Markers + reference

Clivia

7 species · Amaryllidaceae · Asparagales

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Species 7
Genome length 157–159 kb
Candidate markers 271
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnQ-UUG-psbK LSC 338 0.0082 1.00 35.2 yes View details
psbK-psbI LSC 404 0.0061 1.00 43.2 yes View details
atpF LSC 1430 0.0051 0.99 40.9 yes View details
trnC-GCA-petN LSC 1057 0.0114 1.00 43.7 yes View details
petN-psbM LSC 1005 0.0087 1.00 43.6 yes View details
trnT-UGU-trnL-UAA LSC 1041 0.0093 0.98 51.9 yes View details
ndhC-trnV-UAC LSC 1599 0.0100 1.00 50.1 yes View details
rbcL-accD LSC 795 0.0100 0.98 44.0 yes View details
petA-psbJ LSC 1130 0.0151 1.00 56.0 yes View details
rps18-rpl20 LSC 261 0.0197 1.00 41.6 yes View details
rpl32-trnL-UAG SSC 816 0.0102 1.00 52.6 yes View details
ndhD SSC 1518 0.0048 1.00 38.3 yes View details
ycf1 SSC 5388 0.0061 1.00 39.8 yes View details
rps19-psbA LSC 154 0.0523 0.94 72.2 no View details
ccsA-ndhD SSC 225 0.0349 1.00 64.9 yes View details
psbI-trnS-GCU LSC 116 0.0350 1.00 62.3 yes View details
petG-trnW-CCA LSC 121 0.0323 1.00 54.4 yes View details
ycf4-cemA LSC 798 0.0085 0.99 54.2 yes View details
rrn4.5-rrn5 IRb 217 0.0132 1.00 53.6 yes View details
rrn5-rrn4.5 IRa 217 0.0132 1.00 53.6 yes View details
rps12-trnV-GAC IRb 1811 0.0034 1.00 51.6 yes View details
trnV-GAC-rps12 IRa 1811 0.0034 1.00 51.6 yes View details
trnE-UUC-trnT-GGU LSC 707 0.0082 1.00 50.5 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnQ-UUG-psbK_p1 trnQ-UUG-psbK CCGTACACTCGATCACGTTT CTTACAGCAGCTTGCCAAAC 757–759 1.000 80.9
trnQ-UUG-psbK_p2 trnQ-UUG-psbK AACAAAAGGCGGGATCACAT CTTACAGCAGCTTGCCAAAC 675–677 1.000 80.4
trnQ-UUG-psbK_p3 trnQ-UUG-psbK ACAAAAGGCGGGATCACATT CTTACAGCAGCTTGCCAAAC 674–676 1.000 80.4
trnQ-UUG-psbK_p4 trnQ-UUG-psbK TCAGAACAAAAGGCGGGATC CTTACAGCAGCTTGCCAAAC 679–681 1.000 79.5
trnQ-UUG-psbK_p5 trnQ-UUG-psbK CCGTACACTCGATCACGTTT TGGAAGGTCAGAACGAGGAA 938–940 1.000 79.0
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGCCCGGATCGTTAGATAAG 521–531 1.000 78.0
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGCCCGGATCGTTAGATAAG 518–528 1.000 76.0
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT GGCCCGGATCGTTAGATAAG 519–529 1.000 76.0
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT GGCCCGGATCGTTAGATAAG 520–530 1.000 76.0
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTATTCCTCGCGTCCGG 547–557 1.000 75.8
psbI-trnS-GCU_p1 psbI-trnS-GCU CTTATCTAACGATCCGGGCC TAAAGCGGCGGATTGCTAAT 227–237 1.000 80.2
psbI-trnS-GCU_p2 psbI-trnS-GCU CTTATCTAACGATCCGGGCC GGGTTCGAATCCCTCTCTCT 182–192 1.000 79.6
psbI-trnS-GCU_p3 psbI-trnS-GCU CTTATCTAACGATCCGGGCC TTCGAATCCCTCTCTCTCCG 179–189 1.000 78.9
psbI-trnS-GCU_p4 psbI-trnS-GCU CTTATCTAACGATCCGGGCC GATGGCTGAGCGGACTAAAG 242–252 1.000 76.9
psbI-trnS-GCU_p5 psbI-trnS-GCU CTTATCTAACGATCCGGGCC CTAAAGCGGCGGATTGCTAA 228–238 1.000 74.9
atpF_p1 atpF CGCTCCTGGAAAGTAGTCAC CCTTCCCGTCCTTCGTTTAG 2415–2449 1.000 83.2
atpF_p2 atpF CGCTCCTGGAAAGTAGTCAC CCGGGAAGGACTGATTTGAG 2467–2501 1.000 82.9
atpF_p3 atpF CGCTCCTGGAAAGTAGTCAC CGGGAAGGACTGATTTGAGG 2466–2500 1.000 82.9
atpF_p4 atpF CGCTCCTGGAAAGTAGTCAC CTCATTGCCGTTTGCTTCTG 2540–2574 1.000 82.8
atpF_p5 atpF CCGAGATTCAGAAGCGGAAA CCTTCCCGTCCTTCGTTTAG 2152–2186 0.571 65.7
trnC-GCA-petN_p1 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC TTAAAGCAGCCCAAGCAAGA 1115–1122 1.000 75.4
trnC-GCA-petN_p2 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC CAGCCCAAGCAAGACTTACT 1109–1116 1.000 73.9
trnC-GCA-petN_p3 trnC-GCA-petN CAGTTCAAATCCGGGTGTCG TTAAAGCAGCCCAAGCAAGA 1114–1121 1.000 72.5
trnC-GCA-petN_p4 trnC-GCA-petN AGTTCAAATCCGGGTGTCG TTAAAGCAGCCCAAGCAAGA 1113–1120 1.000 72.3
trnC-GCA-petN_p5 trnC-GCA-petN CCAGTTCAAATCCGGGTGT TTAAAGCAGCCCAAGCAAGA 1115–1122 1.000 71.4
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA AAAACAGTCAGCCAAAATGA 1105–1115 1.000 49.9
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA AAAAACAGTCAGCCAAAATGA 1106–1116 1.000 48.9
petN-psbM_p3 petN-psbM AGTAAGTCTTGCTTGGGCTG AAAACAGTCAGCCAAAATGA 1111–1121 1.000 48.4
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA AAACAGTCAGCCAAAATGAT 1104–1114 1.000 48.0
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA AACAGTCAGCCAAAATGATT 1103–1113 1.000 48.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Clivia caulescens PP853196.1 158142 View on NCBI ↗
Clivia gardenii NC_059569.1 158156 View on NCBI ↗
Clivia miniata NC_048961.1 158114 View on NCBI ↗
Clivia miniata var. citrina MW561118.1 158112 View on NCBI ↗
Clivia mirabilis PP836161.1 158914 View on NCBI ↗
Clivia nobilis PP868377.1 157131 View on NCBI ↗
Clivia robusta MW660367.1 157130 View on NCBI ↗