Markers + reference

Desmidorchis

2 species · Apocynaceae · Gentianales

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Species 2
Genome length 162–162 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 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
trnH-GUG-psbA LSC 328 0.0061 1.00 56.6 yes View details
rps16 LSC 1095 0.0018 1.00 59.9 yes View details
rps16-trnQ-UUG LSC 1291 0.0016 0.99 61.1 yes View details
trnS-GCU-trnR-UCU LSC 1429 0.0007 0.99 60.5 yes View details
rpoB-trnC-GCA LSC 1235 0.0016 1.00 59.7 yes View details
psbZ-trnG-GCC LSC 332 0.0000 0.96 42.0 yes View details
rbcL-accD LSC 515 0.0021 0.92 62.2 yes View details
ycf1 SSC 6009 0.0002 1.00 52.6 no View details
ycf1 SSC 6009 0.0002 1.00 40.5 yes View details
petD LSC 1333 0.0000 0.96 62.7 yes View details
atpB-rbcL LSC 778 0.0013 0.98 61.0 yes View details
trnG-GCC LSC 71 0.0141 1.00 60.6 yes View details
trnK-UUU-rps16 LSC 806 0.0000 0.98 60.4 yes View details
matK LSC 1557 0.0026 1.00 60.1 yes View details
trnE-UUC-trnT-GGU LSC 1023 0.0010 1.00 59.3 yes View details
psaA-ycf3 LSC 970 0.0010 1.00 59.3 yes View details
psbE-petL LSC 1135 0.0009 1.00 59.3 yes View details
psbC LSC 1422 0.0007 1.00 59.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 398 1.000 78.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 412 1.000 78.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 411 1.000 78.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 413 1.000 78.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 447 1.000 76.6
trnK-UUU_p1 trnK-UUU TGCTAGTGTCAACTAATATCGA CGATTGTATTTATGCACTTCT 2808–2820 1.000 40.5
trnK-UUU_p2 trnK-UUU TGCTAGTGTCAACTAATATCGATCT CGATTGTATTTATGCACTTCT 2808–2820 1.000 40.5
trnK-UUU_p3 trnK-UUU TGCTAGTGTCAACTAATATCGA CGATTGTATTTATGCACTTCTT 2808–2820 1.000 40.5
trnK-UUU_p4 trnK-UUU TGCTAGTGTCAACTAATATCGATCT CGATTGTATTTATGCACTTCTT 2808–2820 1.000 40.5
trnK-UUU_p5 trnK-UUU TGCTAGTGTCAACTAATATCGA CGATTGTATTTATGCACTTCTTT 2808–2820 1.000 40.5
matK_p1 matK TGTTACACCAACATTTCAGA AAGTTTACCCGTTTCCGAGG 1760 1.000 40.2
matK_p2 matK TGTTACACCAACATTTCAGA TTTGCTAACCCCAAAACCGT 1689 1.000 40.2
matK_p3 matK TGTTACACCAACATTTCAGAA AAGTTTACCCGTTTCCGAGG 1760 1.000 40.2
matK_p4 matK TGTTACACCAACATTTCAGAA TTTGCTAACCCCAAAACCGT 1689 1.000 40.2
matK_p5 matK TGTTACACCAACATTTCAGA ACCCGTTTCCGAGGTATCTA 1754 1.000 40.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TCAAAAGGGTGGGGGTTTTT 944–957 1.000 78.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCAAAAGGGTGGGGGTTTT 945–958 1.000 78.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTTCAAAAGGGTGGGGGTTT 946–959 1.000 78.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTTTCAAAAGGGTGGGGGTT 947–960 1.000 78.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAAAAGGGTGGGGGTTTTT 882–895 1.000 77.7
rps16_p1 rps16 ACGGGAAAAGGAAAAAGGGG CTCCGACGTCTACAAAGCAA 1268 1.000 77.4
rps16_p2 rps16 ATATACAAGCAACTGCCCCC CTCCGACGTCTACAAAGCAA 1217–1218 1.000 76.8
rps16_p3 rps16 ACGGGAAAAGGAAAAAGGGG GACTCCGACGTCTACAAAGC 1270 1.000 74.8
rps16_p4 rps16 ATATACAAGCAACTGCCCCC GACTCCGACGTCTACAAAGC 1219–1220 1.000 74.2
rps16_p5 rps16 ACGAGTAGAACGGGAAAAGG CTCCGACGTCTACAAAGCAA 1277 1.000 73.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAATGGATCATGGCCTT GAGGTTCGAATCCTTCCGTC 1372–1385 1.000 78.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGGATCATGGCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1366–1379 1.000 77.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAATGGATCATGGCCTT TAAACTAAATGGGGCGTGGC 1429–1442 1.000 75.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCATGGCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1365–1378 1.000 75.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAATGGATCATGGCCTT TTCGGAGGTTCGAATCCTTC 1376–1389 1.000 74.2

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
Desmidorchis penicillata PP101941.1 161776 View on NCBI ↗
Desmidorchis retrospiciens PP291741.1 162277 View on NCBI ↗