Markers + reference

Sagina

4 species · Caryophyllaceae · Caryophyllales

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Species 4
Genome length 150–151 kb
Candidate markers 270
Primer pairs 100

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 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 651 0.0242 0.97 67.8 yes View details
rps16-trnQ-UUG LSC 676 0.0331 0.92 66.0 yes View details
atpH-atpI LSC 670 0.0237 1.00 51.8 yes View details
rpoB-trnC-GCA LSC 930 0.0201 1.00 49.2 yes View details
psaA-ycf3 LSC 1140 0.0164 0.98 65.2 yes View details
trnT-UGU-trnL-UAA LSC 731 0.0253 0.99 63.3 yes View details
psbE-petL LSC 1254 0.0183 0.99 48.7 yes View details
rpl16 LSC 1282 0.0169 1.00 55.5 yes View details
ycf1 IRb 1875 0.0031 1.00 45.0 no View details
rpl32-trnL-UAG SSC 674 0.0529 1.00 70.5 yes View details
ycf1 SSC 5538 0.0132 1.00 46.5 yes View details
psbL-psbF LSC 27 0.0432 1.00 71.8 yes View details
ycf3-trnS-GGA LSC 769 0.0173 0.99 66.4 yes View details
trnH-GUG-psbA LSC 265 0.0495 0.98 65.9 yes View details
trnE-UUC-trnT-GGU LSC 613 0.0203 0.99 65.5 yes View details
petA-psbJ LSC 965 0.0185 1.00 63.0 yes View details
ndhC-trnV-UAC LSC 941 0.0172 1.00 62.1 yes View details
rpl33-rps18 LSC 262 0.0262 1.00 62.0 yes View details
trnR-ACG-trnN-GUU IRb 414 0.0069 0.98 61.8 yes View details
trnN-GUU-trnR-ACG IRa 414 0.0069 0.98 61.8 yes View details
rps2-rpoC2 LSC 266 0.0220 0.97 60.9 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 100 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 AGCTGCGATTGAAGTTCCAT 318–341 1.000 85.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTGCGATTGAAGTTCCAT 332–355 1.000 84.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCGATTGAAGTTCCAT 331–354 1.000 84.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCGATTGAAGTTCCAT 333–356 1.000 84.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCTGCGATTGAAGTTCCATC 317–340 1.000 82.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AGAGCGGAGGTTTTTAAAGA 759–796 1.000 58.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC AGAGCGGAGGTTTTTAAAGA 760–797 1.000 57.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAGCGGAGGTTTTTAAAGA 710–747 1.000 57.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTGTAGACGAATCC AGAGCGGAGGTTTTTAAAGA 772–809 1.000 57.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTGTAGACGAATCCC AGAGCGGAGGTTTTTAAAGA 771–808 1.000 57.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 728–779 1.000 85.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TAAGGCATCGGGTTTTGGTC 739–790 1.000 85.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTAAGGCATCGGGTTTTGGT 729–780 1.000 83.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTGGTAAGGCATCGGGTTTT 732–783 1.000 83.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGGTAAGGCATCGGGTTTTG 731–782 1.000 83.5
atpH-atpI_p1 atpH-atpI CCAGTGACCCAAGAAAACGA TTTTGCAACTTTAGCCGCAG 1372–1374 1.000 81.3
atpH-atpI_p2 atpH-atpI CCAGTGACCCAAGAAAACGA TCCACAAACCATTCCGACAG 1882–1884 1.000 80.8
atpH-atpI_p3 atpH-atpI CCAGTGACCCAAGAAAACGA TACAGTTACCTCACGGGGAG 1703–1705 1.000 80.6
atpH-atpI_p4 atpH-atpI CCAGTGACCCAAGAAAACGA CGCCCTTGGGTTCCTTTTAT 1788–1790 1.000 80.5
atpH-atpI_p5 atpH-atpI CCAGTGACCCAAGAAAACGA TGTCTGGTGTGGAAGTAGGT 2014 0.250 48.9
rps2-rpoC2_p1 rps2-rpoC2 ACCAAAATGAACTCCCGCTT ACGAACATTAGCGTTCCCTT 436–440 1.000 79.7
rps2-rpoC2_p2 rps2-rpoC2 AATGAACTCCCGCTTCCATC ACGAACATTAGCGTTCCCTT 431–435 1.000 79.4
rps2-rpoC2_p3 rps2-rpoC2 CCGCTTCCATCATCTCTTCC ACGAACATTAGCGTTCCCTT 422–426 1.000 78.9
rps2-rpoC2_p4 rps2-rpoC2 CCCGCTTCCATCATCTCTTC ACGAACATTAGCGTTCCCTT 423–427 1.000 78.8
rps2-rpoC2_p5 rps2-rpoC2 AAAATGAACTCCCGCTTCCA ACGAACATTAGCGTTCCCTT 433–437 1.000 77.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT AGTATATTACCCCGCACCCA 1769–1787 1.000 81.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCCCTACACAAGCAAACTGT AGTATATTACCCCGCACCCA 1960–1978 1.000 81.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCCTACACAAGCAAACTGT TATTACCCCGCACCCAATTG 1963 0.250 49.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TATTACCCCGCACCCAATTG 1772 0.250 49.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGGGGCTTTGCAATATTTG TATTACCCCGCACCCAATTG 1652 0.250 49.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Sagina apetala subsp. apetala PP165065.1 150421 View on NCBI ↗
Sagina japonica NC_087615.1 151449 View on NCBI ↗
Sagina maxima PQ573026.1 151464 View on NCBI ↗
Sagina procumbens PP165066.1 151446 View on NCBI ↗