Markers + reference

Adenocalymma

12 species · Bignoniaceae · Lamiales

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Species 12
Genome length 157–161 kb
Candidate markers 268
Primer pairs 75

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 8 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD LSC 1725 0.1643 0.89 79.5 yes View details
ycf4 LSC 576 0.1483 0.96 83.1 yes View details
ycf4-cemA LSC 880 0.0569 1.00 84.8 yes View details
trnN-GUU-ycf1 IRb 1163 0.2271 0.72 75.6 yes View details
ycf1 IRb 5409 0.0949 0.99 77.9 yes View details
ycf1 IRa 5409 0.0239 0.99 64.1 no View details
ycf1-trnN-GUU IRa 1163 0.2248 0.71 75.4 yes View details
rpoA LSC 1053 0.0683 0.96 84.2 yes View details
trnR-ACG-trnN-GUU IRb 486 0.0541 1.00 83.1 yes View details
rbcL-accD LSC 997 0.0532 0.97 82.3 yes View details
ndhD-psaC SSC 132 0.0444 0.95 81.5 yes View details
rpl32-trnL-UAC SSC 878 0.0325 0.99 80.9 yes View details
rrn16 IRb 1491 0.0615 1.00 79.5 yes View details
ccsA-ndhD SSC 232 0.0688 1.00 79.2 yes View details
rrn16 IRa 1491 0.0031 1.00 45.5 no 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rbcL-accD_p1 rbcL-accD CGATGCGAAGACAGAGGAAA GGTTGCTAAGCCTGCGATAT 306–1146 0.833 84.4
rbcL-accD_p2 rbcL-accD CGATGCGAAGACAGAGGAAA GATTTCATGTTCCCCGGTCA 363–388 0.417 61.8
rbcL-accD_p3 rbcL-accD CGATGCGAAGACAGAGGAAA TGATTTCATGTTCCCCGGTC 364–389 0.417 61.8
rbcL-accD_p4 rbcL-accD TGTTCGATGCGAAGACAGAG GGTTGCTAAGCCTGCGATAT 416–441 0.417 61.8
rbcL-accD_p5 rbcL-accD TGTTCGATGCGAAGACAGAG GATTTCATGTTCCCCGGTCA 367–392 0.417 61.6
accD_p1 accD CGATGCGAAGACAGAGGAAA CAGGCATAAGCGCTTTTTCC 2623–2982 0.667 77.9
accD_p2 accD CGATGCGAAGACAGAGGAAA GCGCCCCTGATCTATTTGAA 2680–2972 0.333 65.0
accD_p3 accD TGTTCGATGCGAAGACAGAG GCGCCCCTGATCTATTTGAA 2684–2961 0.250 61.6
accD_p4 accD CGATGCGAAGACAGAGGAAA AAGAAACCGTAAAGGCCCAG 2984 0.083 42.5
accD_p5 accD CGATGCGAAGACAGAGGAAA GAAACCGTAAAGGCCCAGAA 2982 0.083 42.5
ycf4_p1 ycf4 TTCAAATAGATCAGGGGCGC TGGCTCGACTGAATGTTCTG 910–990 0.833 84.4
ycf4_p2 ycf4 GGAAAAAGCGCTTATGCCTG TGCATGGATTTGGATACGCA 995–1123 0.833 84.2
ycf4_p3 ycf4 TTCAAATAGATCAGGGGCGC TGCATGGATTTGGATACGCA 992–1066 0.750 81.3
ycf4_p4 ycf4 TTCAAATAGATCAGGGGCGC ACAAGACAGAAATGGGCCAG 1242–1344 0.750 81.1
ycf4_p5 ycf4 TTCAAATAGATCAGGGGCGC CAAGACAGAAATGGGCCAGT 1241–1343 0.750 81.1
ycf4-cemA_p1 ycf4-cemA TCGTGATGCTTTTCTACGGG GGAATTCCTGAGCCCAAGAG 1609–1700 0.833 84.2
ycf4-cemA_p2 ycf4-cemA CGTGATGCTTTTCTACGGGA GAGAAATCCACCAGGGCAAA 1277–1348 0.750 80.0
ycf4-cemA_p3 ycf4-cemA CGTGATGCTTTTCTACGGGA GGAATTCCTGAGCCCAAGAG 1628–1699 0.750 78.7
ycf4-cemA_p4 ycf4-cemA TTCTTCTGGTGACCCGTACT GGAATTCCTGAGCCCAAGAG 1395–1427 0.417 59.9
ycf4-cemA_p5 ycf4-cemA TAGTGGTCGGAACTTCCAGT GGAATTCCTGAGCCCAAGAG 1753–1763 0.167 46.6
rpoA_p1 rpoA ACGTGTGTATCTAGGGAGGG CCGAGAACTGGTTCACGTAG 1678–1784 1.000 91.3
rpoA_p2 rpoA ACGTGTGTATCTAGGGAGGG CGAGAACTGGTTCACGTAGG 1677–1783 1.000 91.3
rpoA_p3 rpoA ACGTGTGTATCTAGGGAGGG GGAAGAGACGCAGCATTACA 1348–1430 0.917 88.0
rpoA_p4 rpoA ACGTGTGTATCTAGGGAGGG CGCTCAAACTGCAACAGAAG 1449–1518 0.917 87.9
rpoA_p5 rpoA ACGTGTGTATCTAGGGAGGG AGGGTACGAGAAAGGGAACA 1478–1546 0.583 74.6
rrn16_p1 rrn16 TCGAATCCGCTTTGTCTACG AACTCAGACGTAGCTCCCTT 1621–1627 0.917 76.6
rrn16_p2 rrn16 CGAATCCGCTTTGTCTACGA AACTCAGACGTAGCTCCCTT 1620–1626 0.917 76.5
rrn16_p3 rrn16 TCGAATCCGCTTTGTCTACG TGTGAAGCAGTGTCAAACCA 1593–1594 0.917 75.9
rrn16_p4 rrn16 CGAATCCGCTTTGTCTACGA TGTGAAGCAGTGTCAAACCA 1592–1593 0.917 75.8
rrn16_p5 rrn16 CGAATCCGCTTTGTCTACGA TTTTGGGTGTGAAGCAGTGT 1599 0.833 72.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Adenocalymma acutissimum NC_037455.1 159752 View on NCBI ↗
Adenocalymma albiflorum NC_037461.1 159488 View on NCBI ↗
Adenocalymma aurantiacum NC_036495.1 159407 View on NCBI ↗
Adenocalymma bracteatum NC_036497.1 159725 View on NCBI ↗
Adenocalymma candolleanum NC_036503.1 158409 View on NCBI ↗
Adenocalymma cristicalyx NC_036498.1 159010 View on NCBI ↗
Adenocalymma divaricatum NC_037456.1 158645 View on NCBI ↗
Adenocalymma hatschbachii NC_036499.1 158786 View on NCBI ↗
Adenocalymma pedunculatum NC_036500.1 158103 View on NCBI ↗
Adenocalymma peregrinum NC_036501.1 159187 View on NCBI ↗
Adenocalymma subspicatum NC_036502.1 157089 View on NCBI ↗
Adenocalymma trifoliatum NC_037459.1 160736 View on NCBI ↗