Markers + reference

Syagrus

4 species · Arecaceae · Arecales

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Species 4
Genome length 155–155 kb
Candidate markers 274
Primer pairs 90

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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 714 0.0079 1.00 64.2 yes View details
trnS-GCU-trnG-UCU; trnG-UCC LSC 1083 0.0045 1.00 59.9 yes View details
psbC LSC 1422 0.0004 1.00 33.8 yes View details
petA-psbJ LSC 935 0.0080 1.00 55.0 yes View details
ycf1 IRb 1347 0.0009 1.00 50.0 no View details
ccsA SSC 969 0.0041 1.00 51.2 yes View details
psaC-ndhE SSC 617 0.0078 1.00 64.1 yes View details
rps15 SSC 273 0.0000 1.00 19.6 yes View details
rps15-ycf1 SSC 394 0.0106 0.99 61.9 yes View details
ycf1 SSC 5598 0.0024 1.00 54.3 yes View details
trnH-GUG-rps19 IRa 204 0.0025 1.00 33.1 yes View details
rps19-psbA LSC 88 0.4697 1.00 78.7 no View details
psbC-trnS-UGA LSC 137 0.0487 1.00 77.5 yes View details
rpl22-rps19 LSC 142 0.0109 0.96 63.2 yes View details
trnT-UGU-trnL-UAA LSC 921 0.0042 1.00 61.8 yes View details
matK-trnK-UUU LSC 818 0.0012 1.00 60.6 yes View details
rpl16 LSC 1589 0.0016 1.00 60.6 yes View details
rpl20-rps12 LSC 679 0.0017 1.00 60.0 yes View details
ndhH-rps15 SSC 113 0.0089 0.99 59.6 yes View details
rpoC1 LSC 2799 0.0011 1.00 56.9 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
matK-trnK-UUU_p1 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA AACGGTAGAGTACTCGGCTT 894–899 1.000 76.9
matK-trnK-UUU_p2 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA ACGGTAGAGTACTCGGCTTT 893–898 1.000 76.9
matK-trnK-UUU_p3 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA GTCGTGCAGTGCAATTCAAT 974–979 1.000 75.4
matK-trnK-UUU_p4 matK-trnK-UUU AAGTGTTGTTGCCGAGATCT AACGGTAGAGTACTCGGCTT 891–896 1.000 75.1
matK-trnK-UUU_p5 matK-trnK-UUU AAGTGTTGTTGCCGAGATCT ACGGTAGAGTACTCGGCTTT 890–895 1.000 75.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACCTACGGGAACTG 829–836 1.000 70.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACGGGAACTG 828–835 1.000 70.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCTACGGGAAC 831–838 1.000 70.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCTACGGGAAC 830–837 1.000 70.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCTACGGGAACT 829–836 1.000 69.7
trnS-GCU-trnG-UCU; trnG-UCC_p1 trnS-GCU-trnG-UCU; trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1157–1200 1.000 52.3
trnS-GCU-trnG-UCU; trnG-UCC_p2 trnS-GCU-trnG-UCU; trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 1160–1203 1.000 51.2
trnS-GCU-trnG-UCU; trnG-UCC_p3 trnS-GCU-trnG-UCU; trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 1159–1202 1.000 51.2
trnS-GCU-trnG-UCU; trnG-UCC_p4 trnS-GCU-trnG-UCU; trnG-UCC AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 1213–1256 1.000 50.7
trnS-GCU-trnG-UCU; trnG-UCC_p5 trnS-GCU-trnG-UCU; trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 1158–1201 1.000 50.4
rpoC1_p1 rpoC1 TGAAACTGGAGAGACCCGAA TTGCTCGTTCGAGAACTACG 2978–2980 1.000 77.6
rpoC1_p2 rpoC1 GGAGAGACCCGAATCCCTAC TTGCTCGTTCGAGAACTACG 2971–2973 1.000 74.5
rpoC1_p3 rpoC1 TGAAACTGGAGAGACCCGAA GCTCGTTCGAGAACTACGAT 2976–2978 1.000 74.2
rpoC1_p4 rpoC1 AACTGGAGAGACCCGAATCC TTGCTCGTTCGAGAACTACG 2975–2977 1.000 73.4
rpoC1_p5 rpoC1 GTGAAACTGGAGAGACCCGA TTGCTCGTTCGAGAACTACG 2979–2981 1.000 71.6
psbC_p1 psbC TTTCCCAAGAAATCCGTGCA TAGCCGAGCCAGAACAGAAA 1585 1.000 71.7
psbC_p2 psbC TTTCCCAAGAAATCCGTGCA GCCGAGCCAGAACAGAAAAA 1583 1.000 71.6
psbC_p3 psbC TTTCCCAAGAAATCCGTGCA TAGCCGAGCCAGAACAGAA 1585 1.000 69.3
psbC_p4 psbC GCAGCGGAAGATCCTGAATT TAGCCGAGCCAGAACAGAAA 1568 1.000 69.2
psbC_p5 psbC AGGTATTCGTGCTTGGATGG TAGCCGAGCCAGAACAGAAA 1512 1.000 69.2
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 244 1.000 81.5
psbC-trnS-UGA_p2 psbC-trnS-UGA CTGTTCTTTCCATGACCCCC GGTTGATAGCTCCGGTCTTG 243 1.000 81.5
psbC-trnS-UGA_p3 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GGTTGATAGCTCCGGTCTTG 283 1.000 81.3
psbC-trnS-UGA_p4 psbC-trnS-UGA CTGTTCTTTCCATGACCCCC GATGGCCGAGTGGTTGATAG 254 1.000 80.8
psbC-trnS-UGA_p5 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GATGGCCGAGTGGTTGATAG 294 1.000 80.6

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
Syagrus coronata NC_029241.1 155053 View on NCBI ↗
Syagrus oleracea PP476489.4 155055 View on NCBI ↗
Syagrus romanzoffiana NC_072146.1 155078 View on NCBI ↗
Syagrus weddelliana NC_079796.1 155182 View on NCBI ↗