Markers + reference

Tipularia

3 species · Orchidaceae · Asparagales

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Species 3
Genome length 143–155 kb
Candidate markers 273
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 929 0.0382 0.84 69.0 yes View details
ndhK LSC 708 0.0383 0.98 72.3 yes View details
ndhF SSC 2220 0.0587 0.25 58.0 yes View details
ndhF-rpl32 SSC 909 0.0393 0.98 70.5 yes View details
rpl32-trnL-UAG SSC 641 0.0350 1.00 69.9 yes View details
ndhE SSC 321 NA 0.00 23.7 yes View details
trnH-GUG-rpl2 IRb 43 0.0620 1.00 84.7 yes View details
rpl2-trnH-GUG IRa 43 0.0620 1.00 84.7 yes View details
psbT-psbN LSC 64 0.0635 0.98 74.7 yes View details
rps3-rpl22 LSC 61 0.0984 1.00 74.4 yes View details
rps11-rpl36 LSC 170 0.0685 0.86 74.3 yes View details
trnT-UGU-trnL-UAA LSC 571 0.0292 0.92 73.2 yes View details
trnR-ACG-trnN-GUU IRb 567 0.0329 0.98 71.5 yes View details
trnN-GUU-trnR-ACG IRa 567 0.0329 0.98 71.5 yes View details
accD-psaI LSC 846 0.0282 0.95 71.2 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TTTTACTTTGGTATGGGTTGA TGATCATATCTAAACTTCACTTCA 2890 0.333 13.3
trnK-UUU_p2 trnK-UUU TTTTTACTTTGGTATGGGTTGA TGATCATATCTAAACTTCACTTCA 2891 0.333 13.3
trnK-UUU_p3 trnK-UUU TTTTACTTTGGTATGGGTTGA TCTAAACTTCACTTCATATTGATCA 2882 0.333 13.3
trnK-UUU_p4 trnK-UUU TTTTACTTTGGTATGGGTTGA TTGATCATATCTAAACTTCACTTCA 2891 0.333 13.3
trnK-UUU_p5 trnK-UUU TTTTTACTTTGGTATGGGTTGA TCTAAACTTCACTTCATATTGATCA 2883 0.333 13.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TACCACTAAACTATACCCGC 872–970 1.000 51.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TTACCACTAAACTATACCCGC 873–971 1.000 50.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TAGTCCACTCAGCCATCTCT TACCACTAAACTATACCCGC 873–971 1.000 48.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CACTTTAGTCCACTCAGCCA TACCACTAAACTATACCCGC 878–976 1.000 48.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACACTTTAGTCCACTCAGCC TACCACTAAACTATACCCGC 879–977 1.000 48.9
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA AGAAAAAGAGCCGGCTATCG ACCAATTTCGCCATATCCCC 661–672 1.000 86.2
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 610–621 1.000 85.9
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA AGAAAAAGAGCCGGCTATCG TAGCGTCTACCAATTTCGCC 669–680 1.000 85.7
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 618–629 1.000 85.3
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 642–653 1.000 84.9
ndhK_p1 ndhK GCACACTGGGAGCGTAAATA AAAAGGAGCGTTGGAATGGT 1023–1036 1.000 86.0
ndhK_p2 ndhK TCTTTACGTAAAGGCCAGCC AAAAGGAGCGTTGGAATGGT 1286–1303 1.000 84.8
ndhK_p3 ndhK GCCAGCCTATCCAACTTTCA AAAAGGAGCGTTGGAATGGT 1273–1290 1.000 84.6
ndhK_p4 ndhK GGGGACGCTCATTGAATGAT AAAAGGAGCGTTGGAATGGT 1404–1421 0.667 70.8
ndhK_p5 ndhK GAAGGGGACGCTCATTGAAT AAAAGGAGCGTTGGAATGGT 1407–1424 0.667 70.6
accD-psaI_p1 accD-psaI CACGGTTTCCTTCCCTTGAA AAGAAACCATTGCGATTGCC 910–952 1.000 83.6
accD-psaI_p2 accD-psaI CACGGTTTCCTTCCCTTGAA CGATTGCCGGAAAGACTAGG 898–940 1.000 83.2
accD-psaI_p3 accD-psaI CACGGTTTCCTTCCCTTGAA CGGAAAGACTAGGCCCACTA 891–933 1.000 82.6
accD-psaI_p4 accD-psaI TCAGCTACACGGTTTCCTTC AAGAAACCATTGCGATTGCC 917–959 1.000 80.1
accD-psaI_p5 accD-psaI TCAGCTACACGGTTTCCTTC CGATTGCCGGAAAGACTAGG 905–947 1.000 79.8
psbT-psbN_p1 psbT-psbN CGAGAACCACCTAAAGTTCCA TCGAAGAACATGGGGACTAG 122–123 1.000 60.3
psbT-psbN_p2 psbT-psbN GCGATCGAATCTATGGAAGCA TCGAAGAACATGGGGACTAG 203–204 1.000 59.0
psbT-psbN_p3 psbT-psbN CGAGAACCACCTAAAGTTCCA TTCGAAGAACATGGGGACTAG 123–124 1.000 58.3
psbT-psbN_p4 psbT-psbN GCGATCGAATCTATGGAAGC TCGAAGAACATGGGGACTAG 203–204 1.000 58.2
psbT-psbN_p5 psbT-psbN GCGATCGAATCTATGGAAGCA TTCGAAGAACATGGGGACTAG 204–205 1.000 57.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Tipularia japonica NC_068106.1 154943 View on NCBI ↗
Tipularia josephi MN990437.1 146816 View on NCBI ↗
Tipularia szechuanica MN990442.1 142799 View on NCBI ↗