Markers + reference

Astrocaryum

17 species · Arecaceae · Arecales

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Species 17
Genome length 156–157 kb
Candidate markers 271
Primer pairs 100

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1059 0.0027 1.00 35.7 yes View details
trnS-GCU-trnG-UCC LSC 863 0.0138 0.91 53.4 yes View details
petN-psbM LSC 514 0.0063 1.00 61.9 yes View details
trnS-UGA-psbZ LSC 335 0.0030 1.00 37.7 yes View details
rbcL-accD LSC 798 0.0050 1.00 45.5 yes View details
petA-psbJ LSC 1013 0.0100 1.00 54.2 yes View details
rpl16 LSC 1529 0.0038 0.99 59.2 yes View details
rpl22 LSC 399 0.0023 0.99 31.2 yes View details
rpl32-trnL-UAG SSC 597 0.0076 1.00 60.7 yes View details
rps15-ycf1 SSC 392 0.0071 1.00 40.4 yes View details
ycf1 SSC 5493 0.0033 1.00 40.6 yes View details
rps19-psbA LSC 231 0.1919 0.55 75.3 no View details
rpl22-rps19 LSC 144 0.0177 0.93 62.6 yes View details
psaC-ndhE SSC 629 0.0050 0.97 57.7 yes View details
accD-psaI LSC 637 0.0048 0.95 56.8 yes View details
rpoB-trnC-GCA LSC 1216 0.0013 0.98 52.7 yes View details
trnK-UUU-rps16 LSC 728 0.0021 1.00 51.7 yes View details
psbC-trnS-UGA LSC 137 0.0272 1.00 51.0 yes View details
trnT-GGU-psbD LSC 996 0.0019 0.98 50.1 yes View details
matK-trnK-UUU LSC 737 0.0008 1.00 49.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TCAACGATTCATATACACTAAGACA ATTGAATAAACCAAGATCTTACC 1113–1116 0.941 39.4
psbA_p2 psbA TCAACGATTCATATACACTAAGACA AATTGAATAAACCAAGATCTTACC 1114–1117 0.941 39.4
psbA_p3 psbA CAACGATTCATATACACTAAGACA ATTGAATAAACCAAGATCTTACC 1112–1115 0.941 39.4
psbA_p4 psbA TCAACGATTCATATACACTAAGACA TGAAAATTGAATAAACCAAGATCT 1118–1121 0.941 39.4
psbA_p5 psbA TCAACGATTCATATACACTAAGACAA ATTGAATAAACCAAGATCTTACC 1113–1116 0.941 39.4
trnK-UUU_p1 trnK-UUU TGCCAATGTCAACCAATCTCA GTCGTGCAGTGCAATTCAAT 2862–2960 1.000 68.9
trnK-UUU_p2 trnK-UUU TGCCAATGTCAACCAATCTCA TCAATGTTTTGACGGGGTCG 2878–2976 1.000 65.5
trnK-UUU_p3 trnK-UUU GCCAATGTCAACCAATCTCA GTCGTGCAGTGCAATTCAAT 2861–2959 1.000 64.4
trnK-UUU_p4 trnK-UUU TGCCAATGTCAACCAATCTC GTCGTGCAGTGCAATTCAAT 2862–2960 1.000 64.4
trnK-UUU_p5 trnK-UUU TGCCAATGTCAACCAATCTCA GTTCAATGTTTTGACGGGGTC 2880–2978 1.000 63.6
matK-trnK-UUU_p1 matK-trnK-UUU TACTTGAACCAGAGGCAGGA AACGGTAGAGTACTCGGCTT 815–913 1.000 79.8
matK-trnK-UUU_p2 matK-trnK-UUU TACTTGAACCAGAGGCAGGA ACGGTAGAGTACTCGGCTTT 814–912 1.000 79.8
matK-trnK-UUU_p3 matK-trnK-UUU GAGGCAGGACCCATTTCATT AACGGTAGAGTACTCGGCTT 804–902 1.000 78.8
matK-trnK-UUU_p4 matK-trnK-UUU GAGGCAGGACCCATTTCATT ACGGTAGAGTACTCGGCTTT 803–901 1.000 78.8
matK-trnK-UUU_p5 matK-trnK-UUU TACTTGAACCAGAGGCAGGA GTCGTGCAGTGCAATTCAAT 895–993 1.000 78.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GCTCAACCTACGGGAACTG 896–899 1.000 71.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GCTCAACCTACGGGAACTG 895–898 1.000 71.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GTGCTCAACCTACGGGAAC 898–901 1.000 71.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GTGCTCAACCTACGGGAAC 897–900 1.000 71.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACGGGAACTG 839–842 1.000 70.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 866–937 1.000 57.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 869–940 1.000 56.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 868–939 1.000 56.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 922–993 1.000 56.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 867–938 1.000 56.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TAAAGGATTTGCAGTCCCCC 1340–1376 1.000 76.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA TAAAGGATTTGCAGTCCCCC 1260–1296 1.000 75.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTCCCTCATTTCCATTCCGG TAAAGGATTTGCAGTCCCCC 1261–1297 1.000 74.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TTTGTTGATCAGGCGACACC 1377–1413 1.000 74.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG GACACCCGGATTTGAACTGG 1363–1399 1.000 74.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Astrocaryum alatum NC_072959.1 155797 View on NCBI ↗
Astrocaryum carnosum OM964746.1 157080 View on NCBI ↗
Astrocaryum chambira OM964750.1 157191 View on NCBI ↗
Astrocaryum chonta OM964751.1 156814 View on NCBI ↗
Astrocaryum ciliatum OM964753.1 156838 View on NCBI ↗
Astrocaryum faranae OM964754.1 156623 View on NCBI ↗
Astrocaryum ferrugineum OM964759.1 156819 View on NCBI ↗
Astrocaryum gratum OM964761.1 156786 View on NCBI ↗
Astrocaryum huicungo OM964765.1 156791 View on NCBI ↗
Astrocaryum javarense OM964767.1 156888 View on NCBI ↗
Astrocaryum macrocalyx OM964770.1 156799 View on NCBI ↗
Astrocaryum minus OM964774.1 156783 View on NCBI ↗
Astrocaryum perangustatum OM964778.1 156840 View on NCBI ↗
Astrocaryum scopatum OM964782.1 156954 View on NCBI ↗
Astrocaryum ulei OM964785.1 156893 View on NCBI ↗
Astrocaryum urostachys OM964790.1 156808 View on NCBI ↗
Astrocaryum vulgare OM964795.1 157458 View on NCBI ↗