Markers + reference

Limnophila

2 species · Plantaginaceae · Lamiales

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Species 2
Genome length 152–152 kb
Candidate markers 268
Primer pairs 90

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 974 0.0681 0.93 80.6 yes View details
atpH-atpI LSC 1023 0.0416 0.99 75.2 yes View details
rpoB-trnC-GCA LSC 1482 0.0466 0.93 75.2 yes View details
trnE-UUC-trnT-GGU LSC 578 0.0702 0.99 82.7 yes View details
petA-psbJ LSC 1143 0.0353 0.84 80.2 yes View details
psaJ-rpl33 LSC 349 0.0867 0.99 78.7 yes View details
ycf1 SSC 5412 0.0367 0.99 61.4 yes View details
ycf1-rps15 SSC 444 0.0498 0.95 74.9 yes View details
ycf1 IRa 1099 0.0164 1.00 54.2 no View details
ndhE-psaC SSC 279 0.0541 0.93 80.3 yes View details
atpA-atpF LSC 57 0.0755 0.93 76.9 yes View details
trnL-UAA-trnF-GAA LSC 276 0.0449 0.97 76.4 yes View details
trnL-UAG-rpl32 SSC 789 0.0474 0.99 74.8 yes View details
trnW-CCA-trnP-UGG LSC 164 0.0671 1.00 73.9 yes View details
psaC-ndhD SSC 121 0.0992 1.00 73.7 yes View details
petG-trnW-CCA LSC 129 0.0620 1.00 73.5 yes View details
rps16-trnQ-UUG LSC 836 0.0309 0.97 71.9 yes View details
psbT-pbf1 LSC 66 0.0606 1.00 71.9 yes View details
psbE-petL LSC 953 0.0260 0.97 71.8 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 911–926 1.000 83.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAACAAACTGAAATGGGGCG 972–987 1.000 83.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 894–909 1.000 83.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAACAAACTGAAATGGGGCG 955–970 1.000 82.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAACAAACTGAAATGGGGCG 973–988 1.000 82.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 981–1029 1.000 56.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 980–1028 1.000 56.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 982–1030 1.000 55.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTACCACTAAACTATACCCGC 981–1029 1.000 55.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 1035–1083 1.000 55.4
atpA-atpF_p1 atpA-atpF ATTGCTCGATACGTTCACGG TATGTTGGGGGCGATGAAAG 145–149 1.000 80.4
atpA-atpF_p2 atpA-atpF ATTGCTCGATACGTTCACGG TTGGGGGCGATGAAAGAAAT 141–145 1.000 79.1
atpA-atpF_p3 atpA-atpF ATTGCTCGATACGTTCACGG GTATGTTGGGGGCGATGAAA 146–150 1.000 78.8
atpA-atpF_p4 atpA-atpF GCTCGATACGTTCACGGATA TATGTTGGGGGCGATGAAAG 142–146 1.000 78.6
atpA-atpF_p5 atpA-atpF ATTGCTCGATACGTTCACGG ATATTGGTATGTTGGGGGCG 152–156 1.000 78.3
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTGATGTTCCTTGGA 1151–1157 1.000 81.0
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA CGCGGCTTATATCGGTGAAT 1087–1093 1.000 81.0
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTGATGTTCCTTGGA 1168–1174 1.000 80.0
atpH-atpI_p4 atpH-atpI GCCAATCCAGCAGCAATAAC CGCGGCTTATATCGGTGAAT 1104–1110 1.000 80.0
atpH-atpI_p5 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTGATGTTCCTTGGA 1163–1169 1.000 79.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCGGATTTGAACTGGGGAAA 2001–2056 1.000 85.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CCGGATTTGAACTGGGGAAA 2193–2248 1.000 85.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TCGTACCCCCTTCCAGTATC 2369–2402 1.000 85.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG TCGTACCCCCTTCCAGTATC 2561–2594 1.000 85.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATATTGGATCCCCGCCTACA TCGTACCCCCTTCCAGTATC 2572–2605 1.000 84.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 681–715 1.000 83.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 660–694 1.000 83.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU ACTTCCTTTCGTGGTACCCT GAACCGATGACTTACGCCTT 725–759 1.000 82.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 657–691 1.000 82.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU ACTTCCTTTCGTGGTACCCT CCATGGCGTTACTCTACCAC 704–738 1.000 82.6

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
Limnophila aromatica PV890005.1 152121 View on NCBI ↗
Limnophila sessiliflora NC_063679.1 152395 View on NCBI ↗