Markers + reference

Garnotia

4 species · Poaceae · Poales

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Species 4
Genome length 140–140 kb
Candidate markers 265
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1217 0.0108 1.00 62.2 yes View details
trnG-UCC-trnT-GGU LSC 1974 0.0110 0.98 60.9 yes View details
trnY-GUA-trnD-GUC LSC 346 0.0173 1.00 56.8 yes View details
trnD-GUC-psbM LSC 1055 0.0093 1.00 59.4 yes View details
rpoC2 LSC 4557 0.0052 1.00 33.2 yes View details
trnT-UGU-trnL-UAA LSC 800 0.0119 0.98 49.4 yes View details
rbcL-psaI LSC 821 0.0101 1.00 53.8 yes View details
psbE-petL LSC 1288 0.0097 0.99 45.5 yes View details
ndhF SSC 2217 0.0058 1.00 48.9 yes View details
rpl32-trnL-UAG SSC 488 0.0120 1.00 52.0 yes View details
ndhH SSC 1182 0.0093 1.00 51.1 yes View details
petB LSC 1407 0.0065 1.00 60.9 yes View details
trnS-GCU-psbD LSC 979 0.0068 0.99 56.9 yes View details
trnT-GGU-trnE-UUC LSC 514 0.0107 1.00 55.8 yes View details
ndhF-rpl32 SSC 814 0.0088 1.00 55.6 yes View details
trnW-CCA-trnP-UGG LSC 139 0.0123 0.98 55.2 yes View details
trnL-UAA-trnF-GAA LSC 386 0.0097 0.96 55.0 yes View details
ndhC-trnV-UAC LSC 978 0.0080 1.00 53.4 yes View details
rpl33-rps18 LSC 288 0.0093 1.00 52.8 yes View details
rps2 LSC 711 0.0038 1.00 52.6 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
trnK-UUU_p1 trnK-UUU AGATTGCTCTTTTCTATTTTCCA GAGCGTCCGGTGTAATTTCA 2622–2632 1.000 41.0
trnK-UUU_p2 trnK-UUU AGATTGCTCTTTTCTATTTTCCA AGCGTCCGGTGTAATTTCAT 2621–2631 1.000 41.0
trnK-UUU_p3 trnK-UUU AGATTGCTCTTTTCTATTTTCCA ATGTTTTGACAGGAGCGTCC 2634–2644 1.000 41.0
trnK-UUU_p4 trnK-UUU AAGATTGCTCTTTTCTATTTTCCA GAGCGTCCGGTGTAATTTCA 2623–2633 1.000 41.0
trnK-UUU_p5 trnK-UUU AAGATTGCTCTTTTCTATTTTCCA AGCGTCCGGTGTAATTTCAT 2622–2632 1.000 41.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1194–1291 1.000 83.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1205–1302 1.000 83.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1198–1295 1.000 82.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1209–1306 1.000 82.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1200–1297 1.000 80.9
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1103–1115 1.000 79.2
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1095–1107 1.000 76.6
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1089–1101 1.000 76.2
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA CTTCGTAACCAGTCGTCCAT 1085–1097 1.000 76.0
trnS-GCU-psbD_p5 trnS-GCU-psbD AGTCCACTCAGCCATCTCTC ACAAAAACGAAACGGTCCCT 1084–1096 1.000 75.4
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2075–2096 1.000 44.5
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 2045–2066 1.000 44.4
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 2041–2062 1.000 43.7
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 2042–2063 1.000 43.7
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2077–2098 1.000 43.6
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 633–635 1.000 68.6
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 612–614 1.000 68.5
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 596–598 1.000 68.5
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 575–577 1.000 68.4
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG GCTGCCTCCTTGAAAGAGAG 601–603 1.000 67.7
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 470–474 1.000 77.7
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 437–441 1.000 75.4
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 436–440 1.000 75.2
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 469–473 1.000 73.5
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 438–442 1.000 72.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Garnotia emodi PP112994.1 139912 View on NCBI ↗
Garnotia stricta var. longiseta MK593551.1 139831 View on NCBI ↗
Garnotia tenella NC_035051.1 139629 View on NCBI ↗
Garnotia thailandica NC_035042.1 139668 View on NCBI ↗