Markers + reference

Lysimachia

63 species · Primulaceae · Ericales

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Species 63
Genome length 153–156 kb
Candidate markers 268
Primer pairs 90

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 427 0.0476 0.97 75.4 yes View details
trnK-UUU-rps16 LSC 631 0.0605 1.00 82.7 yes View details
rps16-trnQ-UUG LSC 1126 0.0404 0.98 79.8 yes View details
trnC-GCA-petN LSC 431 0.0326 1.00 68.1 yes View details
petN-psbM LSC 397 0.0711 0.99 77.8 yes View details
trnF-GAA-ndhJ LSC 718 0.0397 1.00 80.9 yes View details
rpl22 LSC 549 0.0445 1.00 77.1 yes View details
ycf1 IRb 996 0.0061 1.00 50.9 no View details
ndhF-rpl32 SSC 901 0.0426 0.99 78.9 yes View details
ycf1 SSC 5568 0.0312 1.00 70.2 yes View details
trnT-GGU-psbD LSC 1208 0.0339 0.98 79.7 yes View details
psbM-trnD-GUC LSC 1202 0.0328 0.98 78.8 yes View details
trnS-GCU-trnG-UCC LSC 700 0.0344 0.99 78.7 yes View details
trnT-UGU-trnL-UAA LSC 814 0.0359 0.99 78.4 yes View details
petA-psbJ LSC 945 0.0272 0.99 77.8 yes View details
rpl32-trnL-UAG SSC 470 0.0455 1.00 77.8 yes View details
rpoB-trnC-GCA LSC 1148 0.0353 0.99 77.5 yes View details
psaA-ycf3 LSC 678 0.0332 0.99 77.5 yes View details
ndhC-trnV-UAC LSC 1036 0.0333 0.99 75.3 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CTGCGACTGCTGTTTTCTTG 848–1159 1.000 90.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TCAGTGCTATGCATGGTTCC 674–985 0.984 89.9
trnH-GUG-psbA_p3 trnH-GUG-psbA ATAGTTATGGGCGAACGACG CTGCGACTGCTGTTTTCTTG 903–1214 0.524 71.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ATAGTTATGGGCGAACGACG TCAGTGCTATGCATGGTTCC 729–1040 0.524 71.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ATAGTTATGGGCGAACGACG CAGTGCTATGCATGGTTCCT 728–1039 0.524 71.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 CAGGGATCTGGCTCTATCCA AAAAGGGTATGTTGCTGCCA 1400–1680 1.000 91.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACAGGGATCTGGCTCTATCC AAAAGGGTATGTTGCTGCCA 1401–1681 1.000 91.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CAGGGATCTGGCTCTATCCA CTATCCCACTGAGCCGTCTA 923–1226 1.000 91.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 ACAGGGATCTGGCTCTATCC CTATCCCACTGAGCCGTCTA 924–1227 1.000 91.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAAAAGCCTTTTTCGCACCC AAAAGGGTATGTTGCTGCCA 1532–1812 0.984 90.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1061–1801 0.968 83.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1064–1804 1.000 82.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG AAATTTAAATGGGGCGTGGC 1118–1858 0.968 81.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA AAATTTAAATGGGGCGTGGC 1121–1861 1.000 80.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GGGTTTTGGTCCCGGTATTC 1082–1822 0.968 80.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC ACGAATCACACTTTTACCACT 632–801 1.000 58.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC AGAACGAATCACACTTTTACCAC 635–804 1.000 57.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC GAACGAATCACACTTTTACCACT 634–803 1.000 57.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC AACGAATCACACTTTTACCACT 633–802 1.000 56.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TTTCGTCCACTCAGCCATCT ACGAATCACACTTTTACCACT 631–800 1.000 55.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCTTCATTTCCATCCCGGA CTTACCACTCGGCCATGTC 947–1237 0.952 78.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCCTTCATTTCCATCCCGG CTTACCACTCGGCCATGTC 948–1238 0.952 78.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCTTCATTTCCATCCCGGA AAAGGATTTGCAGTCCCCC 968–1258 0.952 75.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCCTTCATTTCCATCCCGG AAAGGATTTGCAGTCCCCC 969–1259 0.952 75.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTCCTTCATTTCCATCCCGG CTTACCACTCGGCCATGTC 949–1239 0.952 73.2
trnC-GCA-petN_p1 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 417–499 1.000 87.0
trnC-GCA-petN_p2 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGAGTCCACTTCTTCCCCAT 478–560 1.000 85.4
trnC-GCA-petN_p3 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC ATTAAACCAGCCCAAGCGAG 425–507 1.000 83.9
trnC-GCA-petN_p4 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC ACCATTAAACCAGCCCAAGC 428–510 1.000 82.3
trnC-GCA-petN_p5 trnC-GCA-petN TTCAAATCTGGGTGTCGCC AGCCCAAGCGAGACTTACTA 415–497 1.000 82.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (63)

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

Species Accession Length (bp) Link
Lysimachia acroadenia PQ783062.1 154207 View on NCBI ↗
Lysimachia alfredii LC758783.1 154880 View on NCBI ↗
Lysimachia auriculata LC758791.1 154634 View on NCBI ↗
Lysimachia barystachys LC758794.1 154333 View on NCBI ↗
Lysimachia candida NC_063330.1 153632 View on NCBI ↗
Lysimachia capillipes LC758781.1 155784 View on NCBI ↗
Lysimachia capillipes var. capillipes PP235248.1 155743 View on NCBI ↗
Lysimachia capillipes var. cavaleriei PP235254.1 155532 View on NCBI ↗
Lysimachia chapaensis PP235256.1 155568 View on NCBI ↗
Lysimachia chekiangensis LC758807.1 155043 View on NCBI ↗
Lysimachia christinae NC_053736.1 154810 View on NCBI ↗
Lysimachia circaeoides LC758808.1 154202 View on NCBI ↗
Lysimachia clethroides NC_064345.1 155110 View on NCBI ↗
Lysimachia congestiflora NC_045275.1 154505 View on NCBI ↗
Lysimachia coreana NC_026197.1 155386 View on NCBI ↗
Lysimachia dabieshanensis PP056236.1 154780 View on NCBI ↗
Lysimachia davurica LC758805.1 155302 View on NCBI ↗
Lysimachia decurrens LC758785.1 154897 View on NCBI ↗
Lysimachia deltoidea var. cinerascens LC758792.1 154908 View on NCBI ↗
Lysimachia europaea LC758812.1 154315 View on NCBI ↗
Lysimachia fistulosa var. wulingensis LC758786.1 154473 View on NCBI ↗
Lysimachia foenum-graecum PP235261.1 155619 View on NCBI ↗
Lysimachia fooningensis PP235263.1 155748 View on NCBI ↗
Lysimachia fordiana NC_065763.1 154399 View on NCBI ↗
Lysimachia fortunei LC758799.1 154983 View on NCBI ↗
Lysimachia fukienensis LC758787.1 154930 View on NCBI ↗
Lysimachia glanduliflora LC758778.1 154811 View on NCBI ↗
Lysimachia grammica LC758800.1 154760 View on NCBI ↗
Lysimachia hemsleyana NC_052863.1 155618 View on NCBI ↗
Lysimachia hemsleyi LC758779.1 154801 View on NCBI ↗
Lysimachia heterobotrys PP235266.1 155678 View on NCBI ↗
Lysimachia heterogenea LC758773.1 154119 View on NCBI ↗
Lysimachia hypericoides LC758790.1 154841 View on NCBI ↗
Lysimachia insignis PP235268.1 154489 View on NCBI ↗
Lysimachia klattiana LC758774.1 154607 View on NCBI ↗
Lysimachia laxa LC758780.1 155669 View on NCBI ↗
Lysimachia leucantha PQ783063.1 153659 View on NCBI ↗
Lysimachia liujiangensis PP235273.1 155767 View on NCBI ↗
Lysimachia lobelioides LC758793.1 154887 View on NCBI ↗
Lysimachia longipes LC758806.1 154213 View on NCBI ↗
Lysimachia maritima NC_059901.1 154939 View on NCBI ↗
Lysimachia mauritiana NC_060700.1 152691 View on NCBI ↗
Lysimachia medogensis PV588044.1 154167 View on NCBI ↗
Lysimachia melampyroides LC758810.1 154520 View on NCBI ↗
Lysimachia microcarpa LC758776.1 155677 View on NCBI ↗
Lysimachia navillei PP235276.1 155679 View on NCBI ↗
Lysimachia paridiformis var. stenophylla LC758802.1 154799 View on NCBI ↗
Lysimachia parvifolia LC758775.1 153622 View on NCBI ↗
Lysimachia patungensis LC758797.1 154872 View on NCBI ↗
Lysimachia pentapetala LC758801.1 155028 View on NCBI ↗
Lysimachia petelotii PP235278.1 155743 View on NCBI ↗
Lysimachia phyllocephala LC758803.1 154769 View on NCBI ↗
Lysimachia pittosporoides PP235280.1 155747 View on NCBI ↗
Lysimachia pseudohenryi LC758777.1 154448 View on NCBI ↗
Lysimachia pseudotrichopoda PP235282.1 155788 View on NCBI ↗
Lysimachia punctata PP484616.1 155353 View on NCBI ↗
Lysimachia rubiginosa LC758811.1 154224 View on NCBI ↗
Lysimachia rupestris PP235284.1 155097 View on NCBI ↗
Lysimachia saxicola PP235288.1 155536 View on NCBI ↗
Lysimachia stenosepala LC758809.1 154118 View on NCBI ↗
Lysimachia thyrsiflora PQ774309.1 155181 View on NCBI ↗
Lysimachia vittiformis PP235290.1 155748 View on NCBI ↗
Lysimachia vulgaris LC758795.1 155313 View on NCBI ↗