Markers + reference

Cornukaempferia

2 species · Zingiberaceae · Zingiberales

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Species 2
Genome length 163–163 kb
Candidate markers 272
Primer pairs 95

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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 1395 0.0588 0.73 85.3 yes View details
psbM-trnD-GUC LSC 1050 0.0173 0.99 69.6 yes View details
trnE-UUC-trnT-GGU LSC 873 0.0213 0.97 66.6 yes View details
trnT-GGU-psbD LSC 1285 0.0250 0.96 61.9 yes View details
trnS-GGA-rps4 LSC 274 0.0471 0.70 62.1 yes View details
clpP1-psbB LSC 473 0.4085 0.99 91.7 yes View details
psbB-psbT LSC 187 0.0000 0.96 43.0 yes View details
ycf1 IRb 3912 0.0123 1.00 51.5 yes View details
psaC-ndhE SSC 626 0.0132 0.61 49.1 yes View details
ycf1 IRa 5448 0.0018 1.00 42.5 no View details
psbC-trnS-UGA LSC 148 0.0473 1.00 79.7 yes View details
psbT-psbN LSC 64 0.1562 1.00 73.0 yes View details
psbJ-psbL LSC 121 0.0331 1.00 71.5 yes View details
ndhF-rpl32 SSC 680 0.0126 0.93 70.3 yes View details
rps16-trnQ-UUG LSC 1423 0.0066 0.96 66.8 yes View details
rps18-rpl20 LSC 203 0.0246 1.00 66.7 yes View details
ndhC-trnV-UAC LSC 1642 0.0065 0.94 66.6 yes View details
trnM-CAU-ycf2 IRb 129 0.0233 1.00 65.9 yes View details
psbE-petL LSC 1230 0.0075 0.98 64.8 yes View details
petN-psbM LSC 1286 0.0086 0.99 64.7 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1470–1514 1.000 83.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1468–1512 1.000 83.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1476–1520 1.000 82.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1452–1496 1.000 82.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA CTCGGAGGTTCGAATCCTTC 1474–1518 1.000 81.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACCTTAGCCGC 1109–1484 1.000 86.8
atpH-atpI_p2 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACCTTAGCCGC 1192–1567 1.000 86.5
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACCTTAGCCGC 1165–1540 1.000 86.0
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATTTTTGCAACCTTAGCCGC 1110–1485 1.000 85.6
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATTTTTGCAACCTTAGCCGC 1169–1544 1.000 85.4
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 1390–1530 1.000 69.1
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 1389–1529 1.000 69.1
petN-psbM_p3 petN-psbM ATGGGGAAGGAGTGGACTTT TGCTACTGCACTGTTCATTCT 1387–1527 1.000 68.1
petN-psbM_p4 petN-psbM ATTGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTCT 1449–1589 1.000 67.9
petN-psbM_p5 petN-psbM TGGGGAAGGAGTGGACTTTA TGCTACTGCACTGTTCATTCT 1386–1526 1.000 66.6
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CCTCGCTGGGATTGTAGTTC 1178–1183 1.000 63.6
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TACACCTCGCTGGGATTGTA 1182–1187 1.000 62.9
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CATACACCTCGCTGGGATTG 1184–1189 1.000 60.7
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA CCTCGCTGGGATTGTAGTTC 1185–1190 1.000 60.4
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1161–1166 1.000 60.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG GAACCGATGACTTACGCCTT 985–1012 1.000 82.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG CCATGGCGTTACTCTACCAC 964–991 1.000 82.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG TGGCGTTACTCTACCACTGA 961–988 1.000 81.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 949–976 1.000 81.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 928–955 1.000 81.6
trnT-GGU-psbD_p1 trnT-GGU-psbD ATTGACCCGCTTCACCTTTT AGCACCATGAAGAGCAACAA 1852–1905 1.000 83.8
trnT-GGU-psbD_p2 trnT-GGU-psbD AAAATTGACCCGCTTCACCT CACCGTCACCATCTTCGAAT 2183–2236 1.000 83.3
trnT-GGU-psbD_p3 trnT-GGU-psbD AAATTGACCCGCTTCACCTT CACCGTCACCATCTTCGAAT 2182–2235 1.000 83.3
trnT-GGU-psbD_p4 trnT-GGU-psbD AATTGACCCGCTTCACCTTT CACCGTCACCATCTTCGAAT 2181–2234 1.000 83.3
trnT-GGU-psbD_p5 trnT-GGU-psbD ATTGACCCGCTTCACCTTTT CACCGTCACCATCTTCGAAT 2180–2233 1.000 83.3

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
Cornukaempferia aurantiflora NC_085809.1 163305 View on NCBI ↗
Cornukaempferia larsenii PP542020.1 162593 View on NCBI ↗