Markers + reference

Cyathodium

2 species · Cyathodiaceae · Marchantiales

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Species 2
Genome length 117–119 kb
Candidate markers 273
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps12 Genome 828 0.3025 0.89 82.0 yes View details
rps7 Genome 468 0.2564 1.00 76.0 yes View details
atpI Genome 747 0.0013 1.00 59.5 yes View details
psaM-trnS-GCU Genome 498 0.0714 0.03 67.2 yes View details
chlL Genome 870 0.0000 1.00 26.5 yes View details
chlL-trnN-GUU Genome 822 0.0028 0.87 62.8 yes View details
rps12-rps7 Genome 57 0.5200 0.88 75.7 yes View details
rps7-ndhB Genome 169 0.4211 0.56 67.3 yes View details
trnV-GAC-rps12 Genome 852 0.0437 0.51 60.2 no View details
psbB Genome 1527 0.0007 1.00 59.1 yes View details
psbZ Genome 189 0.0053 1.00 55.5 yes View details
ycf2 Genome 6132 0.0003 1.00 52.7 yes View details
trnM-CAU-trnV-GAC Genome 782 0.0000 0.46 52.0 yes View details
atpB-rbcL Genome 696 0.0000 0.42 51.5 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps12_p1 rps12 CGGGAAGCCGTATGAAATGA ACTTTCTTCCCTCTTCCCGA 1388 0.500 59.4
rps12_p2 rps12 CGGGAAGCCGTATGAAATGA TTTTCCTTGTGCCGAGACAA 1256 0.500 59.2
rps12_p3 rps12 AGTCCGGTTTCGTAGAGTGA ACTTTCTTCCCTCTTCCCGA 1360 0.500 59.0
rps12_p4 rps12 AGTCCGGTTTCGTAGAGTGA TTTTCCTTGTGCCGAGACAA 1228 0.500 58.8
rps12_p5 rps12 CGGGAAGCCGTATGAAATGA CGTAAGGGGTTTTGGAGGAG 1600 0.500 58.7
rps12-rps7_p1 rps12-rps7 TACGCGTTAGCTACACAACC ACTTTCTTCCCTCTTCCCGA 882 0.500 59.6
rps12-rps7_p2 rps12-rps7 TACGCGTTAGCTACACAACC TTTTCCTTGTGCCGAGACAA 750 0.500 59.5
rps12-rps7_p3 rps12-rps7 TACGCGTTAGCTACACAACC CGTAAGGGGTTTTGGAGGAG 1094 0.500 59.0
rps12-rps7_p4 rps12-rps7 GAGGAGGAAGGGTCAAGGAT ACTTTCTTCCCTCTTCCCGA 1175 0.500 58.9
rps12-rps7_p5 rps12-rps7 GAGGAGGAAGGGTCAAGGAT TTTTCCTTGTGCCGAGACAA 1043 0.500 58.7
rps7_p1 rps7 TACGCGTTAGCTACACAACC CGTAAGGGGTTTTGGAGGAG 1094 0.500 59.0
rps7_p2 rps7 TACGCGTTAGCTACACAACC GACGTAAGGGGTTTTGGAGG 1096 0.500 58.4
rps7_p3 rps7 TCAACAAGGGCGTTCTAGTG CGTAAGGGGTTTTGGAGGAG 1305 0.500 57.8
rps7_p4 rps7 GTCAACAAGGGCGTTCTAGT CGTAAGGGGTTTTGGAGGAG 1306 0.500 57.8
rps7_p5 rps7 TCAACAAGGGCGTTCTAGTG GACGTAAGGGGTTTTGGAGG 1307 0.500 57.2
rps7-ndhB_p1 rps7-ndhB TCGGGAAGAGGGAAGAAAGT AACGAATCGCACTCCTTCAT 972 0.500 56.7
rps7-ndhB_p2 rps7-ndhB TCGGGAAGAGGGAAGAAAGT CCGTTTCTCCACCGGATAAA 811 0.500 56.7
rps7-ndhB_p3 rps7-ndhB TTGTCTCGGCACAAGGAAAA AACGAATCGCACTCCTTCAT 1104 0.500 56.5
rps7-ndhB_p4 rps7-ndhB TTGTCTCGGCACAAGGAAAA CCGTTTCTCCACCGGATAAA 943 0.500 56.5
rps7-ndhB_p5 rps7-ndhB TCGGGAAGAGGGAAGAAAGT TCCGTTTCTCCACCGGATAA 812 0.500 56.3
atpI_p1 atpI TGACAAACCGTTTTATGTGTTTCT AGATTCAAGGTGGAATGAAAACA 926 1.000 40.1
atpI_p2 atpI TGACAAACCGTTTTATGTGT AGATTCAAGGTGGAATGAAAACA 926 1.000 40.1
atpI_p3 atpI TGACAAACCGTTTTATGTGTT AGATTCAAGGTGGAATGAAAACA 926 1.000 40.1
atpI_p4 atpI TGACAAACCGTTTTATGTGTTTC AGATTCAAGGTGGAATGAAAACA 926 1.000 40.1
atpI_p5 atpI TGACAAACCGTTTTATGTGTTTCT AGATTCAAGGTGGAATGAAAACAA 926 1.000 40.1
psaM-trnS-GCU_p1 psaM-trnS-GCU AGCTTTAAGACTAGGGAAGGA TACGGAGAGAGAGGGATTCG 138–622 1.000 53.3
psaM-trnS-GCU_p2 psaM-trnS-GCU AGCTTTAAGACTAGGGAAGGA CGGAGAGAGAGGGATTCGAA 136–620 1.000 52.9
psaM-trnS-GCU_p3 psaM-trnS-GCU AGCTTTAAGACTAGGGAAGGAA TACGGAGAGAGAGGGATTCG 138–622 1.000 51.6
psaM-trnS-GCU_p4 psaM-trnS-GCU AGCTTTAAGACTAGGGAAGGAA CGGAGAGAGAGGGATTCGAA 136–620 1.000 51.1
psaM-trnS-GCU_p5 psaM-trnS-GCU AGCTTTAAGACTAGGGAAGGA GATTCGAACCCTCGGTACAA 124–608 1.000 50.1

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
Cyathodium cavernarum NC_088074.1 118752 View on NCBI ↗
Cyathodium smaragdinum MW429509.1 116912 View on NCBI ↗