Markers + reference

Orinus

2 species · Poaceae · Poales

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Species 2
Genome length 134–134 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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1097 0.0027 1.00 53.6 yes View details
petN-trnC-GCA LSC 848 0.0051 0.92 65.6 yes View details
psaA-ycf3 LSC 631 0.0079 1.00 63.3 yes View details
atpB LSC 1497 0.0020 1.00 46.0 yes View details
petA LSC 963 0.0000 1.00 25.4 yes View details
petA-psbJ LSC 827 0.0109 1.00 65.1 yes View details
ndhF SSC 2220 0.0036 1.00 46.9 yes View details
ndhF-rpl32 SSC 924 0.0056 0.96 62.9 yes View details
rpl32-trnL-UAG SSC 525 0.0154 0.99 66.7 yes View details
ccsA SSC 969 0.0031 1.00 50.6 yes View details
trnT-GGU LSC 65 0.0308 1.00 67.9 yes View details
ccsA-ndhD SSC 190 0.0370 0.99 66.7 yes View details
trnD-GUC-psbM LSC 1008 0.0050 0.99 62.3 yes View details
trnC-GCA-rpoB LSC 985 0.0051 1.00 61.9 yes View details
atpF LSC 1408 0.0022 0.98 61.9 yes View details
atpB-rbcL LSC 792 0.0051 1.00 61.8 yes View details
ndhC-trnV-UAC LSC 926 0.0043 1.00 61.6 yes View details
psbM-petN LSC 808 0.0050 0.99 61.4 yes View details
rbcL LSC 1428 0.0035 1.00 60.8 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
rps16_p1 rps16 GCACGACATAAATGCAGCAA TCTCGATACCACTTTGCAATGA 1257–1262 1.000 60.5
rps16_p2 rps16 GCACGACATAAATGCAGCAA CTCGATACCACTTTGCAATGA 1256–1261 1.000 56.9
rps16_p3 rps16 GCACGACATAAATGCAGCAA TCTCGATACCACTTTGCAATG 1257–1262 1.000 56.9
rps16_p4 rps16 GCACGACATAAATGCAGCAA TCGATACCACTTTGCAATGA 1255–1260 1.000 54.7
rps16_p5 rps16 GCACGACATAAATGCAGCAA CTCGATACCACTTTGCAATGAA 1256–1261 1.000 54.5
trnT-GGU_p1 trnT-GGU AGCCCTTTTAACTCAGTGGT TGGGCATCTCATACTAAACGA 234–236 1.000 50.9
trnT-GGU_p2 trnT-GGU AGGCATAAGTCATCGGTTCA TGGGCATCTCATACTAAACGA 197–199 1.000 50.9
trnT-GGU_p3 trnT-GGU TGGTAAGGCATAAGTCATCGG TGGGCATCTCATACTAAACGA 202–204 1.000 50.1
trnT-GGU_p4 trnT-GGU GGTAAGGCATAAGTCATCGGT TGGGCATCTCATACTAAACGA 201–203 1.000 50.1
trnT-GGU_p5 trnT-GGU GTGGTAGAGTAATGCCATGGT TGGGCATCTCATACTAAACGA 219–221 1.000 49.3
trnD-GUC-psbM_p1 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC TCATTTTGGCTGGCTGTTTT 1172–1213 1.000 66.0
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TCATTTTGGCTGGCTGTTTT 1205–1246 1.000 65.2
trnD-GUC-psbM_p3 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC AATCATTTTGGCTGGCTGTT 1174–1215 1.000 64.2
trnD-GUC-psbM_p4 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC ATCATTTTGGCTGGCTGTTT 1173–1214 1.000 64.2
trnD-GUC-psbM_p5 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC TCATTTTGGCTGGCTGTTTTT 1172–1213 1.000 63.9
psbM-petN_p1 psbM-petN AAAACAGCCAGCCAAAATGA TAGTAAGTCTCGCTTGGGCT 910–915 1.000 69.3
psbM-petN_p2 psbM-petN AAAACAGCCAGCCAAAATGA GGGGGAGAAGTGGACTCTAG 847–852 1.000 68.8
psbM-petN_p3 psbM-petN AAAACAGCCAGCCAAAATGA AGTAGTCTGGGGGAGAAGTG 855–860 1.000 68.6
psbM-petN_p4 psbM-petN AAACAGCCAGCCAAAATGAT TAGTAAGTCTCGCTTGGGCT 909–914 1.000 67.4
psbM-petN_p5 psbM-petN AACAGCCAGCCAAAATGATT TAGTAAGTCTCGCTTGGGCT 908–913 1.000 67.4
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 834–897 1.000 74.7
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 836–899 1.000 74.3
petN-trnC-GCA_p3 petN-trnC-GCA CTAGAGTCCACTTCTCCCCC AGTTCAAATCTGGGTGCCG 897–960 1.000 74.2
petN-trnC-GCA_p4 petN-trnC-GCA CACTTCTCCCCCAGACTACT AGTTCAAATCTGGGTGCCG 889–952 1.000 74.0
petN-trnC-GCA_p5 petN-trnC-GCA TCGCTAGAGTCCACTTCTCC AGTTCAAATCTGGGTGCCG 900–963 1.000 73.9
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1067–1069 1.000 77.4
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1066–1068 1.000 77.4
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AAGTTCTTCTGCCAAGCCTT 1131–1133 1.000 77.0
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AGTTCTTCTGCCAAGCCTTG 1130–1132 1.000 76.8
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CAAGTTCTTCTGCCAAGCCT 1132–1134 1.000 76.8

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
Orinus kokonoricus NC_042859.1 133953 View on NCBI ↗
Orinus thoroldii NC_068120.1 134218 View on NCBI ↗