Markers + reference

Taxillus

14 species · Loranthaceae · Santalales

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Species 14
Genome length 122–124 kb
Candidate markers 236
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 10 remaining regions by MarkerSeek score (out of 236 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnR-UCU LSC 464 0.0564 0.96 78.5 yes View details
rpoB-trnC-GCA LSC 685 0.0564 0.92 86.7 yes View details
trnE-UUC-trnT-GGU LSC 402 0.0467 0.99 76.2 yes View details
psaA-ycf3 LSC 600 0.0385 0.99 93.4 yes View details
trnF-GAA-trnM-CAU LSC 437 0.0485 0.75 66.6 yes View details
accD-psaI LSC 554 0.0525 0.95 81.0 yes View details
infA LSC 237 0.0344 0.97 64.4 yes View details
ycf1 IRb 948 0.0073 1.00 50.0 no View details
ccsA-psaC SSC 292 0.0810 0.92 70.4 yes View details
ycf1 SSC 5010 0.0245 1.00 66.8 yes View details
atpB-rbcL LSC 677 0.0301 1.00 87.9 yes View details
trnC-GCA-petN LSC 288 0.0473 0.98 83.4 yes View details
trnH-GUG-psbA LSC 141 0.0465 1.00 81.9 yes View details
trnS-UGA-psbZ LSC 375 0.0425 0.97 79.4 yes View details
petN-psbM LSC 780 0.0285 0.98 77.7 yes View details
trnT-UGU-trnL-UAA LSC 573 0.0437 0.97 77.7 yes View details
rps2-rpoC2 LSC 198 0.0427 0.99 76.9 yes View details
trnD-GUC-trnY-GUA LSC 316 0.0379 0.99 76.6 yes View details
psbA-matK LSC 561 0.0308 1.00 75.5 yes View details
trnT-GGU-psbD LSC 928 0.0300 0.98 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 CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 254–340 1.000 85.6
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 253–339 1.000 85.6
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 255–341 1.000 85.5
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ACCGTGCTAACCTTGGTATG 255–341 1.000 85.1
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC ACCGTGCTAACCTTGGTATG 254–340 1.000 85.1
psbA-matK_p1 psbA-matK GCTTTCACTTGTGCGTCTCT ACGATCTAGTCAATCATTCATGA 617–633 0.929 48.1
psbA-matK_p2 psbA-matK GCTTTCACTTGTGCGTCTCT TCAACGATCTAGTCAATCATTCA 620–636 0.929 48.0
psbA-matK_p3 psbA-matK TTTCACTTGTGCGTCTCTCT TCAACGATCTAGTCAATCATTCA 618–634 0.929 48.0
psbA-matK_p4 psbA-matK GCTTTCACTTGTGCGTCTCT CAACGATCTAGTCAATCATTCATGA 619–635 0.929 48.0
psbA-matK_p5 psbA-matK GCTTTCACTTGTGCGTCTCT TCAACGATCTAGTCAATCATTCATG 620–636 0.929 48.0
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA TGTGGGCATTTCTGTTTCGA 1111–1266 1.000 91.5
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU CGCATAACTCGTACAACGGA TGTGGGCATTTCTGTTTCGA 1130–1285 1.000 91.0
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA GTTTCGAGAGTAGGATCCGC 1098–1253 1.000 90.7
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA CCCGCTATTAATGTGGGCAT 1122–1265 0.786 80.4
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU CGCATAACTCGTACAACGGA CCCGCTATTAATGTGGGCAT 1141–1284 0.786 79.8
rps2-rpoC2_p1 rps2-rpoC2 GGTGCCATTCTAGGATTCCA ACGATTCTCAGAAGATTAGGA 322 0.071 2.9
rps2-rpoC2_p2 rps2-rpoC2 GGTGCCATTCTAGGATTCCA AACGATTCTCAGAAGATTAGGA 323 0.071 2.9
rps2-rpoC2_p3 rps2-rpoC2 AGGTGCCATTCTAGGATTCC ACGATTCTCAGAAGATTAGGA 323 0.071 2.9
rps2-rpoC2_p4 rps2-rpoC2 GGTGCCATTCTAGGATTCCA AAACGATTCTCAGAAGATTAGGA 324 0.071 2.9
rps2-rpoC2_p5 rps2-rpoC2 GGTGCCATTCTAGGATTCCA ACGATTCTCAGAAGATTAGGAT 322 0.071 2.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTCATTTCCATCCCAGAGC CCGGATTTGAACTGGGGAAA 724–835 0.929 88.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCTCATTTCCATCCCAGAGC AACTGGGGAAAGGGGATTTG 715–826 0.929 86.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCTCATTTCCATCCCAGAGC GGGGATTTCGGGTCTTTTGT 758–869 0.857 85.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCTCATTTCCATCCCAGAGC ACAGAATTGGGGGATTTCGG 767–878 0.857 85.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCTCATTTCCATCCCAGAGC ATTTGAACTGGGGAAAGGGG 720–818 0.857 83.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAT 246–376 1.000 89.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TAAAGCAGCCCAAGCGATAC 244–374 1.000 88.7
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCGATA 245–375 1.000 88.0
trnC-GCA-petN_p4 trnC-GCA-petN GTATCATTTTGGCGGCATGG ATTAAAGCAGCCCAAGCGAT 298–428 0.929 86.2
trnC-GCA-petN_p5 trnC-GCA-petN GTATCATTTTGGCGGCATGG TAAAGCAGCCCAAGCGATAC 296–426 0.929 85.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Taxillus levinei NC_058836.1 122231 View on NCBI ↗
Taxillus liquidambaricola NC_058838.1 123074 View on NCBI ↗
Taxillus lonicerifolius NC_058843.1 121753 View on NCBI ↗
Taxillus matsudae NC_058842.1 122319 View on NCBI ↗
Taxillus pseudochinensis NC_058837.1 122812 View on NCBI ↗
Taxillus rhododendricola NC_058841.1 122641 View on NCBI ↗
Taxillus sericus NC_088731.1 123879 View on NCBI ↗
Taxillus sutchuenensis NC_036307.1 122562 View on NCBI ↗
Taxillus sutchuenensis var. duclouxii PZ127291.1 122537 View on NCBI ↗
Taxillus theifer NC_058839.1 122127 View on NCBI ↗
Taxillus thibetensis NC_088730.1 122497 View on NCBI ↗
Taxillus tsaii NC_058840.1 122635 View on NCBI ↗
Taxillus vestitus NC_045109.1 122200 View on NCBI ↗
Taxillus yadoriki NC_051553.1 122192 View on NCBI ↗