Markers + reference

Boesenbergia

2 species · Zingiberaceae · Zingiberales

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Species 2
Genome length 163–164 kb
Candidate markers 276
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpF-atpH LSC 496 0.0283 1.00 59.4 yes View details
petN-psbM LSC 1299 0.0195 0.99 56.4 yes View details
trnD-GUC-trnY-GUA LSC 455 0.0288 0.99 65.7 yes View details
ycf3-trnS-GGA LSC 633 0.0243 0.97 67.9 yes View details
petB LSC 1461 0.0132 0.98 57.4 yes View details
ndhF-rpl32 SSC 651 0.0420 0.99 76.8 yes View details
psaC-ndhE SSC 644 0.0316 0.98 68.6 yes View details
ndhG-ndhI SSC 402 0.0262 0.95 59.9 yes View details
ndhA SSC 2159 0.0139 1.00 64.6 yes View details
psbC-trnS-UGA LSC 146 0.0548 1.00 81.8 yes View details
trnH-GUG-rpl2 IRb 46 0.0652 1.00 70.2 yes View details
rpl2-trnH-GUG IRa 46 0.0652 1.00 70.2 yes View details
rrn16-trnI-GAU IRb 305 0.0328 1.00 65.3 yes View details
trnI-GAU-rrn16 IRa 305 0.0328 1.00 65.3 yes View details
psbE-petL LSC 1236 0.0098 0.99 65.2 yes View details
trnS-GCU-trnG-GCC LSC 705 0.0158 0.99 65.1 yes View details
atpB-rbcL LSC 835 0.0085 0.99 64.9 yes View details
petD-rpoA LSC 187 0.0214 1.00 64.8 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-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGGAGATACCCCTTCCCTTA 815–818 1.000 78.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGGAGATACCCCTTCCCTTA 814–817 1.000 78.9
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC AGTATCAAGCGGGTCGAGTA CGGAGATACCCCTTCCCTTA 899–902 1.000 78.3
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC GAGCGGAGAAAGAGGGATTC CGGAGATACCCCTTCCCTTA 871–874 1.000 76.9
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GTCGAGTAATCAGAGCGAGC CGGAGATACCCCTTCCCTTA 887–890 1.000 76.7
atpF-atpH_p1 atpF-atpH GTCGTCGATTCGGCATTAGA TGGTTGTGGCATTAGCACTT 1098–1112 1.000 81.3
atpF-atpH_p2 atpF-atpH GTCGTCGATTCGGCATTAGA TATTGCGAGACAACCGGAAG 1187–1201 1.000 81.2
atpF-atpH_p3 atpF-atpH GTCGTCGATTCGGCATTAGA ATTTCTGCCGCTTCCGTTAT 1288–1302 1.000 80.8
atpF-atpH_p4 atpF-atpH TCGTCGAGATTGTGCACTTT TATTGCGAGACAACCGGAAG 876–899 1.000 80.6
atpF-atpH_p5 atpF-atpH TTCGTCGAGATTGTGCACTT TATTGCGAGACAACCGGAAG 877–900 1.000 80.6
petN-psbM_p1 petN-psbM GTCTACTGACTCCATCCGGA GCCTTCCAGTCCCAATTGAA 2506 0.500 59.0
petN-psbM_p2 petN-psbM TATCCAGACTCACGAGGGTC GCCTTCCAGTCCCAATTGAA 2422 0.500 59.0
petN-psbM_p3 petN-psbM AGTATGGGGAAGGAGTGGAC GCCTTCCAGTCCCAATTGAA 1969 0.500 58.4
petN-psbM_p4 petN-psbM GTATGGGGAAGGAGTGGACT GCCTTCCAGTCCCAATTGAA 1968 0.500 58.4
petN-psbM_p5 petN-psbM TATCCAGACTCACGAGGGTC ATGCCTTCCAGTCCCAATTG 2424 0.500 58.4
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA AATTCTTCCTGGGTCGATGC 630–634 1.000 81.2
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GATCGGATCCTAGTTCGGGA AATTCTTCCTGGGTCGATGC 634–638 1.000 81.0
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGGACGGACTGTAAATTCG 597–601 1.000 78.9
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA ATCGGATCCTAGTTCGGGAC AATTCTTCCTGGGTCGATGC 633–637 1.000 78.7
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGACGGACTGTAAATTCGT 596–600 1.000 78.7
psbC-trnS-UGA_p1 psbC-trnS-UGA CTTTCCATGACCCCTCTTCG GAGAGATGGCTGAGTGGTTG 261–264 1.000 82.0
psbC-trnS-UGA_p2 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG GAGAGATGGCTGAGTGGTTG 339–342 1.000 81.7
psbC-trnS-UGA_p3 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG GCTGAGTGGTTGATAGCTCC 331–334 1.000 81.5
psbC-trnS-UGA_p4 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG GGCTGAGTGGTTGATAGCTC 332–335 1.000 81.5
psbC-trnS-UGA_p5 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG GGTTGATAGCTCCGGTCTTG 324–327 1.000 81.5
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TGGCCACAATTGAAGAGGTC ACGGAAAGAGAGGGATTCGA 779–787 1.000 81.2
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TGGCCACAATTGAAGAGGTC TTCCAATGCTACGCCTTGAA 729–737 1.000 81.1
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTTTCTCCGGAAGTTGTCGG ACGGAAAGAGAGGGATTCGA 819–827 1.000 80.8
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTTCTCCGGAAGTTGTCGG TTCCAATGCTACGCCTTGAA 769–777 1.000 80.7
ycf3-trnS-GGA_p5 ycf3-trnS-GGA GGCCACAATTGAAGAGGTCT ACGGAAAGAGAGGGATTCGA 778–786 1.000 80.3

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
Boesenbergia kingii MW326451.1 163198 View on NCBI ↗
Boesenbergia rotunda MZ411538.1 163817 View on NCBI ↗