Markers + reference

Brachycorythis

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 153–153 kb
Candidate markers 272
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 617 0.0211 1.00 66.2 yes View details
rpoB-trnC-GCA LSC 1261 0.0064 0.99 63.3 yes View details
petA-psbJ LSC 799 0.0050 1.00 48.7 yes View details
rps11 LSC 417 0.0000 1.00 23.7 yes View details
rpl14 LSC 369 0.0000 1.00 32.9 yes View details
rpl16 LSC 1574 0.0032 0.99 52.0 yes View details
rps3-rpl22 LSC 78 0.0536 0.72 78.1 yes View details
rpl36-infA LSC 126 0.0364 0.87 75.5 yes View details
rpl16-rps3 LSC 159 0.0252 1.00 67.0 yes View details
matK-trnK-UUU LSC 1072 0.0047 1.00 61.7 yes View details
trnT-UGU-trnL-UAA LSC 1042 0.0020 0.98 61.7 yes View details
clpP-psbB LSC 651 0.0046 1.00 61.4 yes View details
rpoA-rps11 LSC 67 0.0149 1.00 61.1 yes View details
psaA-ycf3 LSC 629 0.0016 0.99 60.9 yes View details
ndhC-trnV-UAC LSC 837 0.0000 0.98 60.7 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
trnK-UUU_p1 trnK-UUU TTCACTTTGGTATGGATTGA TTGTGCAGTACAATTCCATT 2994 0.500 20.0
trnK-UUU_p2 trnK-UUU TTTCACTTTGGTATGGATTGA TTGTGCAGTACAATTCCATT 2995 0.500 20.0
trnK-UUU_p3 trnK-UUU TTTTCACTTTGGTATGGATTGA TTGTGCAGTACAATTCCATT 2996 0.500 20.0
trnK-UUU_p4 trnK-UUU TTTTTCACTTTGGTATGGATTGA TTGTGCAGTACAATTCCATT 2997 0.500 20.0
trnK-UUU_p5 trnK-UUU TTTTCACTTTGGTATGGATTG TTGTGCAGTACAATTCCATT 2996 0.500 20.0
matK-trnK-UUU_p1 matK-trnK-UUU AAGGAGCAGCGGATATAGGA ATCCGGGTTGCTAACTCAAC 1200–1207 1.000 77.2
matK-trnK-UUU_p2 matK-trnK-UUU AGGAGCAGCGGATATAGGAA ATCCGGGTTGCTAACTCAAC 1199–1206 1.000 77.2
matK-trnK-UUU_p3 matK-trnK-UUU AAGGAGCAGCGGATATAGGA ACGGTAGAGTACTCGGCTTT 1182–1189 1.000 76.7
matK-trnK-UUU_p4 matK-trnK-UUU AGGAGCAGCGGATATAGGAA AACGGTAGAGTACTCGGCTT 1182–1189 1.000 76.7
matK-trnK-UUU_p5 matK-trnK-UUU AGGAGCAGCGGATATAGGAA ACGGTAGAGTACTCGGCTTT 1181–1188 1.000 76.7
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AACGGAAAGACCCCTTAACT 724–733 1.000 68.4
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC AACGGAAAGACCCCTTAACT 723–732 1.000 68.4
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GATCAGGGGAATCGGAGAGA AACGGAAAGACCCCTTAACT 789–798 1.000 68.3
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATCAGGGGAATCGGAGAGAG AACGGAAAGACCCCTTAACT 788–797 1.000 68.3
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CAAGTGATCAGGGGAATCGG AACGGAAAGACCCCTTAACT 794–803 1.000 68.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TAAAGGATTTGCAGTCCCCC 1397–1409 1.000 75.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG CGACACCCAGATTCGAACTG 1421–1433 1.000 74.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TTTGTTGATCAGGCGACACC 1434–1446 1.000 73.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT TAAAGGATTTGCAGTCCCCC 1398–1410 1.000 72.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG ATAAAGGATTTGCAGTCCCCC 1398–1410 1.000 71.5
psaA-ycf3_p1 psaA-ycf3 CCCATTCCTCGAAAGACGTT GGACAGGCTTGGTTTGATCA 814–822 1.000 79.4
psaA-ycf3_p2 psaA-ycf3 CCCATTCCTCGAAAGACGTT TGGACAGGCTTGGTTTGATC 815–823 1.000 79.4
psaA-ycf3_p3 psaA-ycf3 CCCATTCCTCGAAAGACGTT ATAGCGCTTACTCCAGGGAA 769–777 1.000 78.5
psaA-ycf3_p4 psaA-ycf3 CCCATTCCTCGAAAGACGTT TAGCGCTTACTCCAGGGAAT 768–776 1.000 78.5
psaA-ycf3_p5 psaA-ycf3 CCCATTCCTCGAAAGACGTT TGGTTTGATCAAGCTGCTGA 805–813 1.000 77.9
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA AGAAAAAGAGCCGGCTATCG ACCAATTTCGCCATATCCCC 1123–1143 1.000 81.0
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA AGAAAAAGAGCCGGCTATCG TAGCGTCTACCAATTTCGCC 1131–1151 1.000 80.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1072–1092 1.000 80.5
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1080–1100 1.000 80.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1104–1124 1.000 79.6

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
Brachycorythis henryi PQ149858.1 153006 View on NCBI ↗
Brachycorythis menglianensis PQ149859.1 152932 View on NCBI ↗