Markers + reference

Plantago

47 species · Plantaginaceae · Lamiales

Back to catalogue

Species 47
Genome length 146–165 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

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-accD LSC 1122 0.2013 0.88 74.8 yes View details
accD LSC 1509 0.1332 0.84 74.1 yes View details
infA-rps8 LSC 899 0.1987 0.13 58.4 yes View details
ndhB IRb 2162 0.1986 0.94 67.7 no View details
rps7 IRb 468 0.1927 0.92 62.1 no View details
rps12 IRb 793 0.2088 0.99 62.7 yes View details
rrn16 IRb 1491 0.2032 0.91 66.3 yes View details
rrn23 IRb 2814 0.2079 0.96 69.5 yes View details
rrn23 IRa 2814 0.1708 0.78 60.4 no View details
rrn16 IRa 1491 0.1726 0.81 61.1 no View details
rps12 IRa 793 0.1932 0.91 64.2 no View details
rps7 IRa 468 0.2200 0.94 61.9 yes View details
ndhB IRa 2162 0.2062 0.91 66.4 yes View details
psbE-petL LSC 785 0.0487 0.97 80.1 yes View details
rpl32-trnL-UAG SSC 606 0.0966 0.95 79.7 yes View details
ndhF-rpl32 SSC 687 0.0830 0.91 79.4 yes View details
trnT-UGU-trnL-UAA LSC 712 0.0521 0.93 78.1 yes View details
rpoB-trnC-GCA LSC 1253 0.0542 0.92 78.0 yes View details
trnT-GGU-psbD LSC 1042 0.0457 0.97 77.9 yes View details
ndhF SSC 2232 0.0547 1.00 76.8 yes View details
petA-psbJ LSC 1048 0.0705 0.85 75.8 yes View details
clpP LSC 1369 0.1034 0.96 75.2 yes View details
psbM-trnD-GUC LSC 537 0.0441 0.98 74.9 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
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TTGTTTCCTACTCACGCGAG CCGGATTTGAACTGGGGAAA 1705–1851 1.000 90.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTGTTTCCTACTCACGCGAG AGCCCAAGCGAGACTTACTA 2268–2481 1.000 90.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTGTTTCCTACTCACGCGAG CCTCTTTTTCTCGCGGGTAA 1828–1948 0.660 77.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTGTTTCCTACTCACGCGAG GAGATTCTCGCGAGTCCATC 2126–2135 0.085 51.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTGTTTCCTACTCACGCGAG GCGGGTAATCATTCTACGGG 1894–1904 0.064 42.9
psbM-trnD-GUC_p1 psbM-trnD-GUC ACTCGTAGTGTGGGGAAGAA CCTGGGGGTAGGGTACTATG 1526–1594 0.149 54.6
psbM-trnD-GUC_p2 psbM-trnD-GUC TCGTAGTGTGGGGAAGAAGT CCTGGGGGTAGGGTACTATG 1524–1592 0.149 54.6
psbM-trnD-GUC_p3 psbM-trnD-GUC CGTAGTGTGGGGAAGAAGTG CCTGGGGGTAGGGTACTATG 1523–1591 0.149 54.0
psbM-trnD-GUC_p4 psbM-trnD-GUC ACGAAATGGAAACCCCCTTC CCTGGGGGTAGGGTACTATG 1080–1090 0.064 43.2
psbM-trnD-GUC_p5 psbM-trnD-GUC CGAAATGGAAACCCCCTTCA CCTGGGGGTAGGGTACTATG 1079–1089 0.064 43.2
trnT-GGU-psbD_p1 trnT-GGU-psbD CATAGTACCCTACCCCCAGG AGCTCGAATTGGCGTAACAT 2137–2698 0.979 90.8
trnT-GGU-psbD_p2 trnT-GGU-psbD CATAGTACCCTACCCCCAGG AAAGGTTGTACCCGTGAACC 1904–2465 0.979 90.7
trnT-GGU-psbD_p3 trnT-GGU-psbD CATAGTACCCTACCCCCAGG CCAGACTGCCCTAGTGGATA 2239–2800 0.979 90.2
trnT-GGU-psbD_p4 trnT-GGU-psbD CATAGTACCCTACCCCCAGG GCTCGAATTGGCGTAACATG 2136–2697 0.979 90.2
trnT-GGU-psbD_p5 trnT-GGU-psbD CATAGTACCCTACCCCCAGG AAAGCGCGGAATGTATTTGC 2446–2993 0.957 89.4
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA CGAAGCCATACCCAATCGAA ACGCAGTCAACTCCATTTGT 1592–1780 0.936 88.8
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA TTGACCTGTTGAACCCTTGG ACGCAGTCAACTCCATTTGT 1529–1717 0.936 88.7
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA CGAAGCCATACCCAATCGAA AGTCATTTCCGCCCCAATAC 2080–2256 0.319 63.9
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA CGAAGCCATACCCAATCGAA AAAGTCATTTCCGCCCCAAT 2082–2258 0.319 63.8
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA TTGACCTGTTGAACCCTTGG AGTCATTTCCGCCCCAATAC 2017–2193 0.319 63.8
rbcL-accD_p1 rbcL-accD ACTACAGTTCGGTGGAGGAA ACACCAGGTCTTCGTCCATA 1319–1507 0.298 63.3
rbcL-accD_p2 rbcL-accD ACTACAGTTCGGTGGAGGAA CAATTGACTAACCTCCCCCG 1929–2056 0.149 56.1
rbcL-accD_p3 rbcL-accD ACTACAGTTCGGTGGAGGAA ACTAACCTCCCCCGTGTTTA 1923–1960 0.064 45.2
rbcL-accD_p4 rbcL-accD GGAGTCAGGAATTAGCTGCC ACTAACCTCCCCCGTGTTTA 1768–1805 0.064 45.1
rbcL-accD_p5 rbcL-accD AATGCTACTGCGGGTACATG ACTAACCTCCCCCGTGTTTA 2399–2436 0.064 44.3
accD_p1 accD TTCGCGAGTGGTGAAAGTAG CGGGATGAGTTGCTAGTGAC 1828–2004 0.149 53.8
accD_p2 accD GTAGTGATTTCGCGAGTGGT CGGGATGAGTTGCTAGTGAC 1836–2012 0.085 51.4
accD_p3 accD TAGTGATTTCGCGAGTGGTG CGGGATGAGTTGCTAGTGAC 1835–2011 0.085 51.4
accD_p4 accD GAAACCCCCGCGAATAGTAG CGGGATGAGTTGCTAGTGAC 1852–1933 0.064 45.9
accD_p5 accD GGGATAACTCAATCGACGGG CGGGATGAGTTGCTAGTGAC 2065–2146 0.064 45.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (47)

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

Species Accession Length (bp) Link
Plantago afra MW877575.1 149501 View on NCBI ↗
Plantago alpina MW877565.1 158089 View on NCBI ↗
Plantago arachnoidea OR911464.1 164019 View on NCBI ↗
Plantago arborescens OR911465.1 149298 View on NCBI ↗
Plantago argentea subsp. liburnica PP541855.1 150092 View on NCBI ↗
Plantago aristata OR911466.1 149887 View on NCBI ↗
Plantago asiatica NC_060521.1 164993 View on NCBI ↗
Plantago asiatica subsp. densiflora OR911468.1 164984 View on NCBI ↗
Plantago asiatica subsp. erosa OR911469.1 164997 View on NCBI ↗
Plantago atrata MW877580.1 149610 View on NCBI ↗
Plantago atrata subsp. fuscescens PP541856.1 149381 View on NCBI ↗
Plantago australis MW877569.1 164785 View on NCBI ↗
Plantago brasiliensis MW877579.1 149817 View on NCBI ↗
Plantago camtschatica OR911470.1 164915 View on NCBI ↗
Plantago cavaleriei OR911471.1 164994 View on NCBI ↗
Plantago cornuti OR911472.1 164975 View on NCBI ↗
Plantago coronopus MW877566.1 159416 View on NCBI ↗
Plantago daltonii OR911473.1 165047 View on NCBI ↗
Plantago depressa NC_041161.1 164617 View on NCBI ↗
Plantago elongata MW877571.1 164083 View on NCBI ↗
Plantago erecta OR911475.1 149381 View on NCBI ↗
Plantago hakusanensis OR911477.1 164956 View on NCBI ↗
Plantago himalaica OR911478.1 164310 View on NCBI ↗
Plantago indica MW877577.1 149345 View on NCBI ↗
Plantago komarovii OR911479.1 165062 View on NCBI ↗
Plantago lagocephala OR911480.1 149672 View on NCBI ↗
Plantago lagopus NC_041420.1 145936 View on NCBI ↗
Plantago lanceolata NC_068049.1 149743 View on NCBI ↗
Plantago lanigera OR911482.1 165021 View on NCBI ↗
Plantago macrorhiza MW877568.1 159456 View on NCBI ↗
Plantago major NC_084063.1 165044 View on NCBI ↗
Plantago maritima NC_028519.1 158358 View on NCBI ↗
Plantago maxima PQ124708.1 165043 View on NCBI ↗
Plantago media NC_028520.1 164130 View on NCBI ↗
Plantago minuta OR911486.1 149658 View on NCBI ↗
Plantago muelleri OR911487.1 165025 View on NCBI ↗
Plantago myosuros OR911488.1 164780 View on NCBI ↗
Plantago pachyphylla OR911490.1 164783 View on NCBI ↗
Plantago rapensis OR911491.1 164798 View on NCBI ↗
Plantago rigida OR911492.1 164143 View on NCBI ↗
Plantago rugelii MW877573.1 164903 View on NCBI ↗
Plantago rupicola OR911493.1 164781 View on NCBI ↗
Plantago sericea MW877584.1 149710 View on NCBI ↗
Plantago strictissima PP541858.1 158056 View on NCBI ↗
Plantago tenuiflora MW877574.1 163739 View on NCBI ↗
Plantago virginica PQ124709.1 164872 View on NCBI ↗
Plantago wonjuenesis (nom. inval.) MK558819.1 164946 View on NCBI ↗