Markers + reference

Thamnosma

2 species · Rutaceae · Sapindales

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Species 2
Genome length 155–156 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 296 0.0237 1.00 51.9 yes View details
trnS-GCU-trnG-GCC LSC 714 0.0244 0.98 66.8 yes View details
atpF LSC 1354 0.0163 1.00 68.6 yes View details
rpoC1 LSC 2845 0.0088 1.00 47.1 yes View details
trnD-GUC-trnY-GUA LSC 480 0.0315 0.99 66.7 yes View details
trnE-UUC-trnT-GGU LSC 762 0.0186 0.99 70.7 yes View details
trnT-GGU-psbD LSC 1196 0.0186 0.99 67.5 yes View details
accD-psaI LSC 744 0.0244 0.99 58.8 yes View details
ndhF-rpl32 SSC 820 0.0337 0.83 66.0 yes View details
rpl32-trnL-UAG SSC 685 0.0365 0.80 70.8 yes View details
ycf1 SSC 5508 0.0135 1.00 60.5 yes View details
rps3-rpl22 LSC 68 0.0588 1.00 77.2 yes View details
rpoC2-rpoC1 LSC 166 0.0422 1.00 76.7 yes View details
ndhK-ndhC LSC 58 0.0357 0.97 72.7 yes View details
ndhD-psaC SSC 170 0.0414 0.99 70.2 yes View details
petA-psbJ LSC 817 0.0160 1.00 68.3 yes View details
ycf3-trnS-GGA LSC 356 0.0291 0.97 66.5 yes View details
psbZ-trnG-UCC LSC 562 0.0160 1.00 65.3 yes View details
psaA-ycf3 LSC 733 0.0096 1.00 64.4 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CTCCGTGTCAACCGCTTAAT ATTTGATCGGGGCGAAATGA 2864–2886 1.000 78.5
trnK-UUU_p2 trnK-UUU CTCCGTGTCAACCGCTTAAT AGAATTTGATCGGGGCGAAA 2867–2889 1.000 77.9
trnK-UUU_p3 trnK-UUU CTCCGTGTCAACCGCTTAAT TTTGATCGGGGCGAAATGAA 2863–2885 1.000 77.5
trnK-UUU_p4 trnK-UUU CTCCGTGTCAACCGCTTAAT TTTTTGTGCTCTTCAGGCCT 2969 0.500 57.2
trnK-UUU_p5 trnK-UUU CTCCGTGTCAACCGCTTAAT TTTGTGCTCTTCAGGCCTAC 2967 0.500 56.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TGTGCCGTTTATCGAATCGT 653–657 1.000 82.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 TTCCACGCCAAGACTTCAAA TGTGCCGTTTATCGAATCGT 754–758 1.000 81.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACTCGACCCAACCTGGATTA TGTGCCGTTTATCGAATCGT 785–789 1.000 81.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGTAAGGGATTTAGTGGGCG TGTGCCGTTTATCGAATCGT 1251–1255 1.000 81.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTGGGCGATCAAACGATAC TGTGCCGTTTATCGAATCGT 1239–1243 1.000 81.0
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CCGACGCTTTAATCCACTCA TGAACGAATCACACTTTTACCAC 779–782 1.000 56.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CCGACGCTTTAATCCACTCA ACGAATCACACTTTTACCACT 776–779 1.000 55.1
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA TGAACGAATCACACTTTTACCAC 837–840 1.000 54.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CCGACGCTTTAATCCACTCA GAACGAATCACACTTTTACCACT 778–781 1.000 54.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACGCTTTAATCCACTCAGCC TGAACGAATCACACTTTTACCAC 776–779 1.000 54.0
atpF_p1 atpF CGTCGGCTTTAATTGTTGCC AGTCGATCTAAAAGAGGAGATCA 1459–1468 1.000 41.5
atpF_p2 atpF GCTCAATACGCTCACGGATA AGTCGATCTAAAAGAGGAGATCA 1492–1501 1.000 41.5
atpF_p3 atpF TCGTCGGCTTTAATTGTTGC AGTCGATCTAAAAGAGGAGATCA 1460–1469 1.000 41.5
atpF_p4 atpF ATTGCTCAATACGCTCACGG AGTCGATCTAAAAGAGGAGATCA 1495–1504 1.000 41.5
atpF_p5 atpF GTCGGCTTTAATTGTTGCCA AGTCGATCTAAAAGAGGAGATCA 1458–1467 1.000 41.5
rpoC2-rpoC1_p1 rpoC2-rpoC1 TATGCCATTCCGAAGTGCTC CGAACTACCGTTGGCCATAT 354 1.000 79.3
rpoC2-rpoC1_p2 rpoC2-rpoC1 GTGAAAGACCAGACTCACCC CGAACTACCGTTGGCCATAT 283 1.000 78.7
rpoC2-rpoC1_p3 rpoC2-rpoC1 TATGCCATTCCGAAGTGCTC ATACAAGGGTTTTGTCGGGC 306 1.000 77.8
rpoC2-rpoC1_p4 rpoC2-rpoC1 GCCATTCCGAAGTGCTCTAT CGAACTACCGTTGGCCATAT 351 1.000 77.7
rpoC2-rpoC1_p5 rpoC2-rpoC1 AGACTCACCCGTTCTGTCAT CGAACTACCGTTGGCCATAT 273 1.000 77.2
rpoC1_p1 rpoC1 CCCAAAGGGCCCTAGAATTC ACGATCTTTGGCTTTGGAACT 2988 0.500 50.3
rpoC1_p2 rpoC1 CCCAAAGGGCCCTAGAATTC TCGAGAACTACGATCTTTGGC 2997 0.500 50.2
rpoC1_p3 rpoC1 CCCAAAGGGCCCTAGAATTC CGAGAACTACGATCTTTGGCT 2996 0.500 50.2
rpoC1_p4 rpoC1 CCCAAAGGGCCCTAGAATTC CGATCTTTGGCTTTGGAACTG 2987 0.500 49.8
rpoC1_p5 rpoC1 CCCAAAGGGCCCTAGAATTC ACGATCTTTGGCTTTGGAAC 2988 0.500 48.4

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
Thamnosma montana NC_063822.1 155641 View on NCBI ↗
Thamnosma texana NC_063824.1 154656 View on NCBI ↗