Markers + reference

Amaranthus

20 species · Amaranthaceae · Caryophyllales

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Species 20
Genome length 150–151 kb
Candidate markers 265
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 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 849 0.0183 0.93 60.4 yes View details
trnS-trnG-UCC LSC 657 0.0200 0.98 65.6 yes View details
psbM-trnD-GUC LSC 1074 0.0121 0.99 59.3 yes View details
rps4-trnT LSC 465 0.0126 1.00 61.3 yes View details
trnT-trnL-UAA LSC 653 0.0107 0.99 57.8 yes View details
accD-psaI LSC 521 0.0156 0.99 65.6 yes View details
ycf1 IRb 1398 0.0019 1.00 29.7 no View details
rpl32-trnL-UAG SSC 1179 0.0211 0.97 65.3 yes View details
ycf1 SSC 5406 0.0080 1.00 38.0 yes View details
psaA-ycf3 LSC 770 0.0099 1.00 65.0 yes View details
trnE-UUC-trnT LSC 494 0.0146 1.00 63.4 yes View details
psaJ-rpl33 LSC 342 0.0129 1.00 61.4 yes View details
atpH-atpI LSC 748 0.0076 1.00 60.0 yes View details
trnC-GCA-petN LSC 502 0.0140 1.00 59.8 yes View details
psbE-petL LSC 871 0.0104 1.00 58.5 yes View details
rpl33-rps18 LSC 285 0.0123 1.00 58.3 yes View details
rps16 LSC 1113 0.0039 1.00 56.8 yes View details
petA-psbJ LSC 927 0.0076 1.00 56.2 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGGCGGAGGTTTTTAAGGAA 859–966 1.000 86.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CAAGAGGGCGGAGGTTTTTA 864–971 1.000 85.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGAGGGCGGAGGTTTTTAAG 862–969 1.000 83.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GAGGGCGGAGGTTTTTAAGG 861–968 1.000 82.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGAATTCCTTGCTTCATCCG GGGCGGAGGTTTTTAAGGAA 898–1005 1.000 82.4
rps16_p1 rps16 TTGTGTGTTGGATTGGCACT TGACTGTCCTGACTGAACCA 1310–1324 1.000 82.2
rps16_p2 rps16 TTTGTGTGTTGGATTGGCAC TGACTGTCCTGACTGAACCA 1311–1325 1.000 79.3
rps16_p3 rps16 TGTGTGTTGGATTGGCACTA TGACTGTCCTGACTGAACCA 1309–1323 1.000 78.8
rps16_p4 rps16 TGTGTTGGATTGGCACTACA TGACTGTCCTGACTGAACCA 1307–1321 1.000 78.8
rps16_p5 rps16 TTGTGTGTTGGATTGGCACT ACCGGTTCCAAATTTGAGGA 1253–1267 1.000 78.6
trnS-trnG-UCC_p1 trnS-trnG-UCC ACGGAAAGAGAGGGATTCGA TCAAACCGGTAGACCCCTTA 788–851 1.000 85.0
trnS-trnG-UCC_p2 trnS-trnG-UCC ACGGAAAGAGAGGGATTCGA AACCGGTAGACCCCTTAACT 785–848 1.000 84.9
trnS-trnG-UCC_p3 trnS-trnG-UCC ACGGAAAGAGAGGGATTCGA AATCAAACCGGTAGACCCCT 790–853 1.000 84.9
trnS-trnG-UCC_p4 trnS-trnG-UCC ACGGAAAGAGAGGGATTCGA ATCAAACCGGTAGACCCCTT 789–852 1.000 84.9
trnS-trnG-UCC_p5 trnS-trnG-UCC TGGAAACGGAAAGAGAGGGA TCAAACCGGTAGACCCCTTA 793–856 1.000 83.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTGCAACTTTAGCTGCAGC 822–837 1.000 83.3
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 793–808 1.000 83.2
atpH-atpI_p3 atpH-atpI AGCGGCAGAAATCAATGGAT TTTGCAACTTTAGCTGCAGC 814–829 1.000 83.1
atpH-atpI_p4 atpH-atpI AGCGGCAGAAATCAATGGAT CGAATCCATGGAGGGTCATC 785–800 1.000 83.0
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT TTTGCAACTTTAGCTGCAGC 878–893 1.000 82.4
trnC-GCA-petN_p1 trnC-GCA-petN TGTTCCCCAGTTCAAATCCG GCCCAAGCGAGACTTACAAT 548–577 1.000 82.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC GCCCAAGCGAGACTTACAAT 603–632 1.000 82.3
trnC-GCA-petN_p3 trnC-GCA-petN TGTTCCCCAGTTCAAATCCG AGAGTCCACTTCTTCCCCAT 610–639 1.000 81.2
trnC-GCA-petN_p4 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGAGTCCACTTCTTCCCCAT 665–694 1.000 81.1
trnC-GCA-petN_p5 trnC-GCA-petN GCAAATCCTTGTTCCCCAGT GCCCAAGCGAGACTTACAAT 557–586 1.000 80.2
psbM-trnD-GUC_p1 psbM-trnD-GUC TCATTTTGGCTGACCGTTTT TCAATTGGTTAGAGCACCGC 872–1272 1.000 71.8
psbM-trnD-GUC_p2 psbM-trnD-GUC AATCATTTTGGCTGACCGTT TCAATTGGTTAGAGCACCGC 874–1274 1.000 69.9
psbM-trnD-GUC_p3 psbM-trnD-GUC ATCATTTTGGCTGACCGTTT TCAATTGGTTAGAGCACCGC 873–1273 1.000 69.9
psbM-trnD-GUC_p4 psbM-trnD-GUC TCATTTTGGCTGACCGTTTTT TCAATTGGTTAGAGCACCGC 872–1272 1.000 69.8
psbM-trnD-GUC_p5 psbM-trnD-GUC TTTGGCTGACCGTTTTTACA TCAATTGGTTAGAGCACCGC 868–1268 1.000 69.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (20)

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

Species Accession Length (bp) Link
Amaranthus albus NC_065857.1 150757 View on NCBI ↗
Amaranthus blitoides NC_065859.1 150668 View on NCBI ↗
Amaranthus blitum NC_056982.1 150775 View on NCBI ↗
Amaranthus capensis NC_065855.1 150708 View on NCBI ↗
Amaranthus caudatus NC_040143.1 150523 View on NCBI ↗
Amaranthus crispus NC_065854.1 150539 View on NCBI ↗
Amaranthus cruentus PP596895.1 150757 View on NCBI ↗
Amaranthus deflexus NC_065853.1 150257 View on NCBI ↗
Amaranthus dubius MZ397802.1 150520 View on NCBI ↗
Amaranthus hybridus NC_053787.1 150759 View on NCBI ↗
Amaranthus hypochondriacus NC_030770.1 150518 View on NCBI ↗
Amaranthus powellii PQ385849.1 150775 View on NCBI ↗
Amaranthus powellii subsp. bouchonii PQ375111.1 150721 View on NCBI ↗
Amaranthus retroflexus MW646089.1 150710 View on NCBI ↗
Amaranthus roxburghianus NC_073000.1 149969 View on NCBI ↗
Amaranthus spinosus NC_065858.1 150524 View on NCBI ↗
Amaranthus standleyanus NC_065856.1 150582 View on NCBI ↗
Amaranthus tricolor NC_065013.1 150718 View on NCBI ↗
Amaranthus tuberculatus NC_085814.1 150680 View on NCBI ↗
Amaranthus viridis MW679034.1 150452 View on NCBI ↗