Markers + reference

Climacoptera

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 150–150 kb
Candidate markers 269
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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 842 0.0351 0.98 70.4 yes View details
rpoB-trnC-GCA LSC 1146 0.0229 0.99 58.0 yes View details
trnS-UGA-psbZ LSC 352 0.0312 1.00 66.4 yes View details
trnS-GGA-rps4 LSC 344 0.0293 0.99 63.1 yes View details
rps3 LSC 663 0.0166 1.00 55.2 yes View details
rpl2 LSC 825 0.0085 1.00 62.7 yes View details
trnN-GUU-ndhF IRb 2056 0.0322 0.94 70.1 yes View details
ndhF-rpl32 SSC 1104 0.0296 0.92 69.7 yes View details
rpl32-trnL-UAG SSC 790 0.0358 0.92 70.2 yes View details
ycf1 SSC 5460 0.0197 1.00 50.4 yes View details
rpl23 LSC 171 0.1135 0.82 87.7 yes View details
psbC-trnS-UGA LSC 210 0.1190 1.00 83.1 yes View details
rps14-psaB LSC 121 0.0413 1.00 76.3 yes View details
ycf3-trnS-GGA LSC 566 0.0236 0.90 73.2 yes View details
trnK-UUU-rps16 LSC 673 0.0244 0.97 72.7 yes View details
rpl23-trnH-GUG IRa 17 0.1765 1.00 72.6 yes View details
rpl23 IRa 21 0.0952 1.00 72.0 yes View details
trnH-GUG-psbA LSC 252 0.0448 0.88 71.4 yes View details
rps4-trnT-UGU LSC 427 0.0342 0.96 69.4 yes View details
psbT-psbN LSC 65 0.0308 1.00 68.8 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 TTCCCTCTAGACCTAGCTGC 293–322 1.000 85.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 307–336 1.000 84.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 306–335 1.000 84.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 308–337 1.000 84.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 342–371 1.000 82.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGCTCAACCTACCGAAACTG 765–780 1.000 80.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCTACCGAAACTG 764–779 1.000 80.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACCTACCGAAACTGT 764–779 1.000 80.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACCGAAACTGT 763–778 1.000 80.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCTACCGAAACT 765–780 1.000 80.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 965–967 1.000 54.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CGAATGACTCGTACAACGGA ACGAATCACACTTTTACCACT 935–937 1.000 53.5
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA AGAACGAATCACACTTTTACCAC 968–970 1.000 53.2
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA GAACGAATCACACTTTTACCACT 967–969 1.000 53.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TCGAAACGGAAAGAGAGGGA ACGAATCACACTTTTACCACT 970–972 1.000 52.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT AGGCCCAGTTAGTAACCACT 1969–1976 1.000 81.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT GGAATGGAGAGGTCTCGGTA 1943–1950 1.000 80.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCGGGCTTTGCAATATTTG AGGCCCAGTTAGTAACCACT 1849–1856 1.000 80.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCGGATTTGAACTGGGGAAA 1720–1722 1.000 80.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCGGGCTTTGCAATATTTG GGAATGGAGAGGTCTCGGTA 1823–1830 1.000 80.7
psbC-trnS-UGA_p1 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GAGAGATGGCTGAGTGGTTG 375–377 1.000 82.1
psbC-trnS-UGA_p2 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GTTGGAGAGATGGCTGAGTG 379–381 1.000 82.1
psbC-trnS-UGA_p3 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGTTGATAGCTCCGGTCTTG 360–362 1.000 82.1
psbC-trnS-UGA_p4 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GCTGAGTGGTTGATAGCTCC 367–369 1.000 82.0
psbC-trnS-UGA_p5 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGCTGAGTGGTTGATAGCTC 368–370 1.000 82.0
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC CCAACCATCAGGAGAAGCAA 472 1.000 80.1
trnS-UGA-psbZ_p2 trnS-UGA-psbZ GAGCTATCAACCACTCAGCC CCAACCATCAGGAGAAGCAA 479 1.000 79.8
trnS-UGA-psbZ_p3 trnS-UGA-psbZ GGAGCTATCAACCACTCAGC CCAACCATCAGGAGAAGCAA 480 1.000 79.8
trnS-UGA-psbZ_p4 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC CCAACCATCAGGAGAAGCAA 487 1.000 79.7
trnS-UGA-psbZ_p5 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC GACCAACCATCAGGAGAAGC 474 1.000 79.6

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
Climacoptera lanata ON929852.1 150081 View on NCBI ↗
Climacoptera subcrassa ON929867.1 150232 View on NCBI ↗