Markers + reference

Chaetophoropsis

2 species · Chaetophoraceae · Chaetophorales

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Species 2
Genome length 104–215 kb
Candidate markers 80
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 80 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl16-atpF Genome 1786 0.4117 0.87 86.1 yes View details
rps12-atpH Genome 2197 0.4362 0.93 81.7 yes View details
rps18-ycf4 Genome 1459 0.4193 0.85 81.1 yes View details
ycf4-rpoA Genome 1171 0.4195 0.75 79.4 yes View details
rpl32-rpoBb Genome 696 0.3505 0.95 84.3 yes View details
rpoA Genome 1767 0.1390 0.95 82.9 yes View details
rpoBb-atpE Genome 694 0.3328 0.97 82.4 yes View details
rpl5-rps7 Genome 599 0.4182 0.90 82.3 yes View details
rpoBb Genome 2232 0.1610 0.94 82.2 yes View details
atpB-rpl5 Genome 1137 0.3701 0.88 82.1 yes View details
atpE-rpoC2 Genome 633 0.3473 0.83 81.1 yes View details
psaJ-rpl14 Genome 192 0.2251 0.99 80.2 yes View details
rpoC2-petL Genome 805 0.2416 0.99 79.7 yes View details
rpl14-rpl16 Genome 478 0.2861 0.81 78.6 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psaJ-rpl14_p1 psaJ-rpl14 AGCAAAAGCAACAACTGGTG ATTTTTGGTCCTGTAGCCCG 321–568 1.000 84.2
psaJ-rpl14_p2 psaJ-rpl14 AAGCAAAAGCAACAACTGGT ATTTTTGGTCCTGTAGCCCG 322–569 1.000 78.1
psaJ-rpl14_p3 psaJ-rpl14 ACCAAGCAAAAGCAACAACT ATTTTTGGTCCTGTAGCCCG 325–572 1.000 78.1
psaJ-rpl14_p4 psaJ-rpl14 AGCAAAAGCAACAACTGGTG GTCCTGTAGCCCGTGAATTA 314–561 1.000 77.9
psaJ-rpl14_p5 psaJ-rpl14 AGCAAAAGCAACAACTGGTG TCCTGTAGCCCGTGAATTAC 313–560 1.000 77.9
rpl14-rpl16_p1 rpl14-rpl16 TCTACGAACACCTTTACGCG TGTATATGGAGGGTTTGCGC 1019 0.500 59.4
rpl14-rpl16_p2 rpl14-rpl16 TCTACGAACACCTTTACGCG CGTATGGGTTCTGGGAAAGG 856 0.500 59.4
rpl14-rpl16_p3 rpl14-rpl16 TCTACGAACACCTTTACGCG GTTTGCGCTTCAAGCTACAG 1007 0.500 59.4
rpl14-rpl16_p4 rpl14-rpl16 GCCAGTATTATCGGCGACAT TGTATATGGAGGGTTTGCGC 851 0.500 59.1
rpl14-rpl16_p5 rpl14-rpl16 GCCAGTATTATCGGCGACAT CGTATGGGTTCTGGGAAAGG 688 0.500 59.1
rpl16-atpF_p1 rpl16-atpF CCTTTCATACGACCACGATGA TCTTTATTGCTCGTTTTACAGA 1877–2081 1.000 52.0
rpl16-atpF_p2 rpl16-atpF TCCTTTCATACGACCACGATG TCTTTATTGCTCGTTTTACAGA 1878–2082 1.000 52.0
rpl16-atpF_p3 rpl16-atpF CCTTTCATACGACCACGATGA TCTTTATTGCTCGTTTTACAGAA 1877–2081 1.000 52.0
rpl16-atpF_p4 rpl16-atpF CCTTTCATACGACCACGATGA TTCTTTATTGCTCGTTTTACAGA 1878–2082 1.000 52.0
rpl16-atpF_p5 rpl16-atpF TCCTTTCATACGACCACGATG TCTTTATTGCTCGTTTTACAGAA 1878–2082 1.000 52.0
atpB-rpl5_p1 atpB-rpl5 ACATGCTTTTACCCCTTGCA AACGTTTTCCCAGAACAGCT 2075 0.500 59.5
atpB-rpl5_p2 atpB-rpl5 AGACTGTAGGACTTGCACCT AACGTTTTCCCAGAACAGCT 1971 0.500 59.4
atpB-rpl5_p3 atpB-rpl5 GCATGATCCCACGATTCACT AACGTTTTCCCAGAACAGCT 2199 0.500 59.3
atpB-rpl5_p4 atpB-rpl5 CTGCATGATCCCACGATTCA AACGTTTTCCCAGAACAGCT 2201 0.500 59.2
atpB-rpl5_p5 atpB-rpl5 ACTGAATCTCCCTTCCCGAA AACGTTTTCCCAGAACAGCT 1920 0.500 59.2
rpl5-rps7_p1 rpl5-rps7 GCTTCACCTACACCACGATT GTGCTAGAGCTATCGCCATC 969 0.500 59.2
rpl5-rps7_p2 rpl5-rps7 GCTTCACCTACACCACGATT TTGAAGTCAAACCACGTCGT 1038 0.500 59.1
rpl5-rps7_p3 rpl5-rps7 GCTTCACCTACACCACGATT TATGGCTCGTAAAGGTGCAC 1256 0.500 59.1
rpl5-rps7_p4 rpl5-rps7 GCTTCACCTACACCACGATT TGAATTCACGTCGTCCAGAC 804 0.500 58.8
rpl5-rps7_p5 rpl5-rps7 GCTTCACCTACACCACGATT CGTGTTGAAGTCAAACCACG 1042 0.500 58.6
rps12-atpH_p1 rps12-atpH ACGTACTCGAGCGACTTTTC ATTGGTCCTGGTATGGGTCA 2554 0.500 59.5
rps12-atpH_p2 rps12-atpH ACGTACTCGAGCGACTTTTC GAGGAAAGATGGCAGAGTGG 2803 0.500 59.4
rps12-atpH_p3 rps12-atpH ACGTACTCGAGCGACTTTTC TTATGCGGTTGAAGGGATCG 2519 0.500 59.3
rps12-atpH_p4 rps12-atpH ACGTACTCGAGCGACTTTTC GGTTATGCGGTTGAAGGGAT 2521 0.500 59.3
rps12-atpH_p5 rps12-atpH ACTCGACCTCCACGAACTAA ATTGGTCCTGGTATGGGTCA 2646 0.500 59.1

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
Chaetophoropsis cf. attenuata FACHB-2291 MN701985.1 104049 View on NCBI ↗
Chaetophoropsis polyrhiza NC_047431.1 214786 View on NCBI ↗