Markers + reference

Alpinia

8 species · Zingiberaceae · Zingiberales

Back to catalogue

Species 8
Genome length 160–164 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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 1030 0.0312 0.81 70.5 yes View details
atpF LSC 1395 0.0172 0.97 60.6 yes View details
atpH-atpI LSC 1233 0.0207 0.92 65.0 yes View details
trnE-UUC-trnT-GGU LSC 843 0.0304 0.70 56.7 yes View details
psbE-petL LSC 1263 0.0201 0.69 64.7 yes View details
ycf1 IRb 1392 0.0034 1.00 40.1 no View details
ndhF-rpl32 SSC 625 0.0312 0.99 73.0 yes View details
rpl32-trnL-UAG SSC 887 0.0392 0.95 78.1 yes View details
ccsA-ndhD SSC 312 0.0496 0.92 75.9 yes View details
psaC-ndhE SSC 694 0.0290 0.92 70.4 yes View details
ycf1 SSC 5457 0.0127 0.99 51.1 yes View details
accD-psaI LSC 521 0.0315 0.93 74.5 yes View details
trnG-GCC-trnfM-CAU LSC 193 0.0316 0.95 72.3 yes View details
ndhC-trnV-UAC LSC 1695 0.0225 0.91 70.2 yes View details
rpl2-trnH-GUG IRa 43 0.0443 1.00 70.2 yes View details
psaJ-rpl33 LSC 626 0.0224 0.96 69.5 yes View details
trnT-UGU-trnL-UAA LSC 653 0.0186 0.98 69.3 yes View details
trnN-GUU-trnR-ACG IRa 573 0.0147 1.00 69.2 yes View details
petN-psbM LSC 1303 0.0191 0.99 68.8 yes View details
trnC-GCA-petN LSC 849 0.0166 0.99 67.7 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
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 869–1099 1.000 62.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 868–1098 1.000 62.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 872–1102 1.000 61.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 871–1101 1.000 61.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 870–1100 1.000 61.3
atpF_p1 atpF CAATTCCGTCGCCTACTTGA TGGTTGTGGCATTAGCACTT 2095–2151 1.000 87.3
atpF_p2 atpF CAATTCCGTCGCCTACTTGA AGGCCAAGCTGTAGAAGGTA 2202–2258 1.000 86.6
atpF_p3 atpF CCGTTTCGGCTACCACAATA TGGTTGTGGCATTAGCACTT 2662–2718 1.000 85.8
atpF_p4 atpF CAATTCCGTCGCCTACTTGA AGGAATTACCGCATTCGCTT 1888–1937 1.000 85.3
atpF_p5 atpF CCGTTTCGGCTACCACAATA AGGAATTACCGCATTCGCTT 2455–2504 1.000 84.2
atpH-atpI_p1 atpH-atpI AAGCAGCAGAAATCAGTGGA ATTTTTGCAACCTTAGCCGC 1196–1315 1.000 83.3
atpH-atpI_p2 atpH-atpI AGCAGCAGAAATCAGTGGAT ATTTTTGCAACCTTAGCCGC 1195–1314 1.000 81.5
atpH-atpI_p3 atpH-atpI GAAGCAGCAGAAATCAGTGG ATTTTTGCAACCTTAGCCGC 1197–1316 1.000 80.6
atpH-atpI_p4 atpH-atpI AAGCAGCAGAAATCAGTGGAT ATTTTTGCAACCTTAGCCGC 1196–1315 1.000 79.2
atpH-atpI_p5 atpH-atpI AGCAGCAGAAATCAGTGGATT ATTTTTGCAACCTTAGCCGC 1195–1314 1.000 79.2
trnC-GCA-petN_p1 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGTCCCCCTAAAGTCCACTC 968–983 1.000 81.5
trnC-GCA-petN_p2 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 898–913 1.000 81.1
trnC-GCA-petN_p3 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGTCCACTCCTTCCCCATAC 957–972 1.000 81.0
trnC-GCA-petN_p4 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC GTCCACTCCTTCCCCATACT 956–971 1.000 81.0
trnC-GCA-petN_p5 trnC-GCA-petN GACATGGCCAAGTGGTAAGG AGTCCCCCTAAAGTCCACTC 1014–1029 1.000 80.7
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 940–1430 1.000 76.1
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 939–1429 1.000 76.1
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 998–1488 1.000 75.6
petN-psbM_p4 petN-psbM ATGGGGAAGGAGTGGACTTT TGCTACTGCACTGTTCATTCT 937–1427 1.000 75.1
petN-psbM_p5 petN-psbM TGGGGAAGGAGTGGACTTTA TGCTACTGCACTGTTCATTCT 936–1426 1.000 73.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 704–964 1.000 86.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 683–943 1.000 86.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 683–943 1.000 86.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 662–922 1.000 86.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 680–940 1.000 86.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Alpinia galanga MZ066611.1 160100 View on NCBI ↗
Alpinia hainanensis NC_048461.1 162387 View on NCBI ↗
Alpinia japonica NC_083220.1 161906 View on NCBI ↗
Alpinia kwangsiensis PV669995.1 162449 View on NCBI ↗
Alpinia ligulata PQ568881.1 163070 View on NCBI ↗
Alpinia nigra NC_062463.1 164343 View on NCBI ↗
Alpinia officinarum MT254526.1 162137 View on NCBI ↗
Alpinia pumila NC_048462.1 161920 View on NCBI ↗