Markers + reference

Trithrinax

2 species · Arecaceae · Arecales

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Species 2
Genome length 158–158 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

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 935 0.0022 0.96 52.2 yes View details
petN-psbM LSC 605 0.0050 1.00 61.6 yes View details
trnS-UGA-psbZ LSC 352 0.0057 1.00 52.8 yes View details
trnT-UGU-trnL-UAA LSC 1009 0.0040 1.00 58.9 yes View details
accD-psaI LSC 772 0.0013 1.00 46.9 yes View details
ycf1 SSC 1347 0.0000 1.00 40.0 no View details
rpl32-trnL-UAG SSC 772 0.0026 1.00 60.2 yes View details
rps15-ycf1 SSC 382 0.0105 1.00 45.5 yes View details
ycf1 SSC 5676 0.0016 0.99 54.6 yes View details
psbC-trnS-UGA LSC 137 0.0219 1.00 65.1 yes View details
trnH-GUG-rpl2 IRb 46 0.0217 1.00 65.0 yes View details
rpl2-trnH-GUG IRa 46 0.0217 1.00 65.0 yes View details
trnI-GAU-trnA-UGC SSC 64 0.0156 1.00 61.5 yes View details
trnA-UGC-trnI-GAU SSC 64 0.0156 1.00 61.5 yes View details
rpoA-rps11 LSC 79 0.0127 1.00 59.8 yes View details
trnS-GCU-trnG-GCC LSC 1273 0.0016 1.00 59.7 yes View details
atpB LSC 1497 0.0013 1.00 59.5 yes View details
rbcL LSC 1464 0.0014 1.00 59.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1346–1347 1.000 51.6
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC GGATTCGAACCCTCGGTATG ACGAATCACACTTTTACCACT 1383–1384 1.000 50.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 1349–1350 1.000 50.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 1348–1349 1.000 50.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 1402–1403 1.000 50.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 960–996 1.000 78.4
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACGTTAGCCGC 988–1024 1.000 78.3
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TAGGTGAATCCATGGAGGGT 961–997 1.000 77.3
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATTTTTGCAACGTTAGCCGC 989–1025 1.000 77.2
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT CCGCGGCTTATATAGGTGAA 972–1008 1.000 77.2
petN-psbM_p1 petN-psbM GTCTCACTTGGGCTGCTTTA TGCTACTGCACTGTTCATTCT 761 1.000 67.6
petN-psbM_p2 petN-psbM ACTTGGGCTGCTTTAATGGT TGCTACTGCACTGTTCATTCT 756 1.000 66.6
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 706 1.000 66.3
petN-psbM_p4 petN-psbM GTAAGTCTCACTTGGGCTGC TGCTACTGCACTGTTCATTCT 765 1.000 64.6
petN-psbM_p5 petN-psbM TAAGTCTCACTTGGGCTGCT TGCTACTGCACTGTTCATTCT 764 1.000 63.9
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
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC ACCAACCATCAGAAGAAGCA 488 1.000 72.2
trnS-UGA-psbZ_p2 trnS-UGA-psbZ CTATCAACCACTCGGCCATC ACCAACCATCAGAAGAAGCA 477 1.000 71.6
trnS-UGA-psbZ_p3 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC GACCAACCATCAGAAGAAGCA 489 1.000 70.1
trnS-UGA-psbZ_p4 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC TGACCAACCATCAGAAGAAGC 490 1.000 70.1
trnS-UGA-psbZ_p5 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC ACCAACCATCAGAAGAAGCAA 488 1.000 70.0
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1059–1060 1.000 79.2
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1067–1068 1.000 78.7
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1091–1092 1.000 78.3
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1099–1100 1.000 77.8
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 1082–1083 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
Trithrinax brasiliensis NC_029951.1 158487 View on NCBI ↗
Trithrinax campestris NC_079816.1 158351 View on NCBI ↗