Markers + reference

Leptochloa

2 species · Poaceae · Poales

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Species 2
Genome length 134–135 kb
Candidate markers 273
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 7 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 394 0.0025 1.00 55.9 yes View details
trnG-UCC-trnM-CAU LSC 991 0.0010 1.00 59.3 yes View details
trnD-GUC-psbM LSC 976 0.0031 1.00 60.5 yes View details
rpoC2-rps2 LSC 287 0.0035 1.00 43.0 yes View details
rps2 LSC 711 0.0014 1.00 59.6 yes View details
ndhC-trnV-UAC LSC 922 0.0011 1.00 59.5 yes View details
petA LSC 963 0.0000 1.00 38.1 yes View details
petA-psbJ LSC 870 0.0069 1.00 62.7 yes View details
rpl33-rps18 LSC 303 0.0037 0.89 57.7 yes View details
rpl16 LSC 1431 0.0007 1.00 59.2 yes View details
rps3 LSC 675 0.0015 1.00 59.6 yes View details
atpI-atpH LSC 776 0.0013 1.00 59.5 yes View details
trnC-GCA-rpoB LSC 1055 0.0009 1.00 59.3 yes View details
ndhH SSC 1182 0.0008 1.00 59.2 yes View details
matK LSC 1542 0.0006 1.00 59.0 yes View details
matK-trnK-UUU LSC 681 0.0000 1.00 58.9 yes View details
rps16 LSC 1052 0.0000 1.00 58.8 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_p1 trnK-UUU ACGCTTGGAAACGATTGGAT AGGAGCGTTCGGTGTAATTC 2729–2730 1.000 78.6
trnK-UUU_p2 trnK-UUU CAACGCTTGGAAACGATTGG AGGAGCGTTCGGTGTAATTC 2731–2732 1.000 77.5
trnK-UUU_p3 trnK-UUU AACGCTTGGAAACGATTGGA AGGAGCGTTCGGTGTAATTC 2730–2731 1.000 76.8
trnK-UUU_p4 trnK-UUU ACGCTTGGAAACGATTGGAT CAGGAGCGTTCGGTGTAATT 2730–2731 1.000 76.4
trnK-UUU_p5 trnK-UUU ACGCTTGGAAACGATTGGAT GAGCGTTCGGTGTAATTCCA 2727–2728 1.000 76.4
matK_p1 matK AGGGGAACATTTCAGAATGGA TGTAACACCCTGTTTTGACCA 1713 1.000 52.2
matK_p2 matK AGGGGAACATTTCAGAATGGAA TGTAACACCCTGTTTTGACCA 1713 1.000 49.9
matK_p3 matK GGGGAACATTTCAGAATGGA TGTAACACCCTGTTTTGACCA 1712 1.000 47.4
matK_p4 matK AGGGGAACATTTCAGAATGG TGTAACACCCTGTTTTGACCA 1713 1.000 47.3
matK_p5 matK AGGGGAACATTTCAGAATGGA TGTAACACCCTGTTTTGACCAT 1713 1.000 46.3
matK-trnK-UUU_p1 matK-trnK-UUU CATAATCGTGGGCAAATGCA AGGAGCGTTCGGTGTAATTC 881–882 1.000 73.1
matK-trnK-UUU_p2 matK-trnK-UUU ACATAATCGTGGGCAAATGC AGGAGCGTTCGGTGTAATTC 882–883 1.000 73.1
matK-trnK-UUU_p3 matK-trnK-UUU CATAATCGTGGGCAAATGCA CAGGAGCGTTCGGTGTAATT 882–883 1.000 70.9
matK-trnK-UUU_p4 matK-trnK-UUU ACATAATCGTGGGCAAATGC CAGGAGCGTTCGGTGTAATT 883–884 1.000 70.9
matK-trnK-UUU_p5 matK-trnK-UUU CATAATCGTGGGCAAATGCA GAGCGTTCGGTGTAATTCCA 879–880 1.000 70.9
rps16_p1 rps16 GCACGACATAAATGCAGCAA ACTCTCGATACCACTTTGCA 1208–1209 1.000 66.6
rps16_p2 rps16 GCACGACATAAATGCAGCAA AACTCTCGATACCACTTTGCA 1209–1210 1.000 64.6
rps16_p3 rps16 GCACGACATAAATGCAGCAA ACTCTCGATACCACTTTGCAA 1208–1209 1.000 64.6
rps16_p4 rps16 GCACGACATAAATGCAGCAA CAACTCTCGATACCACTTTGC 1210–1211 1.000 62.0
rps16_p5 rps16 GCACGACATAAATGCAGCAA AACTCTCGATACCACTTTGCAA 1209–1210 1.000 62.0
psbK-psbI_p1 psbK-psbI CGTGGATGTTATGCCTGTCA TTTACTCCTCACGTCCAGGA 585 1.000 77.6
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTACTCCTCACGTCCAGGA 536 1.000 77.3
psbK-psbI_p3 psbK-psbI TTAGCGTTTGTTTGGCAAGC TTTACTCCTCACGTCCAGGA 545 1.000 76.5
psbK-psbI_p4 psbK-psbI CGTGGATGTTATGCCTGTCA ACTCCTCACGTCCAGGATTA 582 1.000 75.7
psbK-psbI_p5 psbK-psbI CGTGGATGTTATGCCTGTCA TACTCCTCACGTCCAGGATT 583 1.000 75.7
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT GGAAAAGCCCCTTATCGGAT 1096 1.000 46.5
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU AGAACGAATCACACTTTTACCAC GGAAAAGCCCCTTATCGGAT 1099 1.000 45.5
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT GGAAAAGCCCCTTATCGGAT 1098 1.000 45.5
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU AACGAATCACACTTTTACCACT GGAAAAGCCCCTTATCGGAT 1097 1.000 44.6
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT GGAAAAGCCCCTTATCGGATT 1096 1.000 43.3

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
Leptochloa pluriflora NC_037169.1 134507 View on NCBI ↗
Leptochloa virgata NC_036692.1 134500 View on NCBI ↗