Markers + reference

Cyclostephanos

2 species · Stephanodiscaceae · Stephanodiscales

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Species 2
Genome length 129–129 kb
Candidate markers 355
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 355 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbX-rbcS Genome 549 0.1336 0.95 82.3 yes View details
ycf45-ffs Genome 671 0.2033 0.98 80.5 yes View details
rpoB-rps20 Genome 437 0.1327 1.00 75.6 yes View details
petA-chlI Genome 574 0.1633 0.96 82.1 yes View details
ycf89-rns Genome 550 0.1336 0.95 83.3 yes View details
thiS-psb28 Genome 499 0.1636 0.98 79.3 yes View details
rns-ycf89 Genome 550 0.1336 0.95 83.3 yes View details
rps19-ycf88 Genome 13 0.2500 0.92 80.1 yes View details
secG-trnfM-CAU Genome 117 0.1455 0.94 79.5 yes View details
trnP-UGG-ycf89 Genome 486 0.1050 0.98 79.4 yes View details
ycf89-trnP-UGG Genome 486 0.1050 0.98 79.4 yes View details
ycf46-ccs1 Genome 7 0.1429 1.00 79.2 yes View details
ccs1-ycf46 Genome 7 0.1429 1.00 79.2 yes View details
trnI-CAU-trnS-GCU Genome 25 0.1600 1.00 78.6 yes View details
pbf1-psbH Genome 84 0.0952 1.00 77.7 yes View details
ssrA-trnR-CCG Genome 54 0.1132 0.98 77.0 yes View details
psaJ-trnP-UGG Genome 116 0.1121 1.00 77.0 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
ssrA-trnR-CCG_p1 ssrA-trnR-CCG GTCGAAACCAAATCAGTCCC GGTTCGATTCCCTTCATGCT 95–96 1.000 75.3
ssrA-trnR-CCG_p2 ssrA-trnR-CCG TGTCGAAACCAAATCAGTCCC GGTTCGATTCCCTTCATGCT 96–97 1.000 73.5
ssrA-trnR-CCG_p3 ssrA-trnR-CCG GTCGAAACCAAATCAGTCCC GGGGTTCGATTCCCTTCATG 97–98 1.000 73.0
ssrA-trnR-CCG_p4 ssrA-trnR-CCG GTCGAAACCAAATCAGTCCC ATTCTGAAAGTCGGGGGTTC 110–111 1.000 70.9
ssrA-trnR-CCG_p5 ssrA-trnR-CCG GTCGAAACCAAATCAGTCCC GATTCTGAAAGTCGGGGGTT 111–112 1.000 70.9
psbX-rbcS_p1 psbX-rbcS TGCTGTCAAACTCGCGATAA GCTCGTAAATCATGCGCTTC 801–818 1.000 89.6
psbX-rbcS_p2 psbX-rbcS TGCTGTCAAACTCGCGATAA TCGGTGGTGGTACTATTGGT 1309–1326 1.000 85.6
psbX-rbcS_p3 psbX-rbcS TGCTGTCAAACTCGCGATAA GAAGCTCGTAAATCATGCGC 804 0.500 59.3
psbX-rbcS_p4 psbX-rbcS TGCTGTCAAACTCGCGATAA ATCCGCATCCTCGTAACAAC 893 0.500 58.9
psbX-rbcS_p5 psbX-rbcS CGTCTCTTGCAACTTCAGGT GCTCGTAAATCATGCGCTTC 1160 0.500 58.9
pbf1-psbH_p1 pbf1-psbH AAGCAGGTCCAAAAGCAGTA TCAGCATTTAACGGGCGTAA 225 1.000 76.8
pbf1-psbH_p2 pbf1-psbH AAGCAGGTCCAAAAGCAGTA TTCAGCATTTAACGGGCGTA 226 1.000 76.8
pbf1-psbH_p3 pbf1-psbH GAAGCAGGTCCAAAAGCAGT TCAGCATTTAACGGGCGTAA 226 1.000 76.6
pbf1-psbH_p4 pbf1-psbH GAAGCAGGTCCAAAAGCAGT TTCAGCATTTAACGGGCGTA 227 1.000 76.6
pbf1-psbH_p5 pbf1-psbH AGCAGGTCCAAAAGCAGTAT TCAGCATTTAACGGGCGTAA 224 1.000 75.0
ycf45-ffs_p1 ycf45-ffs CCCGCATTTCAACTTGCAAT TCCACTGCTCTACCAACTGA 1418–1420 1.000 87.9
ycf45-ffs_p2 ycf45-ffs CCCGCATTTCAACTTGCAAT ATCGCATCAATAAACGGCCT 1706–1708 1.000 87.6
ycf45-ffs_p3 ycf45-ffs CCCGCATTTCAACTTGCAAT AACTGAGCTATCCGGGCTTA 1404–1406 1.000 86.3
ycf45-ffs_p4 ycf45-ffs CCCGCATTTCAACTTGCAAT CCCCCTAGGCACAGTAGAAT 1539 0.500 57.8
ycf45-ffs_p5 ycf45-ffs CCCGCATTTCAACTTGCAAT ACTGAGCTATCCGGGCTTAA 1405 0.500 57.7
rpoB-rps20_p1 rpoB-rps20 GTTTCTCCCTGCCAATTCCA AAGTTCCATTCTTTGCGGGT 1702–1747 1.000 84.4
rpoB-rps20_p2 rpoB-rps20 GTTTCTCCCTGCCAATTCCA AGTTCCATTCTTTGCGGGTT 1701–1746 1.000 84.4
rpoB-rps20_p3 rpoB-rps20 TGGTTTCTCCCTGCCAATTC AAGTTCCATTCTTTGCGGGT 1704–1749 1.000 84.4
rpoB-rps20_p4 rpoB-rps20 TGGTTTCTCCCTGCCAATTC AGTTCCATTCTTTGCGGGTT 1703–1748 1.000 84.4
rpoB-rps20_p5 rpoB-rps20 GTTTCTCCCTGCCAATTCCA TGCGGGTTATTTCGACGATT 1689–1734 1.000 84.4
petA-chlI_p1 petA-chlI GCCGTGGACAAGTTTATCCA GCAAAAGCACATGCAGCATA 1137–1144 1.000 88.1
petA-chlI_p2 petA-chlI GCCGTGGACAAGTTTATCCA GGTATGCATGCCGAAATTCG 1401–1408 1.000 87.3
petA-chlI_p3 petA-chlI GCCGTGGACAAGTTTATCCA TCGTCATCCTGCTCGATTTG 1483–1490 1.000 86.7
petA-chlI_p4 petA-chlI GCCGTGGACAAGTTTATCCA CAATTCGTCATCCTGCTCGA 1487–1494 1.000 86.6
petA-chlI_p5 petA-chlI GCCGTGGACAAGTTTATCCA GAGCGAATTGTAGATGCCCA 1269 0.500 58.2

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
Cyclostephanos invisitatus PV423702.1 129222 View on NCBI ↗
Cyclostephanos tholiformis PV423699.1 129413 View on NCBI ↗