Markers + reference

Fargesia

18 species · Poaceae · Poales

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Species 18
Genome length 140–140 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 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
psbA LSC 1062 0.0006 1.00 33.1 yes View details
trnS-GCU-psbD LSC 983 0.0017 1.00 39.7 yes View details
trnG-UCC-trnT-GGU LSC 1972 0.0022 1.00 57.0 yes View details
atpF LSC 1392 0.0013 1.00 46.4 yes View details
trnT-UGU-trnL-UAA LSC 820 0.0038 1.00 54.5 yes View details
rbcL LSC 1434 0.0016 1.00 37.1 yes View details
rbcL-psaI LSC 1286 0.0019 1.00 47.6 yes View details
ycf4-cemA LSC 400 0.0035 1.00 46.5 yes View details
rpl33-rps18 LSC 263 0.0041 1.00 48.9 yes View details
rpl16 LSC 1508 0.0020 1.00 37.8 yes View details
ndhF-rpl32 SSC 889 0.0029 1.00 54.8 yes View details
rpl32-trnL-UAG SSC 702 0.0029 1.00 47.9 yes View details
rps19-psbA LSC 129 0.0239 0.99 65.6 no View details
rps16-trnQ-UUG LSC 1533 0.0010 1.00 54.5 yes View details
rpl14-rpl16 LSC 109 0.0111 1.00 53.1 yes View details
trnC-GCA-rpoB LSC 1180 0.0012 1.00 51.0 yes View details
psbE-petL LSC 1228 0.0019 1.00 49.6 yes View details
matK-trnK-UUU LSC 692 0.0013 1.00 49.5 yes View details
petB LSC 1484 0.0003 0.99 49.1 yes View details
trnF-GAA-ndhJ LSC 584 0.0023 1.00 47.6 yes View details
matK LSC 1536 0.0009 1.00 47.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1159 0.944 66.4
psbA_p2 psbA TTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1160 0.944 66.4
psbA_p3 psbA TCTGGCTTTCCTTCCTTCAAA AATACGTGTGCTTGGGAGTC 1159 0.944 64.4
psbA_p4 psbA TTCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1160 0.944 64.4
psbA_p5 psbA TTTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1161 0.944 64.4
matK_p1 matK AGGGAACATTTCAGAAGAACA ATGCAACACCCTGTTTTGAC 1725 1.000 41.8
matK_p2 matK AGGGAACATTTCAGAAGAACA AATGCAACACCCTGTTTTGAC 1726 1.000 40.6
matK_p3 matK AGGGAACATTTCAGAAGAACA GCAACACCCTGTTTTGACCA 1723 1.000 40.6
matK_p4 matK AGGGAACATTTCAGAAGAACA TGCAACACCCTGTTTTGACC 1724 1.000 40.6
matK_p5 matK AGGGAACATTTCAGAAGAACAT ATGCAACACCCTGTTTTGAC 1725 1.000 40.6
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 860–865 1.000 69.3
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGG CGTGCGGTGTAATTCCATTG 860–865 1.000 67.5
matK-trnK-UUU_p3 matK-trnK-UUU CTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 859–864 1.000 67.5
matK-trnK-UUU_p4 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT TGGGTTGCTAACTCAATGGT 801–806 1.000 63.0
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGTA CGTGCGGTGTAATTCCATTG 860–865 1.000 62.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1546–1620 1.000 82.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1557–1631 1.000 82.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1550–1624 1.000 81.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1561–1635 1.000 80.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAAACCAGAAATGGGGCGT 1606–1680 1.000 80.6
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACTCTACCAAGGGCTATAGTCA 1036–1058 1.000 61.1
trnS-GCU-psbD_p2 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACTCTACCAAGGGCTATAGTCA 1022–1044 1.000 58.1
trnS-GCU-psbD_p3 trnS-GCU-psbD AGTCCACTCAGCCATCTCTC ACTCTACCAAGGGCTATAGTCA 1017–1039 1.000 57.3
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACTCTACCAAGGGCTATAGTCAT 1036–1058 1.000 56.7
trnS-GCU-psbD_p5 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA AACTCTACCAAGGGCTATAGTCA 1037–1059 1.000 56.4
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2103–2174 1.000 43.5
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTACGTCTTACCATGGCA 2116–2187 1.000 42.8
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTACCATGGC 2117–2188 1.000 42.8
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC CCATGGCATTACTCTACCACC 2106–2177 1.000 42.5
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2105–2176 1.000 42.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (18)

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

Species Accession Length (bp) Link
Fargesia albocerea NC_043891.1 139617 View on NCBI ↗
Fargesia angustissima NC_072282.1 139706 View on NCBI ↗
Fargesia canaliculata NC_043936.1 139606 View on NCBI ↗
Fargesia communis NC_043934.1 139605 View on NCBI ↗
Fargesia daminiu NC_043942.1 139652 View on NCBI ↗
Fargesia decurvata NC_043933.1 139642 View on NCBI ↗
Fargesia dracocephala NC_063836.1 139638 View on NCBI ↗
Fargesia edulis NC_043945.1 139572 View on NCBI ↗
Fargesia funiushanensis NC_043940.1 139622 View on NCBI ↗
Fargesia grossa NC_043944.1 139601 View on NCBI ↗
Fargesia hygrophila NC_043938.1 139602 View on NCBI ↗
Fargesia nana PV367265.1 139601 View on NCBI ↗
Fargesia nitida NC_024715.1 139535 View on NCBI ↗
Fargesia qinlingensis NC_040002.1 139640 View on NCBI ↗
Fargesia setosa NC_043939.1 139653 View on NCBI ↗
Fargesia spathacea NC_024716.1 139767 View on NCBI ↗
Fargesia stenoclada NC_043935.1 139622 View on NCBI ↗
Fargesia yunnanensis NC_024717.1 139609 View on NCBI ↗