Markers + reference

Parthenium

2 species · Asteraceae · Asterales

Back to catalogue

Species 2
Genome length 152–153 kb
Candidate markers 212
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 212 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-matK LSC 560 0.0537 1.00 73.2 yes View details
matK-rps16 LSC 1419 0.0353 1.00 64.8 yes View details
trnS-GCU-psbM LSC 2384 0.1637 0.88 83.9 yes View details
psbM-rpoB LSC 2017 0.1876 0.89 91.5 yes View details
ndhC-atpE LSC 2091 0.0295 0.99 62.9 yes View details
rpl32-ndhF SSC 1093 0.0466 0.94 80.4 yes View details
ndhF-trnN SSC 1558 0.0066 0.58 42.5 yes View details
trnH-psbA LSC 331 0.0547 0.99 74.8 yes View details
petA-psbJ LSC 866 0.0295 0.90 74.7 yes View details
clpP-psbB LSC 499 0.0343 0.94 74.2 yes View details
psbC-trnS-UGA LSC 264 0.0717 0.95 74.0 yes View details
psbL-psbF LSC 22 0.0455 1.00 73.7 yes View details
ycf3 LSC 34 0.1176 1.00 72.6 yes View details
ndhD-ccsA SSC 241 0.0407 0.92 72.2 yes View details
atpl-atpH LSC 1156 0.0320 1.00 70.9 yes View details
ndhI-ndhG SSC 370 0.0676 1.00 70.2 yes View details
psaJ-rpl33 LSC 450 0.0390 0.97 69.7 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG TCCCTCTAGACTTAGCTGCT 400–508 1.000 73.4
trnH-psbA_p2 trnH-psbA CAATCCACTGCCTTGATCCA TCCCTCTAGACTTAGCTGCT 414–522 1.000 73.3
trnH-psbA_p3 trnH-psbA AATCCACTGCCTTGATCCAC TCCCTCTAGACTTAGCTGCT 413–521 1.000 73.3
trnH-psbA_p4 trnH-psbA ACAATCCACTGCCTTGATCC TCCCTCTAGACTTAGCTGCT 415–523 1.000 73.3
trnH-psbA_p5 trnH-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACTTAGCTGCT 401–509 1.000 71.4
psbA-matK_p1 psbA-matK CAGACGGAAACTAAGCTCCC GAGCGCTTTGGCCGTATATA 1283–1298 1.000 81.8
psbA-matK_p2 psbA-matK CCAGACGGAAACTAAGCTCC GAGCGCTTTGGCCGTATATA 1284–1299 1.000 81.8
psbA-matK_p3 psbA-matK CCCAGACGGAAACTAAGCTC GAGCGCTTTGGCCGTATATA 1285–1300 1.000 81.8
psbA-matK_p4 psbA-matK CGGAAACTAAGCTCCCACTC GAGCGCTTTGGCCGTATATA 1279–1294 1.000 81.8
psbA-matK_p5 psbA-matK CGGAAACTAAGCTCCCACTC GTACGCGGTCAAATGCTAGA 1456–1471 1.000 81.8
matK-rps16_p1 matK-rps16 GTTGTGCCCCAAAAATGGAG CCCAGAACAAGGAAACACCA 2264–2288 1.000 81.0
matK-rps16_p2 matK-rps16 TTGTGCCCCAAAAATGGAGT CCCAGAACAAGGAAACACCA 2263–2287 1.000 80.7
matK-rps16_p3 matK-rps16 GTTGTGCCCCAAAAATGGAG GCCGTACGAGGAGAAAACTT 1965–1994 1.000 80.6
matK-rps16_p4 matK-rps16 TTGTGCCCCAAAAATGGAGT GCCGTACGAGGAGAAAACTT 1964–1993 1.000 80.4
matK-rps16_p5 matK-rps16 GTTGTGCCCCAAAAATGGAG AGCCGTCTATCGAATCGTTG 1897–1925 1.000 80.3
trnS-GCU-psbM_p1 trnS-GCU-psbM CTTTCGTCCACTCAGCCATC ACGTAAAAACAGCCAGTCAA 2287–2438 1.000 69.5
trnS-GCU-psbM_p2 trnS-GCU-psbM CTTTCGTCCACTCAGCCATC ACGTAAAAACAGCCAGTCAAA 2287–2438 1.000 67.6
trnS-GCU-psbM_p3 trnS-GCU-psbM CTTTCGTCCACTCAGCCATC TGCTACTGCACTGTTCATTT 2337–2488 1.000 67.5
trnS-GCU-psbM_p4 trnS-GCU-psbM TTTCGTCCACTCAGCCATCT ACGTAAAAACAGCCAGTCAA 2286–2437 1.000 66.4
trnS-GCU-psbM_p5 trnS-GCU-psbM CTTTCGTCCACTCAGCCATC TGCTACTGCACTGTTCATTTT 2337–2488 1.000 65.8
psbM-rpoB_p1 psbM-rpoB TTGACTGGCTGTTTTTACGT CTTCTGCCAAACCCTGATCA 2189–2251 1.000 72.9
psbM-rpoB_p2 psbM-rpoB TTTGACTGGCTGTTTTTACGT CTTCTGCCAAACCCTGATCA 2190–2252 1.000 71.1
psbM-rpoB_p3 psbM-rpoB TTGACTGGCTGTTTTTACGT TCTTCTGCCAAACCCTGATC 2190–2252 1.000 70.6
psbM-rpoB_p4 psbM-rpoB TTGACTGGCTGTTTTTACGT CTCTTCTGCCAAACCCTGAT 2191–2253 1.000 70.5
psbM-rpoB_p5 psbM-rpoB TTGACTGGCTGTTTTTACGT TGCCAAACCCTGATCAATGA 2185–2247 1.000 69.7
atpl-atpH_p1 atpl-atpH CCCGTCATGTTCCTTGGATT ATAACGGAAGCGGCAGAAAT 1290–1338 1.000 81.0
atpl-atpH_p2 atpl-atpH CCCGTCATGTTCCTTGGATT TACCTTGACCAACTCCAGGT 1346–1394 1.000 80.3
atpl-atpH_p3 atpl-atpH CCCGTCATGTTCCTTGGATT AGCCAATCCAGCAGCAATAA 1306–1354 1.000 80.1
atpl-atpH_p4 atpl-atpH CCCGTCATGTTCCTTGGATT AATAACGGAAGCGGCAGAAA 1291–1339 1.000 79.8
atpl-atpH_p5 atpl-atpH CCCGTCATGTTCCTTGGATT GCAGTACCTTGACCAACTCC 1350–1398 1.000 79.7

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
Parthenium argentatum NC_013553.1 152803 View on NCBI ↗
Parthenium hysterophorus NC_086650.1 151881 View on NCBI ↗