Markers + reference

Astilbe

5 species · Saxifragaceae · Saxifragales

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Species 5
Genome length 156–157 kb
Candidate markers 270
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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 858 0.0110 1.00 54.5 yes View details
psbZ-trnG-UCC LSC 633 0.0209 0.98 68.2 yes View details
trnT-UGU-trnL-UAA LSC 1020 0.0096 1.00 49.5 yes View details
ndhC-trnV-UAC LSC 1117 0.0071 0.99 61.1 yes View details
petA-psbJ LSC 810 0.0135 0.95 50.7 yes View details
rpl16 LSC 1451 0.0103 0.99 54.8 yes View details
ycf1 IRb 1172 0.0058 1.00 36.5 yes View details
ndhF-rpl32 SSC 1127 0.0117 1.00 59.1 yes View details
rps15-ycf1 SSC 422 0.0213 1.00 50.6 yes View details
ycf1 SSC 5604 0.0052 1.00 34.5 no View details
psbM-trnD-GUC LSC 1224 0.0094 0.99 64.5 yes View details
trnR-UCU-atpA LSC 210 0.0119 0.99 61.8 yes View details
psbC-trnS-UGA LSC 233 0.0215 1.00 60.5 yes View details
trnD-GUC-trnY-GUA LSC 400 0.0097 1.00 59.1 yes View details
trnH-GUG-psbA LSC 335 0.0191 1.00 57.1 yes View details
petN-psbM LSC 650 0.0109 1.00 57.1 yes View details
trnC-GCA-petN LSC 734 0.0079 1.00 57.0 yes View details
trnG-GCC-trnR-UCU LSC 187 0.0182 1.00 56.6 yes View details
ycf4-cemA LSC 943 0.0085 1.00 56.5 yes View details
trnY-GUA-trnE-UUC LSC 64 0.0250 1.00 55.9 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 GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 389–404 1.000 85.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 392–407 1.000 84.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 403–418 1.000 84.8
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 402–417 1.000 84.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 404–419 1.000 84.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAGGCAGCGGTTTTTAAGGA 1036–1046 1.000 82.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AGGCAGCGGTTTTTAAGGAA 1035–1045 1.000 82.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAGGCAGCGGTTTTTAAGGA 1035–1045 1.000 82.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGGCAGCGGTTTTTAAGGAA 1034–1044 1.000 82.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 1079–1089 1.000 82.6
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 254–267 1.000 69.4
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 257–270 1.000 69.1
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 260–273 1.000 68.6
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 263–276 1.000 68.3
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 258–271 1.000 66.9
trnR-UCU-atpA_p1 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT GAGGAAGCAGAAGCCCTTTT 364–375 1.000 79.0
trnR-UCU-atpA_p2 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT CATTCACCGAGGAAGCAGAA 372–383 1.000 78.8
trnR-UCU-atpA_p3 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT AAGACATTCACCGAGGAAGC 376–387 1.000 78.8
trnR-UCU-atpA_p4 trnR-UCU-atpA GGAATGAAAGGCGTCCATTG GAGGAAGCAGAAGCCCTTTT 367–378 1.000 78.4
trnR-UCU-atpA_p5 trnR-UCU-atpA GGAATGAAAGGCGTCCATTG CATTCACCGAGGAAGCAGAA 375–386 1.000 78.2
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 824–849 1.000 82.3
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 768–793 1.000 82.3
trnC-GCA-petN_p3 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGAGTCCACTTCTTCCCCAT 885–910 1.000 80.4
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 829–854 1.000 80.4
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 786–811 1.000 80.0
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 798–812 1.000 70.6
petN-psbM_p2 petN-psbM GGGGACACAATTCACATGGA TGCTACTGCACTGTTCATTCT 820–834 1.000 70.0
petN-psbM_p3 petN-psbM AGGGGACACAATTCACATGG TGCTACTGCACTGTTCATTCT 821–835 1.000 70.0
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 737–751 1.000 69.3
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 798–812 1.000 66.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Astilbe chinensis NC_060775.1 157231 View on NCBI ↗
Astilbe koreana NC_060776.1 156752 View on NCBI ↗
Astilbe rivularis NC_066493.1 156240 View on NCBI ↗
Astilbe taquetii PQ412805.1 156968 View on NCBI ↗
Astilbe uljinensis PQ412804.1 157142 View on NCBI ↗