Markers + reference

Flemingia

4 species · Fabaceae · Fabales

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Species 4
Genome length 153–153 kb
Candidate markers 265
Primer pairs 90

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 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 326 0.0191 0.71 37.2 yes View details
trnK-UUU-rbcL LSC 956 0.0098 0.98 58.4 yes View details
trnG-GCC-psbZ LSC 753 0.0103 0.97 51.6 yes View details
trnC-GCA-rpoB LSC 833 0.0072 0.99 46.6 yes View details
trnQ-UUG-rps16 LSC 522 0.0134 0.99 61.4 yes View details
psaJ-rpl33 LSC 508 0.0049 0.99 51.9 yes View details
rpl33-rps18 LSC 248 0.0565 1.00 80.1 yes View details
rps3-rps19 LSC 522 0.0143 0.98 48.5 yes View details
ycf1 IRb 522 0.0019 1.00 37.5 no View details
ccsA SSC 978 0.0048 1.00 37.9 yes View details
rps15-ycf1 SSC 386 0.0299 0.99 69.2 yes View details
ycf1 SSC 5352 0.0057 1.00 42.5 yes View details
ccsA-ndhD SSC 246 0.0247 0.96 66.3 yes View details
trnT-GGU-trnE-UUC LSC 760 0.0057 0.99 63.5 yes View details
ycf3-psaA LSC 797 0.0052 1.00 63.1 yes View details
petN-trnC-GCA LSC 884 0.0038 0.99 62.0 yes View details
rpl20-rps12 LSC 813 0.0070 1.00 55.5 yes View details
rpl2-trnH-GUG IRa 121 0.0179 1.00 55.4 no View details
atpE-trnM-CAU LSC 137 0.0085 0.94 53.4 yes View details
trnS-UGA-psbC LSC 203 0.0057 1.00 52.7 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 90 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 CTGCGATTGAAGCTCCATCT 283–379 1.000 84.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTGCGATTGAAGCTCCATCT 297–393 1.000 84.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTGCGATTGAAGCTCCATCT 296–392 1.000 84.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CTGCGATTGAAGCTCCATCT 298–394 1.000 84.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGTGTAGCTGGTGTATTCGG 713–809 1.000 83.4
trnK-UUU-rbcL_p1 trnK-UUU-rbcL TGGACGAACCAATTGCTTCA AGTCCTGAATTAGCTGCTGC 1115–1116 1.000 82.3
trnK-UUU-rbcL_p2 trnK-UUU-rbcL TGGACGAACCAATTGCTTCA GAGGCTAGCAAATGGAGTCC 1130–1131 1.000 82.2
trnK-UUU-rbcL_p3 trnK-UUU-rbcL CCGCTCTTAAAAGCCGAGTA AGTCCTGAATTAGCTGCTGC 1073–1074 1.000 80.3
trnK-UUU-rbcL_p4 trnK-UUU-rbcL CCGCTCTTAAAAGCCGAGTA GAGGCTAGCAAATGGAGTCC 1088–1089 1.000 80.2
trnK-UUU-rbcL_p5 trnK-UUU-rbcL TAGAGCCGCTCTTAAAAGCC AGTCCTGAATTAGCTGCTGC 1078–1079 1.000 80.1
atpE-trnM-CAU_p1 atpE-trnM-CAU CGAGCTAGGACACGAGTAGA TGGAGGCGGTGATAAATGAC 262–270 1.000 79.9
atpE-trnM-CAU_p2 atpE-trnM-CAU TAGACGAGCTAGGACACGAG TGGAGGCGGTGATAAATGAC 266–274 1.000 79.9
atpE-trnM-CAU_p3 atpE-trnM-CAU CGAGCTAGGACACGAGTAGA TATTGCTTTCATACGGCGGG 220–228 1.000 79.8
atpE-trnM-CAU_p4 atpE-trnM-CAU CGAGCTAGGACACGAGTAGA GGAGGCGGTGATAAATGACC 261–269 1.000 79.3
atpE-trnM-CAU_p5 atpE-trnM-CAU TAGACGAGCTAGGACACGAG GGAGGCGGTGATAAATGACC 265–273 1.000 79.2
ycf3-psaA_p1 ycf3-psaA AGCCCTTACCCCTGGTAATT AATGACCAGGTTTTGCCCAT 958–995 1.000 80.8
ycf3-psaA_p2 ycf3-psaA AGCCCTTACCCCTGGTAATT ATGACCAGGTTTTGCCCATT 957–994 1.000 80.8
ycf3-psaA_p3 ycf3-psaA AGCTATAGCCCTTACCCCTG AATGACCAGGTTTTGCCCAT 964–1001 1.000 80.6
ycf3-psaA_p4 ycf3-psaA AGCTATAGCCCTTACCCCTG ATGACCAGGTTTTGCCCATT 963–1000 1.000 80.6
ycf3-psaA_p5 ycf3-psaA AGCCCTTACCCCTGGTAATT TGCCCATTCCTCGAAAGAAG 945–982 1.000 80.1
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CGAAGGTTGGTCAAGTAACA 876–903 1.000 62.9
trnG-GCC-psbZ_p2 trnG-GCC-psbZ ATAACTAAGTGGGGGCGGAT CGAAGGTTGGTCAAGTAACA 913–940 1.000 62.7
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CGAAGGTTGGTCAAGTAACAA 876–903 1.000 61.1
trnG-GCC-psbZ_p4 trnG-GCC-psbZ ATAACTAAGTGGGGGCGGAT CGAAGGTTGGTCAAGTAACAA 913–940 1.000 60.9
trnG-GCC-psbZ_p5 trnG-GCC-psbZ TAACTAAGTGGGGGCGGATA CGAAGGTTGGTCAAGTAACA 912–939 1.000 60.3
trnS-UGA-psbC_p1 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG ACCTGTTCTTTCCATGACTCC 316–326 1.000 71.4
trnS-UGA-psbC_p2 trnS-UGA-psbC ATAGCCCCGGTCTTGAAAAC ACCTGTTCTTTCCATGACTCC 296–306 1.000 70.8
trnS-UGA-psbC_p3 trnS-UGA-psbC GCTTTTGGAGAGATGGCTGA ACCTGTTCTTTCCATGACTCC 323–333 1.000 70.5
trnS-UGA-psbC_p4 trnS-UGA-psbC AGCTTTTGGAGAGATGGCTG ACCTGTTCTTTCCATGACTCC 324–334 1.000 70.5
trnS-UGA-psbC_p5 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG ATTTATGGCACGCGGGAAG 386–396 1.000 69.5

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
Flemingia macrophylla NC_065865.1 152937 View on NCBI ↗
Flemingia philippinensis PV464028.1 153024 View on NCBI ↗
Flemingia prostrata NC_065863.1 153033 View on NCBI ↗
Flemingia stricta NC_086853.1 152940 View on NCBI ↗