Markers + reference

Turpinia

2 species · Staphyleaceae · Crossosomatales

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Species 2
Genome length 160–160 kb
Candidate markers 269
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1508 0.0020 0.99 60.4 yes View details
psbK-psbI LSC 324 0.0000 1.00 34.2 yes View details
psbI-trnS-GCU LSC 202 0.0101 0.98 60.2 yes View details
trnC-GCA-petN LSC 953 0.0042 1.00 61.4 yes View details
psaA-ycf3 LSC 767 0.0052 1.00 61.9 yes View details
ycf3 LSC 1970 0.0010 1.00 58.4 yes View details
clpP LSC 2107 0.0033 1.00 59.4 yes View details
petB LSC 1439 0.0014 1.00 59.7 yes View details
trnF-GAA-ndhJ LSC 707 0.0000 0.97 61.8 yes View details
ndhC-trnV-UAC LSC 756 0.0000 0.97 61.4 yes View details
rpl32-trnL-UAG SSC 1072 0.0010 0.98 61.1 yes View details
trnK-UUU-rps16 LSC 918 0.0011 1.00 59.7 yes View details
accD-psaI LSC 695 0.0014 1.00 59.7 yes View details
cemA LSC 696 0.0014 1.00 59.6 yes View details
matK LSC 1521 0.0013 1.00 59.5 yes View details
rbcL-accD LSC 775 0.0013 1.00 59.5 yes View details
rps16 LSC 1154 0.0009 1.00 59.3 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
trnK-UUU_p1 trnK-UUU TGCGGATTTCTATACATATGATTTCG TGTTTTGATTGTGTCGTGAA 2691–2697 1.000 40.2
trnK-UUU_p2 trnK-UUU TGCGGATTTCTATACATATGATTTCG TGTTTTGATTGTGTCGTGAAA 2691–2697 1.000 40.2
trnK-UUU_p3 trnK-UUU GCGGATTTCTATACATATGATTTCGA TGTTTTGATTGTGTCGTGAA 2690–2696 1.000 40.2
trnK-UUU_p4 trnK-UUU TGCGGATTTCTATACATATGATTTCG ATGTTTTGATTGTGTCGTGA 2692–2698 1.000 40.2
trnK-UUU_p5 trnK-UUU AGAATGCGGATTTCTATACAT TGTTTTGATTGTGTCGTGAA 2695–2701 1.000 40.2
matK_p1 matK TCAGCCCTTACTCTTACGACA TCCTCTACCCTCGGTTCAAA 1669 1.000 68.0
matK_p2 matK CAGCCCTTACTCTTACGACA TCCTCTACCCTCGGTTCAAA 1668 1.000 67.0
matK_p3 matK TCAGCCCTTACTCTTACGACA AATCCTCTACCCTCGGTTCA 1671 1.000 66.1
matK_p4 matK TCAGCCCTTACTCTTACGACA ATCCTCTACCCTCGGTTCAA 1670 1.000 66.1
matK_p5 matK CAGCCCTTACTCTTACGACA ATCCTCTACCCTCGGTTCAA 1669 1.000 65.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AACAGGCGCTCAATCTACAG 1043–1046 1.000 78.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AACAGGCGCTCAATCTACAG 1042–1045 1.000 78.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TATTTCAACGAAGGCGGGAG 1010–1013 1.000 78.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTCAACGAAGGCGGGAG 1009–1012 1.000 78.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTGAAACAGGCGCTCAATCT 1046–1049 1.000 78.1
rps16_p1 rps16 ATACAATTCCCCCACACCCT GTACCGACTGAACCGATGAC 1268–1269 1.000 76.9
rps16_p2 rps16 ATACAATTCCCCCACACCCT ACCGACTGAACCGATGACTA 1266–1267 1.000 76.3
rps16_p3 rps16 ATACAATTCCCCCACACCCT TACCGACTGAACCGATGACT 1267–1268 1.000 76.3
rps16_p4 rps16 ATACAATTCCCCCACACCCT TGTACCGACTGAACCGATGA 1269–1270 1.000 74.0
rps16_p5 rps16 ATACAATTCCCCCACACCCT ATGTACCGACTGAACCGATG 1270–1271 1.000 73.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATCAAAATGGGGCGTGG 1639–1652 1.000 79.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1581–1594 1.000 78.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACATCGCTTCAAACGAAG GAAATCAAAATGGGGCGTGG 1619–1632 1.000 78.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACATCGCTTCAAACGAAG GAGGTTCGAATCCTTCCGTC 1561–1574 1.000 78.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAAATCAAAATGGGGCGTGG 1653–1666 1.000 77.5
psbK-psbI_p1 psbK-psbI CCAAATTACCCGAGGCCTAC TTCTTCACGCCCAGGATTAC 548 1.000 76.5
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGCCCAGGATTAC 462 1.000 76.4
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTCTTCACGCCCAGGATTAC 459 1.000 74.4
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTCTTCACGCCCAGGATTAC 460 1.000 74.4
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTCTTCACGCCCAGGATTAC 461 1.000 74.4

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
Turpinia arguta NC_050925.1 160139 View on NCBI ↗
Turpinia montana NC_051997.1 160111 View on NCBI ↗