Markers + reference

Cymbopogon

10 species · Poaceae · Poales

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Species 10
Genome length 140–140 kb
Candidate markers 261
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnT-GGU-trnE-UUC LSC 547 0.0086 1.00 59.6 yes View details
trnC-GCA-rpoB LSC 1218 0.0032 1.00 57.0 yes View details
trnR-UCU-rps14 LSC 384 0.0137 1.00 56.2 yes View details
rbcL-psaI LSC 823 0.0057 1.00 56.7 yes View details
psbE-petL LSC 1266 0.0035 1.00 53.7 yes View details
ndhF-rpl32 SSC 853 0.0043 1.00 53.8 yes View details
rpl32-trnL-UAG SSC 453 0.0088 1.00 45.8 yes View details
ccsA SSC 966 0.0033 1.00 35.4 yes View details
matK-rps16 LSC 1288 0.0021 1.00 62.0 yes View details
rps16-trnQ-UUG LSC 1498 0.0023 1.00 58.6 yes View details
ccsA-ndhD SSC 178 0.0202 1.00 55.0 yes View details
ndhC-trnM-CAU LSC 1762 0.0016 1.00 52.8 yes View details
trnT-UGU-trnF-GAA LSC 1716 0.0023 1.00 52.4 yes View details
atpB-rbcL LSC 796 0.0025 1.00 51.6 yes View details
trnV-GAC-rps12 IRa 1756 0.0005 1.00 50.8 yes View details
rps12-trnV-GAC IRb 1756 0.0003 1.00 50.6 yes View details
trnM-CAU-ycf2 IRb 1321 0.0003 1.00 49.9 yes View details
atpI-atpH LSC 834 0.0011 1.00 49.3 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
matK-rps16_p1 matK-rps16 ACGAAGTAGTGTTGACGAGA GGTGCTCAACCTACAAGAACA 1383–1425 1.000 60.7
matK-rps16_p2 matK-rps16 TGAAAGAGAAGTGGGTAGACG GGTGCTCAACCTACAAGAACA 1401–1443 1.000 58.9
matK-rps16_p3 matK-rps16 AGAGAAGTGGGTAGACGAAG GGTGCTCAACCTACAAGAACA 1397–1439 1.000 58.5
matK-rps16_p4 matK-rps16 TTCCTGAAAGAGAAGTGGGT GGTGCTCAACCTACAAGAACA 1405–1447 1.000 58.2
matK-rps16_p5 matK-rps16 TCCTGAAAGAGAAGTGGGTAGA GGTGCTCAACCTACAAGAACA 1404–1446 1.000 57.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1542–1619 1.000 82.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1553–1630 1.000 81.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1546–1623 1.000 81.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1557–1634 1.000 80.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1548–1625 1.000 79.4
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 609–617 1.000 72.3
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 646–654 1.000 72.2
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 630–638 1.000 72.2
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 667–675 1.000 72.1
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG GCTGCCTCCTTGAAAGAGAG 635–643 1.000 71.4
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CTTCTCAAGTTCTTCCGCCA 1362–1382 1.000 80.6
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG TCTCAAGTTCTTCCGCCAAG 1360–1380 1.000 80.6
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG ACTTCTCAAGTTCTTCCGCC 1363–1383 1.000 80.6
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG TTCCGCCAAGCCTTGATTAA 1350–1370 1.000 80.3
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CTTCCGCCAAGCCTTGATTA 1351–1371 1.000 80.0
atpI-atpH_p1 atpI-atpH TAGCCGCAGCCTATATAGGT CAGTACCTTGACCAACTCCG 952–970 1.000 77.0
atpI-atpH_p2 atpI-atpH ATTTTTGCAACGTTAGCCGC CAGTACCTTGACCAACTCCG 965–983 1.000 76.5
atpI-atpH_p3 atpI-atpH TAGCCGCAGCCTATATAGGT GCAGTACCTTGACCAACTCC 953–971 1.000 76.1
atpI-atpH_p4 atpI-atpH TAGCCGCAGCCTATATAGGT AAGCAGCAGCAATTAGTGGA 886–904 1.000 76.1
atpI-atpH_p5 atpI-atpH TAGCCGCAGCCTATATAGGT GCCAATCCAGCAGCAATAAC 908–926 1.000 76.0
trnR-UCU-rps14_p1 trnR-UCU-rps14 AGAAGACCTCTGTCCTATCCA ATGCATGTTTGTTACCGGGT 459–463 1.000 65.7
trnR-UCU-rps14_p2 trnR-UCU-rps14 AGAAGACCTCTGTCCTATCCA TCCGGACACATACTTCGAGA 487–491 1.000 65.3
trnR-UCU-rps14_p3 trnR-UCU-rps14 AGGTTTAGAAGACCTCTGTCCT ATGCATGTTTGTTACCGGGT 465–469 1.000 65.0
trnR-UCU-rps14_p4 trnR-UCU-rps14 AGAAGACCTCTGTCCTATCCA TTACCGGGTGCAACAAGATC 448–452 1.000 65.0
trnR-UCU-rps14_p5 trnR-UCU-rps14 AGGTTTAGAAGACCTCTGTCCT TCCGGACACATACTTCGAGA 493–497 1.000 64.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Cymbopogon bhutanicus PV085078.1 139701 View on NCBI ↗
Cymbopogon citratus NC_042144.1 139708 View on NCBI ↗
Cymbopogon densiflorus NC_059821.1 140062 View on NCBI ↗
Cymbopogon distans MT083936.1 139868 View on NCBI ↗
Cymbopogon flexuosus NC_035040.1 139715 View on NCBI ↗
Cymbopogon nardus NC_070103.1 139823 View on NCBI ↗
Cymbopogon obtectus NC_059822.1 139704 View on NCBI ↗
Cymbopogon pospischilii NC_059823.1 140219 View on NCBI ↗
Cymbopogon schoenanthus NC_059824.1 139648 View on NCBI ↗
Cymbopogon winterianus NC_080535.1 139823 View on NCBI ↗