Markers + reference

Trapa

15 species · Lythraceae · Myrtales

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Species 15
Genome length 155–156 kb
Candidate markers 267
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 853 0.0011 1.00 42.2 yes View details
psbK-psbI LSC 394 0.0111 1.00 55.0 yes View details
atpF LSC 1321 0.0004 1.00 30.0 yes View details
atpH-atpI LSC 1094 0.0008 1.00 44.7 yes View details
psaA-ycf3 LSC 705 0.0012 1.00 42.5 yes View details
trnF-GAA-ndhJ LSC 848 0.0011 1.00 40.8 yes View details
trnP-UGG-psaJ LSC 487 0.0014 1.00 41.5 yes View details
petD LSC 1225 0.0000 1.00 40.0 yes View details
ndhG-ndhI SSC 411 0.0020 1.00 37.6 yes View details
atpA-atpF LSC 69 0.0156 0.99 53.8 yes View details
trnT-UGU-trnL-UAA LSC 1094 0.0000 1.00 47.4 yes View details
accD-psaI LSC 719 0.0002 1.00 43.4 yes View details
clpP LSC 2020 0.0004 1.00 43.2 yes View details
rpoA LSC 1023 0.0007 1.00 43.2 yes View details
trnC-GCA-petN LSC 877 0.0002 1.00 42.9 yes View details
rpl2-trnH-GUG IRa 178 0.0000 1.00 42.0 no View details
cemA LSC 690 0.0004 1.00 41.8 yes View details
atpI LSC 744 0.0002 1.00 41.5 yes View details
trnE-UUC-trnT-GGU LSC 632 0.0002 1.00 41.5 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGGGAGCTGGGTTACAAAAG TCCGATTGTTGTATCCACACA 2677 1.000 64.3
trnK-UUU_p2 trnK-UUU TGGGAGCTGGGTTACAAAAG TGATTGATTGTGTCGTGCAA 2720 1.000 64.0
trnK-UUU_p3 trnK-UUU TGGGAGCTGGGTTACAAAAG TTGATTGATTGTGTCGTGCA 2721 1.000 64.0
trnK-UUU_p4 trnK-UUU TGGGAGCTGGGTTACAAAAG TGTGTCGTGCAATTTTATCCC 2712 1.000 63.1
trnK-UUU_p5 trnK-UUU GGGAGCTGGGTTACAAAAGG TCCGATTGTTGTATCCACACA 2676 1.000 63.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 982–988 1.000 78.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 981–987 1.000 78.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 991–997 1.000 77.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAAAGGCGCTCAACC 986–992 1.000 77.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 985–991 1.000 77.1
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 529–532 1.000 74.2
psbK-psbI_p2 psbK-psbI ATGCCCGTAATACCCCTTCT TCTTCACGTCCAGGATTACG 568–571 1.000 73.0
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 526–529 1.000 72.2
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 527–530 1.000 72.2
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 528–531 1.000 72.2
atpA-atpF_p1 atpA-atpF CGTCGGCTCTAATGGTTACC TGTTTGGGGCGATGAATGAA 116–124 1.000 84.1
atpA-atpF_p2 atpA-atpF CGTCGGCTCTAATGGTTACC ATTGGAATGTTTGGGGCGAT 123–131 1.000 83.6
atpA-atpF_p3 atpA-atpF CAATGCCGTCACCTACTTGA TGTTTGGGGCGATGAATGAA 212–220 1.000 82.3
atpA-atpF_p4 atpA-atpF CAATGCCGTCACCTACTTGA ATGTTTGGGGCGATGAATGA 213–221 1.000 81.8
atpA-atpF_p5 atpA-atpF CAATGCCGTCACCTACTTGA ATTGGAATGTTTGGGGCGAT 219–227 1.000 81.7
atpF_p1 atpF ATGCCTACAGTAGAAGTACT AGTGATACAAAAAGAACTCTATTTGA 1395–1405 1.000 40.5
atpF_p2 atpF AATGCCTACAGTAGAAGTACT AGTGATACAAAAAGAACTCTATTTGA 1396–1406 1.000 40.5
atpF_p3 atpF ATGCCTACAGTAGAAGTACT TCTTTAAGTGATACAAAAAGAACTCT 1401–1411 1.000 40.5
atpF_p4 atpF AATGCCTACAGTAGAAGTACT TCTTTAAGTGATACAAAAAGAACTCT 1402–1412 1.000 40.5
atpF_p5 atpF ATGCCTACAGTAGAAGTACT GTGATACAAAAAGAACTCTATTTGA 1394–1404 1.000 40.5
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCAATGGAGGGTCAT 1183–1189 1.000 79.9
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCAATGGAGGGTCAT 1149–1155 1.000 79.8
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG ATTTTTGCAACCTTAGCCGC 1214–1220 1.000 79.5
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACCTTAGCCGC 1180–1186 1.000 79.4
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT GCGAATCAATGGAGGGTCAT 1205–1211 1.000 79.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Trapa acornis NC_064355.1 155537 View on NCBI ↗
Trapa arcuata MW579854.1 155555 View on NCBI ↗
Trapa bicornis NC_049010.1 155539 View on NCBI ↗
Trapa bicornis var. taiwanensis MW727502.1 155539 View on NCBI ↗
Trapa cochinchinensis NC_064354.1 155538 View on NCBI ↗
Trapa japonica NC_058222.1 155555 View on NCBI ↗
Trapa kozhevnikoviorum NC_057633.1 155545 View on NCBI ↗
Trapa litwinowii MW579853.1 155535 View on NCBI ↗
Trapa manshurica MW579857.1 155547 View on NCBI ↗
Trapa manshurica var. bispinosa MW579851.1 155495 View on NCBI ↗
Trapa natans NC_042895.1 155553 View on NCBI ↗
Trapa natans var. quadrispinosa NC_054282.1 155554 View on NCBI ↗
Trapa potaninii MW579852.1 155555 View on NCBI ↗
Trapa pseudoincisa MW579855.1 155556 View on NCBI ↗
Trapa sibirica MW579856.1 155548 View on NCBI ↗