Markers + reference

Ulnaria

2 species · Ulnariaceae · Licmophorales

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Species 2
Genome length 116–116 kb
Candidate markers 332
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 332 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB LSC 4137 0.0728 1.00 71.7 yes View details
rpoC2 LSC 4338 0.0877 1.00 72.9 yes View details
ftsH LSC 1872 0.0780 1.00 75.3 yes View details
ycf45 LSC 1347 0.0861 1.00 77.3 yes View details
syfB SSC 2121 0.1221 1.00 77.6 yes View details
ycf35 SSC 369 0.0954 0.99 74.5 yes View details
trnV(TAC)-trnY(GTA) LSC 180 0.1860 0.96 82.4 yes View details
trnP(TGG)-psaA IRa 298 0.1147 0.94 82.1 no View details
rns-trnI(GAT) IRb 56 0.0545 0.98 80.5 yes View details
trnI(GAT)-rns IRa 56 0.0545 0.98 80.5 yes View details
trnM(CAT)-trnS(GCT) LSC 90 0.2237 0.84 80.4 yes View details
rpl14-rps17 SSC 10 0.1000 1.00 79.6 yes View details
petA LSC 945 0.0550 1.00 78.8 yes View details
ycf45-trnP(TGG) IRb 230 0.1469 0.92 78.8 yes View details
ccs1 SSC 1266 0.1003 1.00 78.8 yes View details
trnK(TTT)-trnR(TCT) LSC 69 0.3636 0.80 78.4 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
trnK(TTT)-trnR(TCT)_p1 trnK(TTT)-trnR(TCT) TAGTTCTGGGTTCGAGTCCC TTCGATTCCTACTGGGCCTA 105–119 1.000 84.7
trnK(TTT)-trnR(TCT)_p2 trnK(TTT)-trnR(TCT) ACCGAATAGTTCTGGGTTCG TTCGATTCCTACTGGGCCTA 111–125 1.000 82.9
trnK(TTT)-trnR(TCT)_p3 trnK(TTT)-trnR(TCT) TAGTTCTGGGTTCGAGTCCC GGGCCTATCGTCTAACGGAT 158–172 1.000 82.5
trnK(TTT)-trnR(TCT)_p4 trnK(TTT)-trnR(TCT) ACCGAATAGTTCTGGGTTCG GGGCCTATCGTCTAACGGAT 164–178 1.000 80.7
trnK(TTT)-trnR(TCT)_p5 trnK(TTT)-trnR(TCT) CCGAATAGTTCTGGGTTCGA TTCGATTCCTACTGGGCCTA 110–124 1.000 80.7
trnV(TAC)-trnY(GTA)_p1 trnV(TAC)-trnY(GTA) TACCGCTGAGTTAATTGCCC GATTTACAATCCGCCCCCTT 234–241 1.000 89.9
trnV(TAC)-trnY(GTA)_p2 trnV(TAC)-trnY(GTA) AGACACTCTACCGCTGAGTT GATTTACAATCCGCCCCCTT 242–249 1.000 89.4
trnV(TAC)-trnY(GTA)_p3 trnV(TAC)-trnY(GTA) CTGTGGCCTTCTGCTTGTAA GATTTACAATCCGCCCCCTT 265–272 1.000 89.0
trnV(TAC)-trnY(GTA)_p4 trnV(TAC)-trnY(GTA) TGTGGCCTTCTGCTTGTAAG GATTTACAATCCGCCCCCTT 264–271 1.000 89.0
trnV(TAC)-trnY(GTA)_p5 trnV(TAC)-trnY(GTA) TACCGCTGAGTTAATTGCCC CGTAACTTGACGTAGCGGAT 251–258 1.000 88.8
trnM(CAT)-trnS(GCT)_p1 trnM(CAT)-trnS(GCT) AGTGGTTAGAGCAGGGGATT CTTTCGACCACTCAGCCATT 161–175 1.000 90.3
trnM(CAT)-trnS(GCT)_p2 trnM(CAT)-trnS(GCT) AGTGGTTAGAGCAGGGGATT TTCGACCACTCAGCCATTTC 159–173 1.000 90.2
trnM(CAT)-trnS(GCT)_p3 trnM(CAT)-trnS(GCT) TGGTTAGAGCAGGGGATTCA CTTTCGACCACTCAGCCATT 159–173 1.000 90.2
trnM(CAT)-trnS(GCT)_p4 trnM(CAT)-trnS(GCT) TGGTTAGAGCAGGGGATTCA TTCGACCACTCAGCCATTTC 157–171 1.000 90.2
trnM(CAT)-trnS(GCT)_p5 trnM(CAT)-trnS(GCT) AGTGGTTAGAGCAGGGGATT GACCACTCAGCCATTTCTCC 156–170 1.000 89.7
petA_p1 petA AGTACACCAAGAAGACGAACT AAGCATCCATCTTTTAAAAAGT 1052 1.000 44.0
petA_p2 petA AGTACACCAAGAAGACGAACT AAAGCATCCATCTTTTAAAAAGT 1053 1.000 44.0
petA_p3 petA AGTACACCAAGAAGACGAACT AGCATCCATCTTTTAAAAAGTATTTCC 1051 1.000 44.0
petA_p4 petA AGTACACCAAGAAGACGAACT GCATCCATCTTTTAAAAAGTATTTCCT 1050 1.000 44.0
petA_p5 petA AGTACACCAAGAAGACGAACT ACTAAAGCATCCATCTTTTAAAAAGT 1056 1.000 43.9
rpoB_p1 rpoB ACCATGTACGCTAGCAGTTG ACCAAATCGAATCCAAGATCCA 1153 1.000 69.3
rpoB_p2 rpoB CACCATGTACGCTAGCAGTT ACCAAATCGAATCCAAGATCCA 1154 1.000 69.2
rpoB_p3 rpoB TGCAGGACAAGCTTCCATTT ACCAAATCGAATCCAAGATCCA 850 0.500 42.1
rpoB_p4 rpoB TTACCTGCAGGACAAGCTTC ACCAAATCGAATCCAAGATCCA 855 0.500 40.6
rpoB_p5 rpoB AAACCACCATGTACGCTAGC ACCAAATCGAATCCAAGATCCA 1158 0.500 40.0
rpoC2_p1 rpoC2 TGCAACTAAAACAGGAGGGAC TGCGTTTCTTCTTCCAACCA 258 0.500 50.5
rpoC2_p2 rpoC2 CCAGATTCTTTTTCCCAGCCT TGCGTTTCTTCTTCCAACCA 848 0.500 50.1
rpoC2_p3 rpoC2 TCCAGATTCTTTTTCCCAGCC TGCGTTTCTTCTTCCAACCA 849 0.500 50.1
rpoC2_p4 rpoC2 CCAGATTCTTTTTCCCAGCC TGCGTTTCTTCTTCCAACCA 848 0.500 49.0
rpoC2_p5 rpoC2 TGCAACTAAAACAGGAGGGA TGCGTTTCTTCTTCCAACCA 258 0.500 48.9

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
Ulnaria acus NC_016731.1 116251 View on NCBI ↗
Ulnaria ulna NC_082433.1 116024 View on NCBI ↗