Markers + reference

Curcuma

21 species · Zingiberaceae · Zingiberales

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Species 21
Genome length 159–164 kb
Candidate markers 272
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 406 0.0209 0.99 61.1 yes View details
trnQ-UUG-psbK LSC 344 0.0086 0.99 46.4 yes View details
atpF LSC 1380 0.0038 1.00 38.0 yes View details
rpoB-trnC-GCA LSC 1087 0.0072 0.98 57.0 yes View details
trnC-GCA-petN LSC 829 0.0060 1.00 47.3 yes View details
petN-psbM LSC 1357 0.0072 1.00 54.3 yes View details
trnS-UGA-psbZ LSC 358 0.0047 0.99 48.7 yes View details
rps4-trnT-UGU LSC 461 0.0112 1.00 60.4 yes View details
trnT-UGU-trnL-UAA LSC 1128 0.0062 0.99 61.7 yes View details
rpl22 LSC 390 0.0040 1.00 39.3 yes View details
ndhF-rpl32 SSC 657 0.0103 1.00 68.6 yes View details
ccsA SSC 990 0.0025 1.00 40.7 yes View details
psaC-ndhE SSC 645 0.0096 1.00 63.1 yes View details
atpH-atpI LSC 1440 0.0039 0.98 60.4 yes View details
matK-trnK-UUU LSC 826 0.0053 1.00 58.5 yes View details
rpl22-rps19 IRb 174 0.0176 1.00 57.6 yes View details
trnD-GUC-trnY-GUA LSC 435 0.0042 1.00 56.3 yes View details
trnE-UUC-trnT-GGU LSC 854 0.0058 1.00 56.1 yes View details
psbE-petL LSC 1245 0.0034 1.00 55.5 yes View details
petD-rpoA LSC 194 0.0140 0.96 55.1 yes View details
ndhC-trnV-UAC LSC 1454 0.0025 0.96 55.0 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU AGAAACTGTTGTTGCCGAGA TGAAGGGTTGGGTTGCTAAC 919–932 1.000 82.6
matK-trnK-UUU_p2 matK-trnK-UUU AGAAACTGTTGTTGCCGAGA GTTTTGAAGGGTTGGGTTGC 923–936 1.000 82.2
matK-trnK-UUU_p3 matK-trnK-UUU AGAAACTGTTGTTGCCGAGA TTTTGAAGGGTTGGGTTGCT 922–935 1.000 81.6
matK-trnK-UUU_p4 matK-trnK-UUU AGAAACTGTTGTTGCCGAGA AACGGTAGAGTACTCGGCTT 897–910 1.000 81.4
matK-trnK-UUU_p5 matK-trnK-UUU AGAAACTGTTGTTGCCGAGA ACGGTAGAGTACTCGGCTTT 896–909 1.000 81.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 480–1570 1.000 86.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 478–1568 1.000 86.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 486–1576 1.000 86.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 462–1552 1.000 85.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA CTCGGAGGTTCGAATCCTTC 484–1574 1.000 85.5
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GAAGGATTCGAACCTCCGAG CGGGCAATTTGGCAAAGAAA 486–515 1.000 80.7
trnQ-UUG-psbK_p2 trnQ-UUG-psbK AGGATTCGAACCTCCGAGTA CGGGCAATTTGGCAAAGAAA 484–513 1.000 79.0
trnQ-UUG-psbK_p3 trnQ-UUG-psbK AAGGATTCGAACCTCCGAGT CGGGCAATTTGGCAAAGAAA 485–514 1.000 78.9
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GAGTAACGGGACCAAAACCC CGGGCAATTTGGCAAAGAAA 469–498 1.000 78.8
trnQ-UUG-psbK_p5 trnQ-UUG-psbK ATTCGAACCTCCGAGTAACG CGGGCAATTTGGCAAAGAAA 481–510 1.000 78.0
atpF_p1 atpF CAATTCCGTCGCCTACTTGA TGGTTGTGGCATTAGCACTT 2083–2125 1.000 83.1
atpF_p2 atpF CAATTCCGTCGCCTACTTGA TATTGCGAGACAACCGGAAG 2172–2214 1.000 83.0
atpF_p3 atpF CAATTCCGTCGCCTACTTGA ATTTCTGCCGCTTCCGTTAT 2273–2315 1.000 82.5
atpF_p4 atpF CCGTTTCGGCTACCACAATA TGGTTGTGGCATTAGCACTT 2650–2692 1.000 82.4
atpF_p5 atpF CCGTTTCGGCTACCACAATA TATTGCGAGACAACCGGAAG 2739–2781 1.000 82.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACCTTAGCCGC 1496–1568 1.000 85.1
atpH-atpI_p2 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACCTTAGCCGC 1579–1651 1.000 84.9
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACCTTAGCCGC 1552–1624 1.000 84.4
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATTTTTGCAACCTTAGCCGC 1497–1569 1.000 83.9
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATTTTTGCAACCTTAGCCGC 1556–1628 1.000 83.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTC AAAGGATTTGCAGTCCCCTG 1197–1318 1.000 85.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTC GCGACACCCAGATTTGAACT 1223–1344 1.000 81.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTC CCTTACCACTTGGCCATGTC 1177–1298 1.000 81.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT AAAGGATTTGCAGTCCCCTG 1198–1319 1.000 81.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTTCCGTCAAGCCCTCATTA AAAGGATTTGCAGTCCCCTG 1193–1314 1.000 80.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (21)

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

Species Accession Length (bp) Link
Curcuma aff. kwangsiensis JC-2013 MW326453.1 162179 View on NCBI ↗
Curcuma alismatifolia NC_050038.1 162715 View on NCBI ↗
Curcuma amarissima NC_050039.1 162158 View on NCBI ↗
Curcuma aromatica NC_046602.1 159723 View on NCBI ↗
Curcuma cochinchinensis PP799046.1 163713 View on NCBI ↗
Curcuma comosa OK327014.1 162272 View on NCBI ↗
Curcuma elata NC_050036.1 162171 View on NCBI ↗
Curcuma flaviflora NC_028729.1 160478 View on NCBI ↗
Curcuma kwangsiensis NC_046685.1 159439 View on NCBI ↗
Curcuma latifolia OK327015.1 162289 View on NCBI ↗
Curcuma longa NC_042886.1 159550 View on NCBI ↗
Curcuma phaeocaulis NC_045242.1 162133 View on NCBI ↗
Curcuma plicata MW326452.1 162169 View on NCBI ↗
Curcuma roscoeana NC_022928.1 159512 View on NCBI ↗
Curcuma ruiliensis MW326454.1 162242 View on NCBI ↗
Curcuma sichuanensis NC_050035.1 162133 View on NCBI ↗
Curcuma viridiflora NC_084109.1 162212 View on NCBI ↗
Curcuma wenyujin NC_045241.1 162266 View on NCBI ↗
Curcuma xanthorrhiza NC_050040.1 162192 View on NCBI ↗
Curcuma yunnanensis NC_050037.1 162133 View on NCBI ↗
Curcuma zedoaria NC_048505.1 162135 View on NCBI ↗