Markers + reference

Zea

7 species · Poaceae · Poales

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Species 7
Genome length 140–141 kb
Candidate markers 269
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU LSC 228 0.0113 1.00 48.1 yes View details
rps16-trnQ-UUG LSC 1443 0.0036 0.81 53.7 yes View details
psbD LSC 1062 0.0043 1.00 34.9 yes View details
trnY-GUA-trnD-GUC LSC 348 0.0041 1.00 35.8 yes View details
psbM-petN LSC 796 0.0054 1.00 37.9 yes View details
trnC-GCA-rpoB LSC 1211 0.0045 1.00 53.6 yes View details
atpB-rbcL LSC 782 0.0062 1.00 54.2 yes View details
petA-psbJ LSC 912 0.0043 0.99 38.2 yes View details
psbE-petL LSC 1090 0.0035 1.00 61.9 yes View details
rpl16 LSC 1466 0.0027 1.00 49.3 yes View details
ndhF-rpl32 SSC 832 0.0048 1.00 57.9 yes View details
rpl33-rps18 LSC 343 0.0051 0.97 56.9 yes View details
trnF-GAA-ndhJ LSC 592 0.0027 1.00 50.9 yes View details
trnG-UCC-trnM-CAU LSC 1959 0.0016 0.96 49.4 yes View details
trnI-CAU-trnL-CAA IRb 3598 0.0002 1.00 47.0 yes View details
rpl32-trnL-UAG SSC 531 0.0038 1.00 47.0 yes View details
trnL-CAA-trnI-CAU IRa 3598 0.0002 1.00 47.0 yes View details
psaA-ycf3 LSC 607 0.0014 1.00 46.8 yes View details
rbcL-psaI LSC 890 0.0006 1.00 46.0 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU AAGACGGTTTTCGGTGCTAG AAATGCAAGCACGATTTGGG 418–419 1.000 79.6
psbA-trnK-UUU_p2 psbA-trnK-UUU AAAGACGGTTTTCGGTGCTA AAATGCAAGCACGATTTGGG 419–420 1.000 79.3
psbA-trnK-UUU_p3 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT AAATGCAAGCACGATTTGGG 420–421 1.000 79.3
psbA-trnK-UUU_p4 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT AAATGCAAGCACGATTTGGG 370–371 1.000 79.1
psbA-trnK-UUU_p5 psbA-trnK-UUU AACACCGAACCATCCAATGT AAATGCAAGCACGATTTGGG 439–440 1.000 78.9
trnK-UUU_p1 trnK-UUU TGAAAAACTCAGATTGCTCT TGATCGTATCTAAGAGATCCT 2614–2626 1.000 40.6
trnK-UUU_p2 trnK-UUU TGAAAAACTCAGATTGCTCTTTTCT TGATCGTATCTAAGAGATCCT 2614–2626 1.000 40.6
trnK-UUU_p3 trnK-UUU TGAAAAACTCAGATTGCTCTT TGATCGTATCTAAGAGATCCT 2614–2626 1.000 40.6
trnK-UUU_p4 trnK-UUU TGAAAAACTCAGATTGCTCT TTGATCGTATCTAAGAGATCCT 2615–2627 1.000 40.6
trnK-UUU_p5 trnK-UUU TGAAAAACTCAGATTGCTCTTTTCT TTGATCGTATCTAAGAGATCCT 2615–2627 1.000 40.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1247–1523 0.857 74.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ACTCGGAGGTTCGAATCCTT 1246–1522 0.857 74.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGTTACTC 1262–1538 0.857 74.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TACTCGGAGGTTCGAATCCT 1258–1534 0.857 74.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC ACTCGGAGGTTCGAATCCTT 1257–1533 0.857 73.9
psbD_p1 psbD AGGTGCTCGAAAATGGTTGA GTCACGACCAGCTAAAACGA 1133 1.000 77.2
psbD_p2 psbD TGAGGTGCTCGAAAATGGTT GTCACGACCAGCTAAAACGA 1135 1.000 77.2
psbD_p3 psbD ATGAGGTGCTCGAAAATGGT GTCACGACCAGCTAAAACGA 1136 1.000 75.3
psbD_p4 psbD AGGTGCTCGAAAATGGTTGA TCACGACCAGCTAAAACGAA 1132 1.000 74.9
psbD_p5 psbD TGAGGTGCTCGAAAATGGTT TCACGACCAGCTAAAACGAA 1134 1.000 74.9
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT GCGAAAAGCCCTTTATCGGA 1982–2065 1.000 50.3
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TCGAACCGATGACTTCTGTC 2028–2111 1.000 50.2
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CGAACCGATGACTTCTGTCT 2027–2110 1.000 50.1
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU AGAACGAATCACACTTTTACCAC GCGAAAAGCCCTTTATCGGA 1985–2068 1.000 49.2
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT GCGAAAAGCCCTTTATCGGA 1984–2067 1.000 49.2
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 472 1.000 76.3
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 439 1.000 73.9
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 438 1.000 73.7
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 471 1.000 72.2
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 440 1.000 70.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Zea luxurians NC_030301.1 140710 View on NCBI ↗
Zea mays NC_001666.2 140384 View on NCBI ↗
Zea mays subsp. huehuetenangensis KR873422.1 140453 View on NCBI ↗
Zea mays subsp. mexicana BK061458.1 140539 View on NCBI ↗
Zea mays subsp. parviglumis BK061463.1 140462 View on NCBI ↗
Zea nicaraguensis KU291447.1 140465 View on NCBI ↗
Zea perennis NC_030300.1 140647 View on NCBI ↗