Markers + reference

Anthoceros

2 species · Anthocerotaceae · Anthocerotales

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Species 2
Genome length 161–161 kb
Candidate markers 278
Primer pairs 90

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 10 remaining regions by MarkerSeek score (out of 278 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ORF51-trnK Genome 878 0.0137 1.00 53.1 yes View details
ycf2 Genome 7182 0.0039 1.00 43.6 yes View details
ycf2-trnD Genome 1821 0.0127 1.00 53.6 yes View details
cysA-trnT Genome 3904 0.0044 1.00 50.6 yes View details
trnT-trnL Genome 736 0.0215 0.95 67.4 yes View details
atpB-rbcL Genome 1185 0.0061 0.96 65.8 yes View details
trnI-ndhB Genome 2042 0.0054 1.00 60.9 yes View details
chlL-trnN Genome 863 0.0081 1.00 63.5 yes View details
petG-trnW Genome 228 0.0219 1.00 65.1 yes View details
cysA Genome 1149 0.0061 1.00 62.3 yes View details
trnP-psaJ Genome 514 0.0078 0.99 62.2 yes View details
ccsA Genome 1017 0.0059 1.00 62.1 yes View details
ORF288 Genome 867 0.0046 1.00 61.4 yes View details
trnH-ycf2 Genome 478 0.0064 0.99 61.3 yes View details
atpI Genome 747 0.0040 1.00 61.1 yes View details
atpB Genome 1479 0.0041 1.00 61.1 yes View details
trnF-ndhJ Genome 464 0.0086 1.00 60.9 yes View details
accD Genome 942 0.0053 1.00 60.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpI_p1 atpI TCACAATCAATTTTTCAAAGAGGT TGCGAAAAATGAAAACTTACA 828 1.000 40.3
atpI_p2 atpI TCACAATCAATTTTTCAAAGAGGT TTGCGAAAAATGAAAACTTACA 829 1.000 40.3
atpI_p3 atpI TTCACAATCAATTTTTCAAAGAGGT TGCGAAAAATGAAAACTTACA 829 1.000 40.3
atpI_p4 atpI TCACAATCAATTTTTCAAAGAGGT TTTGCGAAAAATGAAAACTTACA 830 1.000 40.3
atpI_p5 atpI TCACAATCAATTTTTCAAAGAGGT TGCGAAAAATGAAAACTTACAT 828 1.000 40.3
ORF51-trnK_p1 ORF51-trnK GCTCAATGTCGGAGAGAAGG GCACTTGAAAGCCGAGTACT 1270–1271 1.000 78.8
ORF51-trnK_p2 ORF51-trnK CAATGTCGGAGAGAAGGACG GCACTTGAAAGCCGAGTACT 1267–1268 1.000 78.7
ORF51-trnK_p3 ORF51-trnK CTAGAGAAGGGGCTCAACCT GCACTTGAAAGCCGAGTACT 1170–1171 1.000 78.4
ORF51-trnK_p4 ORF51-trnK AATGTCGGAGAGAAGGACGA GCACTTGAAAGCCGAGTACT 1266–1267 1.000 78.1
ORF51-trnK_p5 ORF51-trnK GGGGCTCAACCTACAGAAAC GCACTTGAAAGCCGAGTACT 1162–1163 1.000 78.0
trnH-ycf2_p1 trnH-ycf2 CATTATGCGCGGGTTCAATC TCCTGTATGAAAATTTGTTTTCT 547–551 1.000 41.5
trnH-ycf2_p2 trnH-ycf2 TGGATTACGGCAGTGGATTG TCCTGTATGAAAATTTGTTTTCT 573–577 1.000 41.4
trnH-ycf2_p3 trnH-ycf2 GGATTACGGCAGTGGATTGT TCCTGTATGAAAATTTGTTTTCT 572–576 1.000 41.4
trnH-ycf2_p4 trnH-ycf2 GTGGATTACGGCAGTGGATT TCCTGTATGAAAATTTGTTTTCT 574–578 1.000 41.4
trnH-ycf2_p5 trnH-ycf2 GATATTGAAAGGGCGGACGT TCCTGTATGAAAATTTGTTTTCT 600–604 1.000 41.3
ycf2_p1 ycf2 TCACGTTTGAATGGTGGAGG ATATTGATTCGTGTTGCTCA 246 1.000 41.3
ycf2_p2 ycf2 TCACGTTTGAATGGTGGAGG TATTGATTCGTGTTGCTCAT 245 1.000 41.3
ycf2_p3 ycf2 TCACGTTTGAATGGTGGAGG AATATTGATTCGTGTTGCTCA 247 1.000 41.3
ycf2_p4 ycf2 TCACGTTTGAATGGTGGAGG AAATATTGATTCGTGTTGCTCA 248 1.000 41.3
ycf2_p5 ycf2 TCACGTTTGAATGGTGGAGG TCAGAGACTAAAAAGCAAGAAACA 343 1.000 40.9
ycf2-trnD_p1 ycf2-trnD TTACTTATGGGGCAAGACGC CTCTCTTTCAAGGAGGCGAC 2820–2826 1.000 80.6
ycf2-trnD_p2 ycf2-trnD TTACTTATGGGGCAAGACGC CAACTGGTTAGAGTACCGCC 2371–2380 1.000 80.6
ycf2-trnD_p3 ycf2-trnD TTACTTATGGGGCAAGACGC ATCGTCTAGTGGCCTAGGAC 2842–2848 1.000 80.5
ycf2-trnD_p4 ycf2-trnD TTACTTATGGGGCAAGACGC CATCGTCTAGTGGCCTAGGA 2843–2849 1.000 80.5
ycf2-trnD_p5 ycf2-trnD TTACTTATGGGGCAAGACGC TTAGAGTACCGCCCTGTCAA 2364–2373 1.000 80.1
cysA_p1 cysA TGAAATTCTTTATGATGGGAGA AGCAAGAATAGCAAAGAAAGCC 1257 1.000 40.4
cysA_p2 cysA TGAAATTCTTTATGATGGGAGA GCAAGAATAGCAAAGAAAGCCT 1256 1.000 40.4
cysA_p3 cysA TGAAATTCTTTATGATGGGAGA TCTCCAGAAAGCAAGAATAGCA 1266 1.000 40.4
cysA_p4 cysA TGAAATTCTTTATGATGGGAGAA AGCAAGAATAGCAAAGAAAGCC 1257 1.000 40.4
cysA_p5 cysA TGAAATTCTTTATGATGGGAGAA GCAAGAATAGCAAAGAAAGCCT 1256 1.000 40.4

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
Anthoceros agrestis NC_049002.1 160790 View on NCBI ↗
Anthoceros punctatus NC_049001.1 160692 View on NCBI ↗