Markers + reference

Euphorbia

69 species · Euphorbiaceae · Malpighiales

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Species 69
Genome length 159–165 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
trnK-UUU-rps16 LSC 1968 0.0837 0.77 75.1 yes View details
trnG-UCC-trnR-UCU LSC 876 0.1113 0.74 78.0 yes View details
psbZ-trnG-GCC LSC 1455 0.0856 0.78 76.0 yes View details
psaA-pafI LSC 1081 0.0630 0.86 74.4 yes View details
ycf1 IRb 1167 0.0392 0.81 66.0 yes View details
ndhF-trnL-UAG SSC 1617 0.0850 0.74 73.6 yes View details
ycf1 SSC 5757 0.0492 0.93 75.8 no View details
rpoB-trnC-GCA LSC 1179 0.0495 0.98 83.1 yes View details
trnT-GGU-psbD LSC 1796 0.0464 0.93 81.9 yes View details
ndhC-trnV-UAC LSC 1213 0.0636 0.91 80.7 yes View details
trnS-GCU-trnG-UCC LSC 573 0.0790 0.84 78.0 yes View details
rpl16 LSC 1606 0.0400 0.98 77.8 yes View details
rps4-trnT-UGU LSC 439 0.0592 0.96 77.4 yes View details
accD-psaI LSC 1290 0.0673 0.86 76.9 yes View details
atpH-atpI LSC 1050 0.0414 0.92 76.3 yes View details
petN-psbM LSC 1281 0.0403 0.93 76.0 yes View details
rbcL-accD LSC 791 0.0476 0.92 75.9 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 TGTTCCGCACCAAGAATTCA ATGGGAGATAGGCAAATGCG 2430–2917 0.493 70.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG ATGGGAGATAGGCAAATGCG 2328–2815 0.464 69.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TTGGGACTCGAACAAATGGG 2345–2715 0.087 54.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 TGTTCCGCACCAAGAATTCA TTGGGACTCGAACAAATGGG 2462–2634 0.072 51.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAACTCATCAGCGGATTCCC TTGGGACTCGAACAAATGGG 2880–2987 0.058 45.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAGTCACACTTTTACCACT 543–731 1.000 77.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAGTCACACTTTTACCACT 542–730 1.000 77.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACGAGTCACACTTTTACCACT 544–732 1.000 74.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACGAGTCACACTTTTACCACT 543–731 1.000 74.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC ACGAGTCACACTTTTACCACT 545–733 1.000 74.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAGAAAAATTGCGTCCAA 666–1228 0.986 76.4
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAGAAAAATTGCGTCCAA 669–1231 0.986 76.2
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 619–1181 1.000 75.3
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 622–1184 1.000 75.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG ATGGAGAAAAATTGCGTCCA 667–1229 0.986 74.6
atpH-atpI_p1 atpH-atpI CAGTGACCCAGGAAAACGAA GGGTGCACTTTTACCTTGGA 1844–2176 0.971 90.5
atpH-atpI_p2 atpH-atpI CCTCAAATCAGTCCTTCCCG GGGTGCACTTTTACCTTGGA 1502–1841 0.899 87.6
atpH-atpI_p3 atpH-atpI TGGACTAAGAAGGGGGAAGG GGGTGCACTTTTACCTTGGA 1553–1892 0.899 87.6
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT GGGTGCACTTTTACCTTGGA 1156–1494 0.855 85.8
atpH-atpI_p5 atpH-atpI CCCGCAGTAGGTTATTGTCC GGGTGCACTTTTACCTTGGA 1486–1823 0.087 52.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TGATCCAACTCTGAGCGGTA GCGTCTTTTGTTGATGAGGC 1417–1928 0.855 84.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCTCATTTCCATCCTCGAGC GCGTCTTTTGTTGATGAGGC 1246–1504 0.348 64.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTCCATCCTCGA GCGTCTTTTGTTGATGAGGC 1248–1506 0.348 64.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCTGTTTCCTACTCACGCG GCGTCTTTTGTTGATGAGGC 1754–1987 0.246 61.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTCTGTTTCCTACTCACGCG CCGGATTTGAACTGGGGAAA 1729–1962 0.246 60.7
petN-psbM_p1 petN-psbM TTTCCCCAGTTCAAATCCGG ATCCCGAGTTTTTGCGAAGT 1404–1940 0.986 89.9
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT ATCCCGAGTTTTTGCGAAGT 1023–1536 0.986 89.3
petN-psbM_p3 petN-psbM GCCTCATCAACAAAAGACGC ATCCCGAGTTTTTGCGAAGT 1379–1915 0.783 82.2
petN-psbM_p4 petN-psbM GCCTCATCAACAAAAGACGC TGTAAGTGGGGGAGAAAGGT 2142 0.014 39.3
petN-psbM_p5 petN-psbM TTTCCCCAGTTCAAATCCGG TGTAAGTGGGGGAGAAAGGT 2167 0.014 38.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (69)

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

Species Accession Length (bp) Link
Euphorbia adenochlora NC_083119.1 163395 View on NCBI ↗
Euphorbia aff. neococcinea Luke s.n. NC_068483.1 164434 View on NCBI ↗
Euphorbia alluaudii NC_068486.1 163091 View on NCBI ↗
Euphorbia bicompacta NC_068482.1 162452 View on NCBI ↗
Euphorbia bicompacta var. rubra MT395029.1 162432 View on NCBI ↗
Euphorbia biselegans NC_068475.1 164326 View on NCBI ↗
Euphorbia bisglobosa NC_068491.1 163593 View on NCBI ↗
Euphorbia brunellii NC_077252.1 162903 View on NCBI ↗
Euphorbia celastroides PX316410.1 163465 View on NCBI ↗
Euphorbia chevalieri NC_077262.1 162481 View on NCBI ↗
Euphorbia cupricola NC_069182.1 164289 View on NCBI ↗
Euphorbia cyparissias PP165067.1 161453 View on NCBI ↗
Euphorbia discoidea NC_068492.1 163738 View on NCBI ↗
Euphorbia drupifera NC_062829.1 164014 View on NCBI ↗
Euphorbia echinulata NC_068467.1 159139 View on NCBI ↗
Euphorbia fauriei NC_067640.1 162834 View on NCBI ↗
Euphorbia fwambensis NC_077255.1 161097 View on NCBI ↗
Euphorbia guentheri NC_068462.1 163326 View on NCBI ↗
Euphorbia hedyotoides NC_068481.1 163811 View on NCBI ↗
Euphorbia helioscopia NC_071843.1 160984 View on NCBI ↗
Euphorbia humifusa NC_062451.1 163329 View on NCBI ↗
Euphorbia hypericifolia NC_072938.1 164981 View on NCBI ↗
Euphorbia invenusta NC_068465.1 163567 View on NCBI ↗
Euphorbia invenusta var. angusta MT394997.1 163296 View on NCBI ↗
Euphorbia jolkinii NC_083120.1 162821 View on NCBI ↗
Euphorbia kansuensis MZ962400.1 164078 View on NCBI ↗
Euphorbia kirkii NC_069183.1 164367 View on NCBI ↗
Euphorbia larica MN646683.1 162358 View on NCBI ↗
Euphorbia lugardae NC_068472.1 163202 View on NCBI ↗
Euphorbia maculata NC_052745.1 162685 View on NCBI ↗
Euphorbia mafingensis NC_069181.1 164254 View on NCBI ↗
Euphorbia magnifica NC_068469.1 164116 View on NCBI ↗
Euphorbia major NC_077259.1 162131 View on NCBI ↗
Euphorbia makinoi NC_072937.1 163059 View on NCBI ↗
Euphorbia mbuinzauensis NC_068461.1 162313 View on NCBI ↗
Euphorbia micractina NC_060656.1 162056 View on NCBI ↗
Euphorbia milii NC_062585.1 163458 View on NCBI ↗
Euphorbia milii var. splendens PX400300.1 163314 View on NCBI ↗
Euphorbia neoarborescens NC_068484.1 163922 View on NCBI ↗
Euphorbia neocrispa NC_077260.1 161020 View on NCBI ↗
Euphorbia neoglabrata NC_068458.1 163289 View on NCBI ↗
Euphorbia neoglaucescens NC_068489.1 163707 View on NCBI ↗
Euphorbia neogossweileri NC_068480.1 163966 View on NCBI ↗
Euphorbia neokaessneri NC_077263.1 159243 View on NCBI ↗
Euphorbia neorubella NC_068463.1 163558 View on NCBI ↗
Euphorbia neospinescens NC_062823.1 164389 View on NCBI ↗
Euphorbia neostolonifera NC_068476.1 163239 View on NCBI ↗
Euphorbia neovirgata NC_068471.1 162840 View on NCBI ↗
Euphorbia nutans NC_072939.1 162841 View on NCBI ↗
Euphorbia orobanchoides NC_068493.1 161947 View on NCBI ↗
Euphorbia pereskiifolia NC_068464.1 162228 View on NCBI ↗
Euphorbia prostrata NC_066811.1 162858 View on NCBI ↗
Euphorbia pseudolaevis NC_068495.1 163919 View on NCBI ↗
Euphorbia pseudomollis NC_069184.1 163703 View on NCBI ↗
Euphorbia pseudonudicaulis NC_077256.1 159753 View on NCBI ↗
Euphorbia pseudopetiolata NC_077258.1 162811 View on NCBI ↗
Euphorbia pudibunda NC_077254.1 163546 View on NCBI ↗
Euphorbia renneyi NC_068460.1 163115 View on NCBI ↗
Euphorbia rhizophora NC_068473.1 163114 View on NCBI ↗
Euphorbia ritchiei NC_068459.1 163058 View on NCBI ↗
Euphorbia royleana NC_073015.1 164178 View on NCBI ↗
Euphorbia rubella NC_077253.1 162721 View on NCBI ↗
Euphorbia schubei NC_068470.1 163009 View on NCBI ↗
Euphorbia smithii MN646684.1 162172 View on NCBI ↗
Euphorbia succulenta NC_068468.1 163002 View on NCBI ↗
Euphorbia syncameronii NC_068490.1 164327 View on NCBI ↗
Euphorbia thymifolia NC_062827.1 163135 View on NCBI ↗
Euphorbia umbellata NC_068494.1 163077 View on NCBI ↗
Euphorbia yattana NC_068477.1 163227 View on NCBI ↗