Markers + reference

Wurfbainia

5 species · Zingiberaceae · Zingiberales

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Species 5
Genome length 164–164 kb
Candidate markers 252
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 252 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpF LSC 1366 0.0060 0.99 38.5 yes View details
petN-psbM LSC 1314 0.0089 1.00 47.0 yes View details
psbM-trnD-GTC LSC 1086 0.0052 1.00 43.4 yes View details
trnE-TTC-trnT-GGT LSC 911 0.0096 0.92 52.5 yes View details
trnT-GGT-psbD LSC 1321 0.0086 0.99 48.6 yes View details
trnS-TGA-psbZ LSC 367 0.0054 1.00 38.0 yes View details
ndhC-trnM-CAT LSC 2564 0.0085 1.00 55.4 yes View details
psbE-petL LSC 1212 0.0118 1.00 55.6 yes View details
ycf1 IRb 3942 0.0019 1.00 39.1 no View details
rpl32-trnL-TAG SSC 889 0.0103 0.98 44.7 yes View details
rps15-ycf1 SSC 1555 0.0090 1.00 54.9 yes View details
ycf1 IRa 3639 0.0032 1.00 35.4 yes View details
ndhA SSC 2128 0.0046 1.00 61.1 yes View details
psaC-ndhE SSC 672 0.0049 0.90 57.4 yes View details
psbC-trnS-TGA LSC 145 0.0372 0.99 55.8 yes View details
psaJ-rpl33 LSC 658 0.0047 0.98 55.2 yes View details
ndhE-ndhG SSC 209 0.0088 0.98 54.0 yes View details
cemA-petA LSC 253 0.0126 1.00 53.7 yes View details
ndhJ-ndhK LSC 104 0.0096 0.99 52.6 yes View details
ccsA-ndhD SSC 286 0.0136 1.00 51.3 yes View details
rps16-trnQ-TTG LSC 1350 0.0053 0.99 50.9 yes View details
psaA-ycf3 LSC 653 0.0025 0.98 50.7 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-TTG_p1 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1424–1452 1.000 80.0
rps16-trnQ-TTG_p2 rps16-trnQ-TTG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1435–1463 1.000 79.5
rps16-trnQ-TTG_p3 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1428–1456 1.000 78.9
rps16-trnQ-TTG_p4 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA AGGATAAAAATGGGGCGTGG 1482–1510 1.000 78.7
rps16-trnQ-TTG_p5 rps16-trnQ-TTG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1439–1467 1.000 78.4
atpF_p1 atpF CAATTCCGTCGCCTACTTGA TGGTTGTGGCATTAGCACTT 2071–2101 1.000 82.0
atpF_p2 atpF CAATTCCGTCGCCTACTTGA AGGAATTACCGCATTCGCTT 1863–1893 1.000 81.9
atpF_p3 atpF CAATTCCGTCGCCTACTTGA AGGCCAAGCTGTAGAAGGTA 2178–2208 1.000 81.6
atpF_p4 atpF CCGTTTCGGCTACCACAATA TGGTTGTGGCATTAGCACTT 2638–2668 1.000 81.5
atpF_p5 atpF CCGTTTCGGCTACCACAATA AGGAATTACCGCATTCGCTT 2430–2460 1.000 81.4
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 1413–1418 1.000 69.8
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 1412–1417 1.000 69.8
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1471–1476 1.000 69.5
petN-psbM_p4 petN-psbM ATGGGGAAGGAGTGGACTTT TGCTACTGCACTGTTCATTCT 1410–1415 1.000 68.9
petN-psbM_p5 petN-psbM TGGGGAAGGAGTGGACTTTA TGCTACTGCACTGTTCATTCT 1409–1414 1.000 67.4
psbM-trnD-GTC_p1 psbM-trnD-GTC AGAATGAACAGTGCAGTAGC CCTCGCTGGGATTGTAGTTC 1212–1214 1.000 62.8
psbM-trnD-GTC_p2 psbM-trnD-GTC AGAATGAACAGTGCAGTAGC TACACCTCGCTGGGATTGTA 1216–1218 1.000 62.1
psbM-trnD-GTC_p3 psbM-trnD-GTC AGAATGAACAGTGCAGTAGC CATACACCTCGCTGGGATTG 1218–1220 1.000 60.0
psbM-trnD-GTC_p4 psbM-trnD-GTC AGGAACTAGAATGAACAGTGCA CCTCGCTGGGATTGTAGTTC 1219–1221 1.000 59.7
psbM-trnD-GTC_p5 psbM-trnD-GTC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1195–1197 1.000 59.5
trnE-TTC-trnT-GGT_p1 trnE-TTC-trnT-GGT TCCTTTCGTAGTACCCCCAG GAACCGATGACTTACGCCTT 955–1050 1.000 84.2
trnE-TTC-trnT-GGT_p2 trnE-TTC-trnT-GGT TCCTTTCGTAGTACCCCCAG CCATGGCGTTACTCTACCAC 934–1029 1.000 83.7
trnE-TTC-trnT-GGT_p3 trnE-TTC-trnT-GGT TCCTTTCGTAGTACCCCCAG TGGCGTTACTCTACCACTGA 931–1026 1.000 83.6
trnE-TTC-trnT-GGT_p4 trnE-TTC-trnT-GGT GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 919–1014 1.000 83.3
trnE-TTC-trnT-GGT_p5 trnE-TTC-trnT-GGT TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 898–993 1.000 83.2
trnT-GGT-psbD_p1 trnT-GGT-psbD GTGGTAGAGTAACGCCATGG TCAAATAGATCATTTTCTTCTTTGGT 1422–1429 1.000 43.0
trnT-GGT-psbD_p2 trnT-GGT-psbD TCAGTGGTAGAGTAACGCCA TCAAATAGATCATTTTCTTCTTTGGT 1425–1432 1.000 43.0
trnT-GGT-psbD_p3 trnT-GGT-psbD GGCGTAAGTCATCGGTTCAA TCAAATAGATCATTTTCTTCTTTGGT 1399–1406 1.000 43.0
trnT-GGT-psbD_p4 trnT-GGT-psbD GTGGTAGAGTAACGCCATGG CAAATAGATCATTTTCTTCTTTGGT 1421–1428 1.000 43.0
trnT-GGT-psbD_p5 trnT-GGT-psbD GGCCCTTTTAACTCAGTGGT TCAAATAGATCATTTTCTTCTTTGGT 1437–1444 1.000 42.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Wurfbainia compacta NC_036992.1 163553 View on NCBI ↗
Wurfbainia longiligularis NC_044774.1 164068 View on NCBI ↗
Wurfbainia neoaurantiaca NC_057208.1 163534 View on NCBI ↗
Wurfbainia villosa NC_044746.1 164068 View on NCBI ↗
Wurfbainia villosa var. xanthioides NC_044747.1 163981 View on NCBI ↗