Markers + reference

Mimosa

4 species · Fabaceae · Fabales

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Species 4
Genome length 163–167 kb
Candidate markers 252
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 252 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhC-trnV-UAC LSC 1314 0.1100 0.71 78.1 yes View details
accD-psaI LSC 782 0.1505 0.58 76.3 yes View details
petA-psbJ LSC 1359 0.0806 0.94 93.8 yes View details
rpl33-rps18 LSC 533 0.1526 0.66 76.9 yes View details
rps8-rpl14 LSC 702 0.1478 0.46 73.0 yes View details
rps3-rps19 LSC 865 0.1802 0.69 76.9 yes View details
ccsA-ndhD SSC 809 0.1363 0.73 76.7 yes View details
ndhA SSC 2657 0.0421 0.95 74.0 yes View details
trnF-GAA-ndhJ LSC 753 0.0503 0.94 84.2 yes View details
rbcL-accD LSC 1067 0.0762 0.91 83.6 yes View details
trnP-UGG-psaJ LSC 435 0.0651 0.94 83.2 yes View details
clpP LSC 2040 0.0563 0.95 82.8 yes View details
trnL-UAA-trnF-GAA LSC 434 0.0524 0.94 81.9 yes View details
rpl32-trnL-UAG SSC 458 0.0744 0.96 81.5 yes View details
ndhF-rpl32 SSC 992 0.0687 0.82 80.3 yes View details
rpl36-rps8 LSC 495 0.0688 0.94 80.2 yes View details
rps15-ycf1 SSC 399 0.0775 0.96 79.7 yes View details
rps11-rpl36 LSC 153 0.0556 0.99 79.0 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
trnL-UAA-trnF-GAA_p1 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TCTACCAGCTGAGCTATCCC 460–488 1.000 87.3
trnL-UAA-trnF-GAA_p2 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TCAGTCCTCTGCTCTACCAG 472–500 1.000 86.1
trnL-UAA-trnF-GAA_p3 trnL-UAA-trnF-GAA TTCAAGTCCCTCTATCCCCA TCTACCAGCTGAGCTATCCC 449–477 1.000 83.6
trnL-UAA-trnF-GAA_p4 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TTCAGTCCTCTGCTCTACCA 473–501 1.000 82.3
trnL-UAA-trnF-GAA_p5 trnL-UAA-trnF-GAA TTCAAGTCCCTCTATCCCCA TCAGTCCTCTGCTCTACCAG 461–489 1.000 82.3
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ TTCAAATCTGGTTCCTGGCA GTTGGATAGGATGGCCCTTG 818–844 1.000 85.1
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ TTCAAATCTGGTTCCTGGCA AGTTGGATAGGATGGCCCTT 819–845 1.000 84.5
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ TTCAAATCTGGTTCCTGGCA ATGGCCCTTGCGTAAAGATT 808–834 1.000 84.1
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ TTCAAATCTGGTTCCTGGCA GATGGCCCTTGCGTAAAGAT 809–835 1.000 82.7
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ TTCAAATCTGGTTCCTGGCA ATGCCCGAAAGTTGGATAGG 828–854 1.000 82.3
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TGCCAAAATAGGAATAAGACTCGA AGAAGGTCTACGGTTCGAGT 1134–1419 1.000 58.3
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TGCCAAAATAGGAATAAGACTCG AGAAGGTCTACGGTTCGAGT 1134–1419 1.000 55.8
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TGCCAAAATAGGAATAAGACTCGA GAAGGTCTACGGTTCGAGTC 1133–1418 1.000 55.5
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TGCCAAAATAGGAATAAGACTCGA GTTCGAGTCCGTATAGCCCT 1122–1407 1.000 54.4
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GGGGCTAAAATTCCAGAAAT AGAAGGTCTACGGTTCGAGT 1160–1445 1.000 54.0
rbcL-accD_p1 rbcL-accD GAGCTGTATTTGCCCGAGAA TTTGGTCGTCACTTCCACTG 1859 0.250 49.4
rbcL-accD_p2 rbcL-accD AAGAGCTGTATTTGCCCGAG TTTGGTCGTCACTTCCACTG 1861 0.250 49.3
rbcL-accD_p3 rbcL-accD AGTCCTGAATTAGCTGCTGC TTTGGTCGTCACTTCCACTG 1263 0.250 49.3
rbcL-accD_p4 rbcL-accD GAGGCTAGCAAATGGAGTCC TTTGGTCGTCACTTCCACTG 1278 0.250 49.3
rbcL-accD_p5 rbcL-accD CGCTGGTACCGTAGTAGGTA TTTGGTCGTCACTTCCACTG 1636 0.250 49.2
accD-psaI_p1 accD-psaI GCTCCATGCTTTCTTTCCTT AGAGGGTAAGTTGCTGAGAGT 529–843 1.000 69.5
accD-psaI_p2 accD-psaI GCTCCATGCTTTCTTTCCTT GGGTAAGTTGCTGAGAGTTGT 526–840 1.000 69.3
accD-psaI_p3 accD-psaI GCTCCATGCTTTCTTTCCTTT AGAGGGTAAGTTGCTGAGAGT 529–843 1.000 67.6
accD-psaI_p4 accD-psaI GCTCCATGCTTTCTTTCCTTT GGGTAAGTTGCTGAGAGTTGT 526–840 1.000 67.4
accD-psaI_p5 accD-psaI GCTCCATGCTTTCTTTCCTT AGGGTAAGTTGCTGAGAGTTG 527–841 1.000 67.1
petA-psbJ_p1 petA-psbJ GTCTCTTGTTCTTCGTGGCA ATTCCGGATTGGGTTCATCC 1458–1579 1.000 88.0
petA-psbJ_p2 petA-psbJ CGTGTCCAAGGTCTCTTGTT ATTCCGGATTGGGTTCATCC 1468–1589 1.000 87.2
petA-psbJ_p3 petA-psbJ TGTTCTTCGTGGCATCTGTT ATTCCGGATTGGGTTCATCC 1452–1573 1.000 87.0
petA-psbJ_p4 petA-psbJ TTGTTCTTCGTGGCATCTGT ATTCCGGATTGGGTTCATCC 1453–1574 1.000 87.0
petA-psbJ_p5 petA-psbJ CGTTACGTGTCCAAGGTCTC ATTCCGGATTGGGTTCATCC 1473–1594 1.000 86.6

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
Mimosa bimucronata NC_061740.1 167340 View on NCBI ↗
Mimosa diplotricha var. inermis OM585629.1 164445 View on NCBI ↗
Mimosa pigra NC_061906.1 165996 View on NCBI ↗
Mimosa pudica NC_042921.1 163237 View on NCBI ↗