Markers + reference

Libidibia

2 species · Fabaceae · Fabales

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Species 2
Genome length 158–158 kb
Candidate markers 267
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnQ-UUG-psbK LSC 506 0.0211 0.93 66.7 yes View details
trnS-GCU-trnR-UCU LSC 1768 0.0186 0.97 63.0 yes View details
trnC-GCA-petN LSC 1060 0.0167 0.96 67.8 yes View details
psbM-trnD-GUC LSC 935 0.0183 1.00 69.7 yes View details
trnT-GGU-trnL-UAA LSC 1181 0.0202 0.97 69.4 yes View details
rps11-rpl36 LSC 234 0.0645 0.93 86.7 yes View details
rps8 LSC 405 0.0000 1.00 20.9 yes View details
rps8-rpl14 LSC 302 0.0938 0.85 86.9 yes View details
rpl16 LSC 1630 0.0101 0.97 56.8 yes View details
rpl32-trnL-UAG SSC 374 0.0355 0.98 68.1 yes View details
ccsA SSC 972 0.0021 1.00 47.0 yes View details
ccsA-ndhD SSC 286 0.0524 1.00 76.1 yes View details
trnF-GAA-ndhJ LSC 737 0.0194 0.98 72.0 yes View details
trnH-GUG-psbA LSC 372 0.0248 0.98 70.5 yes View details
trnL-UAG-ccsA SSC 128 0.0408 0.77 70.2 yes View details
ndhC-trnV-UAC LSC 586 0.0124 0.96 69.3 yes View details
trnG-UCC-trnfM-CAU LSC 174 0.0287 1.00 68.9 yes View details
rpl33-rps18 LSC 205 0.0248 0.99 68.1 yes View details
psaJ-rpl33 LSC 519 0.0175 0.99 67.8 yes View details
petN-psbM LSC 887 0.0136 0.99 67.1 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 105 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 TTCCCTCTAGACCTAGCTGC 442–447 1.000 81.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 456–461 1.000 81.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 455–460 1.000 81.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 457–462 1.000 81.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGAGCTAACCTTGGTATGG 491–496 1.000 80.0
trnK-UUU_p1 trnK-UUU TCTCTGCCTTATTTTACCTCA TGCGATTGTATCTACACATCCT 2739–2762 1.000 40.7
trnK-UUU_p2 trnK-UUU TTCTCTGCCTTATTTTACCTCA TGCGATTGTATCTACACATCCT 2740–2763 1.000 40.7
trnK-UUU_p3 trnK-UUU TCTCTGCCTTATTTTACCTCA TTGCGATTGTATCTACACATCCT 2740–2763 1.000 40.7
trnK-UUU_p4 trnK-UUU TCTCTGCCTTATTTTACCTCAT TGCGATTGTATCTACACATCCT 2739–2762 1.000 40.7
trnK-UUU_p5 trnK-UUU TCTCTGCCTTATTTTACCTCA TGCGATTGTATCTACACATCC 2739–2762 1.000 40.7
trnQ-UUG-psbK_p1 trnQ-UUG-psbK TACTCTGGGACGGAAGGATT AGGCTTCAGGTAATTTTGCGA 638–670 1.000 71.2
trnQ-UUG-psbK_p2 trnQ-UUG-psbK TACTCTGGGACGGAAGGATT GGCTTCAGGTAATTTTGCGA 637–669 1.000 70.5
trnQ-UUG-psbK_p3 trnQ-UUG-psbK TACTCTGGGACGGAAGGATT AGGCTTCAGGTAATTTTGCG 638–670 1.000 70.4
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AGGCTTCAGGTAATTTTGCGA 600–632 1.000 70.2
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GGCTTCAGGTAATTTTGCGA 599–631 1.000 69.5
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 1839–1840 1.000 67.0
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 1838–1839 1.000 67.0
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 1845–1846 1.000 66.4
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 1844–1845 1.000 66.3
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA AGAAGACCTCTGTCCTATCCA 1893–1894 1.000 65.8
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1096–1126 1.000 82.6
trnC-GCA-petN_p2 trnC-GCA-petN GTATCATTTTGGCGGCATGG AGCCCAAGCGAGACTTACTA 1148–1178 1.000 81.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 1157–1187 1.000 80.8
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTTCCCCATACTACGAGGG 1147–1177 1.000 80.6
trnC-GCA-petN_p5 trnC-GCA-petN GTATCATTTTGGCGGCATGG AGAGTCCACTTCTTCCCCAT 1209–1239 1.000 80.1
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACTGCCTTCTTGC 1025–1028 1.000 76.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT GTTCCTACTGCCTTCTTGCT 1024–1027 1.000 76.3
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT AGTTCCTACTGCCTTCTTGC 964–967 1.000 74.8
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT GTTCCTACTGCCTTCTTGCT 963–966 1.000 74.8
petN-psbM_p5 petN-psbM CCCTCGTAGTATGGGGAAGA GTTCCTACTGCCTTCTTGCT 973–976 1.000 74.5

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
Libidibia coriaria NC_026677.1 158045 View on NCBI ↗
Libidibia paraguariensis PV870830.1 158156 View on NCBI ↗