Markers + reference

Zingiber

23 species · Zingiberaceae · Zingiberales

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Species 23
Genome length 162–164 kb
Candidate markers 273
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1411 0.0210 1.00 68.8 yes View details
atpH-atpI LSC 1436 0.0179 0.98 74.6 yes View details
petN-psbM LSC 1288 0.0245 0.99 69.4 yes View details
rbcL-accD LSC 771 0.0415 0.99 70.3 yes View details
petA-psbJ LSC 883 0.0184 1.00 69.9 yes View details
ycf2 IRb 6870 0.0020 0.99 32.6 yes View details
ycf1 IRb 3879 0.0101 1.00 46.8 no View details
rpl32-trnL-UAG SSC 884 0.0200 0.99 63.4 yes View details
psaC-ndhE SSC 701 0.0359 0.98 77.5 yes View details
ycf1 IRa 5457 0.0124 1.00 55.6 yes View details
ycf2 IRa 6870 0.0019 0.99 31.0 no View details
trnI-CAU-ycf2 IRb 179 0.0635 1.00 79.8 yes View details
psbT-psbN LSC 64 0.0712 1.00 77.2 yes View details
ycf2-trnI-CAU IRa 179 0.0442 1.00 75.2 yes View details
psbC-trnS-UGA LSC 148 0.0412 0.99 68.4 yes View details
ndhF-rpl32 SSC 668 0.0172 1.00 66.5 yes View details
trnfM-CAU-rps14 LSC 153 0.0409 0.99 65.7 yes View details
trnT-GGU-psbD LSC 1281 0.0134 0.99 63.3 yes View details
ccsA-ndhD SSC 275 0.0295 0.98 62.8 yes View details
ndhC-trnV-UAC LSC 1579 0.0081 0.99 62.0 yes View details
rrn4.5-rrn5 IRb 227 0.0347 1.00 62.0 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 1268–1527 0.913 87.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1266–1525 0.913 87.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1274–1533 0.913 87.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1250–1509 0.913 86.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA CTCGGAGGTTCGAATCCTTC 1272–1531 0.913 86.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACCTTAGCCGC 656–1542 0.957 89.3
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACCTTAGCCGC 712–1598 0.957 88.7
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA ATTTTTGCAACCTTAGCCGC 657–1543 0.957 88.2
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC ATTTTTGCAACCTTAGCCGC 716–1602 0.957 88.1
atpH-atpI_p5 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACCTTAGCCGC 739–1625 0.870 85.7
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 1161–1396 1.000 79.8
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 1160–1395 1.000 79.8
petN-psbM_p3 petN-psbM ATGGGGAAGGAGTGGACTTT TGCTACTGCACTGTTCATTCT 1158–1393 1.000 78.8
petN-psbM_p4 petN-psbM TGGGGAAGGAGTGGACTTTA TGCTACTGCACTGTTCATTCT 1157–1392 1.000 77.3
petN-psbM_p5 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTC 1160–1395 1.000 75.6
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGTCTCTGCGTAACCAATCA 1260–1418 1.000 87.0
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGTCTCTGCGTAACCAATCA 1263–1421 1.000 86.9
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGTCTCTGCGTAACCAATCA 1237–1395 1.000 85.4
trnT-GGU-psbD_p4 trnT-GGU-psbD GGCCCTTTTAACTCAGTGGT GGTCTCTGCGTAACCAATCA 1275–1433 1.000 85.2
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CGGTCTCTGCGTAACCAATC 1261–1419 1.000 84.3
psbC-trnS-UGA_p1 psbC-trnS-UGA CTTTCCATGACCCCTCTTCG GAGAGATGGCTGAGTGGTTG 256–301 1.000 89.9
psbC-trnS-UGA_p2 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG GAGAGATGGCTGAGTGGTTG 334–379 1.000 88.0
psbC-trnS-UGA_p3 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG GCTGAGTGGTTGATAGCTCC 326–371 1.000 87.9
psbC-trnS-UGA_p4 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG GGCTGAGTGGTTGATAGCTC 327–372 1.000 87.9
psbC-trnS-UGA_p5 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG GGTTGATAGCTCCGGTCTTG 319–364 1.000 87.8
trnfM-CAU-rps14_p1 trnfM-CAU-rps14 AAGGTTATGAGCCTTGCGAG TTACCGGGCGCAATAAGATC 224–240 1.000 90.6
trnfM-CAU-rps14_p2 trnfM-CAU-rps14 ACAGGATTTGAACCCGTGAC TTACCGGGCGCAATAAGATC 247–263 1.000 89.6
trnfM-CAU-rps14_p3 trnfM-CAU-rps14 AAGGTTATGAGCCTTGCGAG ATGTTTATTACCGGGCGCAA 231–247 1.000 89.5
trnfM-CAU-rps14_p4 trnfM-CAU-rps14 AAGGTTATGAGCCTTGCGAG TGTTTATTACCGGGCGCAAT 230–246 1.000 89.5
trnfM-CAU-rps14_p5 trnfM-CAU-rps14 TTTGAACCCGTGACCTCAAG TTACCGGGCGCAATAAGATC 241–257 0.913 86.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

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

Species Accession Length (bp) Link
Zingiber cochleariforme OP869986.1 163665 View on NCBI ↗
Zingiber densissimum OP869975.1 163607 View on NCBI ↗
Zingiber ellipticum OP869976.1 163455 View on NCBI ↗
Zingiber flavomaculosum OP869987.1 163298 View on NCBI ↗
Zingiber fragile OR337869.1 163381 View on NCBI ↗
Zingiber koshunense OP869977.1 163394 View on NCBI ↗
Zingiber leptorrhizum NC_072309.1 162956 View on NCBI ↗
Zingiber longiglande OR337871.1 163125 View on NCBI ↗
Zingiber mioga NC_057615.1 163541 View on NCBI ↗
Zingiber montanum NC_053656.1 164464 View on NCBI ↗
Zingiber neotruncatum OP869978.1 162481 View on NCBI ↗
Zingiber odoriferum PQ550047.1 163538 View on NCBI ↗
Zingiber officinale NC_044775.1 162621 View on NCBI ↗
Zingiber orbiculatum OP869979.1 163527 View on NCBI ↗
Zingiber purpureum OP869980.1 163135 View on NCBI ↗
Zingiber recurvatum OR337876.1 163129 View on NCBI ↗
Zingiber roseum OR337877.1 163529 View on NCBI ↗
Zingiber simaoense OR337878.1 163551 View on NCBI ↗
Zingiber smilesianum OP869981.1 163640 View on NCBI ↗
Zingiber striolatum NC_065159.1 163711 View on NCBI ↗
Zingiber xishuangbannaense OP869982.1 163487 View on NCBI ↗
Zingiber yingjiangense OP869983.1 163623 View on NCBI ↗
Zingiber yunnanense OR337880.1 163772 View on NCBI ↗