Markers + reference

Blitum

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 152–153 kb
Candidate markers 270
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 670 0.0271 0.99 63.5 yes View details
trnT-GGU-psbD LSC 1236 0.0187 0.99 59.2 yes View details
trnT-UGU-trnL-UAA LSC 768 0.0321 0.97 72.3 yes View details
psbE-petL LSC 1146 0.0255 0.99 67.5 yes View details
rpl22 LSC 600 0.0233 1.00 58.3 yes View details
ycf1 IRb 1458 0.0027 1.00 48.0 no View details
ndhF SSC 2235 0.0125 1.00 58.3 yes View details
ndhF-rpl32 SSC 845 0.0203 0.99 68.9 yes View details
rpl32-trnL-UAG SSC 1082 0.0355 0.78 78.3 yes View details
ndhA SSC 2207 0.0114 0.99 49.9 yes View details
ycf1 SSC 5535 0.0158 1.00 47.5 yes View details
rrn23-rrn4.5 IRb 61 0.0656 1.00 73.8 yes View details
rrn4.5-rrn23 IRa 61 0.0656 1.00 73.8 yes View details
ndhI-ndhA SSC 111 0.0450 1.00 71.0 yes View details
trnS-GCU-trnG-UCC LSC 637 0.0243 0.97 70.8 yes View details
cemA-petA LSC 267 0.0449 1.00 70.7 yes View details
atpH-atpI LSC 772 0.0183 0.99 70.3 yes View details
trnR-UCU-atpA LSC 87 0.0482 0.95 69.7 yes View details
ycf4-cemA LSC 666 0.0153 0.98 69.6 yes View details
rps4-trnT-UGU LSC 419 0.0296 0.97 68.7 yes View details
trnP-UGG-psaJ LSC 430 0.0211 0.99 68.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGAATTTCGACTTAATCAAACGA 734–738 1.000 43.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAATTTCGACTTAATCAAACGA 733–737 1.000 43.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTCGACTTAATCAAACGAAG 730–734 1.000 43.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCGACTTAATCAAACGAAG 729–733 1.000 43.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAATTTCGACTTAATCAAACGAAG 733–737 1.000 43.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AATCAAACCGTTAGACCCCT 789–803 1.000 69.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATCAAACCGTTAGACCCCTT 788–802 1.000 69.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGAATGACTCGTACAACGGA AATCAAACCGTTAGACCCCT 759–773 1.000 69.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGAATGACTCGTACAACGGA ATCAAACCGTTAGACCCCTT 758–772 1.000 69.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TGGAAACGGAAAGAGAGGGA ATCAAACCGTTAGACCCCTT 793–807 1.000 68.9
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TCAATGCTGGAATCAGACCG 808–809 1.000 80.7
trnR-UCU-atpA_p2 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GCAGGAGATGTTTCGGCTTA 887–888 1.000 80.6
trnR-UCU-atpA_p3 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG TCAATGCTGGAATCAGACCG 811–812 1.000 80.5
trnR-UCU-atpA_p4 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG GCAGGAGATGTTTCGGCTTA 890–891 1.000 80.4
trnR-UCU-atpA_p5 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CCAATAGTCGAGACCCAAGC 905–906 1.000 80.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCACTGGAAGGTCAT 823–830 1.000 81.6
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT GCGAATCACTGGAAGGTCAT 879–886 1.000 80.9
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCCGCAG 852–859 1.000 80.7
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA GCGAATCACTGGAAGGTCAT 839–846 1.000 80.7
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCACTGGAAGGTCAT 824–831 1.000 80.4
trnT-GGU-psbD_p1 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA ACAAAAACGAAACGGTCCCT 1363–1375 1.000 77.5
trnT-GGU-psbD_p2 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA CAAAAACGAAACGGTCCCTC 1362–1374 1.000 76.3
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA TCCCTCCGTAACCAGTCATC 1348–1360 1.000 75.4
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCATGGTAAGGCGTAAGTC ACAAAAACGAAACGGTCCCT 1373–1385 1.000 74.1
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA AAAAACGAAACGGTCCCTCC 1361–1373 1.000 74.0
rps4-trnT-UGU_p1 rps4-trnT-UGU AGTCCAGGTAAAGCCCCTAG CTCAGAGGTTAGAGCATCGC 542–544 1.000 81.7
rps4-trnT-UGU_p2 rps4-trnT-UGU GTCCAGGTAAAGCCCCTAGA CTCAGAGGTTAGAGCATCGC 541–543 1.000 81.6
rps4-trnT-UGU_p3 rps4-trnT-UGU TCCAGGTAAAGCCCCTAGAC CTCAGAGGTTAGAGCATCGC 540–542 1.000 81.6
rps4-trnT-UGU_p4 rps4-trnT-UGU AGTCCAGGTAAAGCCCCTAG ATGGTCATCGGTTCGAATCC 510–512 1.000 81.0
rps4-trnT-UGU_p5 rps4-trnT-UGU TCCAGGTAAAGCCCCTAGAC ATGGTCATCGGTTCGAATCC 508–510 1.000 81.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Blitum bonus-henricus OR884979.1 152606 View on NCBI ↗
Blitum virgatum subsp. virgatum OR884978.1 152351 View on NCBI ↗