Markers + reference

Cephalantheropsis

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 158–158 kb
Candidate markers 280
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 8 remaining regions by MarkerSeek score (out of 280 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1187 0.0076 1.00 63.1 yes View details
atpI-rps2 LSC 297 0.0067 1.00 56.4 yes View details
rpoC2 LSC 4143 0.0007 1.00 54.3 yes View details
trnC-GCA-petN LSC 781 0.0026 1.00 60.2 yes View details
petN-psbM LSC 792 0.0025 1.00 60.2 yes View details
trnD-GUC-trnY-GUA LSC 286 0.0070 1.00 51.1 yes View details
rpl33 LSC 201 0.0050 1.00 46.4 yes View details
clpP LSC 2294 0.0017 1.00 58.1 yes View details
clpP-psbB LSC 675 0.0000 0.99 60.2 yes View details
psbE-petL LSC 1158 0.0017 1.00 59.7 yes View details
ndhK LSC 774 0.0013 1.00 59.5 yes View details
psbB-psbT LSC 533 0.0038 1.00 59.5 yes View details
trnT-UGU-trnL-UAA LSC 586 0.0017 1.00 59.4 yes View details
ndhC-trnV-UAC LSC 1080 0.0009 1.00 59.4 yes View details
atpB-rbcL LSC 952 0.0010 1.00 59.4 yes View details
psbA LSC 1062 0.0009 1.00 59.3 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
psbA_p1 psbA AGCAATCCCCCAAGATCTTG GTGCTTGGGAGTCCTTGAAA 1187 1.000 76.3
psbA_p2 psbA CAAGATCTTGGGGGATTGCT GTGCTTGGGAGTCCTTGAAA 1177 1.000 76.3
psbA_p3 psbA AGCAATCCCCCAAGATCTTG AATACGTGTGCTTGGGAGTC 1194 1.000 75.7
psbA_p4 psbA CAAGATCTTGGGGGATTGCT AATACGTGTGCTTGGGAGTC 1184 1.000 75.7
psbA_p5 psbA CAACAAGATAGCAATCCCCCA GTGCTTGGGAGTCCTTGAAA 1196 1.000 71.8
rps16_p1 rps16 GGTACTAGTTACCCTATCCTT TCAATTGCATACGGTTCCAA 1275 1.000 40.6
rps16_p2 rps16 GGTACTAGTTACCCTATCCTT TGCATACGGTTCCAAATTCA 1270 1.000 40.6
rps16_p3 rps16 GGTACTAGTTACCCTATCCTT TGGTTCAGCCAATGACTATTCA 1312 1.000 40.5
rps16_p4 rps16 GGTACTAGTTACCCTATCCTT ATGTATCGATTGGTTCAGCC 1322 1.000 40.5
rps16_p5 rps16 GGTACTAGTTACCCTATCCTTT TGGTTCAGCCAATGACTATTCA 1312 1.000 40.5
trnG-GCC_p1 trnG-GCC GCCGCAGTGGAACAAAATAC AGACGGATTTAGGGAATACA 978 1.000 40.9
trnG-GCC_p2 trnG-GCC GCCGCAGTGGAACAAAATAC AGACGGATTTAGGGAATACAA 978 1.000 40.3
trnG-GCC_p3 trnG-GCC CCGCAGTGGAACAAAATACG AGACGGATTTAGGGAATACA 977 1.000 40.1
trnG-GCC_p4 trnG-GCC CCGCAGTGGAACAAAATACG AGACGGATTTAGGGAATACAA 977 1.000 40.1
trnG-GCC_p5 trnG-GCC TGCCGCAGTGGAACAAAATA AGACGGATTTAGGGAATACA 979 1.000 40.1
atpI-rps2_p1 atpI-rps2 TGGCCTACTTCTACACCTGA TGTGAGGGCCGTTCTAGTTA 404 1.000 74.9
atpI-rps2_p2 atpI-rps2 GCTGGCCTACTTCTACACCT TGTGAGGGCCGTTCTAGTTA 406 1.000 73.4
atpI-rps2_p3 atpI-rps2 TGGCCTACTTCTACACCTGA ATTTGTGAGGGCCGTTCTAG 407 1.000 72.2
atpI-rps2_p4 atpI-rps2 CTGGCCTACTTCTACACCTG TGTGAGGGCCGTTCTAGTTA 405 1.000 72.1
atpI-rps2_p5 atpI-rps2 ATGCTGGCCTACTTCTACAC TGTGAGGGCCGTTCTAGTTA 408 1.000 71.9
rpoC2_p1 rpoC2 TGGACATGATTCGATAAGGT TGATGGTTATCATGCGACCG 284 1.000 45.9
rpoC2_p2 rpoC2 TGGACATGATTCGATAAGGT GATGGTTATCATGCGACCGA 283 1.000 45.8
rpoC2_p3 rpoC2 TGGACATGATTCGATAAGGTT TGATGGTTATCATGCGACCG 284 1.000 44.9
rpoC2_p4 rpoC2 TTGGACATGATTCGATAAGGT TGATGGTTATCATGCGACCG 285 1.000 44.9
rpoC2_p5 rpoC2 TGGACATGATTCGATAAGGTT GATGGTTATCATGCGACCGA 283 1.000 44.8
trnC-GCA-petN_p1 trnC-GCA-petN CCAGTTCGAATCTGGGTGTC TAAAGCAGCCCAAGTGAGAC 854–871 1.000 76.5
trnC-GCA-petN_p2 trnC-GCA-petN CCAGTTCGAATCTGGGTGTC ACCATTAAAGCAGCCCAAGT 859–876 1.000 75.5
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTA TAAAGCAGCCCAAGTGAGAC 877–894 1.000 74.5
trnC-GCA-petN_p4 trnC-GCA-petN CCAGTTCGAATCTGGGTGTC GCAGCCCAAGTGAGACTTAC 850–867 1.000 73.6
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTA ACCATTAAAGCAGCCCAAGT 882–899 1.000 73.5

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
Cephalantheropsis halconensis NC_084154.1 157880 View on NCBI ↗
Cephalantheropsis obcordata NC_050868.1 157918 View on NCBI ↗