Markers + reference

Sagittaria

2 species · Alismataceae · Alismatales

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Species 2
Genome length 177–177 kb
Candidate markers 269
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 3216 0.0016 1.00 56.2 yes View details
trnQ-UUG-trnG-UCC LSC 2082 0.0005 1.00 57.8 yes View details
rpoC2 LSC 4734 0.0034 0.98 56.4 yes View details
psbM-trnD-GUC LSC 863 0.0012 1.00 59.4 yes View details
accD-psaI LSC 1292 0.0023 1.00 60.1 yes View details
rpl22-rps19 LSC 1193 0.0028 0.91 63.9 yes View details
ycf2 IRb 7065 0.0000 0.98 54.4 no View details
ycf2 IRa 7065 0.0001 0.99 53.2 yes View details
trnN-GUU-ycf1 IRb 804 0.0000 0.93 63.0 yes View details
ycf1-trnN-GUU IRa 804 0.0000 0.93 63.0 yes View details
rpoA LSC 1035 0.0019 1.00 59.9 yes View details
trnF-GAA-ndhJ LSC 655 0.0015 1.00 59.6 yes View details
ccsA SSC 969 0.0010 1.00 59.3 yes View details
psbE-petL LSC 1189 0.0008 1.00 59.2 yes View details
ndhF-rpl32 SSC 1350 0.0000 1.00 58.8 yes View details
ycf3 LSC 1986 0.0005 1.00 58.0 yes View details
rpl23-trnH-GUG IRa 247 0.0000 0.94 56.9 no View details
trnT-UGU-trnL-UAA LSC 2593 0.0000 1.00 56.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 AGCTTGTTACGTTAAGAAGACA TCTTATATGCATGCTTATACGT 278–476 1.000 40.6
rps16_p2 rps16 AAGCTTGTTACGTTAAGAAGACA TCTTATATGCATGCTTATACGT 279–477 1.000 40.6
rps16_p3 rps16 AGCTTGTTACGTTAAGAAGACAA TCTTATATGCATGCTTATACGT 278–476 1.000 40.6
rps16_p4 rps16 AGCTTGTTACGTTAAGAAGACA ATCTTATATGCATGCTTATACGT 279–477 1.000 40.6
rps16_p5 rps16 GCTTGTTACGTTAAGAAGACA TCTTATATGCATGCTTATACGT 277–475 1.000 40.6
trnQ-UUG-trnG-UCC_p1 trnQ-UUG-trnG-UCC GTCCAGTCATTCGGAGGTTC CATCGTTAGCTTGGAAGGCT 2229 1.000 79.7
trnQ-UUG-trnG-UCC_p2 trnQ-UUG-trnG-UCC GTCCAGTCATTCGGAGGTTC CGTTAGCTTGGAAGGCTAGG 2226 1.000 79.5
trnQ-UUG-trnG-UCC_p3 trnQ-UUG-trnG-UCC GAGGTTCGAATCCTTCCGTC CATCGTTAGCTTGGAAGGCT 2216 1.000 79.2
trnQ-UUG-trnG-UCC_p4 trnQ-UUG-trnG-UCC GAGGTTCGAATCCTTCCGTC CGTTAGCTTGGAAGGCTAGG 2213 1.000 79.0
trnQ-UUG-trnG-UCC_p5 trnQ-UUG-trnG-UCC GTCCAGTCATTCGGAGGTTC GTTAGCTTGGAAGGCTAGGG 2225 1.000 77.3
rpoC2_p1 rpoC2 TTATATGGGGCTAGGGGTCG TCCCGAGGAAGTGCATATCT 852–900 1.000 84.3
rpoC2_p2 rpoC2 ATGTCGGGTAAGTGAGGGAA TCCCGAGGAAGTGCATATCT 1261–1309 1.000 83.9
rpoC2_p3 rpoC2 TGTCGGGTAAGTGAGGGAAT TCCCGAGGAAGTGCATATCT 1260–1308 1.000 83.9
rpoC2_p4 rpoC2 TTATATGGGGCTAGGGGTCG TTTCATTCCCGAGGAAGTGC 858–906 1.000 83.6
rpoC2_p5 rpoC2 TGTCGGGTAAGTGAGGGAAT TTTCATTCCCGAGGAAGTGC 1266–1314 1.000 83.1
psbM-trnD-GUC_p1 psbM-trnD-GUC TGCGAGAATATTGACTTCCA TATTGTACGGCTCATGGGGA 974 1.000 50.3
psbM-trnD-GUC_p2 psbM-trnD-GUC TGCGAGAATATTGACTTCCA GCTCATGGGGACTGTAGTTC 965 1.000 49.4
psbM-trnD-GUC_p3 psbM-trnD-GUC TGCGAGAATATTGACTTCCA AGTTCAATTGGTCAGAGCGT 950 1.000 47.5
psbM-trnD-GUC_p4 psbM-trnD-GUC TGCGAGAATATTGACTTCCA TTCAATTGGTCAGAGCGTCG 948 1.000 47.4
psbM-trnD-GUC_p5 psbM-trnD-GUC TGCGAGAATATTGACTTCCAT TATTGTACGGCTCATGGGGA 974 1.000 47.2
ycf3_p1 ycf3 CTTGATTGGACCCTCTCAGG TATGAGATCGTTTTCCCGGG 2128 1.000 67.2
ycf3_p2 ycf3 CTTGATTGGACCCTCTCAGG TTATGAGATCGTTTTCCCGGG 2129 1.000 64.9
ycf3_p3 ycf3 CTTGATTGGACCCTCTCAGG ATGAGATCGTTTTCCCGGG 2127 1.000 60.1
ycf3_p4 ycf3 CTTGATTGGACCCTCTCAGG ATGAGATCGTTTTCCCGGGG 2127 1.000 59.8
ycf3_p5 ycf3 TCTTGATTGGACCCTCTCAG TATGAGATCGTTTTCCCGGG 2129 1.000 58.8
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA AAAGCCAGCTATCGGAATCG ACCAATTTCGCCATATCCCC 2686–2688 1.000 79.0
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA AAAGCCAGCTATCGGAATCG TAGCGTCTACCAATTTCGCC 2694–2696 1.000 78.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 2673–2675 1.000 78.1
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 2681–2683 1.000 77.6
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA AAATGCGATGCTCTAACCCC ACCAATTTCGCCATATCCCC 2645–2647 1.000 77.5

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
Sagittaria graminea NC_067603.1 176871 View on NCBI ↗
Sagittaria trifolia NC_044119.1 177417 View on NCBI ↗