Markers + reference

Chenopodium

14 species · Amaranthaceae · Caryophyllales

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Species 14
Genome length 152–152 kb
Candidate markers 267
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petN-psbM LSC 678 0.0153 1.00 50.4 yes View details
psaA-ycf3 LSC 810 0.0136 1.00 51.2 yes View details
ycf3-trnS-GGA LSC 934 0.0153 0.99 50.6 yes View details
rps4-trnT-UGU LSC 392 0.0302 0.99 68.5 yes View details
trnT-UGU-trnL-UAA LSC 771 0.0178 1.00 58.5 yes View details
psbE-petL LSC 1086 0.0121 1.00 47.8 yes View details
psaJ-rpl33 LSC 403 0.0290 1.00 43.8 yes View details
ndhF SSC 2247 0.0105 1.00 48.8 yes View details
ndhF-rpl32 SSC 960 0.0168 1.00 54.4 yes View details
rpl32-trnL-UAG SSC 1073 0.0187 1.00 65.4 yes View details
ycf1 SSC 5646 0.0109 1.00 50.9 yes View details
rps16-trnQ-UUG LSC 609 0.0143 0.99 62.7 yes View details
trnE-UUC-trnT-GGU LSC 503 0.0156 0.99 61.8 yes View details
rpl2-trnH-GUG IRa 144 0.0037 1.00 58.5 no View details
trnH-GUG-psbA LSC 140 0.0276 1.00 58.0 yes View details
psbM-trnD-GUC LSC 786 0.0117 1.00 54.0 yes View details
rrn23-rrn4.5 IRb 92 0.0401 1.00 54.0 yes View details
rrn4.5-rrn23 IRa 92 0.0401 1.00 54.0 yes View details
psbI-trnS-GCU LSC 199 0.0240 0.99 52.3 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 95 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 CTAGACCTAGCCGCTATCGA 195–209 0.857 81.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCTAGACCTAGCCGCTATCG 196–210 0.857 81.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTAGACCTAGCCGCTATCGA 209–223 0.857 80.9
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCTAGACCTAGCCGCTATCG 210–224 0.857 80.9
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTAGACCTAGCCGCTATCGA 208–222 0.857 80.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACGGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 683–703 1.000 84.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 662–682 1.000 84.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 673–693 1.000 83.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACGGATCATGTCCTT TAAGGCATCGGGTTTTGGTC 713–733 1.000 83.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 692–712 1.000 83.2
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA GTCATTCGTACCGAGGGTTC 251–260 1.000 84.2
psbI-trnS-GCU_p2 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA AGTCATTCGTACCGAGGGTT 252–261 1.000 81.2
psbI-trnS-GCU_p3 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA TTTTCAACGGGGAGAGATGG 312–321 1.000 79.5
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA GATGGCTGAGTGGACGAAAG 297–306 1.000 78.7
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA GAGTCATTCGTACCGAGGGT 253–262 1.000 77.6
petN-psbM_p1 petN-psbM ATGGGGAAGAAGTGGACTCT AAAACGGTTAGCCAGAATGA 715–727 1.000 60.4
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT AAAAACGGTTAGCCAGAATGA 716–728 1.000 58.9
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT AAACGGTTAGCCAGAATGAT 714–726 1.000 58.5
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT AACGGTTAGCCAGAATGATT 713–725 1.000 58.5
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT TGTAAAAACGGTTAGCCAGA 719–731 1.000 57.6
psbM-trnD-GUC_p1 psbM-trnD-GUC TCATTCTGGCTAACCGTTTT TCAATTGGTTAGAGCACCGC 949–956 1.000 55.8
psbM-trnD-GUC_p2 psbM-trnD-GUC TCATTCTGGCTAACCGTTTTT TCAATTGGTTAGAGCACCGC 949–956 1.000 54.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AATCATTCTGGCTAACCGTT TCAATTGGTTAGAGCACCGC 951–958 1.000 53.9
psbM-trnD-GUC_p4 psbM-trnD-GUC ATCATTCTGGCTAACCGTTT TCAATTGGTTAGAGCACCGC 950–957 1.000 53.9
psbM-trnD-GUC_p5 psbM-trnD-GUC TCTGGCTAACCGTTTTTACA TCAATTGGTTAGAGCACCGC 945–952 1.000 53.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 560–597 1.000 85.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 558–595 1.000 85.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 539–576 1.000 84.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 537–574 1.000 84.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 557–594 1.000 84.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Chenopodium acuminatum NC_054154.1 152200 View on NCBI ↗
Chenopodium album NC_034950.1 152167 View on NCBI ↗
Chenopodium amaranticolor PP727303.1 152193 View on NCBI ↗
Chenopodium berlandieri NC_085145.1 152194 View on NCBI ↗
Chenopodium berlandieri subsp. nuttalliae PP952099.1 152125 View on NCBI ↗
Chenopodium bryoniifolium NC_085144.1 152166 View on NCBI ↗
Chenopodium ficifolium NC_041200.1 151823 View on NCBI ↗
Chenopodium hircinum PP952100.1 152068 View on NCBI ↗
Chenopodium karoi PP234530.1 152047 View on NCBI ↗
Chenopodium quinoa NC_034949.1 152099 View on NCBI ↗
Chenopodium sonorense PP952103.1 152075 View on NCBI ↗
Chenopodium subglabrum PP952104.1 152103 View on NCBI ↗
Chenopodium suecicum OR654989.1 151865 View on NCBI ↗
Chenopodium watsonii PP952105.1 152098 View on NCBI ↗