Markers + reference

Potamogeton

5 species · Potamogetonaceae · Alismatales

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Species 5
Genome length 156–156 kb
Candidate markers 266
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1218 0.0178 0.99 62.1 yes View details
trnQ-UUG-psbK LSC 828 0.0142 0.98 60.4 yes View details
atpF LSC 1583 0.0078 0.99 53.6 yes View details
atpI-rps2 LSC 246 0.0337 0.96 72.0 yes View details
rps2 LSC 717 0.0033 1.00 46.5 yes View details
trnC-GCA-petN LSC 752 0.0134 0.97 63.0 yes View details
petN-psbM LSC 1039 0.0177 0.88 73.2 yes View details
psbM-trnD-GUC LSC 1034 0.0114 0.98 57.4 yes View details
trnT-GGU-psbD LSC 1063 0.0120 0.96 61.0 yes View details
ycf4-cemA LSC 610 0.0152 0.99 55.1 yes View details
ndhF-rpl32 SSC 976 0.0143 0.99 61.1 yes View details
rpl32-trnL-UAG SSC 613 0.0178 1.00 58.2 yes View details
ycf1 SSC 5391 0.0091 1.00 47.7 yes View details
ndhG-ndhI SSC 551 0.0129 1.00 67.9 yes View details
ndhD-psaC SSC 126 0.0413 1.00 66.4 yes View details
trnF-GAA-ndhJ LSC 640 0.0112 0.98 63.6 yes View details
trnE-UUC-trnT-GGU LSC 518 0.0141 0.96 62.7 yes View details
accD-psaI LSC 865 0.0101 1.00 62.3 yes View details
trnS-GCU-trnG-UCC LSC 863 0.0113 0.99 61.8 yes View details
petD-rpoA LSC 181 0.0200 0.99 60.3 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCCAGACAAGTTGGGATCCT GAGGTTCGAATCCTTCCGTC 1401–1439 1.000 83.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1302–1340 1.000 83.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTTCCACATCG GAGGTTCGAATCCTTCCGTC 1283–1321 1.000 82.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAGCTCCATCGTGCACTATT GAGGTTCGAATCCTTCCGTC 1432–1470 1.000 82.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AACTATGTCGAGCCAAGAGC GAGGTTCGAATCCTTCCGTC 1368–1406 1.000 81.9
trnQ-UUG-psbK_p1 trnQ-UUG-psbK CCTTACCACTTGGCCACG CTCGAATGAGGGGCAGAATT 834–926 1.000 67.2
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GTTGCCTTACCACTTGGCC CTCGAATGAGGGGCAGAATT 838–930 1.000 67.1
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GCCTTACCACTTGGCCAC CTCGAATGAGGGGCAGAATT 835–927 1.000 64.8
trnQ-UUG-psbK_p4 trnQ-UUG-psbK TTGCCTTACCACTTGGCCA CTCGAATGAGGGGCAGAATT 837–929 1.000 63.7
trnQ-UUG-psbK_p5 trnQ-UUG-psbK TTGCCTTACCACTTGGCC CTCGAATGAGGGGCAGAATT 837–929 1.000 63.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 906–948 1.000 56.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 905–947 1.000 56.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 909–951 1.000 55.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 908–950 1.000 55.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGAACCCTCGGTACAAACAA ACGAATCACACTTTTACCACT 943–985 1.000 55.3
atpF_p1 atpF CAGAGCAATACCCACCGTAC GTATTGCGAGACAGCCAGAA 2119–2149 1.000 82.6
atpF_p2 atpF TCCGTTGCTACTGCTGTTTT GTATTGCGAGACAGCCAGAA 2469–2499 1.000 82.5
atpF_p3 atpF ATCCCCTACCTGAAGTACGG GTATTGCGAGACAGCCAGAA 2035–2065 1.000 82.5
atpF_p4 atpF CAGAGCAATACCCACCGTAC TGGATTGGTCGTGGCATTAG 2034–2064 1.000 82.5
atpF_p5 atpF TCCGTTGCTACTGCTGTTTT TGGATTGGTCGTGGCATTAG 2384–2414 1.000 82.4
atpI-rps2_p1 atpI-rps2 GGCCTACCTCTACACCTGAT CGGCCAATGATGACGCTATA 401–425 1.000 85.2
atpI-rps2_p2 atpI-rps2 GTTGGCCTACCTCTACACCT CGGCCAATGATGACGCTATA 404–428 1.000 82.4
atpI-rps2_p3 atpI-rps2 TTGGCCTACCTCTACACCTG CGGCCAATGATGACGCTATA 403–427 1.000 82.4
atpI-rps2_p4 atpI-rps2 GTGCACTTGTAAACCCCCTA CGGCCAATGATGACGCTATA 439–463 1.000 81.1
atpI-rps2_p5 atpI-rps2 GGCCTACCTCTACACCTGAT GTATCCGCAGTTTGTGAGGG 351–375 1.000 81.1
rps2_p1 rps2 GATAAGTACTTGGGCGTGCA CTTGGTAGAAGGTTCCGTCG 1170–1194 1.000 82.9
rps2_p2 rps2 TGATAAGTACTTGGGCGTGC CTTGGTAGAAGGTTCCGTCG 1171–1195 1.000 82.9
rps2_p3 rps2 GATAAGTACTTGGGCGTGCA TCCTTGGTAGAAGGTTCCGT 1172–1196 1.000 82.8
rps2_p4 rps2 TGATAAGTACTTGGGCGTGC TCCTTGGTAGAAGGTTCCGT 1173–1197 1.000 82.8
rps2_p5 rps2 GATTCCGAACAGCTATGGCA CTTGGTAGAAGGTTCCGTCG 1228–1252 1.000 82.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Potamogeton crispus NC_069582.1 155884 View on NCBI ↗
Potamogeton distinctus NC_077520.1 156354 View on NCBI ↗
Potamogeton maackianus NC_077521.1 156488 View on NCBI ↗
Potamogeton perfoliatus NC_029814.1 156226 View on NCBI ↗
Potamogeton wrightii NC_077522.1 156315 View on NCBI ↗