Markers + reference

Haemanthus

3 species · Amaryllidaceae · Asparagales

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Species 3
Genome length 153–156 kb
Candidate markers 268
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petA-psbJ LSC 1000 0.0140 1.00 68.1 yes View details
trnN-GUU-rpl32 IRb 4907 0.0100 0.87 42.5 yes View details
rpl32-trnL-UAG SSC 547 0.0140 1.00 57.0 yes View details
ndhD SSC 1418 0.0080 0.99 49.4 yes View details
ndhA SSC 1253 0.1417 0.98 79.4 yes View details
ndhH SSC 1191 0.0194 1.00 61.5 yes View details
ycf1 SSC 5445 0.0103 1.00 45.3 yes View details
ndhI-ndhA SSC 88 0.0455 1.00 68.7 yes View details
ccsA-ndhD SSC 240 0.0389 1.00 67.3 yes View details
trnE-UUC-trnT-GGU LSC 712 0.0140 1.00 64.9 yes View details
atpB-rbcL LSC 875 0.0061 1.00 64.3 yes View details
petG-trnW-CCA LSC 117 0.0345 0.99 61.4 yes View details
atpH-atpI LSC 470 0.0128 1.00 60.1 yes View details
trnT-UGU-trnL-UAA LSC 898 0.0097 1.00 58.3 yes View details
ndhB IRb 2232 0.0009 1.00 57.8 yes View details
ndhB IRa 2232 0.0009 1.00 57.8 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 532–554 1.000 81.7
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 588–610 1.000 80.8
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 533–555 1.000 80.5
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 592–614 1.000 80.2
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC ATAGGGGAATCCATGGAGGG 547–569 1.000 80.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 793–855 1.000 84.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 772–834 1.000 83.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 769–831 1.000 83.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 755–817 1.000 83.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 734–796 1.000 83.2
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 945–985 1.000 82.0
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 953–993 1.000 81.4
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 977–1017 1.000 81.0
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 985–1025 1.000 80.5
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 968–1008 1.000 80.2
atpB-rbcL_p1 atpB-rbcL TGGGCCAATAATTTGAGCGA AGTCTCTGTTTGTGGTGACA 983–1008 1.000 69.6
atpB-rbcL_p2 atpB-rbcL CTGGGCCAATAATTTGAGCG AGTCTCTGTTTGTGGTGACA 984–1009 1.000 66.7
atpB-rbcL_p3 atpB-rbcL TGGGCCAATAATTTGAGCGA AGTCTCTGTTTGTGGTGACAT 983–1008 1.000 65.8
atpB-rbcL_p4 atpB-rbcL CGGGGGAAAAACAACATCCA AGTCTCTGTTTGTGGTGACA 1007–1032 1.000 65.3
atpB-rbcL_p5 atpB-rbcL TCTTCAAGTGTGGAAACCGC AGTCTCTGTTTGTGGTGACA 946–971 1.000 65.2
petA-psbJ_p1 petA-psbJ GGCCTTTTGTTCTTCTTGGC GGTTCATATTCCGGGTTGGG 1135–1137 1.000 78.0
petA-psbJ_p2 petA-psbJ GGCCTTTTGTTCTTCTTGGC CATATTCCGGGTTGGGTTCA 1131–1133 1.000 77.1
petA-psbJ_p3 petA-psbJ GGCCTTTTGTTCTTCTTGGC GTTCATATTCCGGGTTGGGT 1134–1136 1.000 77.1
petA-psbJ_p4 petA-psbJ GGCCTTTTGTTCTTCTTGGC CGGTTCATATTCCGGGTTGG 1136–1138 1.000 75.0
petA-psbJ_p5 petA-psbJ GGCCTTTTGTTCTTCTTGGC TATTCCGGGTTGGGTTCATC 1129–1131 1.000 74.8
petG-trnW-CCA_p1 petG-trnW-CCA GTGCTCAGTTGGACCTTTGA AGCGCTCTTAGTTCAGTTCG 211–212 1.000 82.6
petG-trnW-CCA_p2 petG-trnW-CCA GTGCTCAGTTGGACCTTTGA CCCTGTCATAAGAAAGCGCT 225–226 1.000 82.3
petG-trnW-CCA_p3 petG-trnW-CCA GTGCTCAGTTGGACCTTTGA TAGACCCGCTAAAGACCCAA 872–877 1.000 80.9
petG-trnW-CCA_p4 petG-trnW-CCA GTGCTCAGTTGGACCTTTGA CCCGATGTATGCAAGACACA 286–287 0.667 66.5
petG-trnW-CCA_p5 petG-trnW-CCA TCAGGTATTCTACGGTCCCC AGCGCTCTTAGTTCAGTTCG 449–450 0.667 66.1

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
Haemanthus albiflos PP853209.1 155667 View on NCBI ↗
Haemanthus coccineus PP853206.1 152659 View on NCBI ↗
Haemanthus humilis PP853208.1 153784 View on NCBI ↗