Markers + reference

Sanicula

21 species · Apiaceae · Apiales

Back to catalogue

Species 21
Genome length 154–156 kb
Candidate markers 269
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH(GTG)-psbA LSC 406 0.0221 1.00 74.0 yes View details
trnS(GCT)-trnG(TCC) LSC 729 0.0118 1.00 60.3 yes View details
trnG(TCC)-trnR(TCT) LSC 215 0.0210 1.00 60.3 yes View details
rpoB-trnC(GCA) LSC 1222 0.0099 1.00 55.9 yes View details
petN-psbM LSC 1050 0.0084 1.00 51.3 yes View details
ycf3-trnS(GGA) LSC 879 0.0099 0.98 57.5 yes View details
petA-psbJ LSC 1076 0.0067 1.00 60.0 yes View details
rpoA LSC 1074 0.0030 1.00 37.3 yes View details
rps15 SSC 273 0.0027 1.00 25.4 yes View details
rps15-ycf1 SSC 401 0.0113 1.00 60.2 yes View details
ycf1 SSC 5313 0.0060 1.00 54.0 yes View details
rpl2-trnH(GTG) IRa 120 0.0040 1.00 66.9 no View details
psbE-petL LSC 917 0.0082 1.00 66.1 yes View details
ndhF-rpl32 SSC 604 0.0069 1.00 64.0 yes View details
atpH-atpI LSC 1177 0.0057 1.00 61.8 yes View details
trnE(TTC)-psbD LSC 1669 0.0055 1.00 61.8 yes View details
trnP(TGG)-psaJ LSC 414 0.0091 1.00 61.3 yes View details
psaJ-rpl33 LSC 429 0.0068 1.00 61.0 yes View details
trnK(TTT)-rps16 LSC 879 0.0061 1.00 60.2 yes View details
rpl22-rps19 LSC 67 0.0132 1.00 60.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH(GTG)-psbA_p1 trnH(GTG)-psbA GATCCACTTGGCTACATCCG TGGAAGTTATGCACGAACGT 493–520 1.000 88.4
trnH(GTG)-psbA_p2 trnH(GTG)-psbA CAATCCACTGCCTTGATCCA TGGAAGTTATGCACGAACGT 507–534 1.000 88.1
trnH(GTG)-psbA_p3 trnH(GTG)-psbA AATCCACTGCCTTGATCCAC TGGAAGTTATGCACGAACGT 506–533 1.000 88.1
trnH(GTG)-psbA_p4 trnH(GTG)-psbA ACAATCCACTGCCTTGATCC TGGAAGTTATGCACGAACGT 508–535 1.000 88.1
trnH(GTG)-psbA_p5 trnH(GTG)-psbA GATCCACTTGGCTACATCCG TGCACGAACGTAATGCTCAT 484–511 1.000 87.5
trnK(TTT)-rps16_p1 trnK(TTT)-rps16 TCCCTCGCTTCATCCAAATG CGGGAACTGTTCGGGATATT 994–1014 1.000 79.6
trnK(TTT)-rps16_p2 trnK(TTT)-rps16 CCGATGGTATGGACGAATCC CGGGAACTGTTCGGGATATT 1011–1031 1.000 79.2
trnK(TTT)-rps16_p3 trnK(TTT)-rps16 CGATGGTATGGACGAATCCC CGGGAACTGTTCGGGATATT 1010–1030 1.000 79.2
trnK(TTT)-rps16_p4 trnK(TTT)-rps16 AAAGCCGAGTACTCTACCGT CGGGAACTGTTCGGGATATT 950–970 1.000 78.8
trnK(TTT)-rps16_p5 trnK(TTT)-rps16 AAGCCGAGTACTCTACCGTT CGGGAACTGTTCGGGATATT 949–969 1.000 78.8
trnS(GCT)-trnG(TCC)_p1 trnS(GCT)-trnG(TCC) ATTAGCAATCCGCCGCTTTA AACCGAAAGACCCCTTAACT 713–851 1.000 74.9
trnS(GCT)-trnG(TCC)_p2 trnS(GCT)-trnG(TCC) ACGGAAAGAGAGGGATTCGA AACCGAAAGACCCCTTAACT 762–900 1.000 73.9
trnS(GCT)-trnG(TCC)_p3 trnS(GCT)-trnG(TCC) ATTAGCAATCCGCCGCTTTA AAACCGAAAGACCCCTTAACT 714–852 1.000 73.0
trnS(GCT)-trnG(TCC)_p4 trnS(GCT)-trnG(TCC) ACGGAAAGAGAGGGATTCGA AAACCGAAAGACCCCTTAACT 763–901 1.000 72.0
trnS(GCT)-trnG(TCC)_p5 trnS(GCT)-trnG(TCC) GCTTTAGTCCACTCAGCCAT AACCGAAAGACCCCTTAACT 699–837 1.000 72.0
trnG(TCC)-trnR(TCT)_p1 trnG(TCC)-trnR(TCT) AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 249–298 1.000 74.1
trnG(TCC)-trnR(TCT)_p2 trnG(TCC)-trnR(TCT) CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 252–301 1.000 73.8
trnG(TCC)-trnR(TCT)_p3 trnG(TCC)-trnR(TCT) AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 255–304 1.000 73.3
trnG(TCC)-trnR(TCT)_p4 trnG(TCC)-trnR(TCT) CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 258–307 1.000 73.0
trnG(TCC)-trnR(TCT)_p5 trnG(TCC)-trnR(TCT) CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 253–302 1.000 71.5
atpH-atpI_p1 atpH-atpI GGCAGAAACCAGTGGATTCA TTTTTGCAACTTTAGCCGCG 1191–1393 1.000 81.3
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1258–1460 1.000 81.0
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 1218–1420 1.000 80.8
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1203–1405 1.000 80.5
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC TTTTTGCAACTTTAGCCGCG 1262–1464 1.000 80.4
rpoB-trnC(GCA)_p1 rpoB-trnC(GCA) CGAGCCCATATCCTTGCTTT TTCAAGACCCAGCCAGTAGA 1977–2048 1.000 86.2
rpoB-trnC(GCA)_p2 rpoB-trnC(GCA) TTGTTTCCTACTCACGCGAG TTCAAGACCCAGCCAGTAGA 1993–2064 1.000 85.9
rpoB-trnC(GCA)_p3 rpoB-trnC(GCA) CCGCCTACACAAGCAAATTG TTCAAGACCCAGCCAGTAGA 2169–2240 1.000 85.7
rpoB-trnC(GCA)_p4 rpoB-trnC(GCA) CTCATTTCCGTCTCGAAGCA CTTACCACTCGGCCATATCG 1218–1275 0.667 70.3
rpoB-trnC(GCA)_p5 rpoB-trnC(GCA) CTCATTTCCGTCTCGAAGCA TTCAAGACCCAGCCAGTAGA 1492–1549 0.667 70.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (21)

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

Species Accession Length (bp) Link
Sanicula astrantiifolia NC_061561.1 155721 View on NCBI ↗
Sanicula brevispina NC_072645.1 155396 View on NCBI ↗
Sanicula chinensis NC_085169.1 155378 View on NCBI ↗
Sanicula coerulescens NC_072644.1 155757 View on NCBI ↗
Sanicula elongata NC_085742.1 155634 View on NCBI ↗
Sanicula flavovirens NC_061752.1 155335 View on NCBI ↗
Sanicula giraldii var. ovicalycina OR865885.1 155792 View on NCBI ↗
Sanicula hacquetioides NC_072641.1 155686 View on NCBI ↗
Sanicula hanyuanensis OR865889.1 155671 View on NCBI ↗
Sanicula lamelligera NC_061292.1 155028 View on NCBI ↗
Sanicula langaoensis OR865887.1 155739 View on NCBI ↗
Sanicula odorata NC_061689.1 154500 View on NCBI ↗
Sanicula orthacantha NC_072642.1 155662 View on NCBI ↗
Sanicula orthacantha var. stolonifera OQ612641.1 155396 View on NCBI ↗
Sanicula oviformis NC_085744.1 155645 View on NCBI ↗
Sanicula pengshuiensis NC_085741.1 155765 View on NCBI ↗
Sanicula rubriflora OR865880.1 155657 View on NCBI ↗
Sanicula rugulosa NC_085743.1 155527 View on NCBI ↗
Sanicula serrata NC_085740.1 155599 View on NCBI ↗
Sanicula tienmuensis NC_072643.1 155717 View on NCBI ↗
Sanicula tienmuensis var. pauciflora OR865886.1 155693 View on NCBI ↗