Markers + reference

Macrotyloma

3 species · Fabaceae · Fabales

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Species 3
Genome length 151–151 kb
Candidate markers 264
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl33-psaJ LSC 509 0.0092 1.00 38.9 yes View details
psbJ-petA LSC 792 0.0084 1.00 63.9 yes View details
trnT-GGU-psbD LSC 1172 0.0074 1.00 61.2 yes View details
psbC LSC 1422 0.0009 1.00 41.4 yes View details
trnL-UAA-trnF-GAA LSC 396 0.0109 1.00 59.1 yes View details
trnF-GAA-ndhJ LSC 791 0.0119 0.99 59.6 yes View details
rbcL-trnK-UUU LSC 876 0.0110 1.00 55.1 yes View details
rpl16 LSC 1428 0.0061 1.00 36.6 yes View details
ycf1 SSC 5361 0.0052 1.00 48.2 yes View details
ndhA SSC 2349 0.0054 1.00 46.0 yes View details
ccsA SSC 987 0.0061 1.00 47.8 yes View details
psbC-trnS-UGA LSC 201 0.0299 1.00 71.5 yes View details
atpH-atpI LSC 1053 0.0044 1.00 63.8 yes View details
psaA-ycf3 LSC 734 0.0073 1.00 63.5 yes View details
petL-psbE LSC 932 0.0050 1.00 62.6 yes View details
rpoB-trnC-GCA LSC 995 0.0060 1.00 61.8 yes View details
trnE-UUC-trnT-GGU LSC 786 0.0076 1.00 61.8 yes View details
rps3-rps19 IRb 539 0.0049 1.00 60.6 yes View details
accD LSC 1506 0.0035 1.00 60.2 yes View details
trnK-UUU-psbA LSC 294 0.0068 1.00 59.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl33-psaJ_p1 rpl33-psaJ CGGATATCTTTACCCTTGGCC CATATCTTTCCGTGGCACCA 643–651 1.000 71.8
rpl33-psaJ_p2 rpl33-psaJ CGGATATCTTTACCCTTGGCC ACATATCTTTCCGTGGCACC 644–652 1.000 71.8
rpl33-psaJ_p3 rpl33-psaJ CGGATATCTTTACCCTTGGCC GCTTTGGCGGGTCTATTGAT 599–607 1.000 69.7
rpl33-psaJ_p4 rpl33-psaJ CGGATATCTTTACCCTTGGCC ATATCTTTCCGTGGCACCAG 642–650 1.000 69.4
rpl33-psaJ_p5 rpl33-psaJ CGGATATCTTTACCCTTGGCC TTTATGGTTCGGGGCTTTGG 612–620 1.000 68.6
petL-psbE_p1 petL-psbE AGACCAATAAATAGAGACGAGGT AGAACGTTCTCCTGTGCTTC 1033–1039 1.000 44.0
petL-psbE_p2 petL-psbE AGACCAATAAATAGAGACGAGGT GTTCTCCTGTGCTTCCAGAC 1028–1034 1.000 43.7
petL-psbE_p3 petL-psbE AGACCAATAAATAGAGACGAGGT CCTGCAATGAATAGGGAGGG 1107–1113 1.000 42.9
petL-psbE_p4 petL-psbE AGACCAATAAATAGAGACGAGGT TCTCCTGTGCTTCCAGACAT 1026–1032 1.000 42.5
petL-psbE_p5 petL-psbE AGACCAATAAATAGAGACGAGGTT AGAACGTTCTCCTGTGCTTC 1033–1039 1.000 41.3
psbJ-petA_p1 psbJ-petA CATATTCCGGATTGGGCTCA CGTGTCGAAGGTCTCTTGTT 931–940 1.000 75.3
psbJ-petA_p2 psbJ-petA ATTCCGGATTGGGCTCATCT CGTGTCGAAGGTCTCTTGTT 928–937 1.000 73.0
psbJ-petA_p3 psbJ-petA TATTCCGGATTGGGCTCATC CGTGTCGAAGGTCTCTTGTT 929–938 1.000 73.0
psbJ-petA_p4 psbJ-petA TCATATTCCGGATTGGGCTC CGTGTCGAAGGTCTCTTGTT 932–941 1.000 73.0
psbJ-petA_p5 psbJ-petA CATATTCCGGATTGGGCTCAT CGTGTCGAAGGTCTCTTGTT 931–940 1.000 71.2
accD_p1 accD CCTGTATGTTTTCATTTTTGATTGCA TCATTTCTTTTGAATACTTCCTCA 1644 1.000 40.4
accD_p2 accD CCTGTATGTTTTCATTTTTGATTGCA ACTTCCTCATTCTTTATTCTTTTCAGT 1629 1.000 40.4
accD_p3 accD CCTGTATGTTTTCATTTTTGATTGCA TCTTTTGAATACTTCCTCATTCT 1639 1.000 40.4
accD_p4 accD TCCTGTATGTTTTCATTTTTGATTGC TCATTTCTTTTGAATACTTCCTCA 1645 1.000 40.4
accD_p5 accD CCTGTATGTTTTCATTTTTGATTGCA TCTTTTCAGTTACTAATCCTCA 1612 1.000 40.4
atpH-atpI_p1 atpH-atpI CAGCAGCAATAACAGAAGCG TCACAAGCGGTATTCAAGCT 1155–1173 1.000 76.7
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC TCACAAGCGGTATTCAAGCT 1162–1180 1.000 76.3
atpH-atpI_p3 atpH-atpI CAATCCCCTCTACAGCTTGC TCACAAGCGGTATTCAAGCT 1233–1251 1.000 75.3
atpH-atpI_p4 atpH-atpI GCAATCCCCTCTACAGCTTG TCACAAGCGGTATTCAAGCT 1234–1252 1.000 75.3
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCT TCACAAGCGGTATTCAAGCT 1185–1203 1.000 74.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTTCTGTTAAGCCCCGATC CCGGATTTGAACTGGGGAAA 1158–1167 1.000 80.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AAAGCCCTTCTGTTAAGCCC CCGGATTTGAACTGGGGAAA 1163–1172 1.000 80.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCTTCTGTTAAGCCCCGATC CTTATCGATCAGGCGACACC 1177–1186 1.000 79.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAAGCCCTTCTGTTAAGCCC CTTATCGATCAGGCGACACC 1182–1191 1.000 78.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCTTCTGTTAAGCCCCGATC AAAAGGATTTGCAGTCCCCC 1140–1149 1.000 78.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Macrotyloma axillare PX659840.1 150989 View on NCBI ↗
Macrotyloma geocarpum PX659841.1 150811 View on NCBI ↗
Macrotyloma uniflorum PX549914.1 151013 View on NCBI ↗