Markers + reference

Zornia

2 species · Fabaceae · Fabales

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Species 2
Genome length 154–155 kb
Candidate markers 265
Primer pairs 115

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 10 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 396 0.0799 0.98 80.2 yes View details
trnL-UAA-trnT-UGU LSC 1018 0.0520 0.89 82.3 yes View details
ycf3-psaA LSC 954 0.0479 0.81 73.2 yes View details
trnG-GCC-psbZ LSC 637 0.0520 0.88 81.2 yes View details
trnC-GCA-rpoB LSC 1156 0.0501 0.83 75.1 yes View details
atpI-atpH LSC 1369 0.0427 0.96 73.3 yes View details
atpA-trnR-UCU LSC 277 0.0620 0.93 77.8 yes View details
psbK-trnQ-UUG LSC 817 0.0626 0.72 73.8 yes View details
trnQ-UUG-rps16 LSC 664 0.0518 0.84 81.1 yes View details
trnP-UGG-psaJ LSC 733 0.0609 0.92 83.0 yes View details
rpl32-trnL-UAG SSC 786 0.0679 0.84 75.5 yes View details
ccsA-ndhD SSC 394 0.1000 0.89 76.6 yes View details
atpH-atpF LSC 481 0.0491 0.97 87.0 yes View details
trnT-GGU-trnE-UUC LSC 671 0.0408 0.95 82.7 yes View details
psbA-trnK-UUU LSC 328 0.0779 0.98 80.1 yes View details
ndhE-ndhG SSC 307 0.0490 0.80 80.1 yes View details
trnS-UGA-psbC LSC 194 0.0481 0.96 78.7 yes View details
atpE-trnM-CAU LSC 155 0.1192 0.97 78.5 yes View details
trnfM-CAU-trnG-GCC LSC 132 0.0579 0.92 77.1 yes View details
psbM-petN LSC 856 0.0437 0.99 77.0 yes View details
ndhG-ndhI SSC 332 0.0387 0.86 76.9 yes View details
psbI-psbK LSC 507 0.0354 0.95 75.2 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 115 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 TTCCCTCTAGACCTAGCTGC 465–466 1.000 85.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 479–480 1.000 84.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 478–479 1.000 84.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 480–481 1.000 84.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGAGCTAACCTTGGTATGG 514–515 1.000 83.1
psbA-trnK-UUU_p1 psbA-trnK-UUU CAATTACAGAAGCGACCCCA CTAGTTCCGGGTTCGAATCC 418–516 1.000 82.9
psbA-trnK-UUU_p2 psbA-trnK-UUU CAATTACAGAAGCGACCCCA CGGCTTGGGGAGAGATTTTT 490–588 1.000 82.6
psbA-trnK-UUU_p3 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA CTAGTTCCGGGTTCGAATCC 440–538 1.000 80.8
psbA-trnK-UUU_p4 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA CGGCTTGGGGAGAGATTTTT 512–610 1.000 80.6
psbA-trnK-UUU_p5 psbA-trnK-UUU TCCAATTACAGAAGCGACCC CGGCTTGGGGAGAGATTTTT 492–590 1.000 80.3
trnK-UUU_p1 trnK-UUU AGATTCATACGAATTTCGCT AGACAACGGGATGGTCTATCT 3000 0.500 20.0
trnK-UUU_p2 trnK-UUU AGATTCATACGAATTTCGCTT AGACAACGGGATGGTCTATCT 3000 0.500 20.0
trnK-UUU_p3 trnK-UUU AGATTCATACGAATTTCGCTTT AGACAACGGGATGGTCTATCT 3000 0.500 20.0
trnK-UUU_p4 trnK-UUU ACGAATTTCGCTTTTTATTTTACCT ACTCTAGACAACGGGATGGT 2997 0.500 20.0
trnK-UUU_p5 trnK-UUU AGATTCATACGAATTTCGCTTTT AGACAACGGGATGGTCTATCT 3000 0.500 20.0
atpE-trnM-CAU_p1 atpE-trnM-CAU CAGACGAGCTAGAACACGAG GAGTGTTGCTTTCATACGGC 251–253 1.000 81.4
atpE-trnM-CAU_p2 atpE-trnM-CAU AGACGAGCTAGAACACGAGT GAGTGTTGCTTTCATACGGC 250–252 1.000 81.3
atpE-trnM-CAU_p3 atpE-trnM-CAU TCAGACGAGCTAGAACACGA GAGTGTTGCTTTCATACGGC 252–254 1.000 81.2
atpE-trnM-CAU_p4 atpE-trnM-CAU CAGACGAGCTAGAACACGAG GCGGGAGTCATTGGTTCAAA 233–235 1.000 80.1
atpE-trnM-CAU_p5 atpE-trnM-CAU AGACGAGCTAGAACACGAGT GCGGGAGTCATTGGTTCAAA 232–234 1.000 80.0
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 979–1068 1.000 86.6
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 987–1076 1.000 86.0
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GGAATCGAACCGATGACCAT 1011–1100 1.000 85.6
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 1019–1108 1.000 85.1
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 993–1082 1.000 84.6
ycf3-psaA_p1 ycf3-psaA TTGGTTGAAGATCACAGGGC CTTCTGGTTCCGGCGAAC 854–1013 1.000 66.9
ycf3-psaA_p2 ycf3-psaA AAGCTATAGCCCTTACCCCC CTTCTGGTTCCGGCGAAC 897–1056 1.000 65.5
ycf3-psaA_p3 ycf3-psaA AAGATCACAGGGCGTTTTGA CTTCTGGTTCCGGCGAAC 847–1006 1.000 65.5
ycf3-psaA_p4 ycf3-psaA AGATCACAGGGCGTTTTGAA CTTCTGGTTCCGGCGAAC 846–1005 1.000 65.5
ycf3-psaA_p5 ycf3-psaA TGAAGATCACAGGGCGTTTT CTTCTGGTTCCGGCGAAC 849–1008 1.000 65.5

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
Zornia diphylla NC_047401.1 155497 View on NCBI ↗
Zornia myriadena MW628944.1 153936 View on NCBI ↗