Markers + reference

Gladiolus

2 species · Iridaceae · Asparagales

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Species 2
Genome length 152–152 kb
Candidate markers 270
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 933 0.0182 1.00 54.2 no View details
ndhF SSC 2217 0.4758 0.93 81.6 yes View details
ndhD SSC 1506 0.4827 0.73 77.3 yes View details
psaC SSC 246 0.4819 0.67 70.4 yes View details
ndhA SSC 2173 0.4758 0.90 80.9 yes View details
ndhH SSC 1182 0.4730 0.86 81.1 yes View details
ycf1 SSC 5412 0.3700 0.83 74.2 yes View details
ccsA SSC 957 0.4635 0.93 83.1 yes View details
ndhF-rpl32 SSC 531 0.4153 0.91 81.2 yes View details
ndhI SSC 540 0.4574 0.89 80.8 yes View details
rpl32-trnL-UAG SSC 789 0.4581 0.80 79.4 yes View details
ndhG SSC 531 0.4640 0.81 78.3 yes View details
ndhH-rps15 SSC 107 0.4020 0.95 77.1 yes View details
rps15 SSC 273 0.5364 0.96 77.1 yes View details
rps15-ycf1 SSC 456 0.4350 0.83 77.1 yes View details
ndhG-ndhI SSC 241 0.5000 0.93 76.8 yes View details
ndhE SSC 306 0.4853 0.89 75.8 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhF_p1 ndhF AGAATGCCGTCGCCTATTTT GATGCATGCTACGATCCGTA 2838 0.500 56.9
ndhF_p2 ndhF GCCGTCGCCTATTTTCACTA GATGCATGCTACGATCCGTA 2833 0.500 56.7
ndhF_p3 ndhF AGAATGCCGTCGCCTATTTT TTGATGCATGCTACGATCCG 2840 0.500 55.7
ndhF_p4 ndhF GCCGTCGCCTATTTTCACTA TTGATGCATGCTACGATCCG 2835 0.500 55.5
ndhF_p5 ndhF AATGCCGTCGCCTATTTTCA GATGCATGCTACGATCCGTA 2836 0.500 55.2
ndhF-rpl32_p1 ndhF-rpl32 GAATTGTGCCGATTTCGCAA ATTGGAAGTCGAGCCATGAC 1475 0.500 59.6
ndhF-rpl32_p2 ndhF-rpl32 GAATTGTGCCGATTTCGCAA GGAAGTCGAGCCATGACAAT 1472 0.500 59.6
ndhF-rpl32_p3 ndhF-rpl32 GGCGGAAAACACCATAGCTA ATTGGAAGTCGAGCCATGAC 911 0.500 59.5
ndhF-rpl32_p4 ndhF-rpl32 GGCGGAAAACACCATAGCTA GGAAGTCGAGCCATGACAAT 908 0.500 59.5
ndhF-rpl32_p5 ndhF-rpl32 CTGCAATTGGTCGTGTGAAC GGAAGTCGAGCCATGACAAT 1254 0.500 59.5
rpl32-trnL-UAG_p1 rpl32-trnL-UAG TACGGATCGTAGCATGCATC AGCGTGTCTACCGATTTCAC 1119 0.500 57.2
rpl32-trnL-UAG_p2 rpl32-trnL-UAG TACGGATCGTAGCATGCATC CAGCGTGTCTACCGATTTCA 1120 0.500 57.1
rpl32-trnL-UAG_p3 rpl32-trnL-UAG TACGGATCGTAGCATGCATC TGGCGAAACCTTGGGTAAAA 1597 0.500 56.7
rpl32-trnL-UAG_p4 rpl32-trnL-UAG TACGGATCGTAGCATGCATC TCGAAGAAATCCAACGGGTC 1447 0.500 56.5
rpl32-trnL-UAG_p5 rpl32-trnL-UAG TACGGATCGTAGCATGCATC TCCTAAGAGCAGCGTGTCTA 1129 0.500 56.2
ccsA_p1 ccsA GTGAAATCGGTAGACACGCT CTCAAAAACTCGCACGAACC 1183 0.500 59.8
ccsA_p2 ccsA GTGAAATCGGTAGACACGCT GGTTCTCAAAAACTCGCACG 1187 0.500 59.8
ccsA_p3 ccsA TGAAATCGGTAGACACGCTG CTCAAAAACTCGCACGAACC 1182 0.500 59.8
ccsA_p4 ccsA TGAAATCGGTAGACACGCTG GGTTCTCAAAAACTCGCACG 1186 0.500 59.8
ccsA_p5 ccsA GTGAAATCGGTAGACACGCT TGCATTACCGGGAATGAGTG 1691 0.500 59.6
ndhD_p1 ndhD GAGGCATGGGGGTCTTATTG AAACAACTCGAAGCATGGGT 2121 0.500 59.7
ndhD_p2 ndhD CGTGCGAGTTTTTGAGAACC AAACAACTCGAAGCATGGGT 1838 0.500 59.7
ndhD_p3 ndhD GGTTCGTGCGAGTTTTTGAG AAACAACTCGAAGCATGGGT 1842 0.500 59.7
ndhD_p4 ndhD GAGGCATGGGGGTCTTATTG GGCATGAAACAACTCGAAGC 2127 0.500 59.6
ndhD_p5 ndhD CGTGCGAGTTTTTGAGAACC GGCATGAAACAACTCGAAGC 1844 0.500 59.6
psaC_p1 psaC GATTGACCAAAAAGCCCGTG ATCACAAGCCGAAACATGGT 938 0.500 58.8
psaC_p2 psaC CCCCCTGCAGTGTACAAAAT ATCACAAGCCGAAACATGGT 1476 0.500 58.7
psaC_p3 psaC GATTGACCAAAAAGCCCGTG GCGATTGGGCTAGCTATTGT 779 0.500 58.6
psaC_p4 psaC GATTGACCAAAAAGCCCGTG AGTCCCTTGGTCCTTTCTCA 521 0.500 58.5
psaC_p5 psaC CCCCCTGCAGTGTACAAAAT GCGATTGGGCTAGCTATTGT 1317 0.500 58.5

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
Gladiolus communis NC_072572.1 151608 View on NCBI ↗
Gladiolus x gandavensis NC_062351.1 151654 View on NCBI ↗