Markers + reference

Stipagrostis

3 species · Poaceae · Poales

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Species 3
Genome length 138–139 kb
Candidate markers 267
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2-rps2 LSC 326 0.0327 1.00 65.6 yes View details
atpA-trnR-UCU LSC 163 0.0123 1.00 39.1 yes View details
rbcL-psaI LSC 983 0.0130 0.94 56.3 yes View details
petA-psbJ LSC 909 0.0117 1.00 57.0 yes View details
rpl16 LSC 1509 0.0084 1.00 53.5 yes View details
rpl32-trnL-UAG SSC 492 0.0203 1.00 60.4 yes View details
ndhD SSC 1503 0.0027 1.00 47.2 yes View details
psbT-psbN LSC 53 0.0629 1.00 74.3 yes View details
psaA-ycf3 LSC 643 0.0073 1.00 64.8 yes View details
trnG-GCC-trnfM-CAU LSC 366 0.0164 1.00 64.3 yes View details
trnY-GUA-trnD-GUC LSC 374 0.0107 1.00 60.9 yes View details
petN-trnC-GCA LSC 929 0.0093 1.00 59.4 yes View details
atpI-atpH LSC 841 0.0056 1.00 59.3 yes View details
psbE-petL LSC 1124 0.0065 1.00 59.3 yes View details
atpB-rbcL LSC 797 0.0042 1.00 58.9 yes View details
rps16 LSC 1110 0.0042 1.00 58.4 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
rps16_p1 rps16 CTGGTGACCCTCTCCTACTT TCTCGATACCACTTTGCAATGA 1196 1.000 60.9
rps16_p2 rps16 CTGGTGACCCTCTCCTACTT CTCGATACCACTTTGCAATGA 1195 1.000 57.3
rps16_p3 rps16 CTGGTGACCCTCTCCTACTT TCTCGATACCACTTTGCAATG 1196 1.000 57.3
rps16_p4 rps16 TGGTGACCCTCTCCTACTTT TCTCGATACCACTTTGCAATGA 1195 1.000 57.1
rps16_p5 rps16 TACTGGTGACCCTCTCCTAC TCTCGATACCACTTTGCAATGA 1198 1.000 56.3
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GTGTAGCGAGCGTAGTTCAA CGAGGCTCATAACCTTGAGG 489–496 1.000 79.4
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GAAGGTACGGGTTCGATTCC CGAGGCTCATAACCTTGAGG 444–451 1.000 79.2
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA CGAGGCTCATAACCTTGAGG 484–491 1.000 79.0
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GTGTAGCGAGCGTAGTTCAA CAGTTTGGTAGCTCACGAGG 504–511 1.000 78.9
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GAAGGTACGGGTTCGATTCC CAGTTTGGTAGCTCACGAGG 459–466 1.000 78.7
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AAATCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 498–506 1.000 76.8
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 465–473 1.000 74.4
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 464–472 1.000 74.2
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AAATCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 497–505 1.000 72.6
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 466–474 1.000 71.0
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 977–978 1.000 71.5
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 979–980 1.000 71.1
petN-trnC-GCA_p3 petN-trnC-GCA CCACTCCTCCCCCATACTAC AGTTCAAATCTGGGTGCCG 1033–1034 1.000 70.4
petN-trnC-GCA_p4 petN-trnC-GCA CCACTCCTCCCCCATACTAC CCAGTTCAAATCTGGGTGCC 1035–1036 1.000 70.0
petN-trnC-GCA_p5 petN-trnC-GCA TCCACTCCTCCCCCATACTA AGTTCAAATCTGGGTGCCG 1034–1035 1.000 69.7
rpoC2-rps2_p1 rpoC2-rps2 AACCCCCATTTACCCCCATT TTTACGCTTTGCCGAGATGT 453–485 1.000 77.3
rpoC2-rps2_p2 rpoC2-rps2 ACCCCCATTTACCCCCATTT TTTACGCTTTGCCGAGATGT 452–484 1.000 77.3
rpoC2-rps2_p3 rpoC2-rps2 AACCCCCATTTACCCCCATT GCTTTGCCGAGATGTAAGGT 448–480 1.000 76.8
rpoC2-rps2_p4 rpoC2-rps2 ACCCCCATTTACCCCCATTT GCTTTGCCGAGATGTAAGGT 447–479 1.000 76.8
rpoC2-rps2_p5 rpoC2-rps2 TCAGAACCCCCATTTACCCC TTTACGCTTTGCCGAGATGT 457–489 1.000 76.5
atpI-atpH_p1 atpI-atpH TTTTGCAACATTAGCCGCAG AGCCAATCCAGCAGCAATAA 942–946 1.000 79.3
atpI-atpH_p2 atpI-atpH TTTTGCAACATTAGCCGCAG GCAGTACCTTGACCAACTCC 986–990 1.000 78.9
atpI-atpH_p3 atpI-atpH TTTTGCAACATTAGCCGCAG AAGCAGCAGCAATTAGTGGA 919–923 1.000 78.9
atpI-atpH_p4 atpI-atpH TTTTGCAACATTAGCCGCAG GCCAATCCAGCAGCAATAAC 941–945 1.000 78.8
atpI-atpH_p5 atpI-atpH TTTTGCAACATTAGCCGCAG ATAACGGAAGCAGCAGCAAT 926–930 1.000 78.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Stipagrostis hirtigluma NC_036112.1 138026 View on NCBI ↗
Stipagrostis pennata NC_060727.1 138725 View on NCBI ↗
Stipagrostis uniplumis var. uniplumis MF460973.1 138019 View on NCBI ↗