Markers + reference

Conocephalum

2 species · Conocephalaceae · Marchantiales

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Species 2
Genome length 121–122 kb
Candidate markers 267
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhB Genome 2019 0.0095 0.99 54.3 yes View details
atpI-atpH Genome 413 0.0545 0.98 74.9 yes View details
psaM-trnS-GCU Genome 383 0.1349 0.99 87.7 yes View details
psbA-trnH-GUG Genome 439 0.0822 0.97 89.1 yes View details
trnH-GUG-ycf2 Genome 335 0.1171 0.99 80.0 yes View details
ycf2 Genome 6534 0.0148 0.98 49.4 yes View details
rps14 Genome 303 0.0000 1.00 20.6 yes View details
cysT-trnL-UAG Genome 248 0.0833 0.97 79.5 yes View details
ycf1-chlN Genome 147 0.0952 1.00 86.9 yes View details
psbZ-trnG-UCC Genome 124 0.1694 1.00 80.5 yes View details
rps7-ndhB Genome 202 0.1542 1.00 80.3 yes View details
trnfM-CAU-rps14 Genome 100 0.0729 0.96 79.5 yes View details
psaJ-rpl33 Genome 114 0.0614 1.00 76.1 yes View details
rpl16-rps3 Genome 63 0.0980 0.81 73.1 yes View details
trnR-UCU-trnG-GCC Genome 82 0.0610 1.00 72.6 yes View details
trnS-UGA-rps4 Genome 226 0.0543 0.98 72.6 yes View details
trnT-UGU-trnL-UAA Genome 201 0.0500 1.00 71.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps7-ndhB_p1 rps7-ndhB TGATGCAGCTAGAGATAATGGG AGATGCATTCTGGTAAAATAGT 356–357 1.000 47.2
rps7-ndhB_p2 rps7-ndhB TGCAGCTAGAGATAATGGGA AGATGCATTCTGGTAAAATAGT 353–354 1.000 47.2
rps7-ndhB_p3 rps7-ndhB TGATGCAGCTAGAGATAATGGG AAGATGCATTCTGGTAAAATAGT 357–358 1.000 47.2
rps7-ndhB_p4 rps7-ndhB TGCAGCTAGAGATAATGGGA AAGATGCATTCTGGTAAAATAGT 354–355 1.000 47.2
rps7-ndhB_p5 rps7-ndhB GATGCAGCTAGAGATAATGGGA AGATGCATTCTGGTAAAATAGT 355–356 1.000 47.2
ndhB_p1 ndhB GGAGCAGCAAGAAAACGTTC CGCGTGTTTACCATTTCACC 2489–2515 1.000 81.8
ndhB_p2 ndhB GGAAAAGCGTTAGCGATTCG CGCGTGTTTACCATTTCACC 2519–2545 1.000 81.5
ndhB_p3 ndhB GGAGCAGCAAGAAAACGTTC GACTCGAACCTCCATGCTTT 2529–2555 1.000 81.3
ndhB_p4 ndhB GGAAAAGCGTTAGCGATTCG GACTCGAACCTCCATGCTTT 2559–2585 1.000 80.9
ndhB_p5 ndhB GCAGCAAGAAAACGTTCAGG CGCGTGTTTACCATTTCACC 2486–2512 1.000 80.1
atpI-atpH_p1 atpI-atpH TTTTTGCTACACTTGCAGCA GCAGCAATAACAGAAGCAGC 507–510 1.000 74.2
atpI-atpH_p2 atpI-atpH TTTTTGCTACACTTGCAGCA AAGCAGCAGAAATCAAGGGG 494–497 1.000 71.5
atpI-atpH_p3 atpI-atpH TTTTTGCTACACTTGCAGCA CCAGCAGCAATAACAGAAGC 510–513 1.000 70.4
atpI-atpH_p4 atpI-atpH ATTTTTGCTACACTTGCAGCA GCAGCAATAACAGAAGCAGC 508–511 1.000 70.3
atpI-atpH_p5 atpI-atpH TTTTTGCTACACTTGCAGCA GCAGCAGAAATCAAGGGGTT 492–495 1.000 69.2
trnR-UCU-trnG-GCC_p1 trnR-UCU-trnG-GCC CCTCTGTCCTATCCTTTAGACG ACCCTTAGCCTTCCAAGCTA 161–162 1.000 59.5
trnR-UCU-trnG-GCC_p2 trnR-UCU-trnG-GCC CCTCTGTCCTATCCTTTAGACG TTCCAAGCTAATGATGCGGG 151–152 1.000 57.4
trnR-UCU-trnG-GCC_p3 trnR-UCU-trnG-GCC GTCCTATCCTTTAGACGATGGAC ACCCTTAGCCTTCCAAGCTA 156–157 1.000 57.3
trnR-UCU-trnG-GCC_p4 trnR-UCU-trnG-GCC CTGTCCTATCCTTTAGACGATGG ACCCTTAGCCTTCCAAGCTA 158–159 1.000 57.2
trnR-UCU-trnG-GCC_p5 trnR-UCU-trnG-GCC TGTCCTATCCTTTAGACGATGGA ACCCTTAGCCTTCCAAGCTA 157–158 1.000 56.7
psaM-trnS-GCU_p1 psaM-trnS-GCU TGACCTCAATTTCAGATAGTCA AACCCTCGGTACAAAAAGCT 551 1.000 48.1
psaM-trnS-GCU_p2 psaM-trnS-GCU TGACCTCAATTTCAGATAGTCA ACCCTCGGTACAAAAAGCTT 550 1.000 48.1
psaM-trnS-GCU_p3 psaM-trnS-GCU TGACCTCAATTTCAGATAGTCA CGGAGAGAGAGGGATTCGAA 569 1.000 47.9
psaM-trnS-GCU_p4 psaM-trnS-GCU TGACCTCAATTTCAGATAGTCAA CGGAGAGAGAGGGATTCGAA 569 1.000 47.9
psaM-trnS-GCU_p5 psaM-trnS-GCU TGACCTCAATTTCAGATAGTCA AACGGAGAGAGAGGGATTCG 571 1.000 47.8
psbA-trnH-GUG_p1 psbA-trnH-GUG GCTCCTGCTGTAAACGGTTA CTGCCTTAATCCACTTGGCT 475–487 1.000 86.2
psbA-trnH-GUG_p2 psbA-trnH-GUG GCTCCTGCTGTAAACGGTTA GATCCACAATCCACTGCCTT 488–500 1.000 86.0
psbA-trnH-GUG_p3 psbA-trnH-GUG GCTCCTGCTGTAAACGGTTA ACTGCCTTAATCCACTTGGC 476–488 1.000 86.0
psbA-trnH-GUG_p4 psbA-trnH-GUG GCTCCTGCTGTAAACGGTTA TTATATTGGGCGAACGACGG 529–541 1.000 85.3
psbA-trnH-GUG_p5 psbA-trnH-GUG GTAACGCTCACAACTTCCCT CTGCCTTAATCCACTTGGCT 516–528 1.000 85.0

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
Conocephalum conicum MT023024.1 120963 View on NCBI ↗
Conocephalum salebrosum MT023022.1 122488 View on NCBI ↗