Markers + reference

Melanthalia

2 species · Gracilariaceae · Gracilariales

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Species 2
Genome length 210–218 kb
Candidate markers 467
Primer pairs 80

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 467 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
clpC-psbW Genome 6359 0.3452 0.57 68.9 yes View details
ompR-orf88 Genome 4879 0.3964 0.76 72.1 yes View details
orf88-orf89 Genome 1240 0.4578 0.72 77.1 yes View details
orf73-orf120 Genome 799 0.4637 0.72 77.3 yes View details
orf120 Genome 363 0.4921 0.87 76.5 yes View details
orf110-rns Genome 4768 0.4367 0.82 74.1 yes View details
psbD-ompR Genome 899 0.1834 0.92 83.4 yes View details
psaC-ycf22 Genome 718 0.1520 0.93 83.2 yes View details
rpl35-bas1 Genome 934 0.2780 0.97 83.2 yes View details
rpl19-dnaB Genome 943 0.2870 0.92 82.9 yes View details
trnR(ccg)-orf460 Genome 1590 0.2083 0.97 81.9 yes View details
syfB-rps1 Genome 503 0.1029 0.95 81.4 yes View details
cemA-orf687 Genome 1405 0.2626 0.85 80.8 yes View details
ycf21-cpcA Genome 1653 0.2571 0.98 80.7 yes View details
rps20-rpl33 Genome 729 0.2626 0.98 80.7 yes View details
ycf46-psaM Genome 648 0.1444 0.99 80.3 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf46-psaM_p1 ycf46-psaM AAACGAATGCGACAGGCTAT TACTGAAGGGGCTAAAGGCT 1295 0.500 59.5
ycf46-psaM_p2 ycf46-psaM GTGGGCGAATCTGAAAAACG TACTGAAGGGGCTAAAGGCT 1310 0.500 59.4
ycf46-psaM_p3 ycf46-psaM TGGGCGAATCTGAAAAACGA TACTGAAGGGGCTAAAGGCT 1309 0.500 58.8
ycf46-psaM_p4 ycf46-psaM TTGTTGATGGGCATACAGGG TACTGAAGGGGCTAAAGGCT 1421 0.500 58.6
ycf46-psaM_p5 ycf46-psaM GGCATACAGGGAACGGAAAA TACTGAAGGGGCTAAAGGCT 1412 0.500 58.4
ycf21-cpcA_p1 ycf21-cpcA TAGCCTCCATTCTGCAGGAA GAGCATCAGTAGCAGTTGCT 2458 0.500 56.5
ycf21-cpcA_p2 ycf21-cpcA TTAGCCTCCATTCTGCAGGA GAGCATCAGTAGCAGTTGCT 2459 0.500 56.5
ycf21-cpcA_p3 ycf21-cpcA TAGCCTCCATTCTGCAGGAA CATGGACTAGGTGGACAAGC 1836 0.500 56.4
ycf21-cpcA_p4 ycf21-cpcA TTAGCCTCCATTCTGCAGGA CATGGACTAGGTGGACAAGC 1837 0.500 56.4
ycf21-cpcA_p5 ycf21-cpcA TAGCCTCCATTCTGCAGGAA ATGGACTAGGTGGACAAGCT 1835 0.500 56.3
psaC-ycf22_p1 psaC-ycf22 AGCAGGTATGACAGGTGGAT ATTCCAGCTCGAATATCGGC 2037 0.500 58.4
psaC-ycf22_p2 psaC-ycf22 CCCCTGGGATGGTTGTAAAG ATTCCAGCTCGAATATCGGC 1450 0.500 58.2
psaC-ycf22_p3 psaC-ycf22 ACTAGTCGAAGCATGGGTCT ATTCCAGCTCGAATATCGGC 1320 0.500 58.1
psaC-ycf22_p4 psaC-ycf22 GGGATGGTTGTAAAGCTGCT ATTCCAGCTCGAATATCGGC 1445 0.500 58.0
psaC-ycf22_p5 psaC-ycf22 TGCTCCTAGAACCGAGGATT ATTCCAGCTCGAATATCGGC 1414 0.500 58.0
trnR(ccg)-orf460_p1 trnR(ccg)-orf460 GTTTCCTCCTGGCCGTAAAA ACAATGGAAAAGGATGCCGA 2795 0.500 57.5
trnR(ccg)-orf460_p2 trnR(ccg)-orf460 GCCTAAAGGTTCAGTCAGCA ACAATGGAAAAGGATGCCGA 2497 0.500 56.8
trnR(ccg)-orf460_p3 trnR(ccg)-orf460 TGCCTAAAGGTTCAGTCAGC ACAATGGAAAAGGATGCCGA 2498 0.500 56.8
trnR(ccg)-orf460_p4 trnR(ccg)-orf460 TTTCCTCCTGGCCGTAAAAG ACAATGGAAAAGGATGCCGA 2794 0.500 56.7
trnR(ccg)-orf460_p5 trnR(ccg)-orf460 AGAGCGTGTAACTCAGAGGA ACAATGGAAAAGGATGCCGA 2178 0.500 56.7
cemA-orf687_p1 cemA-orf687 GCACCGGAAAGAAAATCTGC GGCAGGCCTATTTGGTTCTT 2369 0.500 58.7
cemA-orf687_p2 cemA-orf687 GCACCGGAAAGAAAATCTGC GTGTGTTGAATGCCATGCAA 2014 0.500 58.6
cemA-orf687_p3 cemA-orf687 GCAGAAGAACTTTCGTTGGC GGCAGGCCTATTTGGTTCTT 2333 0.500 58.5
cemA-orf687_p4 cemA-orf687 GCAGAAGAACTTTCGTTGGC GTGTGTTGAATGCCATGCAA 1978 0.500 58.5
cemA-orf687_p5 cemA-orf687 CTAGTACAGGCACCACCAAC GGCAGGCCTATTTGGTTCTT 2080 0.500 58.1
rps20-rpl33_p1 rps20-rpl33 CGACAATAACGGGAAAGGAGT TGTTTTGCAGTAAGCCCTGT 1718 0.500 51.2
rps20-rpl33_p2 rps20-rpl33 CGACAATAACGGGAAAGGAGT GTTGCTTCTGCTGTTTTGCA 1729 0.500 51.2
rps20-rpl33_p3 rps20-rpl33 TGACAGCCTCATGATTTAGCC TGTTTTGCAGTAAGCCCTGT 1594 0.500 50.9
rps20-rpl33_p4 rps20-rpl33 CGACAATAACGGGAAAGGAGT GTGGCCTGATGTGTGAAGAT 1966 0.500 50.8
rps20-rpl33_p5 rps20-rpl33 TGACAGCCTCATGATTTAGCC GTTGCTTCTGCTGTTTTGCA 1605 0.500 50.8

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
Melanthalia abscissa PP328475.1 209722 View on NCBI ↗
Melanthalia intermedia NC_039145.1 218416 View on NCBI ↗