Markers + reference

Cyclorhiza

4 species · Apiaceae · Apiales

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Species 4
Genome length 155–156 kb
Candidate markers 264
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 374 0.0401 1.00 72.1 yes View details
trnK-UUU-rps16 LSC 882 0.0201 0.99 61.7 yes View details
psbK-psbI LSC 414 0.0270 1.00 64.0 yes View details
trnT-GGU-psbD LSC 1420 0.0149 0.99 66.0 yes View details
ycf3-trnS-GGA LSC 880 0.0164 0.99 64.2 yes View details
ndhC-trnV-UAC LSC 1177 0.0149 0.99 58.4 yes View details
petA-psbJ LSC 748 0.0218 1.00 59.1 yes View details
5S ribosomal RNA-trnR-ACG IRb 271 0.0387 0.95 79.0 yes View details
ndhF SSC 2247 0.0111 1.00 51.2 yes View details
ndhF-rpl32 SSC 1180 0.0193 1.00 63.2 yes View details
trnR-ACG-5S ribosomal RNA IRa 271 0.0387 0.95 79.0 yes View details
clpP-psbB LSC 472 0.0106 0.99 67.2 yes View details
atpI-rps2 LSC 253 0.0283 1.00 65.4 yes View details
rpl22-rps19 LSC 68 0.0224 0.97 64.0 yes View details
trnE-UUC-trnT-GGU LSC 827 0.0133 0.98 63.5 yes View details
atpF-atpH LSC 376 0.0116 1.00 63.1 yes View details
trnF-GAA-ndhJ LSC 372 0.0157 0.99 63.1 yes View details
rpl32-trnL-UAG SSC 893 0.0121 1.00 61.6 yes View details
ndhG-ndhI SSC 412 0.0214 0.98 61.3 yes View details
trnT-UGU-trnL-UAA LSC 789 0.0169 0.99 61.1 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 105 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 CCCTCTAGATCTAGCTGCTGT 437–444 1.000 76.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCCTCTAGATCTAGCTGCTGT 451–458 1.000 76.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCCTCTAGATCTAGCTGCTGT 450–457 1.000 76.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCCTCTAGATCTAGCTGCTGT 452–459 1.000 76.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCCCTCTAGATCTAGCTGCTG 438–445 1.000 76.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAGGCGGAGGTTTTTAAGT 937–963 1.000 61.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAGGCGGAGGTTTTTAAGT 938–964 1.000 61.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAGGCGGAGGTTTTTAAGT 947–973 1.000 60.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAGGCGGAGGTTTTTAAGT 939–965 1.000 60.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGCGGAGGTTTTTAAGT 938–964 1.000 60.1
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAAAGTTTGAGAGTAAGCA 467–481 1.000 53.4
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGAAAAGTTTGAGAGTAAGCA 464–478 1.000 51.4
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACGAAAAGTTTGAGAGTAAGCA 465–479 1.000 51.4
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACGAAAAGTTTGAGAGTAAGCA 466–480 1.000 51.4
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACGAAAAGTTTGAGAGTAAGCA 468–482 1.000 50.9
atpF-atpH_p1 atpF-atpH TGGCCCAAAGAAACGAAAGA GCCTGGTTGTAGCATTAGCA 457–469 1.000 79.6
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG GCCTGGTTGTAGCATTAGCA 488–500 1.000 79.0
atpF-atpH_p3 atpF-atpH GTGGCCCAAAGAAACGAAAG GCCTGGTTGTAGCATTAGCA 458–470 1.000 79.0
atpF-atpH_p4 atpF-atpH TGGCCCAAAGAAACGAAAGA TGGCCTGGTTGTAGCATTAG 459–471 1.000 78.2
atpF-atpH_p5 atpF-atpH AGTGGCCCAAAGAAACGAAA GCCTGGTTGTAGCATTAGCA 459–471 1.000 78.2
atpI-rps2_p1 atpI-rps2 TGGAACAGGATAGAACATTCA CAGCCAACGATGACGCTATA 351–378 1.000 48.0
atpI-rps2_p2 atpI-rps2 TGGAACAGGATAGAACATTCA TGTGAAGGGCGTTCTAGCTA 289–316 1.000 47.7
atpI-rps2_p3 atpI-rps2 TGGAACAGGATAGAACATTCA TTTGTGAAGGGCGTTCTAGC 291–318 1.000 47.6
atpI-rps2_p4 atpI-rps2 TGGAACAGGATAGAACATTCA GCAATTTGTGAAGGGCGTTC 295–322 1.000 47.6
atpI-rps2_p5 atpI-rps2 TGGAACAGGATAGAACATTCAT CAGCCAACGATGACGCTATA 351–378 1.000 47.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 931–957 1.000 82.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 896–922 1.000 82.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 928–954 1.000 81.8
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TTGAACCGATGACTTACGCC 933–959 1.000 80.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTGTAGTACCCTACCCCCAG GAACCGATGACTTACGCCTT 966–992 1.000 79.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Cyclorhiza peucedanifolia OR399517.1 155169 View on NCBI ↗
Cyclorhiza puana OR399518.1 156008 View on NCBI ↗
Cyclorhiza purpureovaginata OQ570477.1 155651 View on NCBI ↗
Cyclorhiza waltonii PQ551023.1 156046 View on NCBI ↗