Markers + reference

Platylobium

6 species · Fabaceae · Fabales

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Species 6
Genome length 151–151 kb
Candidate markers 261
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhJ LSC 477 0.0099 1.00 38.0 yes View details
trnL-UAA-trnT-UGU LSC 842 0.0165 1.00 63.4 yes View details
trnS-UGA-psbC LSC 219 0.0429 1.00 64.2 yes View details
trnC-GCA-rpoB LSC 771 0.0136 1.00 55.5 yes View details
trnG-GCC-trnS-GCU LSC 584 0.0176 1.00 53.5 yes View details
psbI-psbK LSC 488 0.0217 1.00 58.8 yes View details
psbK-rps16 LSC 1013 0.0137 1.00 58.0 yes View details
rps16-accD LSC 454 0.0148 1.00 45.7 yes View details
trnP-UGG-psaJ LSC 672 0.0101 0.97 57.7 yes View details
psaJ-rpl33 LSC 547 0.0194 1.00 54.3 yes View details
clpP LSC 1946 0.0120 0.98 56.5 yes View details
rpl32-trnL-UAG SSC 585 0.0170 1.00 40.9 yes View details
rps15-ycf1 SSC 347 0.0148 1.00 48.4 yes View details
trnW-CCA-trnP-UGG LSC 169 0.0398 0.93 66.4 yes View details
trnG-UCC-psbZ LSC 723 0.0118 0.95 64.1 yes View details
ycf3-psaA LSC 887 0.0109 0.96 61.0 yes View details
ndhF-rpl32 SSC 589 0.0101 1.00 61.0 yes View details
trnR-UCU-trnG-GCC LSC 201 0.0210 0.97 59.5 yes View details
atpB LSC 1497 0.0048 1.00 58.9 yes View details
rps3-rps19 LSC 573 0.0091 0.99 58.9 yes View details
ndhJ-trnF-GAA LSC 651 0.0135 1.00 58.1 yes View details
ndhG-ndhI SSC 452 0.0167 0.98 57.9 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpB_p1 atpB CCGATCAACTAACTTTGTTAGGG GGCAATAGGCGCATGATTTT 1698–1699 1.000 46.3
atpB_p2 atpB CCGATCAACTAACTTTGTTAGGG TGGCAATAGGCGCATGATTT 1699–1700 1.000 45.6
atpB_p3 atpB CCGATCAACTAACTTTGTTAGGG TGGCAATAGGCGCATGATT 1699–1700 1.000 41.5
atpB_p4 atpB ACCGATCAACTAACTTTGTTAGG GGCAATAGGCGCATGATTTT 1699–1700 1.000 41.1
atpB_p5 atpB CCGATCAACTAACTTTGTTAGGG GCAATAGGCGCATGATTTTGT 1697–1698 1.000 40.9
ndhJ_p1 ndhJ AGTATCCTCATCCTCCCACG CCTCGTGTCACCAGTTCAAA 1298–1308 1.000 82.5
ndhJ_p2 ndhJ GTATCCTCATCCTCCCACGA CCTCGTGTCACCAGTTCAAA 1297–1307 1.000 82.5
ndhJ_p3 ndhJ AGTATCCTCATCCTCCCACG AGAATGGTCGGGATAGCTCA 1343–1353 1.000 82.1
ndhJ_p4 ndhJ GTATCCTCATCCTCCCACGA AGAATGGTCGGGATAGCTCA 1342–1352 1.000 82.1
ndhJ_p5 ndhJ TATAGTACAGTTCGGGGCGT CCTCGTGTCACCAGTTCAAA 1594–1609 1.000 82.0
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA GGCTGGCCTTTACGTAAAGA CCTCGTGTCACCAGTTCAAA 738–748 1.000 82.3
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA AGGCTGGCCTTTACGTAAAG CCTCGTGTCACCAGTTCAAA 739–749 1.000 82.2
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA GGCTGGCCTTTACGTAAAGA AGAATGGTCGGGATAGCTCA 783–793 1.000 81.8
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA AGGCTGGCCTTTACGTAAAG AGAATGGTCGGGATAGCTCA 784–794 1.000 81.8
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA CCGAAAGTTGGATAGGCTGG CCTCGTGTCACCAGTTCAAA 752–762 1.000 80.4
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 587–900 1.000 83.1
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU CCGTACCAAGGCTCAATTCA GCGATGCTCTAACCTCTGAG 617–930 1.000 82.6
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU GTTTCCGTACCAAGGCTCAA GCGATGCTCTAACCTCTGAG 621–934 1.000 82.6
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 586–932 1.000 82.1
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU AAGTTTCCGTACCAAGGCTC GCGATGCTCTAACCTCTGAG 623–936 1.000 82.0
ycf3-psaA_p1 ycf3-psaA AAGATCACCGAGCGTTTTGA TTTGACTTCTGGTTCCGGTG 896–944 1.000 84.0
ycf3-psaA_p2 ycf3-psaA AGATCACCGAGCGTTTTGAA TTTGACTTCTGGTTCCGGTG 895–943 1.000 84.0
ycf3-psaA_p3 ycf3-psaA TGAAGATCACCGAGCGTTTT TTTGACTTCTGGTTCCGGTG 898–946 1.000 84.0
ycf3-psaA_p4 ycf3-psaA TTGAAGATCACCGAGCGTTT TTTGACTTCTGGTTCCGGTG 899–947 1.000 84.0
ycf3-psaA_p5 ycf3-psaA TTGGTTGAAGATCACCGAGC TTTGACTTCTGGTTCCGGTG 903–951 1.000 83.8
trnG-UCC-psbZ_p1 trnG-UCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTGATGGTTGGTCGAGT 350–874 1.000 78.6
trnG-UCC-psbZ_p2 trnG-UCC-psbZ CGTCTTCTCCTTGGCAAAGA TGCTTCTTCTGATGGTTGGT 350–879 1.000 77.0
trnG-UCC-psbZ_p3 trnG-UCC-psbZ CGTCTTCTCCTTGGCAAAGA TCTTCTGATGGTTGGTCGAG 350–875 1.000 76.3
trnG-UCC-psbZ_p4 trnG-UCC-psbZ CGTCTTCTCCTTGGCAAAGA TGCTTCTTCTGATGGTTGGTC 351–879 1.000 74.9
trnG-UCC-psbZ_p5 trnG-UCC-psbZ CGTCTTCTCCTTGGCAAAGA TTGCTTCTTCTGATGGTTGGT 351–880 1.000 74.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Platylobium infecundum NC_088720.1 151477 View on NCBI ↗
Platylobium montanum NC_088725.1 151314 View on NCBI ↗
Platylobium obtusangulum x Platylobium triangulare NC_088721.1 150674 View on NCBI ↗
Platylobium parviflorum NC_088723.1 151132 View on NCBI ↗
Platylobium reflexum NC_088724.1 151305 View on NCBI ↗
Platylobium triangulare NC_088719.1 150887 View on NCBI ↗