Markers + reference

Trimezia

2 species · Iridaceae · Asparagales

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Species 2
Genome length 151–153 kb
Candidate markers 270
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 7 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-trnT-GGU LSC 582 0.0378 0.95 75.2 yes View details
trnT-GGU-psbD LSC 1105 0.0386 0.94 76.0 yes View details
trnT-UGU-trnL-UAA LSC 791 0.0417 0.91 72.9 yes View details
accD-psaI LSC 615 0.0422 0.77 67.6 yes View details
petA-psbJ LSC 1130 0.0484 0.93 76.2 yes View details
clpP1 LSC 2052 0.0294 0.98 61.6 yes View details
clpP1-psbB LSC 415 0.0594 0.97 73.7 yes View details
ycf1 IRb 963 0.0187 1.00 54.5 no View details
ndhF SSC 2229 0.0211 1.00 54.4 yes View details
ndhF-rpl32 SSC 880 0.0620 0.92 77.7 yes View details
rpl32-trnL-UAG SSC 965 0.0431 0.96 76.2 yes View details
ycf1 SSC 5445 0.0295 0.99 56.3 yes View details
rpl16-rps3 LSC 152 0.0567 0.93 76.6 yes View details
psbC-trnS-UGA LSC 134 0.0720 0.93 76.1 yes View details
psaB-psaA LSC 25 0.0400 1.00 75.5 yes View details
psbI-trnS-GCU LSC 147 0.0752 0.90 74.5 yes View details
psaC-ndhE SSC 363 0.0435 0.89 73.0 yes View details
trnK-UUU-rps16 LSC 679 0.0387 0.95 72.5 yes View details
psbK-psbI LSC 404 0.0340 0.95 72.5 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA TCAAGAAAGAACTTCGAGTT 717–744 1.000 46.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TCAAGAAAGAACTTCGAGTT 719–746 1.000 46.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TTCAAGAAAGAACTTCGAGT 720–747 1.000 46.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TTCAAGAAAGAACTTCGAGTT 720–747 1.000 46.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TTTCAAGAAAGAACTTCGAGT 721–748 1.000 46.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGTCCCGGATCGTTAGA 521–526 1.000 85.2
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGTCCCGGATCGTTAGATA 519–524 1.000 83.4
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGTCCCGGATCGTTAGAT 520–525 1.000 83.4
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTACGTCCCGGATCGTTAGA 518–523 1.000 83.2
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTACGTCCCGGATCGTTAGA 519–524 1.000 83.2
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GGGTTCGAATCCCTCTCTCT 180–194 1.000 79.1
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTCGAATCCCTCTCTCTCCG 177–191 1.000 78.3
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA GGGTTCGAATCCCTCTCTCT 180–194 1.000 76.7
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TTCGAATCCCTCTCTCTCCG 177–191 1.000 76.0
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTTCGAATCCCTCTCTCTCC 178–192 1.000 71.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 702–723 1.000 84.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TACCGCTGAGTTAAAAGGGC 667–688 1.000 83.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 643–664 1.000 83.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 664–685 1.000 83.5
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 699–720 1.000 82.9
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1209–1269 1.000 83.8
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA CCCTCCGTAACCAATCATCC 1193–1253 1.000 83.7
trnT-GGU-psbD_p3 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA CAAAAACGAAACGGTCCCTC 1208–1268 1.000 82.6
trnT-GGU-psbD_p4 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA ACAAAAACGAAACGGTCCCT 1172–1232 1.000 82.4
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA CCCTCCGTAACCAATCATCC 1156–1216 1.000 82.4
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GAGAGATGGCTGAGTGGTTG 247–256 1.000 84.3
psbC-trnS-UGA_p2 psbC-trnS-UGA CTGTTCTTTCCATGACCCCC GAGAGATGGCTGAGTGGTTG 246–255 1.000 84.3
psbC-trnS-UGA_p3 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGCTGAGTGGTTGATAGCTC 240–249 1.000 84.2
psbC-trnS-UGA_p4 psbC-trnS-UGA CTGTTCTTTCCATGACCCCC GGCTGAGTGGTTGATAGCTC 239–248 1.000 84.2
psbC-trnS-UGA_p5 psbC-trnS-UGA ATCGCGATTTGGAACCTGTT GAGAGATGGCTGAGTGGTTG 261–270 1.000 83.8

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
Trimezia candida NC_072573.1 151102 View on NCBI ↗
Trimezia steyermarkii NC_072662.1 152777 View on NCBI ↗