Markers + reference

Xanthium

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–152 kb
Candidate markers 264
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 408 0.0477 0.98 84.4 yes View details
trnC-petN LSC 818 0.0186 0.99 70.8 yes View details
psbM-trnD LSC 658 0.0213 1.00 63.1 yes View details
trnE-rpoB LSC 912 0.0156 0.98 59.6 yes View details
rpl2 IRb 1487 0.0020 1.00 45.7 no View details
ycf1 SSC 5151 0.0235 0.98 58.6 yes View details
psaC SSC 246 0.0041 1.00 40.8 yes View details
rpl32-ndhF SSC 801 0.0164 0.99 61.2 yes View details
ndhF SSC 2232 0.0072 1.00 47.2 yes View details
rpl2 IRa 1487 0.0020 1.00 45.7 yes View details
psaC-ndhD SSC 91 0.1124 0.98 83.4 yes View details
rps19-rpl2 IRb 78 0.1268 0.91 76.8 yes View details
psbI-trnS LSC 156 0.0467 0.96 74.8 yes View details
atpI-atpH LSC 1170 0.0129 0.99 67.1 yes View details
trnS-psbZ LSC 339 0.0236 1.00 66.9 yes View details
clpP-psbB LSC 483 0.0128 0.97 66.4 yes View details
rpl16-rps3 LSC 167 0.0323 0.93 66.4 yes View details
petA-psbJ LSC 788 0.0152 1.00 66.1 yes View details
rrn5-trnR IRb 281 0.0154 0.93 65.4 yes View details
trnR-rrn5 IRa 281 0.0154 0.93 65.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 519–527 1.000 80.7
trnH-psbA_p2 trnH-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 533–541 1.000 80.6
trnH-psbA_p3 trnH-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 532–540 1.000 80.6
trnH-psbA_p4 trnH-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 534–542 1.000 80.5
trnH-psbA_p5 trnH-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 520–528 1.000 80.2
psbI-trnS_p1 psbI-trnS CGTAATCCTGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 267–272 1.000 75.5
psbI-trnS_p2 psbI-trnS CGTAATCCTGGACGTGAAGA CGAGTTATTCGTACCGAGGG 215–220 1.000 74.1
psbI-trnS_p3 psbI-trnS CGTAATCCTGGACGTGAAGAA ATTGGGAGAGATGGCTGAGT 267–272 1.000 73.2
psbI-trnS_p4 psbI-trnS CCTATCCAATGATCCAGGACG ATTGGGAGAGATGGCTGAGT 286–291 1.000 72.1
psbI-trnS_p5 psbI-trnS CGTAATCCTGGACGTGAAGA GATGGCTGAGTGGACGAAAG 258–263 1.000 71.4
trnC-petN_p1 trnC-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 863–874 1.000 80.6
trnC-petN_p2 trnC-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 881–892 1.000 78.4
trnC-petN_p3 trnC-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 862–873 1.000 74.7
trnC-petN_p4 trnC-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 871–882 1.000 74.6
trnC-petN_p5 trnC-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 920–931 1.000 73.8
psbM-trnD_p1 psbM-trnD GGAACTAAAATGAACAGTGCAGT TTCAATAGGCAAGAGCACCG 775–777 1.000 51.8
psbM-trnD_p2 psbM-trnD AAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 769–771 1.000 51.4
psbM-trnD_p3 psbM-trnD ACTAAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 772–774 1.000 50.4
psbM-trnD_p4 psbM-trnD AGGAACTAAAATGAACAGTGCAG TTCAATAGGCAAGAGCACCG 776–778 1.000 49.8
psbM-trnD_p5 psbM-trnD AGGAACTAAAATGAACAGTGCA TTCAATAGGCAAGAGCACCG 776–778 1.000 48.9
trnE-rpoB_p1 trnE-rpoB GGGACTTGAACCCTCGTTTT TGCCAAACCCTGATCAATGA 1035–1046 1.000 77.2
trnE-rpoB_p2 trnE-rpoB TAACCACTGGACCATAGGGG TGCCAAACCCTGATCAATGA 994–1005 1.000 76.5
trnE-rpoB_p3 trnE-rpoB CCCTCGTTTTCTCCGTGAAA TGCCAAACCCTGATCAATGA 1025–1036 1.000 76.4
trnE-rpoB_p4 trnE-rpoB TTGAACCCTCGTTTTCTCCG TGCCAAACCCTGATCAATGA 1030–1041 1.000 76.3
trnE-rpoB_p5 trnE-rpoB TCTTGGTATACCCCCAGAGG TGCCAAACCCTGATCAATGA 1053–1064 1.000 73.4
atpI-atpH_p1 atpI-atpH CCCGTCATGTTCCTTGGATT ATAACGGAAGCGGCAGAAAT 1294–1304 1.000 80.3
atpI-atpH_p2 atpI-atpH CCCGTCATGTTCCTTGGATT TACCTTGACCAACTCCAGGT 1350–1360 1.000 79.6
atpI-atpH_p3 atpI-atpH CCCGTCATGTTCCTTGGATT AGCCAATCCAGCAGCAATAA 1310–1320 1.000 79.4
atpI-atpH_p4 atpI-atpH CCCGTCATGTTCCTTGGATT AATAACGGAAGCGGCAGAAA 1295–1305 1.000 79.1
atpI-atpH_p5 atpI-atpH CCCGTCATGTTCCTTGGATT GCAGTACCTTGACCAACTCC 1354–1364 1.000 79.0

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
Xanthium spinosum NC_054222.1 152422 View on NCBI ↗
Xanthium strumarium NC_072298.1 151852 View on NCBI ↗