Markers + reference

Thyrsostachys

2 species · Poaceae · Poales

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Species 2
Genome length 139–140 kb
Candidate markers 269
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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0019 1.00 49.6 yes View details
trnG-UCC-trnT-GGU LSC 2643 0.0080 0.99 61.8 yes View details
rpoC2 LSC 4518 0.0020 1.00 40.4 yes View details
rbcL-accD LSC 496 0.0161 1.00 52.1 yes View details
petA-psbJ LSC 984 0.0061 1.00 62.4 yes View details
ndhF SSC 2220 0.0018 1.00 45.5 yes View details
rpl32-trnL-UAG SSC 718 0.0070 1.00 52.2 yes View details
rps19-psbA LSC 137 0.0292 1.00 69.3 no View details
trnF-GAA-ndhJ LSC 582 0.0052 1.00 61.5 yes View details
rpoA-rps11 LSC 64 0.0156 1.00 61.5 yes View details
petN-trnC-GCA LSC 900 0.0044 1.00 61.3 yes View details
clpP-psbB LSC 512 0.0059 1.00 60.7 yes View details
ycf3-trnS-GGA LSC 606 0.0000 0.98 60.5 yes View details
rps16-trnQ-UUG LSC 1048 0.0029 1.00 60.4 yes View details
psbM-petN LSC 736 0.0027 1.00 60.3 yes View details
trnC-GCA-rpoB LSC 1170 0.0017 0.99 60.3 yes View details
petD LSC 1231 0.0024 1.00 60.2 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 TCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1159 1.000 68.6
psbA_p2 psbA TTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1160 1.000 68.6
psbA_p3 psbA TCTGGCTTTCCTTCCTTCAAA AATACGTGTGCTTGGGAGTC 1159 1.000 66.6
psbA_p4 psbA TTCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1160 1.000 66.6
psbA_p5 psbA TTTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1161 1.000 66.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1130–1137 1.000 78.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1141–1148 1.000 78.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1134–1141 1.000 77.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1145–1152 1.000 76.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1136–1143 1.000 75.6
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU CATCGTTAGCTTGGAAGGCT CCATGGCATTACTCTACCACC 2831–2855 1.000 71.8
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU CGTTAGCTTGGAAGGCTAGG CCATGGCATTACTCTACCACC 2828–2852 1.000 71.6
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU CATCGTTAGCTTGGAAGGCT GACTTACGTCTTACCATGGCA 2844–2868 1.000 71.1
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU CATCGTTAGCTTGGAAGGCT TGACTTACGTCTTACCATGGC 2845–2869 1.000 71.1
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU CGTTAGCTTGGAAGGCTAGG GACTTACGTCTTACCATGGCA 2841–2865 1.000 70.9
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 898 1.000 67.7
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT GTAGTATGGGGGAGGAGTGG 842 1.000 66.7
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTCT TAGTATGGGGGAGGAGTGGA 841 1.000 66.0
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTC TAGTAAGTCTCGCTTGGGCT 898 1.000 63.5
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT AGTAGTATGGGGGAGGAGTG 843 1.000 62.7
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 949–954 1.000 70.7
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 951–956 1.000 70.3
petN-trnC-GCA_p3 petN-trnC-GCA CCACTCCTCCCCCATACTAC AGTTCAAATCTGGGTGCCG 1005–1010 1.000 69.6
petN-trnC-GCA_p4 petN-trnC-GCA CCACTCCTCCCCCATACTAC CCAGTTCAAATCTGGGTGCC 1007–1012 1.000 69.2
petN-trnC-GCA_p5 petN-trnC-GCA TCCACTCCTCCCCCATACTA AGTTCAAATCTGGGTGCCG 1006–1011 1.000 68.9
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1254–1267 1.000 77.4
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1253–1266 1.000 77.4
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AAGTTCTTCTGCCAAGCCTT 1318–1331 1.000 77.0
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AGTTCTTCTGCCAAGCCTTG 1317–1330 1.000 76.9
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CAAGTTCTTCTGCCAAGCCT 1319–1332 1.000 76.9

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
Thyrsostachys oliveri NC_068070.1 139454 View on NCBI ↗
Thyrsostachys siamensis MW366537.1 139522 View on NCBI ↗