Markers + reference

Typha

5 species · Typhaceae · Poales

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Species 5
Genome length 161–162 kb
Candidate markers 271
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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 1638 0.0308 0.98 79.4 yes View details
trnT-UGU-trnL-UAA LSC 1210 0.0251 0.98 73.2 yes View details
ndhC-trnV-UAC LSC 1091 0.0121 1.00 68.3 yes View details
accD-psaI LSC 1133 0.0206 0.99 64.5 yes View details
rpl16 LSC 1503 0.0101 1.00 57.9 yes View details
ndhF SSC 2214 0.0057 1.00 46.8 yes View details
ccsA SSC 981 0.0063 1.00 49.2 yes View details
psaC-ndhE SSC 718 0.0288 0.97 76.6 yes View details
rps15-ycf1 SSC 457 0.0328 0.95 66.9 yes View details
ycf1 SSC 5517 0.0067 1.00 43.7 yes View details
trnK-UUU-rps16 LSC 716 0.0128 0.99 68.4 yes View details
rps8-rpl14 LSC 189 0.0116 1.00 66.7 yes View details
psbI-trnS-GCU LSC 130 0.0200 1.00 65.7 yes View details
psaA-ycf3 LSC 653 0.0057 0.97 65.6 yes View details
ycf4-cemA LSC 867 0.0077 0.99 65.5 yes View details
ccsA-ndhD SSC 249 0.0260 1.00 65.5 yes View details
rpl22-rps19 IRb 113 0.0265 1.00 64.7 yes View details
rpoB-trnC-GCA LSC 1045 0.0079 0.99 64.4 yes View details
trnG-GCC-trnfM-CAU LSC 216 0.0099 1.00 64.2 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTCAACCTACAGGAACGGTT 804–827 1.000 76.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTCAACCTACAGGAACGGTT 803–826 1.000 76.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAGGGCGCTCAACCTAC 813–836 1.000 74.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGGCGCTCAACCTAC 812–835 1.000 74.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTCAACCTACAGGAACGGTTT 803–826 1.000 73.8
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA TAAAGCGGCGGATTGCTAAT 221–224 1.000 74.7
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA ATTGGGAGAGATGGCTGAGT 245–248 1.000 73.9
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA ATGGCTGAGTGGACTAAAGC 235–238 1.000 71.6
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGACGTGAGGAA TAAAGCGGCGGATTGCTAAT 220–223 1.000 71.1
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA GAGAGATGGCTGAGTGGACT 240–243 1.000 70.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1585–1800 1.000 60.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TAGGGAACGGAAAGAGAGGG ACGAATCACACTTTTACCACT 1640–1855 1.000 59.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 1634–1849 1.000 59.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 1588–1803 1.000 59.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 1587–1802 1.000 59.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TGCCGTCAAGCCTTGATTAA AAAGGATTTGCAGTCCCCTG 1137–1187 1.000 82.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTGAAATTCTGCCGTCAAGC AAAGGATTTGCAGTCCCCTG 1146–1196 1.000 82.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CTGCCGTCAAGCCTTGATTA AAAGGATTTGCAGTCCCCTG 1138–1188 1.000 81.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA AAAGGATTTGCAGTCCCCTG 1062–1112 1.000 81.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAATTCTGCCGTCAAGCCTT AAAGGATTTGCAGTCCCCTG 1143–1193 1.000 81.0
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC CTTGAGGTCACGGGTTCAAA 265–294 1.000 84.4
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GAGAAGATGCGGGTTCGATT CTTGAGGTCACGGGTTCAAA 266–295 1.000 84.4
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU ATGCGGATATGGTCGAATGG CTTGAGGTCACGGGTTCAAA 306–335 1.000 83.9
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC GTCACGGGTTCAAATCCTGT 259–288 1.000 83.8
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GAGAAGATGCGGGTTCGATT GTCACGGGTTCAAATCCTGT 260–289 1.000 83.8
psaA-ycf3_p1 psaA-ycf3 TGAGAAATGACCGGGTTTGG TTGAAGATCACGAAGCGCTT 764–789 1.000 80.5
psaA-ycf3_p2 psaA-ycf3 TGAGAAATGACCGGGTTTGG GCTATAGCGCTTACTCCAGG 809–834 1.000 79.1
psaA-ycf3_p3 psaA-ycf3 TGAGAAATGACCGGGTTTGG CCGATCAAGCTGCTGAGTAT 838–863 1.000 77.7
psaA-ycf3_p4 psaA-ycf3 TGAGAAATGACCGGGTTTGG TCCGATCAAGCTGCTGAGTA 839–864 1.000 77.7
psaA-ycf3_p5 psaA-ycf3 TGAGAAATGACCGGGTTTGG TGGTTGAAGATCACGAAGCG 767–792 1.000 77.5

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
Typha angustifolia PP790750.1 161597 View on NCBI ↗
Typha latifolia NC_013823.1 161572 View on NCBI ↗
Typha lugdunensis NC_061353.1 161338 View on NCBI ↗
Typha orientalis NC_050678.1 160969 View on NCBI ↗
Typha przewalskii NC_061354.1 161614 View on NCBI ↗