Markers + reference

Hyophorbe

2 species · Arecaceae · Arecales

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Species 2
Genome length 158–158 kb
Candidate markers 270
Primer pairs 85

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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 28.7 yes View details
atpF LSC 1358 0.0029 1.00 60.6 yes View details
rpoC1 LSC 2808 0.0014 1.00 56.8 yes View details
accD-psaI LSC 850 0.0083 1.00 63.7 yes View details
rpl32-trnL-UAG SSC 796 0.0063 1.00 62.4 yes View details
ndhD SSC 1413 0.0000 1.00 35.0 yes View details
ndhD-psaC SSC 211 0.0332 1.00 71.6 yes View details
psaC-ndhE SSC 652 0.0105 0.87 67.3 yes View details
ycf1 SSC 5367 0.0024 1.00 53.9 yes View details
rps19-psbA LSC 151 0.0822 0.97 88.1 no View details
rpl22-rps19 IRb 53 0.0208 0.91 67.8 yes View details
petN-psbM LSC 773 0.0039 0.99 62.4 yes View details
trnS-GCU-trnG-UCC LSC 1224 0.0025 0.99 61.0 yes View details
trnT-UGU-trnL-UAA LSC 1003 0.0040 1.00 61.0 yes View details
ycf3-trnS-UGA LSC 620 0.0032 1.00 60.6 yes View details
trnT-GGU-psbD LSC 1039 0.0029 1.00 60.5 yes View details
rps16-trnQ-UUG LSC 1102 0.0027 1.00 60.4 yes View details
trnF-GAA-ndhJ LSC 752 0.0027 1.00 60.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TTGCTCCATTCCTTCAACGA GTGCTTGGGAGTCCTTGAAA 1149 1.000 75.4
psbA_p2 psbA TTGCTCCATTCCTTCAACGA AATACGTGTGCTTGGGAGTC 1156 1.000 74.8
psbA_p3 psbA TGCTCCATTCCTTCAACGAT GTGCTTGGGAGTCCTTGAAA 1148 1.000 73.6
psbA_p4 psbA TGCTCCATTCCTTCAACGAT AATACGTGTGCTTGGGAGTC 1155 1.000 72.9
psbA_p5 psbA TGCTCCATTCCTTCAACGATT GTGCTTGGGAGTCCTTGAAA 1148 1.000 71.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1192–1193 1.000 79.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1190–1191 1.000 79.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1198–1199 1.000 79.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1199–1200 1.000 79.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAAATTCGAAATGGGGCGTG 1251–1252 1.000 79.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGGAAAGACCCCTTAACT 1329–1340 1.000 67.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGAAGAAGCGGAGAGAGAGG AACGGAAAGACCCCTTAACT 1385–1396 1.000 65.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AAACGGAAAGACCCCTTAACT 1330–1341 1.000 65.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA AACGGAAAGACCCCTTAACT 1377–1388 1.000 65.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AACGGAAAGACCCCTTAACT 1315–1326 1.000 64.5
atpF_p1 atpF ACTAATTTCGTCGGCTCGAA AGAACTCTGTTCTTTGTTAGTCCT 1512–1517 1.000 40.5
atpF_p2 atpF ACTAATTTCGTCGGCTCGAA AGTCCTATCTATAAGAGGAGAGCA 1494–1499 1.000 40.5
atpF_p3 atpF GGCTCGAAGGGTTACCATTA AGAACTCTGTTCTTTGTTAGTCCT 1500–1505 1.000 40.5
atpF_p4 atpF ACTAATTTCGTCGGCTCGAA AGAACTCTGTTCTTTGTTAGTCC 1512–1517 1.000 40.5
atpF_p5 atpF ACTAATTTCGTCGGCTCGAA GAACTCTGTTCTTTGTTAGTCCT 1511–1516 1.000 40.5
rpoC1_p1 rpoC1 GAGAGACCCGAATCCCTACA TTGCTCGTTCGAGAACTACG 2979–2987 1.000 79.2
rpoC1_p2 rpoC1 AGAGACCCGAATCCCTACAG TTGCTCGTTCGAGAACTACG 2978–2986 1.000 79.2
rpoC1_p3 rpoC1 TGAAACTGGAGAGACCCGAA TTGCTCGTTCGAGAACTACG 2987–2995 1.000 77.5
rpoC1_p4 rpoC1 GAGAGACCCGAATCCCTACA GCTCGTTCGAGAACTACGAT 2977–2985 1.000 75.9
rpoC1_p5 rpoC1 AGAGACCCGAATCCCTACAG GCTCGTTCGAGAACTACGAT 2976–2984 1.000 75.9
petN-psbM_p1 petN-psbM GTCTCACTTGGGCTGCTTTA TGCTACTGCACTGTTCATTCT 929–944 1.000 68.5
petN-psbM_p2 petN-psbM ACTTGGGCTGCTTTAATGGT TGCTACTGCACTGTTCATTCT 924–939 1.000 67.5
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 874–889 1.000 67.2
petN-psbM_p4 petN-psbM GTAAGTCTCACTTGGGCTGC TGCTACTGCACTGTTCATTCT 933–948 1.000 65.5
petN-psbM_p5 petN-psbM TAAGTCTCACTTGGGCTGCT TGCTACTGCACTGTTCATTCT 932–947 1.000 64.7

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
Hyophorbe lagenicaulis NC_067837.1 157676 View on NCBI ↗
Hyophorbe verschaffeltii NC_067838.1 157712 View on NCBI ↗