Markers + reference

Lolium

2 species · Poaceae · Poales

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Species 2
Genome length 135–135 kb
Candidate markers 271
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 28.1 yes View details
rps16-trnQ-UUG LSC 782 0.0064 1.00 62.4 yes View details
ndhJ LSC 480 0.0187 1.00 56.5 yes View details
rbcL-psaI LSC 1182 0.0135 1.00 66.5 yes View details
rps11-rpl36 LSC 192 0.0156 1.00 48.5 yes View details
ndhF-rpl32 SSC 770 0.0043 0.91 62.8 yes View details
rpl32-trnL-UAG SSC 656 0.0259 1.00 73.7 yes View details
rps19-psbA LSC 121 0.0579 1.00 82.2 no View details
ndhC-trnV-UAC LSC 894 0.0024 0.94 64.7 yes View details
petA-psbJ LSC 788 0.0025 1.00 60.2 yes View details
atpI-atpH LSC 569 0.0035 1.00 60.1 yes View details
petN-trnC-GCA LSC 898 0.0022 1.00 60.0 yes View details
ycf3-trnS-GGA LSC 596 0.0034 1.00 59.9 yes View details
psbB LSC 1527 0.0020 1.00 59.8 yes View details
ndhI SSC 543 0.0037 1.00 59.7 yes View details
clpP-psbB LSC 537 0.0037 1.00 59.6 yes View details
atpB-rbcL LSC 793 0.0013 1.00 59.5 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
psbA_p1 psbA TCCTATATGTTAGCAGAAAAACC TATGTGTGCTTGGGAGTCCT 1133 1.000 40.0
psbA_p2 psbA TTCCTATATGTTAGCAGAAAAACC TATGTGTGCTTGGGAGTCCT 1134 1.000 40.0
psbA_p3 psbA TCCTATATGTTAGCAGAAAAACC TGGGAGTCCTTGCAATTTGA 1123 1.000 40.0
psbA_p4 psbA TCCTATATGTTAGCAGAAAAACC ATATGTGTGCTTGGGAGTCC 1134 1.000 40.0
psbA_p5 psbA TCCTATATGTTAGCAGAAAAACC GCTTGGGAGTCCTTGCAATT 1126 1.000 40.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 856–887 1.000 78.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 867–898 1.000 78.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 860–891 1.000 77.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 871–902 1.000 77.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 862–893 1.000 75.9
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 947–965 1.000 70.5
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 949–967 1.000 70.1
petN-trnC-GCA_p3 petN-trnC-GCA CCACTCCTCCCCCATACTAC AGTTCAAATCTGGGTGCCG 1003–1021 1.000 69.5
petN-trnC-GCA_p4 petN-trnC-GCA CCACTCCTCCCCCATACTAC CCAGTTCAAATCTGGGTGCC 1005–1023 1.000 69.0
petN-trnC-GCA_p5 petN-trnC-GCA TCCACTCCTCCCCCATACTA AGTTCAAATCTGGGTGCCG 1004–1022 1.000 68.8
atpI-atpH_p1 atpI-atpH TTTTGCAACATTAGCCGCAG GCAATAACAGAAGCAGCAGC 659 1.000 79.0
atpI-atpH_p2 atpI-atpH TTTTGCAACATTAGCCGCAG GCAGCAATAACAGAAGCAGC 662 1.000 79.0
atpI-atpH_p3 atpI-atpH TTTTGCAACATTAGCCGCAG GCAGTACCTTGACCAACTCC 716 1.000 78.2
atpI-atpH_p4 atpI-atpH TTTTGCAACATTAGCCGCAG AAGCAGCAGCAATTAGTGGA 649 1.000 78.1
atpI-atpH_p5 atpI-atpH TTTTGCAACATTAGCCGCAG GCCAATCCAGCAGCAATAAC 671 1.000 78.0
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TCTCCTGAGGTTGTCGGAAT TTCCAATGCTACGCCTTCAA 729 1.000 78.2
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TCTCCTGAGGTTGTCGGAAT AGTTCCAATGCTACGCCTTC 731 1.000 77.6
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTCTCCTGAGGTTGTCGGAA TTCCAATGCTACGCCTTCAA 730 1.000 76.4
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTCTCCTGAGGTTGTCGGA TTCCAATGCTACGCCTTCAA 731 1.000 76.4
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TGAAATTTCCATTTGCGCGG TTCCAATGCTACGCCTTCAA 665 1.000 76.4
ndhJ_p1 ndhJ CGTTTCATCTAGGAACAGAACG TCTTGCATCCGAAATGTGAA 622 1.000 41.2
ndhJ_p2 ndhJ CGTTTCATCTAGGAACAGAACG TTCTTGCATCCGAAATGTGA 623 1.000 41.2
ndhJ_p3 ndhJ TCCGTTTCATCTAGGAACAGA TCTTGCATCCGAAATGTGAA 624 1.000 41.2
ndhJ_p4 ndhJ TCCGTTTCATCTAGGAACAGA TTCTTGCATCCGAAATGTGA 625 1.000 41.2
ndhJ_p5 ndhJ CGTTTCATCTAGGAACAGAACG CTTTCTTGCATCCGAAATGTGA 625 1.000 41.2

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
Lolium multiflorum NC_019651.1 135175 View on NCBI ↗
Lolium perenne NC_009950.1 135282 View on NCBI ↗