Markers + reference

Tournefortia

2 species · Heliotropiaceae · Boraginales

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Species 2
Genome length 156–156 kb
Candidate markers 261
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 279 0.1412 0.91 78.5 yes View details
rps16-trnQ-UUG LSC 1096 0.0542 0.89 82.3 yes View details
trnS-GCU-trnG-UCC LSC 833 0.0413 0.90 75.2 yes View details
trnE-UUC-trnT-GGU LSC 440 0.0488 0.93 74.3 yes View details
accD-psaI LSC 739 0.0405 0.97 70.0 yes View details
petA-psbJ LSC 1031 0.0434 0.98 70.9 yes View details
ndhF SSC 2247 0.0290 1.00 59.8 yes View details
ndhE SSC 306 0.0196 1.00 49.8 yes View details
ndhE-ndhG SSC 218 0.1436 0.93 80.7 yes View details
ycf1 SSC 5502 0.0329 0.99 58.1 yes View details
trnF-GAA-ndhJ LSC 665 0.0392 1.00 80.8 yes View details
trnL-UAG-ccsA SSC 110 0.0784 0.93 80.7 yes View details
psbI-trnS-GCU LSC 122 0.0603 0.95 80.4 yes View details
trnG-UCC-trnR-UCU LSC 192 0.0500 0.94 78.8 yes View details
trnS-GGA-rps4 LSC 282 0.0567 1.00 78.3 yes View details
rpl32-trnL-UAG SSC 740 0.0442 0.95 77.9 yes View details
rps15-ycf1 SSC 368 0.0468 0.93 76.7 yes View details
psaA-ycf3 LSC 832 0.0408 0.91 76.0 yes View details
ccsA-ndhD SSC 250 0.0736 0.92 75.5 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 95 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 TCGAAGCTCCATCTACAAATGG 321–326 1.000 73.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGAAGCTCCATCTACAAATGG 335–340 1.000 73.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCGAAGCTCCATCTACAAATGG 334–339 1.000 73.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCGAAGCTCCATCTACAAATGG 336–341 1.000 73.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGAAGCTCCATCTACAAATGG 320–325 1.000 73.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTC GCTATTCGGAGGTTCGAGTC 1075–1165 1.000 86.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTC TATTCGGAGGTTCGAGTCCT 1073–1163 1.000 84.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTC ATTCGGAGGTTCGAGTCCTT 1072–1162 1.000 84.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GCTATTCGGAGGTTCGAGTC 1102–1192 1.000 83.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GCTATTCGGAGGTTCGAGTC 1101–1191 1.000 83.8
psbI-trnS-GCU_p1 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TAAAGCGGCGGATTGCTAAT 220–225 1.000 82.2
psbI-trnS-GCU_p2 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TTTCAATTGGGAGAGGTGGC 249–254 1.000 81.7
psbI-trnS-GCU_p3 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT GGTGGCTGAGTGGACTAAAG 235–240 1.000 81.5
psbI-trnS-GCU_p4 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT AGGTGGCTGAGTGGACTAAA 236–241 1.000 80.1
psbI-trnS-GCU_p5 psbI-trnS-GCU AATGATCCAGGGCGTAATCC TAAAGCGGCGGATTGCTAAT 221–226 1.000 79.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 848–907 1.000 58.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CTTTAGTCCACTCAGCCACC ACGAATCACACTTTTACCACT 833–892 1.000 57.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 897–956 1.000 57.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TTTAGTCCACTCAGCCACCT ACGAATCACACTTTTACCACT 832–891 1.000 56.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 849–908 1.000 56.3
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 271–272 1.000 69.5
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 274–275 1.000 69.2
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 277–278 1.000 68.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 280–281 1.000 68.4
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 275–276 1.000 67.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CCTGAACCACTAGACGATGG GAACCGATGACTTACGCCTT 497–519 1.000 82.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CTGAACCACTAGACGATGGG GAACCGATGACTTACGCCTT 496–518 1.000 82.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CCTGAACCACTAGACGATGG CCATGGCGTTACTCTACCAC 476–498 1.000 82.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CTGAACCACTAGACGATGGG CCATGGCGTTACTCTACCAC 475–497 1.000 82.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CTGAACCACTAGACGATGGG TGGCGTTACTCTACCACTGA 472–494 1.000 81.9

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
Tournefortia montana NC_066795.1 155891 View on NCBI ↗
Tournefortia sibirica PV946886.1 155530 View on NCBI ↗