Markers + reference

Eclipta

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–152 kb
Candidate markers 269
Primer pairs 85

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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnC-GCA LSC 750 0.0040 1.00 54.3 yes View details
ycf4-cemA LSC 825 0.0024 1.00 60.1 yes View details
clpP LSC 2035 0.0010 0.99 59.0 yes View details
ycf1 IRb 597 0.0000 1.00 39.9 no View details
ndhF-rpl32 SSC 1013 0.0049 1.00 61.6 yes View details
rpl32-trnL-UAG SSC 775 0.0078 1.00 63.5 yes View details
ndhD SSC 1503 0.0007 1.00 47.7 yes View details
ndhA SSC 2118 0.0014 1.00 58.3 yes View details
ycf1 SSC 5067 0.0012 1.00 38.4 yes View details
ndhD-psaC SSC 117 0.0256 1.00 67.2 yes View details
trnT-UGU-trnL-UAA LSC 575 0.0018 0.98 60.8 yes View details
atpB-rbcL LSC 768 0.0013 0.99 60.3 yes View details
atpF LSC 1256 0.0016 1.00 59.7 yes View details
petD LSC 1213 0.0016 1.00 59.7 yes View details
rpoA-rps11 LSC 80 0.0125 1.00 59.7 yes View details
rps2 LSC 711 0.0014 1.00 59.6 yes View details
psbE-petL LSC 1294 0.0015 1.00 59.6 yes View details
rpl16 LSC 1430 0.0007 1.00 59.6 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 900–901 1.000 78.5
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 882–883 1.000 76.3
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 836–837 1.000 74.6
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 901–902 1.000 74.3
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 818–819 1.000 72.5
rps2_p1 rps2 GGCTGTGTATCTACGCCAAT AGTCAGAAATAGTAACCGATTCGA 896 1.000 42.6
rps2_p2 rps2 TTCAAAAGGGAGAGGCAGTG AGTCAGAAATAGTAACCGATTCGA 814 1.000 42.3
rps2_p3 rps2 GGCTGTGTATCTACGCCAAT TGAGAGTCAGAAATAGTAACCGA 900 1.000 42.3
rps2_p4 rps2 TTCAAAAGGGAGAGGCAGTG TGAGAGTCAGAAATAGTAACCGA 818 1.000 42.0
rps2_p5 rps2 GGCTGTGTATCTACGCCAAT TCTATGAAGGTTCCGAAATGA 868 1.000 41.1
atpF_p1 atpF ACAAAAAGAACTCTGTTCGA ATTTCGTCGGCTTGAATGGT 1391 1.000 40.1
atpF_p2 atpF ACAAAAAGAACTCTGTTCGA GTCGGCTTGAATGGTTACCA 1386 1.000 40.1
atpF_p3 atpF ACAAAAAGAACTCTGTTCGA TCGTCGGCTTGAATGGTTAC 1388 1.000 40.1
atpF_p4 atpF ACAAAAAGAACTCTGTTCGA TTTCGTCGGCTTGAATGGTT 1390 1.000 40.1
atpF_p5 atpF ACAAAAAGAACTCTGTTCGA TTGCTCAATACGTTCACGGA 1422 1.000 40.1
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 618–625 1.000 80.2
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 626–633 1.000 79.7
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 650–657 1.000 79.3
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 658–665 1.000 78.7
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 632–639 1.000 78.3
atpB-rbcL_p1 atpB-rbcL CTGGCGGAAAAGCTACATCT CACCAGCTTTGAATCCAACAC 923–929 1.000 72.2
atpB-rbcL_p2 atpB-rbcL CTGGCGGAAAAGCTACATCT ACCAGCTTTGAATCCAACACT 922–928 1.000 72.0
atpB-rbcL_p3 atpB-rbcL GGCAACCCCAGAACTAGAAG CACCAGCTTTGAATCCAACAC 850–856 1.000 71.6
atpB-rbcL_p4 atpB-rbcL GATACGCCCCAGGTTCTTTT CACCAGCTTTGAATCCAACAC 880–886 1.000 71.5
atpB-rbcL_p5 atpB-rbcL GGCAACCCCAGAACTAGAAG ACCAGCTTTGAATCCAACACT 849–855 1.000 71.3
ycf4-cemA_p1 ycf4-cemA GAGCCATTCCATTGACTCGT GAGAAATCCACCAGGGCAAA 1005 1.000 79.3
ycf4-cemA_p2 ycf4-cemA CTCCACGGGAAATGGAACAA GAGAAATCCACCAGGGCAAA 969 1.000 78.8
ycf4-cemA_p3 ycf4-cemA TTGGCCTATTTCTTGCGTGT GAGAAATCCACCAGGGCAAA 937 1.000 78.8
ycf4-cemA_p4 ycf4-cemA AAAAAGCTGCTGAATTGGCC GAGAAATCCACCAGGGCAAA 951 1.000 78.2
ycf4-cemA_p5 ycf4-cemA AAAGCTGCTGAATTGGCCTA GAGAAATCCACCAGGGCAAA 949 1.000 77.8

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
Eclipta alba NC_039774.1 151733 View on NCBI ↗
Eclipta prostrata NC_030773.1 151757 View on NCBI ↗