Markers + reference

Myriophyllum

5 species · Haloragaceae · Saxifragales

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Species 5
Genome length 159–160 kb
Candidate markers 267
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 2016 0.1238 0.94 82.5 yes View details
trnC-GCA-trnT-GGU LSC 1232 0.0918 0.93 82.3 yes View details
lhbA-trnG-UCC LSC 984 0.1221 0.89 79.9 yes View details
psaA-ycf3 LSC 1235 0.0941 0.81 76.7 yes View details
trnT-UGU-trnL-UAA LSC 1148 0.1044 0.98 87.9 yes View details
rpl16 LSC 1715 0.0583 0.96 82.1 yes View details
ycf1 IRb 1026 0.0520 1.00 80.8 no View details
rpl32-trnL-UAG SSC 1230 0.1007 0.96 84.3 yes View details
ycf1 SSC 5319 0.0712 0.99 77.9 yes View details
trnF-GAA-ndhJ LSC 713 0.0504 0.99 90.2 yes View details
trnD-GUC-psbM LSC 971 0.0622 0.99 86.3 yes View details
trnS-GCU-trnG-GCC LSC 890 0.0585 0.97 86.0 yes View details
trnT-GGU-psbD LSC 1538 0.0490 0.98 85.6 yes View details
rps3-rps19 LSC 727 0.0527 0.99 84.7 yes View details
trnK-UUU-rps16 LSC 896 0.0696 0.96 84.1 yes View details
trnW-CCA-trnP-UGG LSC 172 0.0643 1.00 84.1 yes View details
rpoB-trnE-UUC LSC 597 0.0782 0.99 83.9 yes View details
rbcL-accD LSC 697 0.0572 0.99 83.6 yes View details
trnY-GUA-trnD-GUC LSC 243 0.0604 1.00 83.4 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AACCCAACCGCTCTTTTGAT TTTTCTTGAGCCGTACGAGG 1752–1783 1.000 90.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACCCAACCGCTCTTTTGATT TTTTCTTGAGCCGTACGAGG 1751–1782 1.000 90.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AACCCAACCGCTCTTTTGAT GCCGTACGAGGAGAAAACTT 1743–1774 1.000 90.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 ACCCAACCGCTCTTTTGATT GCCGTACGAGGAGAAAACTT 1742–1773 1.000 90.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACACCTCGGAGACAGGTAAA TTTTCTTGAGCCGTACGAGG 1908–1939 0.600 68.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CTCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 1630–2112 1.000 91.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1607–2089 1.000 90.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1618–2100 1.000 89.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1628–2110 1.000 88.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1629–2111 1.000 88.0
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 959–1165 1.000 63.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 958–1164 1.000 63.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 962–1168 1.000 61.9
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 961–1167 1.000 61.9
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 960–1166 1.000 61.9
rpoB-trnE-UUC_p1 rpoB-trnE-UUC ATGGTCCAATGCTTTTCGGT ATCAGCAAATTTTTGGGCCG 1208–1233 0.600 66.4
rpoB-trnE-UUC_p2 rpoB-trnE-UUC ATGGTCCAATGCTTTTCGGT AAATTTTGTCCCCTGTCCCC 1612 0.200 47.2
rpoB-trnE-UUC_p3 rpoB-trnE-UUC CCCCACCTACACAAGCAAAT AAATTTTGTCCCCTGTCCCC 1898 0.200 47.2
rpoB-trnE-UUC_p4 rpoB-trnE-UUC CGTCAAGCCCTGATCAAGAA AAATTTTGTCCCCTGTCCCC 1282 0.200 47.0
rpoB-trnE-UUC_p5 rpoB-trnE-UUC GACTCACACGAGCCCATATC AAATTTTGTCCCCTGTCCCC 1712 0.200 46.7
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC GGCAATATGTCTACGCTGGT CAACTTCCGCCTTGACAGG 331–342 1.000 74.3
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC TGGCAATATGTCTACGCTGG CAACTTCCGCCTTGACAGG 332–343 1.000 74.2
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CAACTTCCGCCTTGACAGG 353–364 1.000 72.7
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CAACTTCCGCCTTGACAGG 352–363 1.000 72.6
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC CGGACTGTAAATTCGTTGGC CAACTTCCGCCTTGACAGG 348–359 1.000 71.5
trnD-GUC-psbM_p1 trnD-GUC-psbM CCTGTCAAGGCGGAAGTTG AGAATAAACAGTGCAGTAGC 864–1119 1.000 52.0
trnD-GUC-psbM_p2 trnD-GUC-psbM AGTTCAATTGGTGAGAGCAC AGAATAAACAGTGCAGTAGC 887–1142 1.000 52.0
trnD-GUC-psbM_p3 trnD-GUC-psbM TGTCAAGGCGGAAGTTGC AGAATAAACAGTGCAGTAGC 862–1117 1.000 52.0
trnD-GUC-psbM_p4 trnD-GUC-psbM TGTAGTTCAATTGGTGAGAGCA AGAATAAACAGTGCAGTAGC 890–1145 1.000 52.0
trnD-GUC-psbM_p5 trnD-GUC-psbM CTGTCAAGGCGGAAGTTGC AGAATAAACAGTGCAGTAGC 863–1118 1.000 52.0

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
Myriophyllum aquaticum NC_048889.1 160465 View on NCBI ↗
Myriophyllum papillosum PV929692.1 159773 View on NCBI ↗
Myriophyllum spicatum NC_037885.1 158860 View on NCBI ↗
Myriophyllum ussuriense PV929694.1 158643 View on NCBI ↗
Myriophyllum verticillatum PV929691.1 160199 View on NCBI ↗