Markers + reference

Evolvulus

2 species · Convolvulaceae · Solanales

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Species 2
Genome length 157–162 kb
Candidate markers 263
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-CGA-trnR-UCU LSC 865 0.0525 0.97 83.7 yes View details
accD LSC 1882 0.0072 0.95 66.6 yes View details
trnN-GUU-ycf1 IRb 3296 0.0053 0.97 51.2 yes View details
trnK-UUU LSC 36 0.6389 1.00 72.6 yes View details
trnK-UUU LSC 37 0.4571 0.95 77.3 yes View details
trnK-UUU-rps16 LSC 362 0.4000 0.98 75.7 yes View details
matK-trnK-UUU LSC 770 0.5027 0.95 83.5 yes View details
matK LSC 1311 0.4595 0.96 82.7 yes View details
trnL-CAA-ycf2 LSC 161 0.0435 1.00 70.1 yes View details
ycf2-trnL-CAA LSC 161 0.0248 1.00 66.8 yes View details
trnI-CAU-ycf2 LSC 533 0.0077 0.97 64.5 yes View details
rps16 LSC 68 0.5000 0.32 64.1 no View details
clpP LSC 2201 0.0051 0.90 63.6 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-CGA-trnR-UCU_p1 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 946–1000 1.000 69.2
trnS-CGA-trnR-UCU_p2 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 949–1003 1.000 68.9
trnS-CGA-trnR-UCU_p3 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 952–1006 1.000 68.5
trnS-CGA-trnR-UCU_p4 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 955–1009 1.000 68.2
trnS-CGA-trnR-UCU_p5 trnS-CGA-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 950–1004 1.000 66.7
accD_p1 accD CATGCAAATAGGGGGCAAGA TGCTTTCTTAGATCTTCTGTTCCT 1956–2029 1.000 47.4
accD_p2 accD TCATGCAAATAGGGGGCAAG TGCTTTCTTAGATCTTCTGTTCCT 1957–2030 1.000 47.4
accD_p3 accD TTCATGCAAATAGGGGGCAA TGCTTTCTTAGATCTTCTGTTCCT 1958–2031 1.000 47.2
accD_p4 accD TTTCATGCAAATAGGGGGCA TGCTTTCTTAGATCTTCTGTTCCT 1959–2032 1.000 47.2
accD_p5 accD TGCAAATAGGGGGCAAGAAA TGCTTTCTTAGATCTTCTGTTCCT 1954–2027 1.000 46.6
clpP_p1 clpP GAATTCGAAGTGCCATGCTA CAAAACCCTACGTTTCCCCA 2244–2412 1.000 70.0
clpP_p2 clpP GAATTCGAAGTGCCATGCTA TCAAAACCCTACGTTTCCCC 2245–2413 1.000 67.9
clpP_p3 clpP GAATTCGAAGTGCCATGCTAT CAAAACCCTACGTTTCCCCA 2244–2412 1.000 66.2
clpP_p4 clpP AATTCGAAGTGCCATGCTAT CAAAACCCTACGTTTCCCCA 2243–2411 1.000 64.2
clpP_p5 clpP ATTCGAAGTGCCATGCTATT CAAAACCCTACGTTTCCCCA 2242–2410 1.000 64.2
trnI-CAU-ycf2_p1 trnI-CAU-ycf2 ATTGAACCTACGACTTCGCC TGAATTCAATTGGGTCCACGA 635–650 1.000 73.1
trnI-CAU-ycf2_p2 trnI-CAU-ycf2 GAACCTACGACTTCGCCAAT TGAATTCAATTGGGTCCACGA 632–647 1.000 73.1
trnI-CAU-ycf2_p3 trnI-CAU-ycf2 ATTGAACCTACGACTTCGCC TCAATTGGGTCCACGAATCT 630–645 1.000 73.0
trnI-CAU-ycf2_p4 trnI-CAU-ycf2 GAACCTACGACTTCGCCAAT TCAATTGGGTCCACGAATCT 627–642 1.000 73.0
trnI-CAU-ycf2_p5 trnI-CAU-ycf2 GATGGTGTGCATCCAGTAGG TGAATTCAATTGGGTCCACGA 656–671 1.000 72.8
ycf2-trnL-CAA_p1 ycf2-trnL-CAA ATGGCTTTTCCCGGATGAAA AAATGGTAGACACGCGAGAC 270 1.000 79.3
ycf2-trnL-CAA_p2 ycf2-trnL-CAA TGGCTTTTCCCGGATGAAAT AAATGGTAGACACGCGAGAC 269 1.000 79.3
ycf2-trnL-CAA_p3 ycf2-trnL-CAA ATGGCTTTTCCCGGATGAAA TGAAATGGTAGACACGCGAG 272 1.000 79.3
ycf2-trnL-CAA_p4 ycf2-trnL-CAA TGGCTTTTCCCGGATGAAAT TGAAATGGTAGACACGCGAG 271 1.000 79.3
ycf2-trnL-CAA_p5 ycf2-trnL-CAA AAGATGGCTTTTCCCGGATG AAATGGTAGACACGCGAGAC 273 1.000 79.3
trnN-GUU-ycf1_p1 trnN-GUU-ycf1 AAAGTCCCCCGATGGTCATA TTAAGCCTTGCCGAAAATCG 646–687 1.000 77.6
trnN-GUU-ycf1_p2 trnN-GUU-ycf1 AAAGTCCCCCGATGGTCATA ATCGTACCGAAAACAGACGA 613–654 1.000 77.0
trnN-GUU-ycf1_p3 trnN-GUU-ycf1 AAAGTCCCCCGATGGTCATA TCGTACCGAAAACAGACGAT 612–653 1.000 77.0
trnN-GUU-ycf1_p4 trnN-GUU-ycf1 CCGAATTGCAACAACTGGTG TTAAGCCTTGCCGAAAATCG 615–656 1.000 76.8
trnN-GUU-ycf1_p5 trnN-GUU-ycf1 CGAATTGCAACAACTGGTGG TTAAGCCTTGCCGAAAATCG 614–655 1.000 76.8

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
Evolvulus alsinoides NC_058590.1 157015 View on NCBI ↗
Evolvulus alsinoides var. oblongus LC729545.1 162367 View on NCBI ↗