Markers + reference

Guilandina

2 species · Fabaceae · Fabales

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Species 2
Genome length 157–157 kb
Candidate markers 269
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5418 0.1801 0.93 76.6 yes View details
ndhH SSC 1182 0.4643 0.94 83.2 yes View details
ndhA SSC 2327 0.4696 0.88 80.0 yes View details
ndhI SSC 486 0.4630 0.89 79.5 yes View details
ndhG SSC 531 0.4894 0.89 80.3 yes View details
ndhE SSC 306 0.4823 0.92 76.7 yes View details
psaC SSC 246 0.5630 0.97 75.7 yes View details
ndhD SSC 1497 0.4824 0.91 82.5 yes View details
trnL-UAG-rpl32 SSC 373 0.4596 0.96 77.8 yes View details
ndhF SSC 2289 0.4470 0.85 79.1 yes View details
ycf1 IRa 743 0.0094 1.00 49.2 no View details
rps16-trnQ-UUG LSC 603 0.1327 0.94 89.3 yes View details
trnH-GUG-psbA LSC 315 0.0780 0.94 88.3 yes View details
trnR-UCU-atpA LSC 290 0.0621 1.00 82.8 yes View details
rpl32-ndhF SSC 758 0.4086 0.86 81.0 yes View details
psbZ-trnG-GCC LSC 523 0.0373 0.98 80.9 yes View details
ccsA SSC 972 0.4440 0.77 78.6 yes View details
ndhA-ndhI SSC 79 0.4800 0.95 77.3 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 85 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 384–390 1.000 87.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 398–404 1.000 86.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 397–403 1.000 86.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 399–405 1.000 86.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGAGCTAACCTTGGTATGG 433–439 1.000 84.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 683–812 1.000 91.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 685–814 1.000 90.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 671–800 1.000 89.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 686–815 1.000 89.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 684–813 1.000 88.6
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTCACTCGGGAAGC 408–493 1.000 68.8
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CCAAGACATTCACTCGGGAA 410–495 1.000 65.9
trnR-UCU-atpA_p3 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AAGACATTCACTCGGGAAGC 443–528 1.000 65.7
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACCAAGACATTCACTCGGGA 411–496 1.000 64.4
trnR-UCU-atpA_p5 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA AAGACATTCACTCGGGAAGC 407–492 1.000 63.2
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCG GCGTCTTCTCTTTGGCAAAG 678–705 1.000 81.0
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG GCGTCTTCTCTTTGGCAAAG 681–708 1.000 79.5
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TCCTGATGGTTGGTCGAGTA GCGTCTTCTCTTTGGCAAAG 674–701 1.000 79.3
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC GCGTCTTCTCTTTGGCAAAG 679–706 1.000 79.1
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTCTCCTGATGGTTGGTCGA GCGTCTTCTCTTTGGCAAAG 677–704 1.000 78.2
ycf1_p1 ycf1 ATCGTTCCATAGCGAATCGG TCAAGATTTACTCGGCCTGC 247 0.500 59.3
ycf1_p2 ycf1 ATCGTTCCATAGCGAATCGG TTTACTCGGCCTGCGTATTC 241 0.500 58.9
ycf1_p3 ycf1 TGGATTTTGGGGCTTGGATC TCAAGATTTACTCGGCCTGC 364 0.500 58.7
ycf1_p4 ycf1 AGATCGCCATTCCAAGCAAA TCAAGATTTACTCGGCCTGC 560 0.500 58.5
ycf1_p5 ycf1 TGGATTTTGGGGCTTGGATC TTTACTCGGCCTGCGTATTC 358 0.500 58.4
ndhH_p1 ndhH GCAGCCGTTTCAGTATGGTA CCGTCTGCTAGAGCTTGAAG 2069 0.500 59.2
ndhH_p2 ndhH GCAGCCGTTTCAGTATGGTA TTTGTTCCGTCTGCTAGAGC 2075 0.500 59.2
ndhH_p3 ndhH GCAGCCGTTTCAGTATGGTA TCAGGTCCAATACGCTGTTG 2027 0.500 59.1
ndhH_p4 ndhH GAAAACCCGGGATCGATTGA CCGTCTGCTAGAGCTTGAAG 1747 0.500 59.1
ndhH_p5 ndhH GAAAACCCGGGATCGATTGA TTTGTTCCGTCTGCTAGAGC 1753 0.500 59.1

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
Guilandina bonduc NC_047380.1 156847 View on NCBI ↗
Guilandina minax PV763356.1 156769 View on NCBI ↗