Markers + reference

Zizania

3 species · Poaceae · Poales

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Species 3
Genome length 136–136 kb
Candidate markers 265
Primer pairs 110

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 573 0.0140 1.00 55.3 yes View details
psbK-psbI LSC 392 0.0170 1.00 54.5 yes View details
trnG-UCC-trnT-GGU LSC 1556 0.0086 1.00 52.0 yes View details
trnY-GUA-trnD-GUC LSC 337 0.0168 1.00 62.9 yes View details
trnD-GUC-psbM LSC 932 0.0086 1.00 59.4 yes View details
petN-trnC-GCA LSC 935 0.0107 1.00 60.8 yes View details
ndhC-trnV-UAC LSC 768 0.0122 1.00 47.3 yes View details
rbcL-psaI LSC 1873 0.0093 1.00 37.0 yes View details
petL-petG LSC 185 0.0036 1.00 29.7 yes View details
trnW-CCA-trnP-UGG LSC 134 0.0299 1.00 54.6 yes View details
rps3 LSC 720 0.0028 1.00 35.1 yes View details
ndhF SSC 2205 0.0079 1.00 48.3 yes View details
ndhF-rpl32 SSC 898 0.0119 1.00 61.1 yes View details
ndhG SSC 531 0.0050 1.00 34.4 yes View details
rps3-rpl22 LSC 51 0.0800 0.98 81.0 yes View details
ycf3-trnS-GGA LSC 647 0.0062 1.00 68.0 yes View details
petG-trnW-CCA LSC 116 0.0632 1.00 65.6 yes View details
psbT-psbN LSC 48 0.0833 1.00 60.5 yes View details
rrn16-trnI-GAU IRb 309 0.0065 1.00 57.2 yes View details
trnI-GAU-rrn16 IRa 309 0.0065 1.00 57.2 yes View details
rps4-trnT-UGU LSC 326 0.0083 0.98 54.4 yes View details
atpB-rbcL LSC 763 0.0100 1.00 53.4 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 ACCAAGAGTCTGGACGAACT AGAAAAAGAAAGAACTTTGAGT 689–695 1.000 42.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 ATCAGTCGCGGTCTTCTAGA AGAAAAAGAAAGAACTTTGAGT 713–719 1.000 41.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATCAGTCGCGGTCTTCTAGA AAGAAAAAGAAAGAACTTTGAGT 714–720 1.000 41.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 ATCAGTCGCGGTCTTCTAGA AGAAAAAGAAAGAACTTTGAGTT 713–719 1.000 41.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 ATCAGTCGCGGTCTTCTAGA AAGAAAAAGAAAGAACTTTGAGTT 714–720 1.000 41.9
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ATTTTTACTCGTCACGCCCA 536–539 1.000 79.8
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ATTTTTACTCGTCACGCCCA 533–536 1.000 77.8
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ATTTTTACTCGTCACGCCCA 534–537 1.000 77.8
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ATTTTTACTCGTCACGCCCA 535–538 1.000 77.8
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTACTCGTCACGCCCAG 535–538 1.000 77.2
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU TTTCCACCGAGCTGAAACAA ACGTCTTACCACGGCATTAC 2137–2140 1.000 81.4
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU TTTCCACCGAGCTGAAACAA CACGTCTTACCACGGCATTA 2138–2141 1.000 81.4
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU CATCGTTAGCTTGGAAGGCT ACGTCTTACCACGGCATTAC 2418–2421 1.000 81.3
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU CATCGTTAGCTTGGAAGGCT CACGTCTTACCACGGCATTA 2419–2422 1.000 81.3
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU CGTTAGCTTGGAAGGCTAGG ACGTCTTACCACGGCATTAC 2415–2418 1.000 81.1
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 398–463 1.000 81.3
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 365–430 1.000 78.9
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 364–429 1.000 78.8
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 397–462 1.000 77.1
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 366–431 1.000 75.6
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 1043–1047 1.000 59.4
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG AGAATGAACAGTGCAGTAGC 1075–1079 1.000 58.0
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AGGAACTAGAATGAACAGTGCA 1050–1054 1.000 56.3
trnD-GUC-psbM_p4 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC AGAATGAACAGTGCAGTAGC 1044–1048 1.000 55.3
trnD-GUC-psbM_p5 trnD-GUC-psbM TAGGTATGCCATACACCCCG AGGAACTAGAATGAACAGTGCA 1082–1086 1.000 54.8
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 979–984 1.000 72.7
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 981–986 1.000 72.3
petN-trnC-GCA_p3 petN-trnC-GCA CCACTCCTCCCCCATACTAC AGTTCAAATCTGGGTGCCG 1035–1040 1.000 71.6
petN-trnC-GCA_p4 petN-trnC-GCA CCACTCCTCCCCCATACTAC CCAGTTCAAATCTGGGTGCC 1037–1042 1.000 71.1
petN-trnC-GCA_p5 petN-trnC-GCA TCCACTCCTCCCCCATACTA AGTTCAAATCTGGGTGCCG 1036–1041 1.000 70.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Zizania aquatica NC_026967.1 136364 View on NCBI ↗
Zizania latifolia NC_029401.1 136461 View on NCBI ↗
Zizania palustris NC_066144.1 136278 View on NCBI ↗