Markers + reference

Chorda

2 species · Chordaceae · Laminariales

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Species 2
Genome length 130–144 kb
Candidate markers 346
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 346 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
dnaB Genome 1746 0.4383 0.30 69.5 yes View details
psbB Genome 1533 0.3810 0.18 66.0 yes View details
rpoC2 Genome 3846 0.4347 0.91 77.9 yes View details
clpC Genome 2679 0.4049 0.25 67.1 yes View details
ccsA-psbK Genome 418 0.4575 0.51 71.6 yes View details
psbC Genome 1425 0.4602 1.00 79.2 yes View details
psbD-trnN-GUU Genome 237 0.4895 1.00 72.5 yes View details
trnV-UAC-trnT-UGU Genome 131 0.3664 1.00 72.6 yes View details
syfB Genome 2301 0.4605 0.96 80.6 yes View details
psbW Genome 345 0.4451 0.98 75.7 yes View details
rnl-trnA-UGC Genome 56 0.3810 0.75 85.8 yes View details
atpI Genome 738 0.3409 0.95 83.6 yes View details
atpD Genome 618 0.4566 0.93 83.1 yes View details
cp74 Genome 1905 0.4053 0.24 82.0 yes View details
psbD Genome 1053 0.4420 0.97 81.3 yes View details
atpA Genome 1506 0.2961 0.98 81.1 yes View details
rps2 Genome 696 0.4152 0.98 80.7 yes View details
ycf39 Genome 960 0.4401 0.98 80.5 yes View details
ycf24 Genome 1446 0.4392 0.98 80.3 yes View details
atpF Genome 525 0.4139 0.87 79.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
dnaB_p1 dnaB GATTGGTGGGGCAAACCTTA GTTTTGCCCATTGAAGGACG 402 0.500 58.9
dnaB_p2 dnaB TGGTGGGGCAAACCTTATTC GTTTTGCCCATTGAAGGACG 399 0.500 58.9
dnaB_p3 dnaB GATTGGTGGGGCAAACCTTA GCAGTTTTGCCCATTGAAGG 405 0.500 57.8
dnaB_p4 dnaB TGGTGGGGCAAACCTTATTC GCAGTTTTGCCCATTGAAGG 402 0.500 57.8
dnaB_p5 dnaB GGTGGGGCAAACCTTATTCT GTTTTGCCCATTGAAGGACG 398 0.500 57.6
psbB_p1 psbB CTTGAAGACGCTGGTGCTAT CCTATACAGCGTTTGGACCA 2509 0.500 54.4
psbB_p2 psbB CTTGAAGACGCTGGTGCTAT ACCTATACAGCGTTTGGACC 2510 0.500 54.4
psbB_p3 psbB AAACACTTGAAGACGCTGGT CCTATACAGCGTTTGGACCA 2514 0.500 54.2
psbB_p4 psbB AAACACTTGAAGACGCTGGT ACCTATACAGCGTTTGGACC 2515 0.500 54.2
psbB_p5 psbB CTCCTGCACGGCAAGAATAT CCTATACAGCGTTTGGACCA 2149 0.500 54.2
rnl-trnA-UGC_p1 rnl-trnA-UGC CCCCCGTAAGCCCTTATTTC CCATCTGGGGGTATAGCTCA 161 0.500 59.6
rnl-trnA-UGC_p2 rnl-trnA-UGC CCCCGTAAGCCCTTATTTCC CCATCTGGGGGTATAGCTCA 160 0.500 59.6
rnl-trnA-UGC_p3 rnl-trnA-UGC TCGTAGCTTGTTTCCAGCTC CCATCTGGGGGTATAGCTCA 236 0.500 59.1
rnl-trnA-UGC_p4 rnl-trnA-UGC CTCGTAGCTTGTTTCCAGCT CCATCTGGGGGTATAGCTCA 237 0.500 59.1
rnl-trnA-UGC_p5 rnl-trnA-UGC ATATCTCCGGCTCGTAGCTT CCATCTGGGGGTATAGCTCA 247 0.500 59.1
atpA_p1 atpA GGGCTAGCTGTTATGGAACC AGGGCCTGAGTTTACAACTTC 2316 0.500 50.6
atpA_p2 atpA GGGCTAGCTGTTATGGAACC GGGCCTGAGTTTACAACTTCT 2315 0.500 50.6
atpA_p3 atpA ATTATGGTGAGCCTGCTTGG AGGGCCTGAGTTTACAACTTC 2396 0.500 50.4
atpA_p4 atpA ATTATGGTGAGCCTGCTTGG GGGCCTGAGTTTACAACTTCT 2395 0.500 50.4
atpA_p5 atpA GGAACCTTCTGCCTTAGGTG GGGCCTGAGTTTACAACTTCT 2301 0.500 49.9
atpD_p1 atpD ACTCACGTTGACCTCTACCA CTGAAACACGTCTGGCAGAT 1650 0.500 58.3
atpD_p2 atpD CCCATAAGTACAGCCCCAAC CTGAAACACGTCTGGCAGAT 1384 0.500 58.0
atpD_p3 atpD ACTCACGTTGACCTCTACCA TGAAACACGTCTGGCAGATT 1649 0.500 57.9
atpD_p4 atpD ACTCACGTTGACCTCTACCA TCGGTTTTACGTAATCGCGA 1471 0.500 57.9
atpD_p5 atpD TGCGATCCCATCTCCTACTT CTGAAACACGTCTGGCAGAT 1271 0.500 57.7
atpF_p1 atpF AGCCTCTGAATATGGATTGGC GCTTAGTTGTGGCCTTAGCT 1260 0.500 49.9
atpF_p2 atpF GGATTGGCGATTTTTGAACCA GCTTAGTTGTGGCCTTAGCT 1247 0.500 48.6
atpF_p3 atpF TGGATTGGCGATTTTTGAACC GCTTAGTTGTGGCCTTAGCT 1248 0.500 48.6
atpF_p4 atpF CCTCTGAATATGGATTGGCGA GCTTAGTTGTGGCCTTAGCT 1258 0.500 47.8
atpF_p5 atpF AGCCTCTGAATATGGATTGGC TTTACGGCTTAGTTGTGGCC 1266 0.500 47.0

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
Chorda asiatica NC_085296.1 130219 View on NCBI ↗
Chorda filum NC_058751.1 143970 View on NCBI ↗