Markers + reference

Libanotis

13 species · Apiaceae · Apiales

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Species 13
Genome length 147–151 kb
Candidate markers 264
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0024 1.00 37.6 yes View details
rps16-trnQ-UUG LSC 1276 0.0120 0.97 55.4 yes View details
trnC-GCA-petN LSC 729 0.0213 0.96 73.2 yes View details
petA-psbJ LSC 959 0.0165 1.00 78.9 yes View details
ycf2-trnL-CAA IRb 1253 0.0330 0.98 80.9 yes View details
ycf1 IRb 2289 0.0072 0.87 45.4 yes View details
ycf1 SSC 5448 0.0060 1.00 59.8 no View details
trnL-CAA-trnH-GUG IRa 1395 0.1078 0.89 84.4 no View details
trnH-GUG-psbA LSC 196 0.0482 1.00 82.8 yes View details
trnE-UUC-trnT-GGU LSC 750 0.0106 0.99 71.4 yes View details
psbE-petL LSC 1005 0.0048 1.00 69.7 yes View details
trnT-GGU-psbD LSC 1444 0.0072 0.99 69.0 yes View details
ndhC-trnV-UAC LSC 1085 0.0103 0.98 68.7 yes View details
ccsA-ndhD SSC 224 0.0249 1.00 68.5 yes View details
atpH-atpI LSC 1115 0.0116 0.99 67.9 yes View details
trnK-UUU-rps16 LSC 710 0.0084 1.00 67.5 yes View details
psbM-trnD-GUC LSC 688 0.0078 1.00 66.6 yes View details
trnG-UCC-trnR-UCU LSC 136 0.0219 1.00 65.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 301–341 1.000 90.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 315–355 1.000 90.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 314–354 1.000 90.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 316–356 1.000 90.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 251–291 1.000 90.4
psbA_p1 psbA GATCCACTTGGCTACATCCG AAATTCGTGTGCTTGGGAGT 1319–1359 1.000 83.1
psbA_p2 psbA CAATCCACTGCCTTGATCCA AAATTCGTGTGCTTGGGAGT 1333–1373 1.000 83.1
psbA_p3 psbA AATCCACTGCCTTGATCCAC AAATTCGTGTGCTTGGGAGT 1332–1372 1.000 83.0
psbA_p4 psbA ACAATCCACTGCCTTGATCC AAATTCGTGTGCTTGGGAGT 1334–1374 1.000 83.0
psbA_p5 psbA GATCCACTTGGCTACATCCG TGCTTGGGAGTCCCTGATAA 1310–1350 1.000 83.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AGGAACTGTTCGGGATCTTT 834–886 1.000 71.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGGAACTGTTCGGGATCTTT 851–903 1.000 71.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AGGAACTGTTCGGGATCTTT 850–902 1.000 71.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTGTTCGGGATCTTT 789–841 1.000 71.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGAACTGTTCGGGATCTTT 790–842 1.000 70.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT TGGAAGTATAGATGGGGCGT 937–1441 1.000 86.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT TGGAAGTATAGATGGGGCGT 938–1442 1.000 86.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT CTTACAGCAGCTTGCCAAAC 1453–1955 1.000 86.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT CTTACAGCAGCTTGCCAAAC 1454–1956 1.000 86.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GATTCCCGCGTGATACACTT CTTACAGCAGCTTGCCAAAC 1810–2312 1.000 86.1
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 216–247 1.000 73.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 219–250 1.000 72.9
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 222–253 1.000 72.3
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 225–256 1.000 71.9
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 220–251 1.000 70.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 1170–1228 1.000 85.4
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 1226–1284 1.000 84.5
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 1186–1244 1.000 84.4
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 1171–1229 1.000 84.2
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 1230–1288 1.000 83.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Libanotis abolinii PP078847.1 148015 View on NCBI ↗
Libanotis acaulis NC_087706.1 147829 View on NCBI ↗
Libanotis condensata NC_087707.1 147763 View on NCBI ↗
Libanotis grubovii NC_087709.1 147471 View on NCBI ↗
Libanotis iliensis NC_087710.1 147795 View on NCBI ↗
Libanotis jinanensis NC_087711.1 147488 View on NCBI ↗
Libanotis lancifolia PP078853.1 147970 View on NCBI ↗
Libanotis lanzhouensis NC_087712.1 147742 View on NCBI ↗
Libanotis laticalycina PP078854.1 150958 View on NCBI ↗
Libanotis schrenkiana NC_087713.1 146960 View on NCBI ↗
Libanotis sibirica NC_087715.1 146836 View on NCBI ↗
Libanotis spodotrichoma NC_062134.1 147348 View on NCBI ↗
Libanotis wannienchun PP078856.1 147774 View on NCBI ↗