Markers + reference

Agrimonia

6 species · Rosaceae · Rosales

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Species 6
Genome length 155–155 kb
Candidate markers 268
Primer pairs 100

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 925 0.0068 0.99 55.6 yes View details
trnS-GCU-trnG-GCC LSC 601 0.0083 0.97 55.6 yes View details
trnR-UCU-atpA LSC 602 0.0202 0.92 75.9 yes View details
rpoC2 LSC 4134 0.0013 1.00 35.6 yes View details
rpoB-trnC-GCA LSC 1008 0.0083 1.00 59.4 yes View details
trnC-GCA-petN LSC 784 0.0064 0.99 53.1 yes View details
ndhC-trnV-UAC LSC 652 0.0119 0.99 49.0 yes View details
accD-psaI LSC 516 0.0173 0.97 59.1 yes View details
rpl16 LSC 1374 0.0055 0.99 44.2 yes View details
rpl32-trnL-UAG SSC 801 0.0093 0.95 61.8 yes View details
petN-psbM LSC 1269 0.0049 0.99 62.8 yes View details
rps19-rpl2 IRb 56 0.0179 0.98 60.0 yes View details
rpl14-rpl16 LSC 168 0.0129 0.99 59.7 yes View details
rps2-rpoC2 LSC 220 0.0276 1.00 58.5 yes View details
trnL-UAA-trnF-GAA LSC 350 0.0053 0.99 58.5 yes View details
psbM-trnD-GUC LSC 1001 0.0030 1.00 58.2 yes View details
trnP-UGG-psaJ LSC 455 0.0059 0.94 57.0 yes View details
trnH-GUG-psbA LSC 332 0.0135 0.94 56.4 yes View details
ndhF-rpl32 SSC 1137 0.0023 0.98 56.0 yes View details
rpl20-rps12 LSC 805 0.0038 1.00 55.6 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 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 TTTCCCTCTAGACCTAGCGG 381–402 1.000 84.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTTCCCTCTAGACCTAGCGG 395–416 1.000 84.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTTCCCTCTAGACCTAGCGG 394–415 1.000 84.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTTCCCTCTAGACCTAGCGG 396–417 1.000 84.7
trnH-GUG-psbA_p5 trnH-GUG-psbA ATTCATTGATGGGCGAACGA TTTCCCTCTAGACCTAGCGG 466 0.167 45.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 988–1014 1.000 80.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCACAGACGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1010–1036 1.000 80.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 999–1025 1.000 80.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CTCCACAGACGATCATGTCC GAGGTTCGAATCCTTCCGTC 1011–1037 1.000 80.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGACGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1009–1035 1.000 76.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AATCAAACCGAAAGACCCTT 696–736 1.000 60.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ATCAAACCGAAAGACCCTTT 695–735 1.000 60.9
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ATCAAACCGAAAGACCCTTT 694–734 1.000 60.9
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC AATCAAACCGAAAGACCCTT 695–735 1.000 60.8
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ATCAAACCGAAAGACCCTTT 749–789 1.000 59.4
trnR-UCU-atpA_p1 trnR-UCU-atpA AATTGGAGTGAAAGGCGTCC CAGGACCAGATGGAACGTTT 661–730 1.000 81.9
trnR-UCU-atpA_p2 trnR-UCU-atpA AGTGAAAGGCGTCCATTGTC CAGGACCAGATGGAACGTTT 655–724 1.000 81.9
trnR-UCU-atpA_p3 trnR-UCU-atpA GAGTGAAAGGCGTCCATTGT CAGGACCAGATGGAACGTTT 656–725 1.000 81.9
trnR-UCU-atpA_p4 trnR-UCU-atpA GTGAAAGGCGTCCATTGTCT CAGGACCAGATGGAACGTTT 654–723 1.000 81.9
trnR-UCU-atpA_p5 trnR-UCU-atpA AATTGGAGTGAAAGGCGTCC ACCGCAGTTCCAAGAAATCA 737–806 1.000 80.9
rps2-rpoC2_p1 rps2-rpoC2 CCTGCTTCCATCATCTCTTCC TTTTTCGGATTTAATGATTCCT 285–294 1.000 46.3
rps2-rpoC2_p2 rps2-rpoC2 AGGTGCCATCCTAGGATTCC TTTTTCGGATTTAATGATTCCT 334–343 1.000 45.4
rps2-rpoC2_p3 rps2-rpoC2 GGTGCCATCCTAGGATTCCA TTTTTCGGATTTAATGATTCCT 333–342 1.000 45.4
rps2-rpoC2_p4 rps2-rpoC2 AGGTGCCATCCTAGGATTCC ACATGATACATCAAAACAATCTT 356–365 1.000 45.1
rps2-rpoC2_p5 rps2-rpoC2 AGGTGCCATCCTAGGATTCC ACATGATACATCAAAACAATCTTT 356–365 1.000 45.1
rpoC2_p1 rpoC2 AATTAAGGACTCATTCGCTC GGATTTGTGCGCCTTTCAAG 200 1.000 40.8
rpoC2_p2 rpoC2 AAATTAAGGACTCATTCGCTC GGATTTGTGCGCCTTTCAAG 201 1.000 40.8
rpoC2_p3 rpoC2 AATTAAGGACTCATTCGCTC AAAGGATTTGTGCGCCTTTC 203 1.000 40.8
rpoC2_p4 rpoC2 AAATTAAGGACTCATTCGCTC AAAGGATTTGTGCGCCTTTC 204 1.000 40.8
rpoC2_p5 rpoC2 AAAATTAAGGACTCATTCGCTC GGATTTGTGCGCCTTTCAAG 202 1.000 40.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Agrimonia coreana NC_058959.1 155362 View on NCBI ↗
Agrimonia eupatoria NC_066021.1 155187 View on NCBI ↗
Agrimonia gorovoii PX425320.1 155211 View on NCBI ↗
Agrimonia nipponica NC_058960.1 155161 View on NCBI ↗
Agrimonia pilosa NC_050051.1 155188 View on NCBI ↗
Agrimonia pilosa var. nepalensis MW387437.1 155147 View on NCBI ↗