAAGGCGGGGG 1155–1250 1.000 83.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TATTTCAAAGAAGGCGGGGG 1154–1249 1.000 83.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TATTTCAAAGAAGGCGGGGG 1093–1188 1.000 83.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTCAAAGAAGGCGGGGG 1092–1187 1.000 83.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TATTTCAAAGAAGGCGGGGG 1102–1197 1.000 82.3
atpA-atpF_p1 atpA-atpF ATGCCATCGCCTACTTGAAG TGGGGCGCTGAAAGAAATAA 198–200 1.000 80.4
atpA-atpF_p2 atpA-atpF ATGCCATCGCCTACTTGAAG TTGGGGCGCTGAAAGAAATA 199–201 1.000 80.4
atpA-atpF_p3 atpA-atpF GATGCCATCGCCTACTTGAA TGGGGCGCTGAAAGAAATAA 199–201 1.000 80.4
atpA-atpF_p4 atpA-atpF GATGCCATCGCCTACTTGAA TTGGGGCGCTGAAAGAAATA 200–202 1.000 80.3
atpA-atpF_p5 atpA-atpF ATGCCATCGCCTACTTGAAG GGGGCGCTGAAAGAAATAAC 197–199 1.000 77.6
trnC-GCA-petN_p1 trnC-GCA-petN AACAAAACAAGCAAACGGGG AGCCCAAGCGAGACTTACTA 637–824 1.000 84.0
trnC-GCA-petN_p2 trnC-GCA-petN AACAAAACAAGCAAACGGGG AGAGTCCACTTCTTCCCCAT 698–885 1.000 82.3
trnC-GCA-petN_p3 trnC-GCA-petN CAAAACAAGCAAACGGGGAA AGCCCAAGCGAGACTTACTA 635–822 1.000 81.7
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 565–752 1.000 81.4
trnC-GCA-petN_p5 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 540–727 1.000 80.5
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 866–878 1.000 71.8
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 805–817 1.000 70.5
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 866–878 1.000 67.6
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTC 805–817 1.000 66.3
petN-psbM_p5 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTCT 867–879 1.000 65.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 963–977 1.000 80.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 926–940 1.000 80.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 942–956 1.000 80.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 905–919 1.000 80.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 939–953 1.000 80.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Toxicodendron diversilobum NC_068850.1 159543 View on NCBI ↗
Toxicodendron griffithii NC_053916.1 159613 View on NCBI ↗
Toxicodendron succedaneum NC_067614.1 159636 View on NCBI ↗
Toxicodendron sylvestre MT211615.1 159600 View on NCBI ↗
Toxicodendron vernicifluum NC_046700.1 159571 View on NCBI ↗