Markers + reference

Bactris

4 species · Arecaceae · Arecales

Back to catalogue

Species 4
Genome length 156–157 kb
Candidate markers 267
Primer pairs 90

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 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0014 1.00 34.5 yes View details
trnS-GCU-trnG-UCC LSC 822 0.0037 1.00 47.8 yes View details
trnD-GUC-trnY-GUA LSC 391 0.0051 1.00 35.9 yes View details
trnS-UGA-psbZ LSC 335 0.0060 1.00 35.5 yes View details
psaI-pafII LSC 332 0.0065 1.00 39.1 yes View details
petA-psbJ LSC 1017 0.0118 1.00 58.2 yes View details
psbE-petL LSC 911 0.0055 1.00 47.5 yes View details
rpl22 LSC 396 0.0013 1.00 27.7 yes View details
rps15-trnN-GUU SSC 6074 0.0024 1.00 45.7 yes View details
rpl22-rps19 IRb 106 0.0472 1.00 81.4 yes View details
rps19-psbA LSC 228 0.0450 0.86 78.8 no View details
psbC-trnS-UGA LSC 137 0.0401 1.00 66.5 yes View details
rpl32-trnL-UAG SSC 804 0.0025 1.00 62.4 yes View details
atpI-rps2 LSC 259 0.0064 1.00 57.7 yes View details
trnT-UGU-trnL-UAA LSC 1030 0.0024 1.00 55.8 yes View details
matK-rps16 LSC 667 0.0025 1.00 51.8 yes View details
ndhC-trnV-UAC LSC 1915 0.0008 1.00 51.1 yes View details
trnT-GGU-psbD LSC 1002 0.0020 1.00 50.9 yes View details
rpoB-trnC-GCA LSC 1222 0.0016 1.00 50.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TTGCTCCATTCCTTCAACGA GTGCTTGGGAGTCCTTGAAA 1149 1.000 75.6
psbA_p2 psbA TTGCTCCATTCCTTCAACGA AATACGTGTGCTTGGGAGTC 1156 1.000 75.0
psbA_p3 psbA TGCTCCATTCCTTCAACGAT GTGCTTGGGAGTCCTTGAAA 1148 1.000 73.8
psbA_p4 psbA TGCTCCATTCCTTCAACGAT AATACGTGTGCTTGGGAGTC 1155 1.000 73.1
psbA_p5 psbA TGCTCCATTCCTTCAACGATT GTGCTTGGGAGTCCTTGAAA 1148 1.000 71.5
matK-rps16_p1 matK-rps16 AGAAAGTGTTGTTGCCGAGA GCTCAACCTACGGGAACTG 804–1764 1.000 68.7
matK-rps16_p2 matK-rps16 AGAAAGTGTTGTTGCCGAGA GTGCTCAACCTACGGGAAC 806–1766 1.000 68.5
matK-rps16_p3 matK-rps16 AGAAAGTGTTGTTGCCGAGA TGCTCAACCTACGGGAACT 805–1765 1.000 67.8
matK-rps16_p4 matK-rps16 AAGTGTTGTTGCCGAGATCT GCTCAACCTACGGGAACTG 801–1761 1.000 66.9
matK-rps16_p5 matK-rps16 AAGTGTTGTTGCCGAGATCT GTGCTCAACCTACGGGAAC 803–1763 1.000 66.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGGAAAGACCCCTTAACT 934–953 1.000 67.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGAAGAAGCGGAGAGAGAGG AACGGAAAGACCCCTTAACT 990–1009 1.000 65.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AAACGGAAAGACCCCTTAACT 935–954 1.000 65.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA AACGGAAAGACCCCTTAACT 982–1001 1.000 65.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AACGGAAAGACCCCTTAACT 920–939 1.000 64.5
atpI-rps2_p1 atpI-rps2 GTTGGCCTACTTCTACACCC TTCCAGCAAATGATGACGCT 432–433 1.000 76.3
atpI-rps2_p2 atpI-rps2 GTTGGCCTACTTCTACACCC TGCAATTTGTGAGGGTCGTT 374–375 1.000 75.4
atpI-rps2_p3 atpI-rps2 GTTGGCCTACTTCTACACCC GCAATTTGTGAGGGTCGTTC 373–374 1.000 75.2
atpI-rps2_p4 atpI-rps2 GTTGGCCTACTTCTACACCC TTGTGAGGGTCGTTCTAGCT 368–369 1.000 74.9
atpI-rps2_p5 atpI-rps2 GGCCTACTTCTACACCCGAT TTCCAGCAAATGATGACGCT 429–430 1.000 74.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TAAAGGATTTGCAGTCCCCC 1369–1370 1.000 74.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA TAAAGGATTTGCAGTCCCCC 1289–1290 1.000 72.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TTTGTTGATCAGGCGACACC 1406–1407 1.000 72.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCCCTCATTTCCATTCCGG TAAAGGATTTGCAGTCCCCC 1290–1291 1.000 72.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG GACACCCGGATTTGAACTGG 1392–1393 1.000 72.2
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA AATTCTTCCTGGGTCGATGC 570 1.000 79.7
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GTGCTCTGACCGATTGAACT AATTCTTCCTGGGTCGATGC 513 1.000 79.6
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGGACGGACTGTAAATTCG 537 1.000 77.2
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA ATCGGATCCTAGTTCGGGAC AATTCTTCCTGGGTCGATGC 573 1.000 77.2
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CATCGGATCCTAGTTCGGGA AATTCTTCCTGGGTCGATGC 574 1.000 77.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Bactris gasipaes NC_072144.1 155604 View on NCBI ↗
Bactris gasipaes var. chichagui NC_058634.1 156646 View on NCBI ↗
Bactris gasipaes var. gasipaes NC_061651.1 156580 View on NCBI ↗
Bactris mexicana NC_079706.1 156774 View on NCBI ↗