Markers + reference

Hymenocallis

2 species · Amaryllidaceae · Asparagales

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Species 2
Genome length 158–163 kb
Candidate markers 263
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-trnG LSC 569 0.1434 0.96 82.5 yes View details
atpF LSC 1639 0.0171 0.96 67.0 yes View details
rpl32-ndhF SSC 941 0.2559 0.99 79.6 yes View details
ndhF SSC 2244 0.3723 1.00 77.6 yes View details
rpl2-rpl23 IRb 35 0.0286 1.00 68.9 yes View details
rpl23-rpl2 IRa 35 0.0286 1.00 68.9 yes View details
petA-psbJ LSC 1112 0.0135 1.00 66.5 yes View details
psbZ-trnG LSC 237 0.0340 0.99 65.6 yes View details
petN-psbM LSC 997 0.0021 0.95 64.7 yes View details
psaA-ycf3 LSC 638 0.0114 0.96 64.7 yes View details
rpl33-rps18 LSC 164 0.0187 0.98 64.5 yes View details
rbcL-accD LSC 811 0.0063 0.98 64.4 yes View details
rps19-psbA LSC 149 0.0138 0.97 63.0 no 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-trnG_p1 trnS-trnG ATTAGCAATCCGCCGCTTTA CCTTGGGATACAAATCGCGA 789–1442 1.000 86.7
trnS-trnG_p2 trnS-trnG ATTAGCAATCCGCCGCTTTA CATCGTTAGCTTGGAAGGCT 1352–2005 1.000 84.5
trnS-trnG_p3 trnS-trnG ATTAGCAATCCGCCGCTTTA CGTTAGCTTGGAAGGCTAGG 1349–2002 1.000 84.2
trnS-trnG_p4 trnS-trnG TTTGAATGCTCCGCTCATGA CCTTGGGATACAAATCGCGA 1476–2126 1.000 83.6
trnS-trnG_p5 trnS-trnG TTTGAATGCTCCGCTCATGA CATCGTTAGCTTGGAAGGCT 2039–2689 1.000 82.6
atpF_p1 atpF ACTAATTTCGTCAGCTCGAA GGCGAGCCAAGTGATACAAA 1761–1811 1.000 54.3
atpF_p2 atpF ACTAATTTCGTCAGCTCGAA GGCGAGCCAAGTGATACAA 1761–1811 1.000 49.5
atpF_p3 atpF ACTAATTTCGTCAGCTCGAA GCGAGCCAAGTGATACAAAA 1760–1810 1.000 48.5
atpF_p4 atpF ACTAATTTCGTCAGCTCGAA AAAGGGCGAGCCAAGTGATA 1765–1815 1.000 47.6
atpF_p5 atpF TACTAATTTCGTCAGCTCGA GGCGAGCCAAGTGATACAAA 1762–1812 1.000 47.4
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 1105–1152 1.000 72.7
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 1054–1101 1.000 71.9
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 1053–1100 1.000 71.9
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTGTTCATTCT 1052–1099 1.000 71.5
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 1111–1158 1.000 71.2
psbZ-trnG_p1 psbZ-trnG TGCTTCTTCTGATGGTTGGT GATCGAACCCGCATCTTCTC 402–404 1.000 70.3
psbZ-trnG_p2 psbZ-trnG TGCTTCTTCTGATGGTTGGT GAACCCGCATCTTCTCCTTG 398–400 1.000 69.3
psbZ-trnG_p3 psbZ-trnG GCTTCTTCTGATGGTTGGTCA GATCGAACCCGCATCTTCTC 401–403 1.000 68.2
psbZ-trnG_p4 psbZ-trnG TGCTTCTTCTGATGGTTGGTC GATCGAACCCGCATCTTCTC 402–404 1.000 68.2
psbZ-trnG_p5 psbZ-trnG TTGCTTCTTCTGATGGTTGGT GATCGAACCCGCATCTTCTC 403–405 1.000 68.1
psaA-ycf3_p1 psaA-ycf3 CCCATTCCTCGAAAGACGTT CGACCAAGCTGCTGAGTATT 805–817 1.000 82.3
psaA-ycf3_p2 psaA-ycf3 CCCATTCCTCGAAAGACGTT ACCAAGCTGCTGAGTATTGG 803–815 1.000 81.4
psaA-ycf3_p3 psaA-ycf3 CCCATTCCTCGAAAGACGTT TTGAAGATCACGAGGCGTTT 732–744 1.000 81.4
psaA-ycf3_p4 psaA-ycf3 CCCATTCCTCGAAAGACGTT TTGGTTGAAGATCACGAGGC 736–748 1.000 81.2
psaA-ycf3_p5 psaA-ycf3 CCCATTCCTCGAAAGACGTT TGAAGATCACGAGGCGTTTC 731–743 1.000 80.4
rbcL-accD_p1 rbcL-accD GCAAATGGAGCCCTGAACTA CCGGTATGTCCAAGAGCATT 1001–1013 1.000 78.1
rbcL-accD_p2 rbcL-accD CGCTGCTTGTGAAGTATGGA CCGGTATGTCCAAGAGCATT 979–991 1.000 76.9
rbcL-accD_p3 rbcL-accD GCAAATGGAGCCCTGAACTA CTCTTCACTTCCCCCGGTAT 1014–1026 1.000 76.7
rbcL-accD_p4 rbcL-accD AAATGGAGCCCTGAACTAGC CCGGTATGTCCAAGAGCATT 999–1011 1.000 75.7
rbcL-accD_p5 rbcL-accD CGCTGCTTGTGAAGTATGGA CTCTTCACTTCCCCCGGTAT 992–1004 1.000 75.5

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
Hymenocallis acutifolia PV409676.1 158457 View on NCBI ↗
Hymenocallis speciosa PP853214.1 163169 View on NCBI ↗