Markers + reference

Kummerowia

2 species · Fabaceae · Fabales

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Species 2
Genome length 147–148 kb
Candidate markers 252
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 252 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl2 LSC 825 NA 0.00 46.2 yes View details
trnH-GUG-psbA LSC 282 0.0554 0.96 85.4 yes View details
trnK-UUU-rbcL LSC 846 0.0221 0.96 61.3 yes View details
trnL-UAA-trnT-UGU LSC 920 0.0197 0.94 65.7 yes View details
psbZ-trnS-UGA LSC 329 0.0214 0.99 61.7 yes View details
petN-trnC-GCA LSC 481 0.0275 0.98 66.7 yes View details
trnG-UCC-trnS-GCU LSC 386 0.0430 0.96 72.4 yes View details
trnS-GCU-psbI LSC 188 0.0291 0.91 60.2 yes View details
trnQ-UUG-psaI LSC 3849 0.0215 0.95 64.2 yes View details
clpP LSC 2064 0.0147 0.99 56.3 yes View details
rps3-rps19 LSC 461 0.0510 0.98 72.7 yes View details
rpl2 LSC 825 0.0036 1.00 51.8 no View details
ndhF-rpl32 SSC 589 0.0375 1.00 68.4 yes View details
ycf1 SSC 5313 0.0191 0.99 52.8 yes View details
trnS-UGA-psbC LSC 227 0.0705 1.00 78.0 yes View details
psbT-psbN LSC 56 0.0536 1.00 77.0 yes View details
ndhD-psaC SSC 128 0.0635 0.98 76.9 yes View details
rps2-atpI LSC 324 0.0332 0.93 76.1 yes View details
trnL-UAG-ccsA SSC 88 0.0568 1.00 72.5 yes View details
ycf3-psaA LSC 677 0.0262 0.96 71.4 yes View details
trnW-CCA-trnP-UGG LSC 194 0.0278 0.93 71.4 yes View details
ndhE-ndhG SSC 219 0.0550 1.00 71.3 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
rpl2_p1 rpl2 CGCTTCAACCGGGTTATTCT ACGTGTCACAGTTAATTACTCCT 956 1.000 54.2
rpl2_p2 rpl2 ATCATTACGCTTCAACCGGG ACGTGTCACAGTTAATTACTCCT 963 1.000 53.6
rpl2_p3 rpl2 ACGCTTCAACCGGGTTATTC ACGTGTCACAGTTAATTACTCCT 957 1.000 51.9
rpl2_p4 rpl2 CGCTTCAACCGGGTTATTCT ACGTGTCACAGTTAATTACTCC 956 1.000 51.0
rpl2_p5 rpl2 ATCATTACGCTTCAACCGGG ACGTGTCACAGTTAATTACTCC 963 1.000 50.4
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCCTCTAGATCTAGCTGCGA 346–356 1.000 83.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TCCCTCTAGATCTAGCTGCG 347–357 1.000 83.3
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCCTCTAGATCTAGCTGCGA 347–357 1.000 83.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TCCCTCTAGATCTAGCTGCG 348–358 1.000 83.1
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGAGCTAACCTTGGTATGG 397–407 1.000 82.2
trnK-UUU-rbcL_p1 trnK-UUU-rbcL AGAGTCGCTCTTAAAAGCCG GAGCCGTATTTGCCAGAGAA 1555–1564 1.000 82.7
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG GAGCCGTATTTGCCAGAGAA 1553–1562 1.000 82.7
trnK-UUU-rbcL_p3 trnK-UUU-rbcL GAGTCGCTCTTAAAAGCCGA GAGCCGTATTTGCCAGAGAA 1554–1563 1.000 82.6
trnK-UUU-rbcL_p4 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG AAGAGCCGTATTTGCCAGAG 1555–1564 1.000 82.6
trnK-UUU-rbcL_p5 trnK-UUU-rbcL AAACCTATCAACGGACTCGC GAGCCGTATTTGCCAGAGAA 2140–2149 1.000 82.1
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT GCGATGCTCTAACCTCTGAG 918–976 1.000 83.2
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT ATCGAGAAAAGCCGGCTATC 970–1028 1.000 82.9
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT GGATTCGAACCGATGACCAT 950–1008 1.000 82.3
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT AAATCGAGAAAAGCCGGCTA 972–1030 1.000 81.0
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT CTAACCTCTGAGCTAAGCGG 910–968 1.000 80.2
ycf3-psaA_p1 ycf3-psaA TTGGTTGAAGATCACTGGGC TTTCACTTCTGGTTCCGGTG 741 1.000 83.9
ycf3-psaA_p2 ycf3-psaA TTGGTTGAAGATCACTGGGC AATGACCTGGTTTTGCCCAT 802 1.000 83.6
ycf3-psaA_p3 ycf3-psaA TTGGTTGAAGATCACTGGGC ATGACCTGGTTTTGCCCATT 801 1.000 83.6
ycf3-psaA_p4 ycf3-psaA TTGGTTGAAGATCACTGGGC TGGTTTTGCCCATTCCTCAA 795 1.000 83.2
ycf3-psaA_p5 ycf3-psaA TGGTTTAATCAAGCCGCTGA ATGACCTGGTTTTGCCCATT 875 1.000 82.4
psbZ-trnS-UGA_p1 psbZ-trnS-UGA ACTTGACCAACCTTCAGGAG CAACCACTCAGCCATCTCTC 455–485 1.000 73.8
psbZ-trnS-UGA_p2 psbZ-trnS-UGA ACTTGACCAACCTTCAGGAG TTCGCCGAGAAAAAGGAGAG 540–570 1.000 73.1
psbZ-trnS-UGA_p3 psbZ-trnS-UGA ACTTGACCAACCTTCAGGAG GTTTTCAAGACCGGGGCTAT 475–505 1.000 73.0
psbZ-trnS-UGA_p4 psbZ-trnS-UGA GGAGAAGCAAATACAACGGG CAACCACTCAGCCATCTCTC 439–469 1.000 71.8
psbZ-trnS-UGA_p5 psbZ-trnS-UGA CTTGACCAACCTTCAGGAGA CAACCACTCAGCCATCTCTC 454–484 1.000 71.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Kummerowia stipulacea PX648295.1 146837 View on NCBI ↗
Kummerowia striata NC_044114.1 148450 View on NCBI ↗