Markers + reference

Pueraria

8 species · Fabaceae · Fabales

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Species 8
Genome length 153–155 kb
Candidate markers 265
Primer pairs 95

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL LSC 1017 0.0074 0.98 57.7 yes View details
rpoC2 LSC 4185 0.0040 1.00 35.5 yes View details
atpI-atpH LSC 1103 0.0076 0.99 39.2 yes View details
trnR-UCU-trnG-UCC LSC 219 0.0305 1.00 62.8 yes View details
psbK-trnQ-UUG LSC 475 0.0088 0.99 50.3 yes View details
trnQ-UUG-rps16 LSC 503 0.0120 0.96 51.4 yes View details
psbE-petL LSC 944 0.0077 1.00 40.8 yes View details
rpl16 LSC 1630 0.0048 0.96 41.3 yes View details
rps3-rps19 LSC 355 0.0200 1.00 46.1 yes View details
ycf1 IRb 468 0.0009 1.00 23.4 no View details
ycf1 SSC 4746 0.0060 1.00 33.8 yes View details
trnH-GUG-psbA LSC 225 0.0190 1.00 55.3 yes View details
psbI-psbK LSC 460 0.0105 1.00 55.1 yes View details
ycf3-psaA LSC 815 0.0054 0.98 54.8 yes View details
trnC-GCA-rpoB LSC 1000 0.0041 0.99 53.8 yes View details
trnT-GGU-trnE-UUC LSC 845 0.0061 0.97 52.4 yes View details
psbM-petN LSC 735 0.0051 0.96 52.1 yes View details
rps14-trnP-GGG LSC 190 0.0190 0.94 52.0 yes View details
ndhF-rpl32 SSC 485 0.0079 1.00 48.2 yes View details
rps2-atpI LSC 240 0.0092 1.00 48.1 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 95 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 CCCTCTAGATCTAGCTGCGA 288–308 1.000 81.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCCCTCTAGATCTAGCTGCG 289–309 1.000 81.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCCTCTAGATCTAGCTGCGA 302–322 1.000 81.2
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCCCTCTAGATCTAGCTGCG 303–323 1.000 81.2
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCCTCTAGATCTAGCTGCGA 301–321 1.000 81.2
trnK-UUU-rbcL_p1 trnK-UUU-rbcL AGAGTCGCTCTTAAAAGCCG AGTCCTGAATTAGCTGCTGC 1125–1139 1.000 83.1
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG AGTCCTGAATTAGCTGCTGC 1123–1137 1.000 83.1
trnK-UUU-rbcL_p3 trnK-UUU-rbcL AGAGTCGCTCTTAAAAGCCG GAGGCTAGCAAATGGAGTCC 1140–1154 1.000 83.0
trnK-UUU-rbcL_p4 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG GAGGCTAGCAAATGGAGTCC 1138–1152 1.000 83.0
trnK-UUU-rbcL_p5 trnK-UUU-rbcL GAGTCGCTCTTAAAAGCCGA AGTCCTGAATTAGCTGCTGC 1124–1138 1.000 83.0
ycf3-psaA_p1 ycf3-psaA AAGTTGCGGAGTCTTGGTTT TTTCACTTCTGGTTCCGGTG 960–969 1.000 81.3
ycf3-psaA_p2 ycf3-psaA AAGTTGCGGAGTCTTGGTTT AATGACCAGGTTTTGCCCAT 1021–1030 1.000 81.2
ycf3-psaA_p3 ycf3-psaA AAGTTGCGGAGTCTTGGTTT ATGACCAGGTTTTGCCCATT 1020–1029 1.000 81.2
ycf3-psaA_p4 ycf3-psaA TTGGTTGAAGATCACAGGGC AATGACCAGGTTTTGCCCAT 933–942 1.000 81.1
ycf3-psaA_p5 ycf3-psaA TTGGTTGAAGATCACAGGGC ATGACCAGGTTTTGCCCATT 932–941 1.000 81.1
rps14-trnP-GGG_p1 rps14-trnP-GGG CATGCATGTTTATTGCCCGG AAGGTTATGAGCCTTGCGAG 263–275 1.000 84.6
rps14-trnP-GGG_p2 rps14-trnP-GGG CATGCATGTTTATTGCCCGG TTTGAACCCGTGACCTCAAG 280–292 1.000 84.2
rps14-trnP-GGG_p3 rps14-trnP-GGG CATGCATGTTTATTGCCCGG GATTTGAACCCGTGACCTCA 282–294 1.000 83.0
rps14-trnP-GGG_p4 rps14-trnP-GGG GACCGCGAGCTAATTATCGA AAGGTTATGAGCCTTGCGAG 322–334 1.000 82.1
rps14-trnP-GGG_p5 rps14-trnP-GGG ACCGCGAGCTAATTATCGAG AAGGTTATGAGCCTTGCGAG 321–333 1.000 82.0
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT AACTTCCTTTCGTAGCACCC 963–993 1.000 82.0
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC AACTTCCTTTCGTAGCACCC 942–972 1.000 81.6
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT GCTGCCTCCTTGAAAGAGAG 918–948 1.000 81.5
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC TGGCGTTACTCTACCACTGA AACTTCCTTTCGTAGCACCC 939–969 1.000 81.4
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TGTCCTGAACCACTAGACGA 897–927 1.000 81.4
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTTATTCT TCTTGCTTGGGCTGCTTTAA 872–890 1.000 53.5
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTTATTCT AGTAAGTCTTGCTTGGGCTG 878–896 1.000 52.0
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTTATTCTAGT TCTTGCTTGGGCTGCTTTAA 872–890 1.000 51.2
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTTATTCT CCCTCGTAGTATGGGGAAGA 828–846 1.000 50.7
psbM-petN_p5 psbM-petN ACTGCACTGTTTATTCTAGTTCCT TCTTGCTTGGGCTGCTTTAA 868–886 1.000 50.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Pueraria alopecuroides NC_084329.1 154753 View on NCBI ↗
Pueraria candollei var. mirifica OM135503.1 153373 View on NCBI ↗
Pueraria edulis NC_065692.1 153471 View on NCBI ↗
Pueraria montana NC_060608.1 153442 View on NCBI ↗
Pueraria montana var. culaishanensis (nom. ined.) OR187861.1 153380 View on NCBI ↗
Pueraria montana var. lobata PX125817.1 153397 View on NCBI ↗
Pueraria montana var. montana MZ145063.1 153442 View on NCBI ↗
Pueraria montana var. thomsonii NC_060607.1 153673 View on NCBI ↗