Markers + reference

Melanoseris

5 species · Asteraceae · Asterales

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Species 5
Genome length 152–153 kb
Candidate markers 272
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 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1114 0.0027 1.00 60.8 yes View details
petN-psbM LSC 473 0.0059 1.00 60.6 yes View details
accD-psaI LSC 727 0.0033 1.00 50.6 yes View details
rpl20 LSC 381 0.0010 1.00 30.8 yes View details
clpP LSC 2054 0.0013 1.00 59.3 yes View details
rpl16-rps3 LSC 1181 0.0030 1.00 46.4 yes View details
ycf1 SSC 5037 0.0032 1.00 53.7 yes View details
ycf1-rps15 SSC 394 0.0056 1.00 45.5 yes View details
ycf1 IRa 495 0.0000 1.00 37.8 no View details
trnF-GAA-ndhJ LSC 625 0.0026 1.00 59.0 yes View details
rpl32-ndhF SSC 1065 0.0019 1.00 58.5 yes View details
rpoC1 LSC 2798 0.0007 1.00 56.8 yes View details
ndhC-trnV-UAC LSC 996 0.0020 1.00 56.4 yes View details
rpoC2 LSC 4146 0.0005 1.00 54.2 yes View details
trnE-UUC-rpoB LSC 895 0.0029 1.00 53.9 yes View details
atpB-rbcL LSC 772 0.0016 1.00 53.5 yes View details
trnK-UUU-rps16 LSC 767 0.0018 1.00 52.8 yes View details
matK LSC 1521 0.0018 1.00 52.7 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
trnK-UUU_p1 trnK-UUU GCCCGTGTCAACCAATATCT TCTGATTGTATCTACATACCCGT 2748 1.000 42.9
trnK-UUU_p2 trnK-UUU GCCCGTGTCAACCAATATCT TCTGATTGTATCTACATACCCGTT 2748 1.000 40.3
trnK-UUU_p3 trnK-UUU GCCCGTGTCAACCAATATCT TTCTGATTGTATCTACATACCCGT 2749 1.000 40.3
trnK-UUU_p4 trnK-UUU GCCCGTGTCAACCAATATCT CTGATTGTATCTACATACCCGT 2747 1.000 40.3
trnK-UUU_p5 trnK-UUU GCCCGTGTCAACCAATATCT CTGATTGTATCTACATACCCGTT 2747 1.000 40.3
matK_p1 matK ATTTACAAGGTTTCATAACGAA ACCCCCAAAATCCTCTACCT 1584 1.000 40.3
matK_p2 matK ATTTACAAGGTTTCATAACGAA AACCCCCAAAATCCTCTACC 1585 1.000 40.3
matK_p3 matK TATTTACAAGGTTTCATAACGAA ACCCCCAAAATCCTCTACCT 1585 1.000 40.3
matK_p4 matK ATTTACAAGGTTTCATAACGAA AACCCCCAAAATCCTCTACCT 1585 1.000 40.3
matK_p5 matK ATTTACAAGGTTTCATAACGAA ACCCCCAAAATCCTCTACCTT 1584 1.000 40.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 886–916 1.000 77.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 885–915 1.000 77.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 901–931 1.000 77.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTCCTTGAAAAAGGCGCTCA 895–925 1.000 77.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC TTCCTTGAAAAAGGCGCTCA 872–902 1.000 75.6
rps16_p1 rps16 AGAAATCACTATCCTACCCTTAGT TCTCTGTACCGACTGAACCA 1234–1260 1.000 41.3
rps16_p2 rps16 AGAAATCACTATCCTACCCT TCTCTGTACCGACTGAACCA 1234–1260 1.000 41.3
rps16_p3 rps16 AGAGCAAGAAAAGAAGGAAA TCTCTGTACCGACTGAACCA 1293–1319 0.800 33.1
rps16_p4 rps16 AGAGCAAGAAAAGAAGGAAAT TCTCTGTACCGACTGAACCA 1293–1319 0.800 33.1
rps16_p5 rps16 AGAGCAAGAAAAGAAGGAAA GTCTCTGTACCGACTGAACC 1294–1320 0.800 33.1
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 635 1.000 60.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 635 1.000 58.6
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 636 1.000 54.4
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 627 1.000 54.3
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 621 1.000 53.5
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT AGTTCTTCTGTCAAACCCTGA 1034–1040 1.000 62.9
trnE-UUC-rpoB_p2 trnE-UUC-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCTGA 993–999 1.000 62.2
trnE-UUC-rpoB_p3 trnE-UUC-rpoB CCCTCGTTTTCTCCGTGAAA AGTTCTTCTGTCAAACCCTGA 1024–1030 1.000 62.1
trnE-UUC-rpoB_p4 trnE-UUC-rpoB TTGAACCCTCGTTTTCTCCG AGTTCTTCTGTCAAACCCTGA 1029–1035 1.000 62.1
trnE-UUC-rpoB_p5 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT TCAAACCCTGATCAATGAACCT 1024–1030 1.000 61.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Melanoseris ciliata PP525143.1 152255 View on NCBI ↗
Melanoseris cyanea PQ586435.1 152497 View on NCBI ↗
Melanoseris decipiens NC_066793.1 152474 View on NCBI ↗
Melanoseris macrantha PP525145.1 152290 View on NCBI ↗
Melanoseris macrocephala PQ586445.1 152558 View on NCBI ↗