Markers + reference

Euterpe

3 species · Arecaceae · Arecales

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Species 3
Genome length 158–159 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0013 1.00 36.2 yes View details
trnQ-UUG-psbK LSC 344 0.0039 1.00 52.8 yes View details
trnS-GCU-trnG-UCC LSC 1127 0.0157 1.00 69.5 yes View details
petN-psbM LSC 759 0.0079 1.00 65.1 yes View details
trnM-CAU-atpE LSC 179 0.0708 1.00 65.4 yes View details
petA-psbJ LSC 937 0.0164 1.00 68.5 yes View details
ndhF-rpl32 SSC 332 0.0120 1.00 54.2 yes View details
rpl32-trnL-UAG SSC 787 0.0059 1.00 39.0 yes View details
rps19-psbA LSC 233 0.0372 1.00 63.7 no View details
rps16-trnQ-UUG LSC 1117 0.0042 1.00 61.8 yes View details
atpF LSC 1343 0.0035 1.00 61.0 yes View details
atpB-rbcL LSC 768 0.0030 1.00 60.8 yes View details
psbM-trnD-GUC LSC 999 0.0027 1.00 60.5 yes View details
psbE-petL LSC 1288 0.0026 1.00 60.5 yes View details
psaJ-rpl33 LSC 553 0.0036 1.00 60.4 yes View details
trnC-GCA-petN LSC 1133 0.0018 1.00 60.2 yes View details
ycf3-trnS-GGA LSC 625 0.0021 1.00 60.1 yes View details
trnT-UGU-trnL-UAA LSC 1018 0.0020 1.00 60.1 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 TGGGTATTGCTCCATTGTTTGA GTGCTTGGGAGTCCTTGAAA 1159 1.000 62.2
psbA_p2 psbA TGGGTATTGCTCCATTGTTTG GTGCTTGGGAGTCCTTGAAA 1159 1.000 62.1
psbA_p3 psbA TGGGTATTGCTCCATTGTTTGA AATACGTGTGCTTGGGAGTC 1166 1.000 61.6
psbA_p4 psbA TGGGTATTGCTCCATTGTTTG AATACGTGTGCTTGGGAGTC 1166 1.000 61.5
psbA_p5 psbA GGGTATTGCTCCATTGTTTGA GTGCTTGGGAGTCCTTGAAA 1158 1.000 59.9
trnK-UUU_p1 trnK-UUU TTTCAAGGACTCCCAAGCAC GTCGTGCAGTGCAATTCAAT 2949–2956 1.000 77.7
trnK-UUU_p2 trnK-UUU GACTCCCAAGCACACGTATT GTCGTGCAGTGCAATTCAAT 2942–2949 1.000 77.1
trnK-UUU_p3 trnK-UUU TTTCAAGGACTCCCAAGCAC TCAATGTTTTGACGGGGTCG 2965–2972 1.000 74.2
trnK-UUU_p4 trnK-UUU GACTCCCAAGCACACGTATT TCAATGTTTTGACGGGGTCG 2958–2965 1.000 73.6
trnK-UUU_p5 trnK-UUU TTTCAAGGACTCCCAAGCAC GTTCAATGTTTTGACGGGGTC 2967–2974 1.000 72.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1204–1208 1.000 79.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1202–1206 1.000 79.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1210–1214 1.000 79.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1211–1215 1.000 79.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAAATTCGAAATGGGGCGTG 1263–1267 1.000 79.7
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GAAGGATTCGAACCTCCGAG GGGCAATTTGGCGAAGAAAA 487–489 1.000 77.8
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GATGGAAACGATCTGGGACG GGGCAATTTGGCGAAGAAAA 507–509 1.000 76.1
trnQ-UUG-psbK_p3 trnQ-UUG-psbK AGGATTCGAACCTCCGAGTA GGGCAATTTGGCGAAGAAAA 485–487 1.000 76.1
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AAGGATTCGAACCTCCGAGT GGGCAATTTGGCGAAGAAAA 486–488 1.000 76.0
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GAGTAACGGGACCAAAACCC GGGCAATTTGGCGAAGAAAA 470–472 1.000 75.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1201–1506 1.000 53.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 1204–1509 1.000 52.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 1203–1508 1.000 52.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 1261–1566 1.000 51.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 1202–1507 1.000 51.5
atpF_p1 atpF ACTAATTTCGTCGGCTCGAA AGAACTCTGTTCTTTGTTAGTCCT 1495–1502 1.000 40.4
atpF_p2 atpF ACTAATTTCGTCGGCTCGAA AGTCCTATCTATAAGAGGAGAGCA 1477–1484 1.000 40.4
atpF_p3 atpF GGCTCGAAGGGTTACCATTA AGAACTCTGTTCTTTGTTAGTCCT 1483–1490 1.000 40.4
atpF_p4 atpF ACTAATTTCGTCGGCTCGAA AGAACTCTGTTCTTTGTTAGTCC 1495–1502 1.000 40.4
atpF_p5 atpF ACTAATTTCGTCGGCTCGAA GAACTCTGTTCTTTGTTAGTCCT 1494–1501 1.000 40.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Euterpe edulis NC_057602.1 158397 View on NCBI ↗
Euterpe oleracea NC_057603.1 158802 View on NCBI ↗
Euterpe precatoria NC_065201.1 159275 View on NCBI ↗