Markers + reference

Galinsoga

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–152 kb
Candidate markers 271
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1131 0.0018 1.00 59.8 yes View details
psbC LSC 1422 0.0000 1.00 31.2 yes View details
psbC-trnS-UGA LSC 234 0.0171 1.00 62.3 yes View details
rbcL-accD LSC 562 0.0036 1.00 60.0 yes View details
clpP LSC 2015 0.0015 1.00 58.5 yes View details
ycf1 SSC 5058 0.0010 1.00 51.3 yes View details
ycf1-rps15 SSC 405 0.0049 1.00 57.5 yes View details
ndhD SSC 1503 0.0020 1.00 48.5 yes View details
trnL-UAG-rpl32 SSC 737 0.0027 1.00 57.4 yes View details
ycf1 IRa 567 0.0000 1.00 39.3 no View details
psaC-ndhD SSC 116 0.0259 1.00 66.9 yes View details
psbE-petL LSC 1277 0.0016 1.00 59.7 yes View details
rps2 LSC 711 0.0014 1.00 59.6 yes View details
accD-psaI LSC 717 0.0014 1.00 59.6 yes View details
trnK-UUU-rps16 LSC 775 0.0013 1.00 59.5 yes View details
psaA-ycf3 LSC 723 0.0014 1.00 59.5 yes View details
atpB-rbcL LSC 783 0.0000 0.99 59.4 yes View details
rpl32-ndhF SSC 905 0.0011 1.00 59.4 yes View details
rps12-ycf15 IRb 986 0.0010 1.00 59.3 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 972–973 1.000 76.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 971–972 1.000 76.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 911–912 1.000 76.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 910–911 1.000 76.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TGGTATGGACGAATCCCTCA TTCCTTGAAAAAGGCGCTCA 968–969 1.000 76.2
rps16_p1 rps16 ACGAATAGAGCAAGAAAAGAAGG TCTCTGTACCGACTGAACCA 1317–1324 1.000 44.9
rps16_p2 rps16 ACGAATAGAGCAAGAAAAGAAGGA TCTCTGTACCGACTGAACCA 1317–1324 1.000 44.2
rps16_p3 rps16 CGAATAGAGCAAGAAAAGAAGGA TCTCTGTACCGACTGAACCA 1316–1323 1.000 42.9
rps16_p4 rps16 ACGAATAGAGCAAGAAAAGAAGG GTCTCTGTACCGACTGAACC 1318–1325 1.000 42.1
rps16_p5 rps16 ACGAATAGAGCAAGAAAAGAAGGA GTCTCTGTACCGACTGAACC 1318–1325 1.000 41.4
rps2_p1 rps2 CTGTGCATCTACGCCAATCT TGAGATTCAGAAATAGTAACCGA 899 1.000 40.1
rps2_p2 rps2 TGCATCTACGCCAATCTACG TGAGATTCAGAAATAGTAACCGA 896 1.000 40.1
rps2_p3 rps2 TTTTTCAAAAGGGGGAGGCA TGAGATTCAGAAATAGTAACCGA 821 1.000 40.1
rps2_p4 rps2 TTTTCAAAAGGGGGAGGCAG TGAGATTCAGAAATAGTAACCGA 820 1.000 40.1
rps2_p5 rps2 CTGTGCATCTACGCCAATCT TTGAGATTCAGAAATAGTAACCGA 900 1.000 40.1
psbC_p1 psbC TTTCTCAAGAAATTCGCGCG GGGAACCGAAGTGACTCCTA 1576 1.000 74.6
psbC_p2 psbC CGGCGGAAGATCCTGAATTT GGGAACCGAAGTGACTCCTA 1558 1.000 73.8
psbC_p3 psbC AGGTATTCGTGCTTGGATGG GGGAACCGAAGTGACTCCTA 1503 1.000 73.8
psbC_p4 psbC GGCGGAAGATCCTGAATTTG GGGAACCGAAGTGACTCCTA 1557 1.000 67.3
psbC_p5 psbC TATTCGTGCTTGGATGGCG GGGAACCGAAGTGACTCCTA 1500 1.000 65.9
psbC-trnS-UGA_p1 psbC-trnS-UGA TCTTCGTAGGGCATTTGTGG GAGAGATGGCTGAGTGGTTG 429 1.000 79.7
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GAGAGATGGCTGAGTGGTTG 346 1.000 79.5
psbC-trnS-UGA_p3 psbC-trnS-UGA TCTTCGTAGGGCATTTGTGG GTCTTTCGGAGAGATGGCTG 437 1.000 79.3
psbC-trnS-UGA_p4 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GTCTTTCGGAGAGATGGCTG 354 1.000 79.1
psbC-trnS-UGA_p5 psbC-trnS-UGA TCTTCGTAGGGCATTTGTGG TCTTTCGGAGAGATGGCTGA 436 1.000 78.7
psaA-ycf3_p1 psaA-ycf3 GAGAAATGACCCGGTCTAGC AGCCGCTGAGTATTGGAAAC 915–918 1.000 76.2
psaA-ycf3_p2 psaA-ycf3 GAGAAATGACCCGGTCTAGC CAAGCCGCTGAGTATTGGAA 917–920 1.000 76.2
psaA-ycf3_p3 psaA-ycf3 GAGAAATGACCCGGTCTAGC AAGCCGCTGAGTATTGGAAA 916–919 1.000 74.4
psaA-ycf3_p4 psaA-ycf3 TTTTACTTCTGGTTCCGGCG AGCCGCTGAGTATTGGAAAC 850–853 1.000 74.1
psaA-ycf3_p5 psaA-ycf3 TTTTACTTCTGGTTCCGGCG CAAGCCGCTGAGTATTGGAA 852–855 1.000 74.1

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
Galinsoga parviflora NC_046787.1 151811 View on NCBI ↗
Galinsoga quadriradiata NC_031853.1 151917 View on NCBI ↗