Markers + reference

Tainia

3 species · Orchidaceae · Asparagales

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Species 3
Genome length 158–158 kb
Candidate markers 274
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0038 1.00 35.0 yes View details
matK-rps16 LSC 1645 0.0183 0.99 62.1 yes View details
trnS-GCU-trnG-UCC LSC 1066 0.0316 1.00 73.3 yes View details
rpoB-trnC-GCA LSC 1418 0.0186 1.00 59.6 yes View details
petN-psbM LSC 735 0.0222 1.00 68.9 yes View details
ndhC-trnV-UAC LSC 357 0.0962 1.00 82.6 yes View details
rbcL-accD LSC 786 0.0271 1.00 67.0 yes View details
clpP-psbB LSC 760 0.0280 0.99 79.4 yes View details
ndhF-rpl32 SSC 813 0.0229 0.97 64.1 yes View details
psaC-ndhE SSC 478 0.0286 1.00 60.7 yes View details
rps19-psbA IRa 647 0.0443 1.00 77.5 no View details
psbB-psbT LSC 470 0.0250 0.99 75.7 yes View details
trnF-GAA-ndhJ LSC 592 0.0183 0.98 74.8 yes View details
psbC-trnS-UGA LSC 144 0.0417 1.00 72.5 yes View details
rps8-rpl14 LSC 199 0.0335 1.00 69.6 yes View details
rrn16-trnI-GAU IRb 302 0.0265 1.00 69.4 yes View details
trnI-GAU-rrn16 IRa 302 0.0265 1.00 69.4 yes View details
ccsA-ndhD SSC 278 0.0336 1.00 66.8 yes View details
rpl16-rps3 LSC 184 0.0217 1.00 66.4 yes View details
rpl32-trnL-UAG SSC 689 0.0136 1.00 65.3 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
psbA_p1 psbA AGCAATCCCCCAAGATCTTG GTGCTTGGGAGTCCTTGAAA 1207–1216 1.000 77.0
psbA_p2 psbA CAAGATCTTGGGGGATTGCT GTGCTTGGGAGTCCTTGAAA 1197–1206 1.000 77.0
psbA_p3 psbA AGCAATCCCCCAAGATCTTG TCGTGTGCAATGAAAACTGC 1525–1537 1.000 76.1
psbA_p4 psbA CAAGATCTTGGGGGATTGCT TCGTGTGCAATGAAAACTGC 1515–1527 1.000 76.1
psbA_p5 psbA CAAGATCTTGGGGGATTGCT AATGAAAACTGCAAGCACGG 1507–1519 1.000 76.0
matK-rps16_p1 matK-rps16 TCCTTGTAATTCTGCCATTT GTGCTCAACCCACAGGAAC 1761–1768 1.000 44.3
matK-rps16_p2 matK-rps16 TCCTTGTAATTCTGCCATTT TGCTCAACCCACAGGAACT 1760–1767 1.000 44.3
matK-rps16_p3 matK-rps16 ATCCTTGTAATTCTGCCATT GTGCTCAACCCACAGGAAC 1762–1769 1.000 44.3
matK-rps16_p4 matK-rps16 ATCCTTGTAATTCTGCCATTT GTGCTCAACCCACAGGAAC 1762–1769 1.000 44.3
matK-rps16_p5 matK-rps16 ATCCTTGTAATTCTGCCATT TGCTCAACCCACAGGAACT 1761–1768 1.000 44.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CTTTAGCCCACTCAGCCATC ACGAATCACACTTTTACCACT 1125–1147 1.000 55.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TAGCAATCCGACGCTTTAGC ACGAATCACACTTTTACCACT 1138–1160 1.000 54.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CTTTAGCCCACTCAGCCATC AGAACGAATCACACTTTTACCAC 1128–1150 1.000 54.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CTTTAGCCCACTCAGCCATC GAACGAATCACACTTTTACCACT 1127–1149 1.000 54.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TAGCAATCCGACGCTTTAGC GAACGAATCACACTTTTACCACT 1140–1162 1.000 53.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG CCTTACCACTTGGCCATGC 1532–1545 1.000 67.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG GCCTTACCACTTGGCCATG 1533–1546 1.000 67.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT CCTTACCACTTGGCCATGC 1533–1546 1.000 64.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT GCCTTACCACTTGGCCATG 1534–1547 1.000 64.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTTCCGTCAAGCCCTGATTA CCTTACCACTTGGCCATGC 1528–1541 1.000 63.5
petN-psbM_p1 petN-psbM GGGACATCATTCGCATGGAT ACGTCAAAACAGTCAGCCAA 831–872 1.000 83.4
petN-psbM_p2 petN-psbM GGGGAAGAAGTGGGCTTTAG ACGTCAAAACAGTCAGCCAA 747–788 1.000 83.4
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTCAAAACAGTCAGCCAA 810–851 1.000 83.0
petN-psbM_p4 petN-psbM TATGGGGAAGAAGTGGGCTT ACGTCAAAACAGTCAGCCAA 750–791 1.000 81.9
petN-psbM_p5 petN-psbM GGGACATCATTCGCATGGAT TACGTCAAAACAGTCAGCCA 832–873 1.000 80.6
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GAGAGATGGCTGAGTGGTTG 267–274 1.000 81.2
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC ATAGCCCCGGTCTTGAAAAC 247–254 1.000 80.6
psbC-trnS-UGA_p3 psbC-trnS-UGA AGCGGGGTTTGAAAAAGGAA GAGAGATGGCTGAGTGGTTG 304–311 1.000 80.4
psbC-trnS-UGA_p4 psbC-trnS-UGA TTCCATGACCCCTCTTAGCT GAGAGATGGCTGAGTGGTTG 259–266 1.000 80.4
psbC-trnS-UGA_p5 psbC-trnS-UGA TTGTGGGACATTTGTGGCAT GAGAGATGGCTGAGTGGTTG 347–354 1.000 79.6

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
Tainia acuminata NC_060558.1 157603 View on NCBI ↗
Tainia cordifolia NC_045851.1 158316 View on NCBI ↗
Tainia dunnii NC_045862.1 158459 View on NCBI ↗