Markers + reference

Caldesia

2 species · Alismataceae · Alismatales

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Species 2
Genome length 173–173 kb
Candidate markers 268
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1594 0.0108 0.98 57.1 yes View details
atpH-atpI LSC 971 0.0072 1.00 59.6 yes View details
accD LSC 1272 0.0086 1.00 51.3 yes View details
accD-psaI LSC 968 0.0093 1.00 59.5 yes View details
petL-petG LSC 176 0.0057 1.00 50.0 yes View details
psaJ-rpl33 LSC 446 0.0615 0.98 83.2 yes View details
rpl22-rps19 LSC 761 0.2055 0.96 82.8 yes View details
rps19 IRb 938 0.1098 1.00 78.9 yes View details
trnN-GUU-rps15 IRb 9815 0.0034 0.75 53.5 yes View details
rps15 IRb 273 0.0037 1.00 43.2 yes View details
ccsA SSC 969 0.0052 1.00 53.7 yes View details
ndhA SSC 2196 0.0051 0.99 47.9 yes View details
petG-trnW-CCA LSC 104 0.0577 1.00 82.2 yes View details
psbZ-trnG-UCC LSC 835 0.0085 0.99 64.4 yes View details
ycf3-trnS-GGA LSC 575 0.0087 1.00 63.6 yes View details
trnM-CAU-psbD LSC 1003 0.0070 1.00 62.8 yes View details
rpl16-rps3 LSC 1221 0.0066 1.00 62.8 yes View details
ndhK LSC 744 0.0067 1.00 62.6 yes View details
trnH-GUG-psbA LSC 292 0.0205 1.00 62.1 yes View details
psaA-ycf3 LSC 557 0.0054 1.00 61.1 yes View details
ycf4-cemA LSC 903 0.0033 1.00 60.7 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 409–426 1.000 79.9
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 359–376 1.000 79.7
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 362–379 1.000 79.7
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATCGCGCTAACCTTGGTATG 412–429 1.000 79.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CTGTTGAAGCTCCATCCACA 343–360 1.000 78.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGGTCCTGTTATTCGGAGGT 1657–1682 1.000 80.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGATGTCCTTCAAGTCGCAC TGGTCCTGTTATTCGGAGGT 1668–1693 1.000 79.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1646–1671 1.000 75.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACCGGTTTTGGTC 1672–1697 1.000 75.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATGATGTCCTTCAAGTCGCA TGGTCCTGTTATTCGGAGGT 1669–1694 1.000 75.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CCGCGGCTTATATAGGTGAA 1044–1045 1.000 74.3
atpH-atpI_p2 atpH-atpI CAGTACCTTGACCAACTCCG CCGCGGCTTATATAGGTGAA 1103–1104 1.000 74.0
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGC 1032–1033 1.000 73.4
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA CCGCGGCTTATATAGGTGAA 1045–1046 1.000 73.2
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC CCGCGGCTTATATAGGTGAA 1104–1105 1.000 73.1
trnM-CAU-psbD_p1 trnM-CAU-psbD GTGGTAGAGTAACGCCATGG CACAAAAACGAAACGGTCCC 1147–1153 1.000 78.6
trnM-CAU-psbD_p2 trnM-CAU-psbD GTGGTAGAGTAACGCCATGG CCACAAAAACGAAACGGTCC 1148–1154 1.000 78.6
trnM-CAU-psbD_p3 trnM-CAU-psbD GTGGTAGAGTAACGCCATGG CCCACAAAAACGAAACGGTC 1149–1155 1.000 78.6
trnM-CAU-psbD_p4 trnM-CAU-psbD TCAGTGGTAGAGTAACGCCA CACAAAAACGAAACGGTCCC 1150–1156 1.000 78.4
trnM-CAU-psbD_p5 trnM-CAU-psbD TCAGTGGTAGAGTAACGCCA CCACAAAAACGAAACGGTCC 1151–1157 1.000 78.4
psbZ-trnG-UCC_p1 psbZ-trnG-UCC TTTGCTTCTCCTGACGGTTG CGGATAGCGGGAATCGAAC 1008–1015 1.000 68.3
psbZ-trnG-UCC_p2 psbZ-trnG-UCC TTTGCTTCTCCTGACGGTTG GATAGCGGGAATCGAACCC 1006–1013 1.000 68.2
psbZ-trnG-UCC_p3 psbZ-trnG-UCC TTTGCTTCTCCTGACGGTTG GGATAGCGGGAATCGAACC 1007–1014 1.000 68.2
psbZ-trnG-UCC_p4 psbZ-trnG-UCC ATTTGCTTCTCCTGACGGTT CGGATAGCGGGAATCGAAC 1009–1016 1.000 67.0
psbZ-trnG-UCC_p5 psbZ-trnG-UCC ATTTGCTTCTCCTGACGGTT GATAGCGGGAATCGAACCC 1007–1014 1.000 66.9
psaA-ycf3_p1 psaA-ycf3 CCCATTCCTCGAAAGACGTT TGGTTGAAGATTACAGGGCG 665–666 1.000 78.9
psaA-ycf3_p2 psaA-ycf3 TTGAGAAATGGCCTGGTCTG TGGTTGAAGATTACAGGGCG 686–687 1.000 78.0
psaA-ycf3_p3 psaA-ycf3 CCCATTCCTCGAAAGACGTT TGGTTTGATCAAGCTGCTGA 740–741 1.000 77.5
psaA-ycf3_p4 psaA-ycf3 CCCATTCCTCGAAAGACGTT GCTATAGCGCTTACTCCAGG 707–708 1.000 76.8
psaA-ycf3_p5 psaA-ycf3 TTGAGAAATGGCCTGGTCTG TGGTTTGATCAAGCTGCTGA 761–762 1.000 76.6

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
Caldesia grandis NC_045925.1 173124 View on NCBI ↗
Caldesia parnassifolia NC_045926.1 173051 View on NCBI ↗