Markers + reference

Acampe

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 147–147 kb
Candidate markers 266
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 871 0.0138 1.00 61.3 yes View details
petN-psbM LSC 856 0.0153 0.99 68.6 yes View details
ndhK LSC 393 0.0102 1.00 45.6 yes View details
rbcL-accD LSC 804 0.0124 1.00 58.4 yes View details
petA-psbJ LSC 941 0.0128 1.00 56.1 yes View details
clpP LSC 2267 0.0058 1.00 51.4 yes View details
rpl16 LSC 1600 0.0133 0.99 52.5 yes View details
ycf1-rpl32 SSC 463 0.0330 0.98 76.5 yes View details
ndhD SSC 874 0.0116 0.99 60.0 yes View details
ndhG SSC 283 0.0142 1.00 46.3 yes View details
ndhG-ndhI SSC 9 0.1111 1.00 76.8 yes View details
rpoC1-rpoB LSC 26 0.0385 1.00 74.6 yes View details
rpoA-rps11 LSC 99 0.0404 1.00 73.9 yes View details
ndhJ-ndhK LSC 126 0.0397 1.00 66.8 yes View details
rps8-rpl14 LSC 228 0.0221 0.99 66.0 yes View details
rpoB-trnC-GCA LSC 1566 0.0072 0.98 64.7 yes View details
matK-trnK-UUU LSC 1129 0.0071 0.99 63.6 yes View details
clpP-psbB LSC 683 0.0089 0.99 63.5 yes View details
psaA-ycf3 LSC 574 0.0087 1.00 63.4 yes View details
atpH-atpI LSC 649 0.0077 1.00 63.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TCCGGGTTGCTAACTCAATG 1272–1276 1.000 71.8
matK-trnK-UUU_p2 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA CGGGTTGCTAACTCAATGGT 1270–1274 1.000 71.3
matK-trnK-UUU_p3 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA GATCCGGGTTGCTAACTCAA 1274–1278 1.000 69.5
matK-trnK-UUU_p4 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TTGATCCGGGTTGCTAACTC 1276–1280 1.000 69.5
matK-trnK-UUU_p5 matK-trnK-UUU TCCTGAAGGAGTAGCGGATAT TCCGGGTTGCTAACTCAATG 1272–1276 1.000 68.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 965–967 1.000 80.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GACCAAAAAGAAATGGGGCG 1026–1028 1.000 80.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 942–944 1.000 79.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GACCAAAAAGAAATGGGGCG 1003–1005 1.000 79.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 963–965 1.000 79.3
atpH-atpI_p1 atpH-atpI CGCAATACCTTCTACGGCTT AACTTTGGCTGCGGCTTATA 818 1.000 79.0
atpH-atpI_p2 atpH-atpI TCCGATAGAAGCAAGCCCTA AACTTTGGCTGCGGCTTATA 767 1.000 78.9
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 746 1.000 78.4
atpH-atpI_p4 atpH-atpI CCGATAGAAGCAAGCCCTAC AACTTTGGCTGCGGCTTATA 766 1.000 78.3
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC AACTTTGGCTGCGGCTTATA 745 1.000 77.8
rpoC1-rpoB_p1 rpoC1-rpoB GGGAAACTGGTCCAATTCGA AGAGGGTGCTCCAGAATCTT 193 1.000 78.6
rpoC1-rpoB_p2 rpoC1-rpoB GGGAAACTGGTCCAATTCGA TTGCTCGTTCGAGAACTACG 168 1.000 78.6
rpoC1-rpoB_p3 rpoC1-rpoB TTGTTGAGGGGAAACTGGTC TTGCTCGTTCGAGAACTACG 176 1.000 77.3
rpoC1-rpoB_p4 rpoC1-rpoB TTGTTGAGGGGAAACTGGTC AGAGGGTGCTCCAGAATCTT 201 1.000 77.2
rpoC1-rpoB_p5 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA AGAGGGTGCTCCAGAATCTT 264 1.000 77.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG CCGGGGATAAAGGATTTGCA 1689–1721 1.000 80.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG ACCGGGGATAAAGGATTTGC 1690–1722 1.000 80.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TCGAACCGGGGATAAAGGAT 1694–1726 1.000 79.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TTCGAACCGGGGATAAAGGA 1695–1727 1.000 77.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT CCGGGGATAAAGGATTTGCA 1690–1722 1.000 76.8
petN-psbM_p1 petN-psbM GATAGGGGCATCATTCGCAT ACGTCAAAACAGTCAGCCAA 984–993 1.000 78.8
petN-psbM_p2 petN-psbM GATAGGGGCATCATTCGCAT ATTGCTACTGCGCTGTTCAT 1036–1045 1.000 78.7
petN-psbM_p3 petN-psbM ATAGGGGCATCATTCGCATG ACGTCAAAACAGTCAGCCAA 983–992 1.000 78.4
petN-psbM_p4 petN-psbM GGGCATCATTCGCATGGATA ACGTCAAAACAGTCAGCCAA 979–988 1.000 78.4
petN-psbM_p5 petN-psbM ATAGGGGCATCATTCGCATG ATTGCTACTGCGCTGTTCAT 1035–1044 1.000 78.3

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
Acampe papillosa MN124418.1 147350 View on NCBI ↗
Acampe rigida MN124419.1 147467 View on NCBI ↗