Markers + reference

Tabernaemontana

2 species · Apocynaceae · Gentianales

Back to catalogue

Species 2
Genome length 158–162 kb
Candidate markers 267
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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 808 0.0191 0.97 61.0 yes View details
rps16-trnQ-UUG LSC 1233 0.0091 0.98 65.4 yes View details
trnE-UUC-trnT-GGU LSC 883 0.0263 0.99 66.5 yes View details
psbZ-trnG-GCC LSC 6220 0.0143 0.44 52.7 yes View details
psaA-ycf3 LSC 803 0.0100 1.00 51.4 yes View details
clpP LSC 2027 0.0069 1.00 48.6 yes View details
ndhF-rpl32 SSC 734 0.0124 0.99 54.3 yes View details
ycf1 SSC 5601 0.0080 1.00 44.4 yes View details
rpoC1-rpoB LSC 5 0.2000 1.00 87.5 yes View details
trnR-ACG-trnN-GUU IRb 589 0.0085 1.00 63.4 yes View details
trnN-GUU-trnR-ACG IRa 589 0.0085 1.00 63.4 yes View details
ycf2-trnL-CAA IRb 680 0.0074 1.00 63.0 yes View details
trnL-CAA-ycf2 IRa 680 0.0074 1.00 63.0 yes View details
trnC-GCA-petN LSC 870 0.0071 0.97 62.9 yes View details
psbE-petL LSC 1175 0.0060 1.00 62.6 yes View details
petN-psbM LSC 1196 0.0076 0.99 61.8 yes View details
trnD-GUC-trnY-GUA LSC 102 0.0294 1.00 61.7 yes View details
atpF LSC 1280 0.0039 0.99 61.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAAAGGGTGGGTGTTTTTAA 902–923 1.000 45.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAAAAGGGTGGGTGTTTTTA 903–924 1.000 45.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGGTGGGTGTTTTTA 841–862 1.000 44.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGGTGGGTGTTTTTAA 840–861 1.000 44.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAAAAGGGTGGGTGTTTTTAA 903–924 1.000 44.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1306–1310 1.000 80.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1317–1321 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1310–1314 1.000 75.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1336–1340 1.000 75.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1318–1322 1.000 75.1
atpF_p1 atpF TTTCGTCAGCTCGAATGGTT AAGAGGGGCGAAGTGATAGA 1438–1440 1.000 78.1
atpF_p2 atpF TTTCGTCAGCTCGAATGGTT AGAGGGGCGAAGTGATAGAA 1437–1439 1.000 78.1
atpF_p3 atpF TCGTCAGCTCGAATGGTTAC AAGAGGGGCGAAGTGATAGA 1436–1438 1.000 77.3
atpF_p4 atpF TCGTCAGCTCGAATGGTTAC AGAGGGGCGAAGTGATAGAA 1435–1437 1.000 77.3
atpF_p5 atpF GTCAGCTCGAATGGTTACCA AGAGGGGCGAAGTGATAGAA 1433–1435 1.000 76.4
rpoC1-rpoB_p1 rpoC1-rpoB CAGGATTTTAGTGGCCCAGG CGAGGATGCTCCAGAATCTT 228 1.000 71.2
rpoC1-rpoB_p2 rpoC1-rpoB CAGGATTTTAGTGGCCCAGG CCGAGGATGCTCCAGAATCT 229 1.000 70.9
rpoC1-rpoB_p3 rpoC1-rpoB AGGCGCTTATTTGTTGAGGA CGAGGATGCTCCAGAATCTT 211 1.000 69.2
rpoC1-rpoB_p4 rpoC1-rpoB ACCTCTCCATTAGGCAGGAT CGAGGATGCTCCAGAATCTT 242 1.000 69.0
rpoC1-rpoB_p5 rpoC1-rpoB CAGGATTTTAGTGGCCCAGG CGAGGATGCTCCAGAATCTTT 228 1.000 69.0
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 961–980 1.000 81.9
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 959–978 1.000 81.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 962–981 1.000 81.3
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 907–926 1.000 80.9
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTCTTCCCCACACTACGAGT 977–996 1.000 79.7
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA TCATTCTAGTTCCTACCGCCT 1282–1292 1.000 72.9
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT TCATTCTAGTTCCTACCGCCT 1280–1290 1.000 72.9
petN-psbM_p3 petN-psbM ACTCGTAGTGTGGGGAAGAA TCTAGTTCCTACCGCCTTTCT 1278–1288 1.000 72.4
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT TCTAGTTCCTACCGCCTTTCT 1276–1286 1.000 72.4
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG TCATTCTAGTTCCTACCGCCT 1279–1289 1.000 72.3

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
Tabernaemontana bovina NC_079611.1 161700 View on NCBI ↗
Tabernaemontana divaricata MZ073339.1 157954 View on NCBI ↗