Markers + reference

Pseudopediastrum

2 species · Hydrodictyaceae · Sphaeropleales

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Species 2
Genome length 187–207 kb
Candidate markers 265
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 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaB SSC 2208 0.4685 0.80 77.9 yes View details
atpB SSC 1446 0.4865 0.82 80.0 yes View details
tufA SSC 1257 0.4716 0.92 82.9 yes View details
tufA-trnV(uac) SSC 1204 0.4544 0.96 83.2 yes View details
rpoC1 SSC 5868 0.4138 0.79 72.9 yes View details
petB SSC 648 0.4351 0.94 83.5 yes View details
petB-rps18 SSC 695 0.4641 0.94 83.4 yes View details
rps18 SSC 426 0.5065 0.90 78.5 yes View details
clpP SSC 1623 0.4578 0.90 82.0 yes View details
DR615_pgp039 SSC 579 0.4387 0.83 79.8 yes View details
cemA SSC 1761 0.0801 0.89 92.6 yes View details
DR615_pgr004-trnS(gcu) IRb 716 0.3551 0.81 86.5 yes View details
trnS(gcu)-DR615_pgr003 IRa 716 0.3551 0.81 86.5 yes View details
rpoBa-psbF LSC 2111 0.1343 0.71 85.7 yes View details
rpl5-rpl14 SSC 917 0.3753 0.92 85.1 yes View details
rps12-psaJ LSC 1083 0.2409 0.81 84.0 yes View details
psaA-rps8 SSC 559 0.1078 0.96 83.9 yes View details
psbF-psbL LSC 344 0.0901 1.00 83.2 yes View details
psbD-psaA LSC 1097 0.2254 0.82 83.2 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
rpoBa-psbF_p1 rpoBa-psbF TGCATGTCCACAAAATCTGG TGTTGGAACAGCTAATGCATG 2110–2248 1.000 65.3
rpoBa-psbF_p2 rpoBa-psbF GCATGTCCACAAAATCTGGT TGTTGGAACAGCTAATGCATG 2109–2247 1.000 65.3
rpoBa-psbF_p3 rpoBa-psbF TGCATGTCCACAAAATCTGGT TGTTGGAACAGCTAATGCATG 2110–2248 1.000 65.3
rpoBa-psbF_p4 rpoBa-psbF TTGCATGTCCACAAAATCTGG TGTTGGAACAGCTAATGCATG 2111–2249 1.000 63.2
rpoBa-psbF_p5 rpoBa-psbF TGCATGTCCACAAAATCTGG GTTGGAACAGCTAATGCATGA 2109–2247 1.000 63.1
psbF-psbL_p1 psbF-psbL CATGCATTAGCTGTTCCAACA ATTGGGATTAGGTCTAGCCA 434–464 1.000 48.8
psbF-psbL_p2 psbF-psbL CATGCATTAGCTGTTCCAACA TTGGGATTAGGTCTAGCCAT 433–463 1.000 48.8
psbF-psbL_p3 psbF-psbL TCATGCATTAGCTGTTCCAAC ATTGGGATTAGGTCTAGCCA 435–465 1.000 46.6
psbF-psbL_p4 psbF-psbL TCATGCATTAGCTGTTCCAAC TTGGGATTAGGTCTAGCCAT 434–464 1.000 46.6
psbF-psbL_p5 psbF-psbL CATGCATTAGCTGTTCCAACA CCCCAATAAAGACTAGTACGGT 475–505 1.000 46.1
rps12-psaJ_p1 rps12-psaJ TCGAGCTGTTTTAATTAATTGTTGA ATCGTTTCTTCCCAGATCCA 1157–1251 1.000 52.0
rps12-psaJ_p2 rps12-psaJ TCGAGCTGTTTTAATTAATTGTTGA TCGTTTCTTCCCAGATCCAT 1156–1250 1.000 52.0
rps12-psaJ_p3 rps12-psaJ TCGAGCTGTTTTAATTAATTGTTGA AATCGTTTCTTCCCAGATCCA 1158–1252 1.000 52.0
rps12-psaJ_p4 rps12-psaJ TCGAGCTGTTTTAATTAATTGTTGA TCGTTTCTTCCCAGATCCATT 1156–1250 1.000 52.0
rps12-psaJ_p5 rps12-psaJ CGAGCTGTTTTAATTAATTGTTGA TCGTTTCTTCCCAGATCCAT 1155–1249 1.000 52.0
psbD-psaA_p1 psbD-psaA CAAAACGGTCTTGACGAAGC TGGTCATTCTTCTTAGCACGT 1209–1221 1.000 78.4
psbD-psaA_p2 psbD-psaA GAAGCCAGTCATCTGCATCA TGGTCATTCTTCTTAGCACGT 1194–1206 1.000 78.3
psbD-psaA_p3 psbD-psaA GCCAGTCATCTGCATCATCA TGGTCATTCTTCTTAGCACGT 1191–1203 1.000 78.3
psbD-psaA_p4 psbD-psaA TTGACGAAGCCAGTCATCTG TGGTCATTCTTCTTAGCACGT 1199–1211 1.000 77.9
psbD-psaA_p5 psbD-psaA GTCTTGACGAAGCCAGTCAT TGGTCATTCTTCTTAGCACGT 1202–1214 1.000 77.9
DR615_pgr004-trnS(gcu)_p1 DR615_pgr004-trnS(gcu) GTTGGAAGTCTGGCAGGAAA CGGATTAGCAATCAGTCGCT 799–971 1.000 90.7
DR615_pgr004-trnS(gcu)_p2 DR615_pgr004-trnS(gcu) TGGAAGTCTGGCAGGAAAAC CGGATTAGCAATCAGTCGCT 797–969 1.000 90.7
DR615_pgr004-trnS(gcu)_p3 DR615_pgr004-trnS(gcu) ACTTGTTGGAAGTCTGGCAG CGGATTAGCAATCAGTCGCT 803–975 1.000 90.6
DR615_pgr004-trnS(gcu)_p4 DR615_pgr004-trnS(gcu) GACTTGTTGGAAGTCTGGCA CGGATTAGCAATCAGTCGCT 804–976 1.000 90.6
DR615_pgr004-trnS(gcu)_p5 DR615_pgr004-trnS(gcu) AGGAAAACTCAACTAGCGCC CGGATTAGCAATCAGTCGCT 785–957 1.000 89.3
cemA_p1 cemA GAAGGAAGCGAAGAAGGAGG GAGCTTCTTCGCTTTGCTTC 1946 0.500 57.9
cemA_p2 cemA GGAAGCGAAGAAGGAGGAAG GAGCTTCTTCGCTTTGCTTC 1943 0.500 57.9
cemA_p3 cemA TACGGAGAGGAGGAAGTTCC GAGCTTCTTCGCTTTGCTTC 1969 0.500 57.0
cemA_p4 cemA CCTACGGAGAGGAGGAAGTT GAGCTTCTTCGCTTTGCTTC 1971 0.500 56.9
cemA_p5 cemA GGAAGCGAAGAAGGAGGAAG TTCTTCGCTTTGCTTCCTCC 1939 0.500 56.1

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
Pseudopediastrum boryanum NC_037920.1 206668 View on NCBI ↗
Pseudopediastrum integrum NC_037921.1 187268 View on NCBI ↗