Markers + reference

Sabal

10 species · Arecaceae · Arecales

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Species 10
Genome length 158–159 kb
Candidate markers 269
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbC LSC 1422 0.0001 1.00 30.9 yes View details
rbcL LSC 1455 0.0014 1.00 45.1 yes View details
rbcL-accD LSC 783 0.0031 1.00 44.2 yes View details
petA-psbJ LSC 1008 0.0034 1.00 42.6 yes View details
psaJ-rpl33 LSC 512 0.0018 1.00 41.5 yes View details
rpl16 LSC 1556 0.0021 1.00 57.1 yes View details
rpl32-trnL-UAG SSC 798 0.0020 1.00 46.4 yes View details
psaC-ndhE SSC 669 0.0036 1.00 44.6 yes View details
rps15-ycf1 SSC 380 0.0054 1.00 41.4 yes View details
ycf1 SSC 5619 0.0012 1.00 38.6 yes View details
psbC-trnS-UGA LSC 137 0.0284 1.00 59.4 yes View details
trnS-GCU-trnG-UCC LSC 1252 0.0024 1.00 57.2 yes View details
ndhC-trnV-UAC LSC 1859 0.0003 0.99 52.4 yes View details
trnH-GUG-psbA IRa 648 0.0005 1.00 51.7 no View details
matK-trnK-UUU LSC 810 0.0012 1.00 49.3 yes View details
trnC-GCA-petN LSC 1107 0.0014 1.00 49.2 yes View details
trnT-UGU-trnL-UAA LSC 994 0.0008 1.00 48.8 yes View details
rps16-trnQ-UUG LSC 1114 0.0012 1.00 46.8 yes View details
ndhF SSC 2238 0.0007 1.00 46.7 yes View details
rpl20-rps12 LSC 712 0.0008 1.00 46.4 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
trnK-UUU_p1 trnK-UUU TGCCAATGTCAACCAATCTCA GTCGTGCAGTGCAATTCAAT 2898–2901 1.000 68.8
trnK-UUU_p2 trnK-UUU TGCCAATGTCAACCAATCTCA TCAATGTTTTGACGGGGTCG 2914–2917 1.000 65.3
trnK-UUU_p3 trnK-UUU GCCAATGTCAACCAATCTCA GTCGTGCAGTGCAATTCAAT 2897–2900 1.000 64.3
trnK-UUU_p4 trnK-UUU TGCCAATGTCAACCAATCTC GTCGTGCAGTGCAATTCAAT 2898–2901 1.000 64.3
trnK-UUU_p5 trnK-UUU TGCCAATGTCAACCAATCTCA GTTCAATGTTTTGACGGGGTC 2916–2919 1.000 63.4
matK-trnK-UUU_p1 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA AACGGTAGAGTACTCGGCTT 887–890 1.000 76.9
matK-trnK-UUU_p2 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA ACGGTAGAGTACTCGGCTTT 886–889 1.000 76.9
matK-trnK-UUU_p3 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA GTCGTGCAGTGCAATTCAAT 977–980 1.000 75.4
matK-trnK-UUU_p4 matK-trnK-UUU AAGTGTTGTTGCCGAGATCT AACGGTAGAGTACTCGGCTT 884–887 1.000 75.1
matK-trnK-UUU_p5 matK-trnK-UUU AAGTGTTGTTGCCGAGATCT ACGGTAGAGTACTCGGCTTT 883–886 1.000 75.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1205–1206 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1203–1204 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1211–1212 1.000 79.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1212–1213 1.000 79.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAAATTCGAAATGGGGCGTG 1264–1265 1.000 79.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1167–1350 1.000 56.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 1170–1353 1.000 55.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 1169–1352 1.000 55.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 1223–1406 1.000 54.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 1168–1351 1.000 54.3
trnC-GCA-petN_p1 trnC-GCA-petN GGGGGACTGCAAATCCTTTA TAAAGCAGCCCAAGTGAGAC 1183–1187 1.000 75.0
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTA ACCATTAAAGCAGCCCAAGT 1188–1192 1.000 74.0
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTA AGAGTCCACTTCTTCCCCAT 1238–1242 1.000 73.6
trnC-GCA-petN_p4 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC TAAAGCAGCCCAAGTGAGAC 1160–1164 1.000 72.5
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTA GCAGCCCAAGTGAGACTTAC 1179–1183 1.000 72.0
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

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Sabal bermudana NC_079746.1 158915 View on NCBI ↗
Sabal causiarum NC_079747.1 158897 View on NCBI ↗
Sabal domingensis NC_026444.1 157835 View on NCBI ↗
Sabal etonia NC_079748.1 158848 View on NCBI ↗
Sabal mauritiiformis NC_079749.1 158888 View on NCBI ↗
Sabal mexicana NC_079750.1 158852 View on NCBI ↗
Sabal minor NC_067827.1 158848 View on NCBI ↗
Sabal palmetto NC_079751.1 157826 View on NCBI ↗
Sabal rosei NC_079752.1 158734 View on NCBI ↗
Sabal uresana NC_079753.1 158784 View on NCBI ↗