Markers + reference

Thunbergia

2 species · Acanthaceae · Lamiales

Back to catalogue

Species 2
Genome length 152–152 kb
Candidate markers 268
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 442 0.0726 0.97 76.7 yes View details
ycf3-trnS-GGA LSC 710 0.0377 0.75 63.8 yes View details
rbcL-accD LSC 701 0.0447 0.99 71.9 yes View details
rpl22 LSC 480 0.0417 1.00 66.9 yes View details
ycf1 IRb 795 0.0176 1.00 54.0 no View details
ndhF SSC 2277 0.0338 1.00 61.8 yes View details
ndhF-rpl32 SSC 504 0.0586 0.98 73.9 yes View details
ycf1 SSC 5523 0.0430 0.99 66.2 yes View details
rpoA-rps11 LSC 65 0.0820 0.94 78.6 yes View details
psbT-psbN LSC 60 0.1333 1.00 78.1 yes View details
rrn16-trnI-GAU IRb 297 0.0438 1.00 77.7 yes View details
trnI-GAU-rrn16 IRa 297 0.0438 1.00 77.7 yes View details
trnG-UCC-trnR-UCU LSC 175 0.0614 0.93 74.8 yes View details
petD-rpoA LSC 158 0.0949 1.00 74.8 yes View details
trnfM-CAU-rps14 LSC 148 0.0432 0.94 73.7 yes View details
psaJ-rpl33 LSC 495 0.0450 0.99 72.9 yes View details
rpl22-rps19 LSC 208 0.1202 1.00 72.8 yes View details
ccsA-ndhD SSC 234 0.0694 0.92 72.5 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 90 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 GAGCTTAGTTTCCGTCTGGG 1128–1129 1.000 82.6
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGTGGGAGCTTAGTTTCCG 1134–1135 1.000 82.6
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGAGCTTAGTTTCCGTCTGG 1129–1130 1.000 82.6
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGGAGCTTAGTTTCCGTCTG 1130–1131 1.000 82.6
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGCTTAGTTTCCGTCTGGG 1142–1143 1.000 82.6
trnK-UUU_p1 trnK-UUU ACTCCCAAGCACACGAATTT GGCAATGGTTTGATTAGCTCG 2970–2972 1.000 74.5
trnK-UUU_p2 trnK-UUU ACTCCCAAGCACACGAATTT AGGGCAATGGTTTGATTAGCT 2972–2974 1.000 74.3
trnK-UUU_p3 trnK-UUU ACTCCCAAGCACACGAATTT GGGCAATGGTTTGATTAGCTC 2971–2973 1.000 71.6
trnK-UUU_p4 trnK-UUU GACTCCCAAGCACACGAATT GGCAATGGTTTGATTAGCTCG 2971–2973 1.000 70.9
trnK-UUU_p5 trnK-UUU GACTCCCAAGCACACGAATT AGGGCAATGGTTTGATTAGCT 2973–2975 1.000 70.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 243–255 1.000 70.4
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 246–258 1.000 70.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 249–261 1.000 69.6
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU GACGTTCAAAGCGCTGAATC AGAAGACCTCTGTCCTATCCA 282–294 1.000 68.7
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU GTTCAAAGCGCTGAATCGAC AGAAGACCTCTGTCCTATCCA 279–291 1.000 68.7
trnfM-CAU-rps14_p1 trnfM-CAU-rps14 GCTACCAAACTGCTCTACCC CGTTGTTTTTCGACCGGAAG 283–292 1.000 83.9
trnfM-CAU-rps14_p2 trnfM-CAU-rps14 AAGGTTATGAGCCTTGCGAG CGTTGTTTTTCGACCGGAAG 302–311 1.000 83.6
trnfM-CAU-rps14_p3 trnfM-CAU-rps14 TTTGAACCCGTGACCTCAAG CGTTGTTTTTCGACCGGAAG 319–328 1.000 83.3
trnfM-CAU-rps14_p4 trnfM-CAU-rps14 GATGTTGCGGAGACAGGATT CGTTGTTTTTCGACCGGAAG 337–346 1.000 83.2
trnfM-CAU-rps14_p5 trnfM-CAU-rps14 ACAGGATTTGAACCCGTGAC CGTTGTTTTTCGACCGGAAG 325–334 1.000 82.7
ycf3-trnS-GGA_p1 ycf3-trnS-GGA ATGCTTGTTGTCCCAACCAT AACCATTTGACCCTTCACCC 1519–1675 1.000 85.7
ycf3-trnS-GGA_p2 ycf3-trnS-GGA ACTTCACCTTCAACAAGCGT AACCATTTGACCCTTCACCC 1257–1413 1.000 85.7
ycf3-trnS-GGA_p3 ycf3-trnS-GGA AGGTGTAGTGCTTCTTCCCT AACCATTTGACCCTTCACCC 1433–1589 1.000 85.6
ycf3-trnS-GGA_p4 ycf3-trnS-GGA GGTACTAGTGGAGTGGGGTT AACCATTTGACCCTTCACCC 1400–1556 1.000 85.5
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTGGTACTAGTGGAGTGGGG AACCATTTGACCCTTCACCC 1402–1558 1.000 85.4
rbcL-accD_p1 rbcL-accD ACTACAGTTCGGTGGAGGAA ACTCTTCTCGGGGGTTTGTA 1548 0.500 59.8
rbcL-accD_p2 rbcL-accD ACTACAGTTCGGTGGAGGAA TACTCTTCTCGGGGGTTTGT 1549 0.500 59.8
rbcL-accD_p3 rbcL-accD TTGAATGCTACTGCGGGTAC ACTCTTCTCGGGGGTTTGTA 2027 0.500 59.7
rbcL-accD_p4 rbcL-accD TTGAATGCTACTGCGGGTAC TACTCTTCTCGGGGGTTTGT 2028 0.500 59.7
rbcL-accD_p5 rbcL-accD TCATGGTATGCACTTCCGTG ACTCTTCTCGGGGGTTTGTA 1827 0.500 59.7

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
Thunbergia erecta MZ555773.1 152202 View on NCBI ↗
Thunbergia grandiflora PX516301.1 151547 View on NCBI ↗