Markers + reference

Lindernia

5 species · Linderniaceae · Lamiales

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Species 5
Genome length 153–154 kb
Candidate markers 271
Primer pairs 95

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
trnH-GUG-psbA LSC 515 0.1009 0.92 73.8 yes View details
trnK-UUU-rps16 LSC 907 0.0609 0.90 82.2 yes View details
rps16-trnQ-UUG LSC 1123 0.0664 1.00 87.5 yes View details
trnC-GCA-petN LSC 831 0.0676 0.98 86.9 yes View details
petN-psbM LSC 997 0.0650 0.98 84.8 yes View details
ndhC-trnV-UAC LSC 1120 0.0549 0.99 79.3 yes View details
accD-psaI LSC 449 0.0795 0.82 76.6 yes View details
rpl32-trnL-UAG SSC 817 0.0822 0.97 83.6 yes View details
ycf1 SSC 5544 0.0500 1.00 72.5 yes View details
psbE-petL LSC 949 0.0471 0.98 88.4 yes View details
trnS-GCU-trnG-CGA LSC 663 0.0517 0.99 86.6 yes View details
trnT-UGU-trnL-UAA LSC 683 0.0594 0.95 86.0 yes View details
trnS-GGA-rps4 LSC 279 0.0556 0.99 82.6 yes View details
trnG-GCC-trnfM-CAU LSC 181 0.1148 0.97 82.5 yes View details
atpH-atpI LSC 983 0.0426 0.98 82.4 yes View details
petA-psbJ LSC 1042 0.0487 0.99 82.4 yes View details
trnT-GGU-psbD LSC 1343 0.0432 0.98 82.0 yes View details
trnM-CAU-atpE LSC 221 0.0769 1.00 82.0 yes View details
trnV-UAC-trnM-CAU LSC 200 0.0742 1.00 81.8 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 95 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 TCAGTGCTATGCATGGTTCC 964–1033 1.000 90.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 978–1047 1.000 90.1
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 963–1032 1.000 90.1
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAGTGCTATGCATGGTTCC 977–1046 1.000 90.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAGTGCTATGCATGGTTCC 979–1048 1.000 90.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAGATCTTCGAAACGTGGGG 1150–1204 1.000 90.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT AAGATCTTCGAAACGTGGGG 1151–1205 1.000 90.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAGATCTTCGAAACGTGGGG 1208 0.400 59.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGCCGTCTATCGAATCGTTG 1258 0.400 59.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCGATCCCGAAGAGAAGGAA 1228 0.400 59.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1196–1244 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1200–1248 1.000 85.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1188–1236 1.000 85.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 1195–1243 1.000 84.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGCTATTC 1217–1265 1.000 83.7
trnS-GCU-trnG-CGA_p1 trnS-GCU-trnG-CGA CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 721–802 1.000 60.6
trnS-GCU-trnG-CGA_p2 trnS-GCU-trnG-CGA AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 720–801 1.000 60.6
trnS-GCU-trnG-CGA_p3 trnS-GCU-trnG-CGA CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 724–805 1.000 59.5
trnS-GCU-trnG-CGA_p4 trnS-GCU-trnG-CGA CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 723–804 1.000 59.5
trnS-GCU-trnG-CGA_p5 trnS-GCU-trnG-CGA AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 722–803 1.000 59.5
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1040–1109 1.000 85.0
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 1057–1126 1.000 84.0
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG TTTTTGCAACTTTAGCCGCG 1052–1121 1.000 83.7
atpH-atpI_p4 atpH-atpI AACGGAAGCAGCAGAAATCA CCGCGGCTTATATAGGTGAA 1025–1094 1.000 83.4
atpH-atpI_p5 atpH-atpI ATCCAGCAGCAATAACGGAA TTTTTGCAACTTTAGCCGCG 1053–1122 1.000 82.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 873–903 1.000 90.1
trnC-GCA-petN_p2 trnC-GCA-petN TTTTGGATCATTTTGGCGGC AGCCCAAGCGAGACTTACTA 929–959 1.000 90.1
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 891–921 1.000 87.9
trnC-GCA-petN_p4 trnC-GCA-petN TTGGATCATTTTGGCGGCAT AGCCCAAGCGAGACTTACTA 927–957 1.000 84.3
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 872–902 1.000 84.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Lindernia procumbens NC_082121.1 153448 View on NCBI ↗
Lindernia rotundifolia NC_082122.1 153360 View on NCBI ↗
Lindernia scutellariiformis NC_082131.1 153942 View on NCBI ↗
Lindernia setulosa NC_082133.1 153688 View on NCBI ↗
Lindernia stricta NC_082132.1 153885 View on NCBI ↗