Markers + reference

Liriope

4 species · Asparagaceae · Asparagales

Back to catalogue

Species 4
Genome length 156–157 kb
Candidate markers 271
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 637 0.0026 1.00 60.7 yes View details
atpF LSC 1373 0.0025 1.00 60.4 yes View details
rpoC2 LSC 4158 0.0004 1.00 36.6 yes View details
trnE-UUC-trnT-GGU LSC 492 0.0041 1.00 44.9 yes View details
rbcL LSC 1461 0.0000 1.00 31.9 yes View details
ycf4-cemA LSC 802 0.0025 1.00 37.3 yes View details
trnN-GUU-ndhF IRb 1144 0.0017 1.00 41.4 yes View details
ndhF-rpl32 SSC 955 0.0017 1.00 56.2 yes View details
ycf1 SSC 5487 0.0012 1.00 53.3 yes View details
trnS-GCU-trnG-UCC LSC 1154 0.0017 1.00 64.8 yes View details
rpl32-trnL-UAG SSC 948 0.0014 0.98 64.4 yes View details
psaC-ndhE SSC 414 0.0000 1.00 59.5 yes View details
ndhC-trnV-UAC LSC 1640 0.0008 1.00 55.1 yes View details
trnT-UGU-trnL-UAA LSC 1010 0.0007 1.00 52.5 yes View details
matK-trnK-UUU LSC 1082 0.0015 1.00 51.1 yes View details
trnC-GCA-petN LSC 929 0.0000 1.00 49.7 yes View details
petN-psbM LSC 895 0.0000 1.00 49.6 yes View details
cemA LSC 738 0.0000 1.00 49.5 yes View details
infA LSC 198 0.0034 0.99 48.0 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 ACCAATGTGTATCTATCCGCC TTCGATCGTATCTACAAATCA 2794–2795 1.000 40.2
trnK-UUU_p2 trnK-UUU ACCAATGTGTATCTATCCGCC TTTCGATCGTATCTACAAATCA 2795–2796 1.000 40.2
trnK-UUU_p3 trnK-UUU CCGCCTAAATAGAAATGCACC TTCGATCGTATCTACAAATCA 2778–2779 1.000 40.2
trnK-UUU_p4 trnK-UUU ACCAATGTGTATCTATCCGCC TCGATCGTATCTACAAATCAT 2793–2794 1.000 40.2
trnK-UUU_p5 trnK-UUU CCAATGTGTATCTATCCGCCT TTCGATCGTATCTACAAATCA 2793–2794 1.000 40.2
matK-trnK-UUU_p1 matK-trnK-UUU ACTAATCGCAACGAGAATGGA TCTGGGTTGCTAACTCAACG 1178–1179 1.000 66.8
matK-trnK-UUU_p2 matK-trnK-UUU ACTAATCGCAACGAGAATGGA AACGGTAGAGTACTCGGCTT 1162–1163 1.000 66.8
matK-trnK-UUU_p3 matK-trnK-UUU ACTAATCGCAACGAGAATGGA ACGGTAGAGTACTCGGCTTT 1161–1162 1.000 66.8
matK-trnK-UUU_p4 matK-trnK-UUU TCGCAACGAGAATGGAATTTC TCTGGGTTGCTAACTCAACG 1173–1174 1.000 65.0
matK-trnK-UUU_p5 matK-trnK-UUU TCGCAACGAGAATGGAATTTC ACGGTAGAGTACTCGGCTTT 1156–1157 1.000 65.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 749 1.000 77.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 748 1.000 77.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 735 1.000 75.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAGGAAC 760 1.000 74.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 758 1.000 73.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GATCAGAGGGAACGGAGAGA ACGAATCGCACTTTTACCACT 1083–1294 1.000 73.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AAGTGATCAGAGGGAACGGA ACGAATCGCACTTTTACCACT 1087–1298 1.000 73.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATCAGAGGGAACGGAGAGAG ACGAATCGCACTTTTACCACT 1082–1293 1.000 73.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GATCAGAGGGAACGGAGAGA ACGAATCGCACTTTTACCAC 1083–1294 1.000 73.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GATCAGAGGGAACGGAGAGA CGAACGAATCGCACTTTTACC 1086–1297 1.000 73.8
atpF_p1 atpF ACTAATTTCGTCAGCTCGAA AAAAAGGGCGAGTCAAGTGA 1547 1.000 52.4
atpF_p2 atpF ACTAATTTCGTCAGCTCGAA GGGCGAGTCAAGTGATACAA 1542 1.000 52.1
atpF_p3 atpF ACTAATTTCGTCAGCTCGAA AGGGCGAGTCAAGTGATACA 1543 1.000 51.6
atpF_p4 atpF ACTAATTTCGTCAGCTCGAA AAAAGGGCGAGTCAAGTGAT 1546 1.000 50.6
atpF_p5 atpF ACTAATTTCGTCAGCTCGAA AAGGGCGAGTCAAGTGATAC 1544 1.000 49.7
rpoC2_p1 rpoC2 ACTACGGGTCGAACCAAAAC AAGAAGCCGAGTAGGTGGAT 249 1.000 78.9
rpoC2_p2 rpoC2 ACTACGGGTCGAACCAAAAC AGAAGCCGAGTAGGTGGATT 248 1.000 78.9
rpoC2_p3 rpoC2 CTACGGGTCGAACCAAAACA AAGAAGCCGAGTAGGTGGAT 248 1.000 78.9
rpoC2_p4 rpoC2 CTACGGGTCGAACCAAAACA AGAAGCCGAGTAGGTGGATT 247 1.000 78.9
rpoC2_p5 rpoC2 GACTACGGGTCGAACCAAAA AGAAGCCGAGTAGGTGGATT 249 1.000 78.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Liriope graminifolia PP078673.1 156995 View on NCBI ↗
Liriope muscari NC_045384.1 156754 View on NCBI ↗
Liriope spicata NC_042227.1 157055 View on NCBI ↗
Liriope spicata var. prolifera MN811645.1 155998 View on NCBI ↗