Markers + reference

Acrocomia

2 species · Arecaceae · Arecales

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Species 2
Genome length 157–157 kb
Candidate markers 270
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 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbC LSC 1422 0.0000 1.00 31.1 yes View details
accD-psaI LSC 631 0.0063 1.00 62.4 yes View details
petA-psbJ LSC 1014 0.0158 1.00 67.9 yes View details
trnP-UGG-psaJ LSC 407 0.0025 1.00 56.1 yes View details
psaJ-rpl33 LSC 552 0.0000 1.00 57.9 yes View details
rpl14 LSC 369 0.0000 1.00 33.9 yes View details
rpl16 LSC 1530 0.0013 1.00 59.5 yes View details
ccsA SSC 969 0.0000 1.00 30.9 yes View details
psaC-ndhE SSC 645 0.0016 0.94 64.4 yes View details
psbC-trnS-UGA LSC 137 0.0219 1.00 65.1 yes View details
ccsA-ndhD SSC 215 0.0140 1.00 60.5 yes View details
trnF-GAA-ndhJ LSC 717 0.0014 1.00 59.6 yes View details
accD LSC 1476 0.0007 1.00 59.1 yes View details
matK LSC 1548 0.0006 1.00 59.0 yes View details
ndhB IRb 2237 0.0004 1.00 57.5 yes View details
ndhB IRa 2237 0.0004 1.00 57.5 yes View details
trnD-GUC-trnY-GUA LSC 431 0.0023 1.00 56.6 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
trnK-UUU_p1 trnK-UUU TGCCAATGTCAACCAATCTCA GTCGTGCAGTGCAATTCAAT 2870 1.000 68.3
trnK-UUU_p2 trnK-UUU TGCCAATGTCAACCAATCTCA TCAATGTTTTGACGGGGTCG 2886 1.000 64.9
trnK-UUU_p3 trnK-UUU GCCAATGTCAACCAATCTCA GTCGTGCAGTGCAATTCAAT 2869 1.000 63.8
trnK-UUU_p4 trnK-UUU TGCCAATGTCAACCAATCTC GTCGTGCAGTGCAATTCAAT 2870 1.000 63.8
trnK-UUU_p5 trnK-UUU TGCCAATGTCAACCAATCTCA GTTCAATGTTTTGACGGGGTC 2888 1.000 63.0
matK_p1 matK TCTCATCACGTCACCAAACC TCCTGCCTCTGGTTCAAGTA 1599 1.000 78.5
matK_p2 matK TCTCATCACGTCACCAAACC AATGAAATGGGTCCTGCCTC 1610 1.000 77.5
matK_p3 matK TCTCATCACGTCACCAAACC CCTGCCTCTGGTTCAAGTAG 1598 1.000 75.6
matK_p4 matK TCTCATCACGTCACCAAACC AAATGAAATGGGTCCTGCCT 1611 1.000 73.7
matK_p5 matK TCTCATCACGTCACCAAACC ATGAAATGGGTCCTGCCTCT 1609 1.000 73.2
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA AATTCTTCCTGGGTCGATGC 610 1.000 79.2
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GTGCTCTGACCGATTGAACT AATTCTTCCTGGGTCGATGC 553 1.000 79.1
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGGACGGACTGTAAATTCG 577 1.000 76.8
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA ATCGGATCCTAGTTCGGGAC AATTCTTCCTGGGTCGATGC 613 1.000 76.7
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CATCGGATCCTAGTTCGGGA AATTCTTCCTGGGTCGATGC 614 1.000 76.7
psbC_p1 psbC TTTCCCAAGAAATCCGTGCA CTAGCCGAGCCAAAACAGAA 1586 1.000 78.4
psbC_p2 psbC TTTCCCAAGAAATCCGTGCA GCCGAGCCAAAACAGAAAAA 1583 1.000 78.2
psbC_p3 psbC TTTCCCAAGAAATCCGTGCA TAGCCGAGCCAAAACAGAAA 1585 1.000 77.8
psbC_p4 psbC GCAGCGGAAGATCCTGAATT CTAGCCGAGCCAAAACAGAA 1569 1.000 75.9
psbC_p5 psbC AGGTATTCGTGCTTGGATGG CTAGCCGAGCCAAAACAGAA 1513 1.000 75.8
psbC-trnS-UGA_p1 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GGTTGATAGCTCCGGTCTTG 283 1.000 79.3
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 244 1.000 79.2
psbC-trnS-UGA_p3 psbC-trnS-UGA CTGTTCTTTCCATGACCCCC GGTTGATAGCTCCGGTCTTG 243 1.000 79.2
psbC-trnS-UGA_p4 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GATGGCCGAGTGGTTGATAG 294 1.000 78.7
psbC-trnS-UGA_p5 psbC-trnS-UGA CTGTTCTTTCCATGACCCCC GATGGCCGAGTGGTTGATAG 254 1.000 78.6
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TGAAAGTTGGATAGGCTGGC 827–831 1.000 78.7
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA ATAGGCTGGCCCTTACGTAA 817–821 1.000 78.1
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ GGAAATGGTCGGGATAGCTC TGAAAGTTGGATAGGCTGGC 873–877 1.000 77.7
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ AATGGTCGGGATAGCTCAGT TGAAAGTTGGATAGGCTGGC 870–874 1.000 77.4
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ ATGGTCGGGATAGCTCAGTT TGAAAGTTGGATAGGCTGGC 869–873 1.000 77.4

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
Acrocomia intumescens NC_072142.1 156590 View on NCBI ↗
Acrocomia totai NC_072143.1 156604 View on NCBI ↗