Markers + reference

Corispermum

4 species · Amaranthaceae · Caryophyllales

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Species 4
Genome length 151–151 kb
Candidate markers 262
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 360 0.0130 1.00 63.0 yes View details
trnD-GUC-trnY-GUA LSC 417 0.0052 1.00 40.4 yes View details
rpl33 LSC 297 0.0152 1.00 51.8 yes View details
rpl22 LSC 672 0.0022 1.00 32.1 yes View details
ycf2-trnL-CAA IRb 652 0.0061 1.00 39.8 yes View details
ndhD SSC 1614 0.0033 1.00 55.5 yes View details
ndhA SSC 2182 0.0029 1.00 44.7 yes View details
ycf1 SSC 5568 0.0039 1.00 55.8 yes View details
ndhB-trnL-CAA IRa 560 0.0000 1.00 34.1 yes View details
rpl22-rps19 LSC 27 0.0741 1.00 67.7 yes View details
rbcL-accD LSC 618 0.0035 1.00 61.1 yes View details
petA-psbJ LSC 972 0.0015 1.00 59.8 yes View details
trnF-GAA-ndhJ LSC 686 0.0022 1.00 58.0 yes View details
rpoC1 LSC 2826 0.0005 1.00 56.4 yes View details
rpoB LSC 3213 0.0008 1.00 55.8 yes View details
psaA-ycf3 LSC 708 0.0038 1.00 54.8 yes View details
rpoC2 LSC 4149 0.0006 1.00 54.3 yes View details
atpH-atpI LSC 701 0.0031 1.00 54.0 yes View details
rps16-trnQ-UUG LSC 610 0.0025 1.00 53.9 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 TTCCCTCTAGACCTAGCTGC 429–430 1.000 80.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 443–444 1.000 80.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 442–443 1.000 80.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 444–445 1.000 80.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 478–479 1.000 78.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACGGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 700–705 1.000 79.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 679–684 1.000 79.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 690–695 1.000 78.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACGGATCATGTCCTT TAAGGCATCGGGTTTTGGTC 730–735 1.000 78.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 709–714 1.000 78.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCCGCAG 786–796 1.000 79.2
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 756–766 1.000 78.9
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCAG 842–852 1.000 78.6
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCCGCAG 802–812 1.000 78.3
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 812–822 1.000 78.3
rpoC2_p1 rpoC2 CCCGATTTAAAGTGCGGTCT AGGAACAGCCCTTCCAATTG 321 1.000 77.6
rpoC2_p2 rpoC2 AAGTGCGGTCTGTTTTTGGT AGGAACAGCCCTTCCAATTG 312 1.000 75.4
rpoC2_p3 rpoC2 AGTGCGGTCTGTTTTTGGTT AGGAACAGCCCTTCCAATTG 311 1.000 75.4
rpoC2_p4 rpoC2 AAAGTGCGGTCTGTTTTTGG AGGAACAGCCCTTCCAATTG 313 1.000 75.1
rpoC2_p5 rpoC2 CCCGATTTAAAGTGCGGTCT GCCCTTCCAATTGCGAATTT 314 1.000 75.0
rpoC1_p1 rpoC1 ACTCGAATTCCACAAGTCCG ACGATCTTTGGCTCTGGAAC 2969–2972 1.000 78.7
rpoC1_p2 rpoC1 CTCGAATTCCACAAGTCCGA ACGATCTTTGGCTCTGGAAC 2968–2971 1.000 76.4
rpoC1_p3 rpoC1 ACTCGAATTCCACAAGTCCG CGATCTTTGGCTCTGGAACT 2968–2971 1.000 76.3
rpoC1_p4 rpoC1 CTCGAATTCCACAAGTCCGA CGATCTTTGGCTCTGGAACT 2967–2970 1.000 74.1
rpoC1_p5 rpoC1 ACTCGAATTCCACAAGTCCG ACTACGATCTTTGGCTCTGG 2972–2975 1.000 71.7
rpoB_p1 rpoB TATATCCCGCGGCAACAAAA TGGATAATGTTTGCTACCCGG 275 1.000 71.7
rpoB_p2 rpoB GTTCAGTCGCCGGTTCATAT TGGATAATGTTTGCTACCCGG 230 1.000 71.6
rpoB_p3 rpoB TCCGCAGCTGCCAATATATC TGGATAATGTTTGCTACCCGG 289 1.000 71.2
rpoB_p4 rpoB TATATCCCGCGGCAACAAAA GGATAATGTTTGCTACCCGGA 274 1.000 70.6
rpoB_p5 rpoB GTTCAGTCGCCGGTTCATAT GGATAATGTTTGCTACCCGGA 229 1.000 70.6

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
Corispermum chinganicum NC_086957.1 150647 View on NCBI ↗
Corispermum declinatum NC_086958.1 150590 View on NCBI ↗
Corispermum pamiricum PP234537.1 150615 View on NCBI ↗
Corispermum patelliforme PV256407.1 150614 View on NCBI ↗