Markers + reference

Tanaecium

2 species · Bignoniaceae · Lamiales

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Species 2
Genome length 159–160 kb
Candidate markers 276
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-accD LSC 454 0.0463 1.00 67.7 yes View details
accD LSC 1749 0.0479 0.94 75.5 yes View details
psaI-ycf4 LSC 512 0.0692 0.93 77.2 yes View details
ycf4 LSC 522 0.0664 0.98 74.8 yes View details
rpl33-rps18 LSC 1094 0.0522 0.44 70.8 yes View details
rps18 LSC 597 0.0325 0.82 69.4 yes View details
rpoA LSC 1131 0.1141 0.89 81.9 yes View details
trnN-GUU-ycf1 IRb 826 0.0400 0.73 71.6 yes View details
ycf1-trnN-GUU IRa 826 0.0400 0.73 71.6 yes View details
rpoA-rps11 LSC 71 0.2295 0.86 75.1 yes View details
clpP LSC 2042 0.0383 0.97 69.7 yes View details
rpl2-trnH-GUG IRa 79 0.0253 0.99 69.3 no View details
psbZ-trnG-UCC LSC 265 0.0344 0.99 69.2 yes View details
petA-psbJ LSC 999 0.0140 1.00 66.9 yes View details
psbK-psbI LSC 382 0.0191 0.96 66.4 yes View details
rps12-clpP LSC 184 0.0489 1.00 66.0 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 488–502 1.000 82.6
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 489–503 1.000 82.6
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT ACGCCCCGGATCATTAGATA 493–507 1.000 82.5
psbK-psbI_p4 psbK-psbI CTTTTGTTTGGCAAGCTGCT TACGCCCCGGATCATTAGAT 494–508 1.000 82.5
psbK-psbI_p5 psbK-psbI GCCAGTCATACCTGTGCTTT ACGCCCCGGATCATTAGATA 525–539 1.000 81.4
psbZ-trnG-UCC_p1 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG TCGAACCCACATCTTCTCCT 431–458 1.000 80.0
psbZ-trnG-UCC_p2 psbZ-trnG-UCC GCTTCTCCTGATGGTTGGTC TCGAACCCACATCTTCTCCT 429–456 1.000 79.6
psbZ-trnG-UCC_p3 psbZ-trnG-UCC CCGTCGTATTTGCTTCTCCT TCGAACCCACATCTTCTCCT 440–467 1.000 79.3
psbZ-trnG-UCC_p4 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG CCACATCTTCTCCTTGGCAA 425–452 1.000 78.9
psbZ-trnG-UCC_p5 psbZ-trnG-UCC GCTTCTCCTGATGGTTGGTC CCACATCTTCTCCTTGGCAA 423–450 1.000 78.5
rbcL-accD_p1 rbcL-accD ACTACAGTTCGGTGGAGGAA GACATTGCCGGGGTGATATT 917 0.500 59.8
rbcL-accD_p2 rbcL-accD ACTACAGTTCGGTGGAGGAA GCCGGGGTGATATTTGTCAT 911 0.500 59.8
rbcL-accD_p3 rbcL-accD GGAGTCTTGAACTAGCTGCC GACATTGCCGGGGTGATATT 762 0.500 59.7
rbcL-accD_p4 rbcL-accD GGAGTCTTGAACTAGCTGCC GCCGGGGTGATATTTGTCAT 756 0.500 59.7
rbcL-accD_p5 rbcL-accD TTGAATGCTACTGCGGGTAC GCCGGGGTGATATTTGTCAT 1390 0.500 59.7
accD_p1 accD GGAGTCTTGAACTAGCTGCC AAAGAAGCCATTGCCATTGC 2690–2797 1.000 85.4
accD_p2 accD ACTACAGTTCGGTGGAGGAA AAAGAAGCCATTGCCATTGC 2845–2952 1.000 85.3
accD_p3 accD GGAGTCTTGAACTAGCTGCC TTGCCATTGCCGGAAATACT 2680–2787 1.000 85.0
accD_p4 accD ACTACAGTTCGGTGGAGGAA TTGCCATTGCCGGAAATACT 2835–2942 1.000 84.9
accD_p5 accD GCTCTGACCGAGATCTTTGG AAAGAAGCCATTGCCATTGC 2877–2984 1.000 84.8
psaI-ycf4_p1 psaI-ycf4 TAGGCCTAGTATTTCCGGCA TTGCATTTTTCCCTCCTGCT 1127–1180 1.000 87.6
psaI-ycf4_p2 psaI-ycf4 GCAATGGCAATGGCTTCTTT CCAGGAAATTGTGGACCACA 754–788 1.000 87.1
psaI-ycf4_p3 psaI-ycf4 TAGGCCTAGTATTTCCGGCA CCAGGAAATTGTGGACCACA 771–805 1.000 87.0
psaI-ycf4_p4 psaI-ycf4 TTTGAAGTTCCACGGCTTCA TTGCATTTTTCCCTCCTGCT 1587 1.000 86.0
psaI-ycf4_p5 psaI-ycf4 TTTGAAGTTCCACGGCTTCA CCAGGAAATTGTGGACCACA 1212–1231 1.000 85.2
ycf4_p1 ycf4 TAGGCCTAGTATTTCCGGCA TTGCATTTTTCCCTCCTGCT 1127–1180 1.000 87.6
ycf4_p2 ycf4 AAAACAGGAGCAGATGCCAA TTGCATTTTTCCCTCCTGCT 652 0.500 59.9
ycf4_p3 ycf4 AAAACAGGAGCAGATGCCAA TGGCTCGACTGAATGTTCTG 715 0.500 59.3
ycf4_p4 ycf4 AAAACAGGAGCAGATGCCAA ACAAGACAGAAATGGGCCAG 1044 0.500 59.3
ycf4_p5 ycf4 AAAACAGGAGCAGATGCCAA CAAGACAGAAATGGGCCAGT 1043 0.500 59.3

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
Tanaecium pyramidatum NC_069627.1 160112 View on NCBI ↗
Tanaecium tetramerum NC_082920.1 159476 View on NCBI ↗