Markers + reference

Lysidice

2 species · Fabaceae · Fabales

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Species 2
Genome length 158–159 kb
Candidate markers 262
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnR-UCU-atpA LSC 386 0.0389 1.00 65.0 yes View details
atpH-atpI LSC 1309 0.0261 0.73 63.8 yes View details
psbZ-trnG-GCC LSC 589 0.0502 0.95 87.1 yes View details
trnT-UGU-trnL-UAA LSC 902 0.0318 0.84 74.3 yes View details
trnL-UAA-trnF-GAA LSC 432 0.0093 1.00 60.8 yes View details
rps3-rps19 LSC 691 0.0279 0.99 64.4 yes View details
rrn4.5S-rrn5S IRb 223 0.0717 1.00 84.0 yes View details
ccsA-ndhD SSC 264 0.0536 0.99 70.0 yes View details
trnR-ACG-rrn5S IRa 273 0.0000 0.93 56.7 yes View details
rrn5S-rrn4.5S IRa 223 0.0717 1.00 84.0 yes View details
accD-psaI LSC 549 0.0171 0.96 70.2 yes View details
psbC-trnS-UGA LSC 234 0.0427 1.00 69.9 yes View details
trnR-ACG-trnN-GUU IRb 725 0.0118 0.93 69.8 yes View details
trnN-GUU-trnR-ACG IRa 725 0.0118 0.93 69.8 yes View details
petA-psbJ LSC 855 0.0114 0.92 69.2 yes View details
trnS-GCU-trnG-UCC LSC 803 0.0129 0.97 69.1 yes View details
trnC-GCA-petN LSC 1102 0.0076 0.95 67.9 yes View details
ndhC-trnV-UAC LSC 573 0.0096 0.91 67.3 yes View details
trnT-GGU-psbD LSC 1356 0.0112 0.85 67.2 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
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATGAATCAAACGAGGGACCC 916–951 1.000 79.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATGAATCAAACGAGGGACCC 915–950 1.000 79.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAGATTAGCAATCCGACGCT ATGAATCAAACGAGGGACCC 924–959 1.000 78.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATGAATCAAACGAGGGACCC 970–1005 1.000 78.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC ATGAATCAAACGAGGGACCC 918–953 1.000 76.8
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGCAGAAGCCCTTGTGAAA 488–516 1.000 68.3
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTTACCGGGGAAGCAGAA 500–528 1.000 67.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTTACCGGGGAAGC 504–532 1.000 67.8
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGCCCTTGTGAAAGAAGCT 482–510 1.000 65.9
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGCAGAAGCCCTTGTGAAAG 487–515 1.000 65.8
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG TTTGCAACTTTAGCTGCTGC 1081–1429 1.000 84.2
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTGCAACTTTAGCTGCTGC 1047–1395 1.000 84.2
atpH-atpI_p3 atpH-atpI TGGTCCAATAGAAGCAAGCC TTTGCAACTTTAGCTGCTGC 1087–1435 1.000 83.4
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTGCAACTTTAGCTGCTGC 1048–1396 1.000 83.1
atpH-atpI_p5 atpH-atpI AATAGAAGCAAGCCCGACAG GCTGCTGCTTATATAGGCGA 1069–1417 1.000 82.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1113–1158 1.000 82.6
trnC-GCA-petN_p2 trnC-GCA-petN TTTATCGTTTTGGCGGCATG AGCCCAAGCGAGACTTACTA 1166–1211 1.000 80.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTTCCCCATACTACGAGGG 1164–1209 1.000 80.6
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1131–1176 1.000 80.3
trnC-GCA-petN_p5 trnC-GCA-petN TTTATCGTTTTGGCGGCATG TCTTCCCCATACTACGAGGG 1217–1262 1.000 78.9
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1312–1506 1.000 82.3
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GACCGGACCAACCTACAAAA 1326–1520 1.000 82.1
trnT-GGU-psbD_p3 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1315–1509 1.000 82.1
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GACCGGACCAACCTACAAAA 1329–1523 1.000 82.0
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TAGACCGGACCAACCTACAA 1328–1522 1.000 81.8
psbC-trnS-UGA_p1 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GAGAGATGGCTGAGTGGTTG 399 1.000 78.8
psbC-trnS-UGA_p2 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GCTGAGTGGTTGATAGCTCC 391 1.000 78.6
psbC-trnS-UGA_p3 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGCTGAGTGGTTGATAGCTC 392 1.000 78.6
psbC-trnS-UGA_p4 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGTTGATAGCTCCGGTCTTG 384 1.000 78.6
psbC-trnS-UGA_p5 psbC-trnS-UGA TAGGTCATTTATGGCACGCG GAGAGATGGCTGAGTGGTTG 433 1.000 78.3

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
Lysidice brevicalyx NC_080273.1 159084 View on NCBI ↗
Lysidice rhodostegia NC_047385.1 158060 View on NCBI ↗