Markers + reference

Cleistogenes

11 species · Poaceae · Poales

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Species 11
Genome length 134–135 kb
Candidate markers 268
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 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
trnG-GCC-trnfM-CAU LSC 356 0.0033 1.00 43.3 yes View details
trnT-GGU-trnE-UUC LSC 539 0.0030 1.00 48.5 yes View details
trnD-GUC-psbM LSC 1082 0.0011 1.00 51.9 yes View details
petN-trnC-GCA LSC 848 0.0028 1.00 53.4 yes View details
trnC-GCA-rpoB LSC 1010 0.0022 1.00 56.7 yes View details
petA-psbJ LSC 929 0.0023 1.00 50.8 yes View details
psbE-petL LSC 1266 0.0014 1.00 52.0 yes View details
ndhF SSC 2220 0.0011 1.00 48.2 yes View details
atpI-atpH LSC 816 0.0011 1.00 54.1 yes View details
trnT-UGU-trnL-UAA LSC 863 0.0009 0.95 53.5 yes View details
petD LSC 1230 0.0007 1.00 49.4 yes View details
matK-trnK-UUU LSC 675 0.0008 1.00 49.0 yes View details
petB LSC 1427 0.0001 1.00 49.0 yes View details
ndhF-rpl32 SSC 920 0.0012 1.00 48.9 yes View details
psbM-petN LSC 788 0.0011 1.00 48.2 yes View details
psaA-ycf3 LSC 661 0.0006 1.00 48.0 yes View details
ycf3 LSC 1999 0.0006 1.00 46.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU TTCCTGAAAGAGAAGTGGGT GTCCGGTGTAATTCCATCGA 825–851 1.000 61.8
matK-trnK-UUU_p2 matK-trnK-UUU TTCCTGAAAGAGAAGTGGGT CGTCCGGTGTAATTCCATCG 826–852 1.000 60.2
matK-trnK-UUU_p3 matK-trnK-UUU TTCCTGAAAGAGAAGTGGGT TTCAATGTTTTGCCAGGAGC 845–871 1.000 59.9
matK-trnK-UUU_p4 matK-trnK-UUU TTCCTGAAAGAGAAGTGGGT TGGGTTGCTAACTCAATGGT 767–793 1.000 59.0
matK-trnK-UUU_p5 matK-trnK-UUU TTCCTGAAAGAGAAGTGGGT TCAATGGTAGAGTACTCGGCT 755–781 1.000 58.7
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA AGTTTTTGGCCCTACAGAGC 518–521 1.000 79.6
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU AATATATGCCGTAGCGAGCG AGTTTTTGGCCCTACAGAGC 531–553 1.000 79.5
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU GACCCAGGCGGATATATCCT AGTTTTTGGCCCTACAGAGC 555–577 1.000 79.1
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT AGTTTTTGGCCCTACAGAGC 522–544 1.000 78.8
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU TAGCGAGCGTAGTTCAATGG AGTTTTTGGCCCTACAGAGC 520–523 1.000 78.6
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 659–664 1.000 68.0
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 638–643 1.000 67.8
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 622–627 1.000 67.8
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 601–606 1.000 67.7
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG GCTGCCTCCTTGAAAGAGAG 627–632 1.000 67.0
trnD-GUC-psbM_p1 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC TCATTTTGGCTGGCTGTTTT 1237–1251 1.000 66.0
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TCATTTTGGCTGGCTGTTTT 1270–1284 1.000 65.2
trnD-GUC-psbM_p3 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC AATCATTTTGGCTGGCTGTT 1239–1253 1.000 64.2
trnD-GUC-psbM_p4 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC ATCATTTTGGCTGGCTGTTT 1238–1252 1.000 64.2
trnD-GUC-psbM_p5 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC TCATTTTGGCTGGCTGTTTTT 1237–1251 1.000 64.0
psbM-petN_p1 psbM-petN AAAACAGCCAGCCAAAATGA AGTATGGGGGAGAAGTGGAC 834–837 1.000 69.2
psbM-petN_p2 psbM-petN AAAACAGCCAGCCAAAATGA GTATGGGGGAGAAGTGGACT 833–836 1.000 69.2
psbM-petN_p3 psbM-petN AAAACAGCCAGCCAAAATGA TAGTAAGTCTCGCTTGGGCT 892–895 1.000 68.9
psbM-petN_p4 psbM-petN AAAACAGCCAGCCAAAATGA TATGGGGGAGAAGTGGACTC 832–835 1.000 68.8
psbM-petN_p5 psbM-petN AAAACAGCCAGCCAAAATGA GGGGGAGAAGTGGACTCTAG 829–832 1.000 68.5
petN-trnC-GCA_p1 petN-trnC-GCA AGTCCACTTCTCCCCCATAC AGTTCAAATCTGGGTGCCG 891–958 1.000 75.2
petN-trnC-GCA_p2 petN-trnC-GCA GTCCACTTCTCCCCCATACT AGTTCAAATCTGGGTGCCG 890–957 1.000 75.2
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 832–899 1.000 75.0
petN-trnC-GCA_p4 petN-trnC-GCA AGTCCACTTCTCCCCCATAC CCAGTTCAAATCTGGGTGCC 893–960 1.000 74.8
petN-trnC-GCA_p5 petN-trnC-GCA GTCCACTTCTCCCCCATACT CCAGTTCAAATCTGGGTGCC 892–959 1.000 74.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Cleistogenes caespitosa MW194082.1 134654 View on NCBI ↗
Cleistogenes caespitosa var. ramosa MW194083.1 134233 View on NCBI ↗
Cleistogenes chinensis MW194084.1 134550 View on NCBI ↗
Cleistogenes festucacea MW194085.1 134594 View on NCBI ↗
Cleistogenes gracilis MW194086.1 134576 View on NCBI ↗
Cleistogenes hackelii MW194087.1 134588 View on NCBI ↗
Cleistogenes hackelii var. nakaii MW194088.1 134531 View on NCBI ↗
Cleistogenes hancei MW194089.1 134549 View on NCBI ↗
Cleistogenes polyphylla MW194090.1 134579 View on NCBI ↗
Cleistogenes songorica MW194091.1 134556 View on NCBI ↗
Cleistogenes squarrosa MW194092.1 134509 View on NCBI ↗