Markers + reference

Zantedeschia

2 species · Araceae · Alismatales

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Species 2
Genome length 175–175 kb
Candidate markers 283
Primer pairs 85

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 8 remaining regions by MarkerSeek score (out of 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 40.0 yes View details
psbA-trnK-UUU LSC 260 0.0000 0.98 54.0 yes View details
psbZ-trnG-GCC LSC 338 0.0000 1.00 34.3 yes View details
trnM-CAU-trnV-UAC LSC 470 0.0043 1.00 58.5 yes View details
rbcL-accD LSC 3529 0.0033 0.86 59.0 yes View details
rps3 LSC 687 0.0000 1.00 37.6 yes View details
rpl22 LSC 384 0.0026 1.00 55.7 yes View details
trnI-CAU-ycf2 IRb 370 0.0415 0.78 76.8 yes View details
ycf2-trnI-CAU IRa 370 0.0415 0.78 76.8 yes View details
rps2 LSC 783 0.0000 0.97 61.7 yes View details
clpP-psbB LSC 995 0.0000 1.00 59.1 yes View details
rps18 LSC 549 0.0000 0.83 59.0 yes View details
petA-psbJ LSC 993 0.0000 1.00 58.8 yes View details
trnG-GCC-trnfM-CAU LSC 162 0.0062 1.00 56.0 yes View details
rpoC2 LSC 4281 0.0000 0.99 54.6 yes View details
trnY-GUA-trnE-UUC LSC 226 0.0000 0.99 53.4 yes View details
matK-trnK-UUU LSC 765 0.0000 1.00 40.0 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA AATGAGGGAGGAGGTTTGGT GTGCTTGGGAGTCCTTGAAA 1166 1.000 77.9
psbA_p2 psbA AATGAGGGAGGAGGTTTGGT TAGCTAATACGCGTGCTTGG 1178 1.000 76.9
psbA_p3 psbA ATGAGGGAGGAGGTTTGGTA GTGCTTGGGAGTCCTTGAAA 1165 1.000 74.6
psbA_p4 psbA TGAGGGAGGAGGTTTGGTAT GTGCTTGGGAGTCCTTGAAA 1164 1.000 74.6
psbA_p5 psbA TGAGGGAGGAGGTTTGGTAT TAGCTAATACGCGTGCTTGG 1176 1.000 73.5
psbA-trnK-UUU_p1 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC CATAGGGAAAGTCGTGTGCA 414–418 1.000 79.9
psbA-trnK-UUU_p2 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ACATAGGGAAAGTCGTGTGC 415–419 1.000 79.9
psbA-trnK-UUU_p3 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC TCGTGTGCAATGAAAACTGC 403–407 1.000 79.7
psbA-trnK-UUU_p4 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC AATGAAAACTGCAAGCACGG 395–399 1.000 79.6
psbA-trnK-UUU_p5 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC CGTGTGCAATGAAAACTGCA 402–406 1.000 79.4
matK-trnK-UUU_p1 matK-trnK-UUU CCATGATCATGAGCAAGTGC TCTGGGTTGCTAACTCAACG 912 1.000 72.5
matK-trnK-UUU_p2 matK-trnK-UUU CCATGATCATGAGCAAGTGC AACGGTAGAGTACTCGGCTT 896 1.000 72.4
matK-trnK-UUU_p3 matK-trnK-UUU CCATGATCATGAGCAAGTGC ACGGTAGAGTACTCGGCTTT 895 1.000 72.4
matK-trnK-UUU_p4 matK-trnK-UUU CCATGATCATGAGCAAGTGC GGGTTGCTAACTCAACGGTA 909 1.000 70.1
matK-trnK-UUU_p5 matK-trnK-UUU CCATGATCATGAGCAAGTGC CTGGGTTGCTAACTCAACGG 911 1.000 67.0
rps2_p1 rps2 TGAAATCCAGGAATAGCCAA CAACGGTCAATCCTCGGTAG 944–968 1.000 51.7
rps2_p2 rps2 TTGAAATCCAGGAATAGCCA CAACGGTCAATCCTCGGTAG 945–969 1.000 51.7
rps2_p3 rps2 TGAAATCCAGGAATAGCCAA AACGGTCAATCCTCGGTAGA 943–967 1.000 51.0
rps2_p4 rps2 TGAAATCCAGGAATAGCCAA ACGGTCAATCCTCGGTAGAA 942–966 1.000 51.0
rps2_p5 rps2 TTGAAATCCAGGAATAGCCA ACGGTCAATCCTCGGTAGAA 943–967 1.000 51.0
rpoC2_p1 rpoC2 TGAGTCTCCTTTTAGGAATCA TATAATCCCGATCCGTGCAG 1066 1.000 40.0
rpoC2_p2 rpoC2 TGAGTCTCCTTTTAGGAATCA TTATAATCCCGATCCGTGCAG 1067 1.000 40.0
rpoC2_p3 rpoC2 ATGAGTCTCCTTTTAGGAATCA TATAATCCCGATCCGTGCAG 1067 1.000 40.0
rpoC2_p4 rpoC2 TGAGTCTCCTTTTAGGAATCAT TATAATCCCGATCCGTGCAG 1066 1.000 40.0
rpoC2_p5 rpoC2 TGAGTCTCCTTTTAGGAATCA TTATAATCCCGATCCGTGCA 1067 1.000 40.0
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC AGGAAAGCGGCGAATTTTTG TCTAGCGGTTCAGGACATCT 389–391 1.000 78.7
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC CAAAGGAAAGCGGCGAATTT TCTAGCGGTTCAGGACATCT 392–394 1.000 78.7
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC AGGAAAGCGGCGAATTTTTG GTCTAGCGGTTCAGGACATC 390–392 1.000 78.2
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC CAAAGGAAAGCGGCGAATTT GTCTAGCGGTTCAGGACATC 393–395 1.000 78.2
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC AGGAAAGCGGCGAATTTTTG TATCGTCTAGCGGTTCAGGA 394–396 1.000 77.2

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
Zantedeschia hybrid cultivar NC_041553.1 175448 View on NCBI ↗
Zantedeschia rehmannii MH743154.1 175067 View on NCBI ↗