Markers + reference

Chaetoseris

6 species · Asteraceae · Asterales

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Species 6
Genome length 153–153 kb
Candidate markers 275
Primer pairs 90

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 10 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnC-GCA-petN LSC 814 0.0011 1.00 43.9 yes View details
petN-psbM LSC 473 0.0020 1.00 41.9 yes View details
psbE-petL LSC 1251 0.0012 1.00 44.0 yes View details
clpP LSC 2041 0.0006 1.00 42.5 yes View details
ycf1 SSC 5064 0.0007 1.00 37.3 yes View details
ndhI SSC 501 0.0012 1.00 38.7 yes View details
ndhD SSC 1521 0.0010 1.00 43.8 yes View details
rpl32-ndhF SSC 1065 0.0009 1.00 38.7 yes View details
ycf1 IRa 472 0.0000 1.00 37.3 no View details
trnT-GGU-psbD LSC 1238 0.0000 0.98 49.0 yes View details
rpl16 LSC 1440 0.0006 1.00 43.6 yes View details
accD-psaI LSC 727 0.0005 1.00 43.5 yes View details
ycf3-trnS-GCU LSC 911 0.0004 1.00 43.4 yes View details
trnL-UAG-rpl32 SSC 899 0.0004 1.00 43.4 yes View details
atpI-atpH LSC 1178 0.0005 0.98 42.1 yes View details
matK-trnK LSC 729 0.0008 1.00 40.5 yes View details
ccsA SSC 969 0.0006 1.00 40.4 yes View details
petD LSC 1192 0.0004 1.00 40.3 yes View details
matK LSC 1521 0.0004 1.00 40.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK TCCTTACTACATACTACATCAACA ACCCCCAAAATCCTCTACCT 1681 1.000 40.0
matK_p2 matK ACATACTACATCAACATTTCAGA ACCCCCAAAATCCTCTACCT 1673 1.000 40.0
matK_p3 matK ACATACTACATCAACATTTCAGAA ACCCCCAAAATCCTCTACCT 1673 1.000 40.0
matK_p4 matK ACTACATACTACATCAACATTTCAGA ACCCCCAAAATCCTCTACCT 1676 1.000 40.0
matK_p5 matK CCTTACTACATACTACATCAACA ACCCCCAAAATCCTCTACCT 1680 1.000 40.0
matK-trnK_p1 matK-trnK ACCATGATCATGAGCAAGTACA AACGGTAGAGTACTCGGCTT 861 1.000 58.8
matK-trnK_p2 matK-trnK ACCATGATCATGAGCAAGTACA ACGGTAGAGTACTCGGCTTT 860 1.000 58.8
matK-trnK_p3 matK-trnK AGAAGTGGTGTTGTTGAGATCT AACGGTAGAGTACTCGGCTT 808 1.000 57.2
matK-trnK_p4 matK-trnK AGAAGTGGTGTTGTTGAGATCT ACGGTAGAGTACTCGGCTTT 807 1.000 57.2
matK-trnK_p5 matK-trnK ACCATGATCATGAGCAAGTACA TTGGGTTGCTAACTCAACGG 876 1.000 57.0
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 870 1.000 78.3
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 888 1.000 76.1
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 869 1.000 72.4
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 878 1.000 72.3
trnC-GCA-petN_p5 trnC-GCA-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 927 1.000 71.7
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 635 1.000 59.7
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 635 1.000 58.0
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 636 1.000 53.7
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 627 1.000 53.7
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 621 1.000 52.9
atpI-atpH_p1 atpI-atpH TCCCTGTCATGTTCCTTGGA ATAACGGAAGCGGCAGAAAT 1292–1314 1.000 79.0
atpI-atpH_p2 atpI-atpH TCCCTGTCATGTTCCTTGGA TACCTTGACCAACTCCAGGT 1348–1370 1.000 78.4
atpI-atpH_p3 atpI-atpH TCCCTGTCATGTTCCTTGGA AGCCAATCCAGCAGCAATAA 1308–1330 1.000 78.1
atpI-atpH_p4 atpI-atpH TCCCTGTCATGTTCCTTGGA AATAACGGAAGCGGCAGAAA 1293–1315 1.000 77.9
atpI-atpH_p5 atpI-atpH TCCCTGTCATGTTCCTTGGA GCAGTACCTTGACCAACTCC 1352–1374 1.000 77.8
trnT-GGU-psbD_p1 trnT-GGU-psbD CGTAAGCCCTCGGTTCAAAT GGACCAGCCTACAAAAACGA 1369–1378 1.000 78.9
trnT-GGU-psbD_p2 trnT-GGU-psbD TCCATGAACCAAGCCCTTTT GGACCAGCCTACAAAAACGA 1425–1434 1.000 77.8
trnT-GGU-psbD_p3 trnT-GGU-psbD TTCCATGAACCAAGCCCTTT GGACCAGCCTACAAAAACGA 1426–1435 1.000 77.8
trnT-GGU-psbD_p4 trnT-GGU-psbD CGTAAGCCCTCGGTTCAAAT ACAAAAACGAAACGGTCCCT 1359–1368 1.000 77.8
trnT-GGU-psbD_p5 trnT-GGU-psbD TAAGCCCTCGGTTCAAATCC GGACCAGCCTACAAAAACGA 1367–1376 1.000 77.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Chaetoseris hastata PQ586436.1 152533 View on NCBI ↗
Chaetoseris hispida PQ586437.1 152542 View on NCBI ↗
Chaetoseris lutea PQ586439.1 152541 View on NCBI ↗
Chaetoseris lyriformis PQ586441.1 152544 View on NCBI ↗
Chaetoseris sichuanensis PQ586443.1 152538 View on NCBI ↗
Chaetoseris yunnanensis PQ586446.1 152522 View on NCBI ↗