Markers + reference

Rodgersia

2 species · Saxifragaceae · Saxifragales

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Species 2
Genome length 157–157 kb
Candidate markers 266
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 1085 0.0028 1.00 60.4 yes View details
psbM-trnD-GUC LSC 1170 0.0017 1.00 59.7 yes View details
psbZ-trnG-UCC LSC 721 0.0042 0.99 62.1 yes View details
rps18 LSC 312 0.0000 1.00 23.3 yes View details
clpP LSC 2000 0.0010 1.00 46.7 yes View details
ycf1 IRb 1141 0.0000 1.00 27.2 yes View details
ndhF SSC 2247 0.0009 1.00 43.5 yes View details
ndhF-rpl32 SSC 1136 0.0026 1.00 60.3 yes View details
ycf1 SSC 5631 0.0007 1.00 52.9 no View details
ycf1-ndhF SSC 42 0.0476 1.00 79.9 yes View details
trnE-UUC-trntT LSC 867 0.0000 0.99 59.9 yes View details
matK LSC 1521 0.0013 1.00 59.5 yes View details
trnS-trnG-GCC LSC 785 0.0013 1.00 59.5 yes View details
trnC-GCA-petN LSC 860 0.0012 1.00 59.4 yes View details
ycf2-trnL-CAA IRb 949 0.0011 1.00 59.4 yes View details
ccsA SSC 957 0.0010 1.00 59.4 yes View details
trnL-CAA-ycf2 IRa 949 0.0011 1.00 59.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TCCATCATAATTCTTTGTGAATGACT TCGACTGTATCTACACATCCT 2693 1.000 40.1
trnK-UUU_p2 trnK-UUU TCCATCATAATTCTTTGTGAATGACT TGTTTTGATTGTGTCATGCA 2739 1.000 40.1
trnK-UUU_p3 trnK-UUU TCCATCATAATTCTTTGTGAATGACT TGTTTTGATTGTGTCATGCAA 2739 1.000 40.1
trnK-UUU_p4 trnK-UUU TCCATCATAATTCTTTGTGAATGACT TTCGACTGTATCTACACATCCT 2694 1.000 40.1
trnK-UUU_p5 trnK-UUU TCAACAGCCATAGATATCTATCT TCGACTGTATCTACACATCCT 2730 1.000 40.1
matK_p1 matK TCAATCCTTACTGCATGAACA TGTTTTGACCGTATCGCACT 1696 1.000 48.6
matK_p2 matK CCTTACTGCATGAACATTTCAGA TGTTTTGACCGTATCGCACT 1691 1.000 47.8
matK_p3 matK TCCTTACTGCATGAACATTTCAG TGTTTTGACCGTATCGCACT 1692 1.000 47.8
matK_p4 matK CAGTTGATTCAATCCTTACTGCA TGTTTTGACCGTATCGCACT 1704 1.000 47.7
matK_p5 matK TCCTTACTGCATGAACATTTCA TGTTTTGACCGTATCGCACT 1692 1.000 46.8
trnS-trnG-GCC_p1 trnS-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 854 1.000 51.8
trnS-trnG-GCC_p2 trnS-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 853 1.000 51.8
trnS-trnG-GCC_p3 trnS-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 857 1.000 50.7
trnS-trnG-GCC_p4 trnS-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 856 1.000 50.7
trnS-trnG-GCC_p5 trnS-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 855 1.000 50.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GGGGAATCTATGGAGGGTCA 1143–1144 1.000 79.0
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCAGCGG 1171–1172 1.000 78.9
atpH-atpI_p3 atpH-atpI AGCGGCAGAAATCAATGGAT GGGGAATCTATGGAGGGTCA 1135–1136 1.000 78.8
atpH-atpI_p4 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCAGCGG 1163–1164 1.000 78.7
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT GGGGAATCTATGGAGGGTCA 1199–1200 1.000 78.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 972 1.000 78.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 916 1.000 78.2
trnC-GCA-petN_p3 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGAGTCCACTTCTTCCCCAT 1033 1.000 76.8
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 977 1.000 76.6
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 934 1.000 76.0
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1281 1.000 58.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TTCAATTGGTCAGAGCACCG 1288 1.000 55.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 1282 1.000 54.3
psbM-trnD-GUC_p4 psbM-trnD-GUC GGAACTAGAATGAACAGTGCAG TTCAATTGGTCAGAGCACCG 1287 1.000 52.8
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TCAATTGGTCAGAGCACCG 1280 1.000 52.4

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
Rodgersia aesculifolia NC_057229.1 157238 View on NCBI ↗
Rodgersia sambucifolia MN496077.1 157289 View on NCBI ↗