Markers + reference

Stylosanthes

4 species · Fabaceae · Fabales

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Species 4
Genome length 156–157 kb
Candidate markers 253
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 9 remaining regions by MarkerSeek score (out of 253 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL LSC 743 0.0290 0.99 64.9 yes View details
trnV-UAC-ndhC LSC 651 0.0466 0.91 79.9 yes View details
trnG-UCC-psbZ LSC 839 0.0366 0.84 74.8 yes View details
atpA-trnR-UCU LSC 284 0.0298 0.99 51.4 yes View details
petA-psbJ LSC 1057 0.0253 0.96 66.2 yes View details
trnW-CCA-trnP-UGG LSC 209 0.0458 0.96 79.4 yes View details
trnP-UGG-psaJ LSC 414 0.0250 1.00 64.4 yes View details
rps11-rpl36 LSC 576 0.0316 0.98 69.5 yes View details
rps3-rps19 LSC 529 0.0382 0.99 61.7 yes View details
ndhF SSC 2256 0.0159 1.00 54.2 yes View details
rpl32-trnL-UAG SSC 773 0.0393 0.97 77.3 yes View details
ycf1 SSC 5205 0.0251 1.00 56.1 yes View details
trnfM-CAU-trnG-UCC LSC 142 0.0331 0.96 71.9 yes View details
trnT-GGU-trnE-UUC LSC 808 0.0274 0.99 71.0 yes View details
rpl20-rps12 LSC 739 0.0199 1.00 69.8 yes View details
trnF-GAA-trnL-UAA LSC 340 0.0291 0.99 68.0 yes View details
psbD-trnT-GGU LSC 1515 0.0206 0.98 68.0 yes View details
atpE-trnM-CAU LSC 138 0.0426 0.99 67.9 yes View details
ndhF-rpl32 SSC 619 0.0256 0.98 67.5 yes View details
ndhJ-trnF-GAA LSC 823 0.0240 1.00 67.1 yes View details
psbK-trnQ-UUG LSC 549 0.0273 0.95 66.5 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
trnK-UUU-rbcL_p1 trnK-UUU-rbcL CCTTTCTGGATCAGTCGTGG AATGAGGGTCGTGATCTTGC 1006–1025 1.000 83.9
trnK-UUU-rbcL_p2 trnK-UUU-rbcL CCTTTCTGGATCAGTCGTGG AGTCCTGAATTAGCTGCTGC 946–965 1.000 83.9
trnK-UUU-rbcL_p3 trnK-UUU-rbcL CATTGATCGCCACCCCATAA AATGAGGGTCGTGATCTTGC 1348–1371 1.000 83.0
trnK-UUU-rbcL_p4 trnK-UUU-rbcL TTGATCGCCACCCCATAATG AATGAGGGTCGTGATCTTGC 1346–1369 1.000 83.0
trnK-UUU-rbcL_p5 trnK-UUU-rbcL TTGATCGCCACCCCATAATG AGTCCTGAATTAGCTGCTGC 1286–1309 1.000 82.9
atpE-trnM-CAU_p1 atpE-trnM-CAU CGAGCTAGGACACGAGTAGA TACTGGACGTCTCAACCCTT 620–632 0.750 73.3
atpE-trnM-CAU_p2 atpE-trnM-CAU AGCTGAAGGCAAGAGACAAC TACTGGACGTCTCAACCCTT 666–678 0.750 72.7
atpE-trnM-CAU_p3 atpE-trnM-CAU GCTGAAGGCAAGAGACAACT TACTGGACGTCTCAACCCTT 665–677 0.750 72.7
atpE-trnM-CAU_p4 atpE-trnM-CAU CTCTGATGGGTGGTTTTGCT TACTGGACGTCTCAACCCTT 799–811 0.750 72.4
atpE-trnM-CAU_p5 atpE-trnM-CAU TGCCGAGAAGAGTAGTGACA TACTGGACGTCTCAACCCTT 741–753 0.750 72.4
trnV-UAC-ndhC_p1 trnV-UAC-ndhC GTTCGAGTCCGTATAGCCCT TCATAGTCGTAAAGCAAAAACA 570–695 1.000 50.1
trnV-UAC-ndhC_p2 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT TCATAGTCGTAAAGCAAAAACA 582–707 1.000 50.0
trnV-UAC-ndhC_p3 trnV-UAC-ndhC GAAGGTCTACGGTTCGAGTC TCATAGTCGTAAAGCAAAAACA 581–706 1.000 50.0
trnV-UAC-ndhC_p4 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT TCATAGTCGTAAAGCAAAAACAT 582–707 1.000 50.0
trnV-UAC-ndhC_p5 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT ATCATAGTCGTAAAGCAAAAACA 583–708 1.000 49.9
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC GGGATAGCTCAGCTGGTAGA 963–971 1.000 83.1
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CCTCGTGTCACCAGTTCAAA 927–935 1.000 82.9
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CTGGTAGAGCAGAGGACTGA 951–959 1.000 82.1
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA ATGCCCGAAAGTTGGATAGG GGGATAGCTCAGCTGGTAGA 974–982 1.000 80.9
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA ATGCCCGAAAGTTGGATAGG CCTCGTGTCACCAGTTCAAA 938–946 1.000 80.6
trnF-GAA-trnL-UAA_p1 trnF-GAA-trnL-UAA TCTACCAGCTGAGCTATCCC AATCGTGAGGGTTCAAGTCC 394–408 1.000 82.4
trnF-GAA-trnL-UAA_p2 trnF-GAA-trnL-UAA TTTGAACTGGTGACACGAGG AATCGTGAGGGTTCAAGTCC 430–444 1.000 81.5
trnF-GAA-trnL-UAA_p3 trnF-GAA-trnL-UAA TCAGTCCTCTGCTCTACCAG AATCGTGAGGGTTCAAGTCC 406–420 1.000 81.1
trnF-GAA-trnL-UAA_p4 trnF-GAA-trnL-UAA GTGCCAGGAACCAGATTTGA AATCGTGAGGGTTCAAGTCC 445–459 1.000 81.0
trnF-GAA-trnL-UAA_p5 trnF-GAA-trnL-UAA TCTACCAGCTGAGCTATCCC GGAAGAGGAAAATCCGTCGA 421–435 1.000 80.4
trnfM-CAU-trnG-UCC_p1 trnfM-CAU-trnG-UCC CTTGAGGTCACGGGTTCAAA TCTTTGCCAAGGAGAAGACG 220–246 1.000 83.4
trnfM-CAU-trnG-UCC_p2 trnfM-CAU-trnG-UCC TGAGGTCACGGGTTCAAATC TCTTTGCCAAGGAGAAGACG 218–244 1.000 82.3
trnfM-CAU-trnG-UCC_p3 trnfM-CAU-trnG-UCC GTAGCTCGCAAGGCTCATAA TCTTTGCCAAGGAGAAGACG 241–267 1.000 81.5
trnfM-CAU-trnG-UCC_p4 trnfM-CAU-trnG-UCC TAGCTCGCAAGGCTCATAAC TCTTTGCCAAGGAGAAGACG 240–266 1.000 81.5
trnfM-CAU-trnG-UCC_p5 trnfM-CAU-trnG-UCC ATTCTTCTCTTTACCGCGGG TCTTTGCCAAGGAGAAGACG 274–300 1.000 80.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Stylosanthes guianensis NC_058691.1 156763 View on NCBI ↗
Stylosanthes hamata NC_039159.1 156502 View on NCBI ↗
Stylosanthes scabra NC_039160.1 156502 View on NCBI ↗
Stylosanthes viscosa NC_039161.1 156244 View on NCBI ↗