Markers + reference

Angraecum

3 species · Orchidaceae · Asparagales

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Species 3
Genome length 151–152 kb
Candidate markers 262
Primer pairs 100

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 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-trnT-GGU LSC 1052 0.0194 0.98 63.9 yes View details
ndhC-trnV-UAC LSC 781 0.0222 0.98 61.1 yes View details
petA-psbJ LSC 1153 0.0237 0.97 65.2 yes View details
clpP-psbB LSC 883 0.0313 0.93 78.1 yes View details
psbB-psbT LSC 639 0.0277 0.90 63.3 yes View details
rpl16 LSC 1704 0.0182 1.00 60.0 yes View details
trnN-GUU-rpl32 SSC 540 0.0417 0.96 75.8 yes View details
ndhD-psaC SSC 499 0.0275 1.00 64.5 yes View details
psaC-ndhE SSC 826 0.0308 0.97 67.0 yes View details
ycf1 SSC 5517 0.0159 0.99 48.6 yes View details
rpoA-rps11 LSC 91 0.0321 0.91 73.1 yes View details
rpoB-trnC-GCA LSC 1450 0.0146 0.98 71.6 yes View details
psbC-trnS-UGA LSC 150 0.0253 0.97 70.5 yes View details
psbM-trnD-GUC LSC 1129 0.0209 0.99 70.0 yes View details
atpF-atpH LSC 175 0.0287 0.99 69.5 yes View details
atpH-atpI LSC 781 0.0166 0.98 69.3 yes View details
trnL-UAG-ccsA SSC 127 0.0420 1.00 68.9 yes View details
rbcL-accD LSC 812 0.0190 0.99 68.5 yes View details
atpB-rbcL LSC 1015 0.0204 1.00 68.1 yes View details
trnT-UGU-trnL-UAA LSC 606 0.0165 1.00 66.1 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpF-atpH_p1 atpF-atpH TAAACTCGAAACTCCCAGCG ATTTATGGACTGGTCGTGGC 295–297 1.000 81.3
atpF-atpH_p2 atpF-atpH TAAACTCGAAACTCCCAGCG GGTCGTGGCATTAGCTCTTT 284–286 1.000 79.6
atpF-atpH_p3 atpF-atpH CCACGGAAACAAAAGAATCGG ATTTATGGACTGGTCGTGGC 262–264 1.000 73.6
atpF-atpH_p4 atpF-atpH CCCACGGAAACAAAAGAATCG ATTTATGGACTGGTCGTGGC 263–265 1.000 73.5
atpF-atpH_p5 atpF-atpH AAACTCGAAACTCCCAGCG ATTTATGGACTGGTCGTGGC 294–296 1.000 73.2
atpH-atpI_p1 atpH-atpI CGCAATACCTTCTACGGCTT AACTTTGGCTGCGGCTTATA 948–973 1.000 81.7
atpH-atpI_p2 atpH-atpI TCCGATAGAAGCAAGCCCTA AACTTTGGCTGCGGCTTATA 897–922 1.000 81.7
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 876–901 1.000 81.3
atpH-atpI_p4 atpH-atpI CCGATAGAAGCAAGCCCTAC AACTTTGGCTGCGGCTTATA 896–921 1.000 81.1
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC AACTTTGGCTGCGGCTTATA 875–900 1.000 80.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG CCGGGGATAAAGGATTTGCA 1362–1605 1.000 83.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG ACCGGGGATAAAGGATTTGC 1363–1606 1.000 83.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TCGAACCGGGGATAAAGGAT 1367–1610 1.000 82.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TTCGAACCGGGGATAAAGGA 1368–1611 1.000 80.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT CCGGGGATAAAGGATTTGCA 1363–1606 1.000 80.3
psbM-trnD-GUC_p1 psbM-trnD-GUC CAGCGCAGTAGCAATAAACG AGTTCAATCGGTCAGAGCAC 1085–1234 1.000 84.7
psbM-trnD-GUC_p2 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT AGTTCAATCGGTCAGAGCAC 1090–1239 1.000 83.3
psbM-trnD-GUC_p3 psbM-trnD-GUC TGAACAGCGCAGTAGCAATA AGTTCAATCGGTCAGAGCAC 1089–1238 1.000 82.3
psbM-trnD-GUC_p4 psbM-trnD-GUC CAGCGCAGTAGCAATAAACG GCCATGCATATAGCTGGGAT 1108–1257 1.000 81.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AATGAACAGCGCAGTAGCAA AGTTCAATCGGTCAGAGCAC 1091–1240 1.000 81.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 1156–1620 1.000 81.6
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 1135–1599 1.000 81.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 1132–1596 1.000 81.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 1134–1598 1.000 80.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 1153–1617 1.000 80.5
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GAGAGATGGCTGAGTGGTTG 266–272 1.000 81.8
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC ATAGCCCCGGTCTTGAAAAC 246–252 1.000 81.3
psbC-trnS-UGA_p3 psbC-trnS-UGA AGCGGGGTTTGAAAAAGGAA GAGAGATGGCTGAGTGGTTG 303–309 1.000 81.0
psbC-trnS-UGA_p4 psbC-trnS-UGA TTCCATGACCCCTCTTAGCT GAGAGATGGCTGAGTGGTTG 258–264 1.000 81.0
psbC-trnS-UGA_p5 psbC-trnS-UGA TTGTGGGACATTTGTGGCAT GAGAGATGGCTGAGTGGTTG 346–352 1.000 80.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Angraecum lecomtei NC_086703.1 151277 View on NCBI ↗
Angraecum sesquipedale NC_086704.1 151818 View on NCBI ↗
Angraecum sororium NC_086705.1 151341 View on NCBI ↗