Markers + reference

Ixeris

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–153 kb
Candidate markers 273
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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 472 0.0000 1.00 22.3 no View details
ndhF SSC 2226 0.4558 0.79 77.5 yes View details
rpl32-trnL-UAG SSC 775 0.4480 0.76 78.2 yes View details
ccsA SSC 969 0.4829 0.69 76.4 yes View details
ndhD SSC 1503 0.4683 0.88 81.7 yes View details
ndhE SSC 306 0.4938 0.79 73.0 yes View details
ndhI SSC 501 0.5068 0.88 79.7 yes View details
ndhA SSC 2124 0.4619 0.87 80.4 yes View details
ndhH SSC 1182 0.4709 0.91 82.7 yes View details
ycf1 SSC 4971 0.4070 0.87 75.1 yes View details
trnH-GUG-psbA LSC 412 0.0537 0.95 83.6 yes View details
ndhF-rpl32 SSC 1088 0.4278 0.86 81.2 yes View details
ndhG SSC 531 0.4623 0.80 78.4 yes View details
rps15-ycf1 SSC 397 0.4867 0.85 76.7 yes View details
ccsA-ndhD SSC 259 0.4661 0.91 76.3 yes View details
ndhH-rps15 SSC 90 0.4074 0.90 75.9 yes View details
ndhD-psaC SSC 115 0.4854 0.90 75.8 yes View details
ndhG-ndhI SSC 352 0.4228 0.85 75.7 yes View details
rps15 SSC 279 0.4367 0.88 75.5 yes View details
trnL-UAG-ccsA SSC 114 0.3918 0.85 74.6 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-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 512–530 1.000 82.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 526–544 1.000 82.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 525–543 1.000 82.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 527–545 1.000 82.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 513–531 1.000 82.2
ndhF_p1 ndhF GGCCCTCCTATCTCTTCCTT AACGAGGTAAGATCCGGTGA 2655 0.500 57.9
ndhF_p2 ndhF GGCCCTCCTATCTCTTCCTT ACGAGGTAAGATCCGGTGAA 2654 0.500 57.9
ndhF_p3 ndhF CTAGCACTGGGTAGACCTCA AACGAGGTAAGATCCGGTGA 2515 0.500 57.6
ndhF_p4 ndhF CTAGCACTGGGTAGACCTCA ACGAGGTAAGATCCGGTGAA 2514 0.500 57.6
ndhF_p5 ndhF CCCTTCCATGCCTCATTTCA ACGAGGTAAGATCCGGTGAA 2988 0.500 57.6
ndhF-rpl32_p1 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG AAGGTAAAGGTCGATGGGGA 1598 0.500 59.4
ndhF-rpl32_p2 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG AGGTAAAGGTCGATGGGGAA 1597 0.500 59.4
ndhF-rpl32_p3 ndhF-rpl32 TGCCGTCGGAAAAAGAAGAA AAGGTAAAGGTCGATGGGGA 1596 0.500 59.3
ndhF-rpl32_p4 ndhF-rpl32 TGCCGTCGGAAAAAGAAGAA AGGTAAAGGTCGATGGGGAA 1595 0.500 59.3
ndhF-rpl32_p5 ndhF-rpl32 TTGCCGTCGGAAAAAGAAGA AGGTAAAGGTCGATGGGGAA 1596 0.500 59.3
rpl32-trnL-UAG_p1 rpl32-trnL-UAG AAAGGAAAGGGTATTGGGCG AGCGTGTCTACCGATTTCAC 908 0.500 58.7
rpl32-trnL-UAG_p2 rpl32-trnL-UAG AAAGGAAAGGGTATTGGGCG CAGCGTGTCTACCGATTTCA 909 0.500 58.7
rpl32-trnL-UAG_p3 rpl32-trnL-UAG GTATTGGGCGGCGTTAAAAG AGCGTGTCTACCGATTTCAC 898 0.500 58.5
rpl32-trnL-UAG_p4 rpl32-trnL-UAG GTATTGGGCGGCGTTAAAAG CAGCGTGTCTACCGATTTCA 899 0.500 58.5
rpl32-trnL-UAG_p5 rpl32-trnL-UAG AAAGGAAAGGGTATTGGGCG GAAGTAGCAAAGCCTTGGGT 1417 0.500 58.1
trnL-UAG-ccsA_p1 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT GAAGTAGCAAAGCCTTGGGT 529 0.500 59.2
trnL-UAG-ccsA_p2 trnL-UAG-ccsA TGAAATCGGTAGACACGCTG GAAGTAGCAAAGCCTTGGGT 528 0.500 59.2
trnL-UAG-ccsA_p3 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT TGATCCACAAAGAAGAGCCG 647 0.500 59.1
trnL-UAG-ccsA_p4 trnL-UAG-ccsA TGAAATCGGTAGACACGCTG TGATCCACAAAGAAGAGCCG 646 0.500 59.1
trnL-UAG-ccsA_p5 trnL-UAG-ccsA TCCCCATCGACCTTTACCTT GAAGTAGCAAAGCCTTGGGT 1086 0.500 59.0
ccsA_p1 ccsA GTGAAATCGGTAGACACGCT GTTTTTGATTCTGGACCGCG 1557 0.500 59.6
ccsA_p2 ccsA TGAAATCGGTAGACACGCTG GTTTTTGATTCTGGACCGCG 1556 0.500 59.6
ccsA_p3 ccsA GTGAAATCGGTAGACACGCT GCTTGCATTACCGGGTATGA 1762 0.500 59.6
ccsA_p4 ccsA TGAAATCGGTAGACACGCTG GCTTGCATTACCGGGTATGA 1761 0.500 59.6
ccsA_p5 ccsA TCCCCATCGACCTTTACCTT GTTTTTGATTCTGGACCGCG 2114 0.500 59.4

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
Ixeris polycephala NC_046514.1 152776 View on NCBI ↗
Ixeris repens NC_057108.1 153017 View on NCBI ↗