Markers + reference

Pentanema

3 species · Asteraceae · Asterales

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Species 3
Genome length 151–152 kb
Candidate markers 267
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 6 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaA-ycf3 LSC 725 0.0009 1.00 47.0 yes View details
ndhC-trnV-UAC LSC 346 0.0000 1.00 32.8 yes View details
ycf2 IRb 6849 0.0031 1.00 27.4 yes View details
ycf2-trnL IRb 419 0.0207 1.00 47.8 yes View details
ycf1 IRb 618 0.0000 1.00 40.0 no View details
ycf1 SSC 5091 0.0005 1.00 52.8 yes View details
trnL-ycf2 IRa 419 0.0207 1.00 47.8 yes View details
ycf2 IRa 6849 0.0031 1.00 27.4 no View details
trnG-UCC-psbD LSC 1391 0.0000 1.00 58.9 yes View details
rps16-trnQ-UUG LSC 902 0.0007 1.00 46.9 yes View details
rpl32-trnL SSC 888 0.0008 1.00 46.7 yes View details
ndhF-rpl32 SSC 1082 0.0006 1.00 46.6 yes View details
ycf3 LSC 1952 0.0003 1.00 45.5 yes View details
clpP LSC 2010 0.0000 1.00 45.2 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 973–975 1.000 78.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 984–986 1.000 78.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CACACCGGATCATGTCCTTC GAGGTTCGAATCCTTCCGTC 993–995 1.000 76.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CACCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 991–993 1.000 76.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1044–1046 1.000 75.6
trnG-UCC_p1 trnG-UCC AGAGTCTGTTAGAGTATTTGAGA ACATATACAGAAGCGCCTCG 909 1.000 40.1
trnG-UCC_p2 trnG-UCC AGAGTCTGTTAGAGTATTTGAGA GCCTCGACAAAAGGTCCATT 895 1.000 40.1
trnG-UCC_p3 trnG-UCC AGAGTCTGTTAGAGTATTTGAGA TATACAGAAGCGCCTCGACA 906 1.000 40.1
trnG-UCC_p4 trnG-UCC AGAGTCTGTTAGAGTATTTGAGAA ACATATACAGAAGCGCCTCG 909 1.000 40.1
trnG-UCC_p5 trnG-UCC AGAGTCTGTTAGAGTATTTGAGAA GCCTCGACAAAAGGTCCATT 895 1.000 40.1
trnG-UCC-psbD_p1 trnG-UCC-psbD AATCAAACCGAAAGACCCCT GAAACGGTCCCTACGTAACC 1550–1552 1.000 72.3
trnG-UCC-psbD_p2 trnG-UCC-psbD ATCAAACCGAAAGACCCCTT GAAACGGTCCCTACGTAACC 1549–1551 1.000 72.3
trnG-UCC-psbD_p3 trnG-UCC-psbD CAATCAAACCGAAAGACCCC GAAACGGTCCCTACGTAACC 1551–1553 1.000 72.0
trnG-UCC-psbD_p4 trnG-UCC-psbD AATCAAACCGAAAGACCCCT GGACCAGCCTACAAAAACGA 1568–1570 1.000 71.4
trnG-UCC-psbD_p5 trnG-UCC-psbD ATCAAACCGAAAGACCCCTT GGACCAGCCTACAAAAACGA 1567–1569 1.000 71.4
psaA-ycf3_p1 psaA-ycf3 AGAAATGACCCGGTTTAGCC CGACCAAGCTGCTGAGTATT 921–922 1.000 79.1
psaA-ycf3_p2 psaA-ycf3 AGAAATGACCCGGTTTAGCC ACCAAGCTGCTGAGTATTGG 919–920 1.000 78.2
psaA-ycf3_p3 psaA-ycf3 CCCATGCCTCGAATGAAGTT CGACCAAGCTGCTGAGTATT 903–904 1.000 78.1
psaA-ycf3_p4 psaA-ycf3 GTTTAGCCCATGCCTCGAAT CGACCAAGCTGCTGAGTATT 909–910 1.000 77.5
psaA-ycf3_p5 psaA-ycf3 TTTAGCCCATGCCTCGAATG CGACCAAGCTGCTGAGTATT 908–909 1.000 77.5
ycf3_p1 ycf3 TGATGGGGCCAACAAACAAT TCCCGCGAGAAGTAATGAGA 2088 1.000 75.9
ycf3_p2 ycf3 TGATGGGGCCAACAAACAAT GGATCATTTTCCCGCGAGAA 2097 1.000 75.2
ycf3_p3 ycf3 TGATGGGGCCAACAAACAAT ATCATTTTCCCGCGAGAAGT 2095 1.000 74.6
ycf3_p4 ycf3 ATTTGACTGATGGGGCCAAC TCCCGCGAGAAGTAATGAGA 2095 1.000 74.6
ycf3_p5 ycf3 ATTTGACTGATGGGGCCAAC GGATCATTTTCCCGCGAGAA 2104 1.000 73.8
ndhC-trnV-UAC_p1 ndhC-trnV-UAC GTCCTTTGCTAATCGGAGCT AGAAGGTCTACGGTTCGAGT 491–492 1.000 75.9
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CGGTCCTTTGCTAATCGGAG AGAAGGTCTACGGTTCGAGT 493–494 1.000 75.0
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CTCCGGTCCTTTGCTAATCG AGAAGGTCTACGGTTCGAGT 496–497 1.000 75.0
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GTCCTTTGCTAATCGGAGCT GAAGGTCTACGGTTCGAGTC 490–491 1.000 73.1
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GGTCCTTTGCTAATCGGAGC AGAAGGTCTACGGTTCGAGT 492–493 1.000 72.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Pentanema ensifolium OR990532.1 151109 View on NCBI ↗
Pentanema hirtum OR990533.1 151105 View on NCBI ↗
Pentanema x haussmannii OR990535.1 152052 View on NCBI ↗