Markers + reference

Stipa

50 species · Poaceae · Poales

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Species 50
Genome length 137–138 kb
Candidate markers 269
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

9 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
trnK-UUU-rps16 LSC 558 0.0092 0.00 37.5 yes View details
trnG-GCC-trnfM-CAU LSC 469 0.0069 0.00 27.5 yes View details
trnG-UCC-trnT-GGU LSC 1625 0.0070 0.00 37.9 yes View details
petN-trnC-GCA LSC 925 0.0074 0.00 26.6 yes View details
rbcL LSC 1431 0.0064 1.00 37.7 yes View details
rbcL-rpl23 LSC 297 0.0117 0.96 47.4 yes View details
ndhF SSC 2220 0.0044 1.00 43.6 yes View details
ndhF-rpl32 SSC 917 0.0078 0.99 60.1 yes View details
rpl32-trnL-UAG SSC 735 0.0069 0.99 55.9 yes View details
infA-rps8 LSC 111 0.0197 1.00 62.2 yes View details
petA-psbJ LSC 815 0.0049 1.00 59.4 yes View details
trnF-GAA-ndhJ LSC 577 0.0041 1.00 58.1 yes View details
ndhC-trnV-UAC LSC 899 0.0033 0.97 55.4 yes View details
trnT-UGU-trnL-UAA LSC 742 0.0052 0.99 54.0 yes View details
rpl22-rps19 IRb 84 0.0075 0.99 53.3 yes View details
ndhA SSC 2122 0.0029 1.00 52.0 yes View details
ycf4-cemA LSC 453 0.0030 1.00 50.2 yes View details
trnW-CCA-trnP-UGG LSC 139 0.0058 1.00 50.0 yes View details
rps3-rpl22 LSC 56 0.0063 1.00 49.1 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
trnK-UUU_p1 trnK-UUU CAACCAAGTCAGCCCAAAGA CGTGCGGTGTAATTCCATTG 2733–2764 1.000 82.0
trnK-UUU_p2 trnK-UUU TCAACCAAGTCAGCCCAAAG CGTGCGGTGTAATTCCATTG 2734–2765 1.000 82.0
trnK-UUU_p3 trnK-UUU GTCAACCAAGTCAGCCCAAA CGTGCGGTGTAATTCCATTG 2735–2766 1.000 79.7
trnK-UUU_p4 trnK-UUU AACCAAGTCAGCCCAAAGAT CGTGCGGTGTAATTCCATTG 2732–2763 1.000 79.1
trnK-UUU_p5 trnK-UUU ACCAAGTCAGCCCAAAGATT CGTGCGGTGTAATTCCATTG 2731–2762 1.000 79.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACT 680–697 1.000 75.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CATAGCCGCACTTAAAAGCC GGTGCTCAACCTACAAGAACT 685–702 1.000 74.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACT 679–696 1.000 71.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAAC 680–697 1.000 71.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTACCAAGAGTCTGGACGA GGTGCTCAACCTACAAGAACT 736–753 1.000 70.9
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GTCGACCCAAGCGGATATAC CGAGGCTCATAACCTTGAGG 605–639 1.000 84.0
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA CGAGGCTCATAACCTTGAGG 565–599 1.000 83.9
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU GTCGACCCAAGCGGATATAC CAGTTTGGTAGCTCACGAGG 620–654 1.000 83.5
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA CAGTTTGGTAGCTCACGAGG 580–614 1.000 83.4
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GTCGACCCAAGCGGATATAC GAGCGGAGTAGAGCAGTTTG 633–667 0.980 82.0
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCACGCCATTACTCTACCAC 1731–1774 1.000 58.1
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT CCACGCCATTACTCTACCAC 1733–1776 1.000 57.1
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACGTCTTACCACGCCATTAC 1739–1775 0.980 56.1
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC ACGTCTTACCACGCCATTAC 1742–1778 0.980 55.0
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ACGTCTTACCACGCCATTAC 1741–1777 0.980 55.0
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 974–1015 1.000 77.1
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 976–1017 1.000 76.7
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CAGTTCAAATCTGGGTGCCG 975–1016 1.000 73.8
petN-trnC-GCA_p4 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGGGGACTGCAAATCCTTTA 999–1040 1.000 72.7
petN-trnC-GCA_p5 petN-trnC-GCA AGCCCAAGCGAGACTTACTA TGCAAATCCTTTATCCCCAGT 992–1033 1.000 71.5
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA ATTTGAACCGATGACCCTCG ACAATCAAGTCCGTAGCGTC 840–912 1.000 85.7
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA CGATGACCCTCGCATTACAA ACAATCAAGTCCGTAGCGTC 832–904 1.000 85.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACAATCAAGTCCGTAGCGTC 810–882 1.000 85.1
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA ATTTGAACCGATGACCCTCG CCGTAGCGTCTACCGATTTC 830–902 1.000 83.9
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA ATTTGAACCGATGACCCTCG CAATCAAGTCCGTAGCGTCT 839–911 1.000 83.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (50)

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

Species Accession Length (bp) Link
Stipa aliena NC_072322.1 137379 View on NCBI ↗
Stipa arabica NC_037024.1 137757 View on NCBI ↗
Stipa austroaltaica NC_062948.1 137831 View on NCBI ↗
Stipa baicalensis NC_072325.1 137842 View on NCBI ↗
Stipa basiplumosa NC_062959.1 137305 View on NCBI ↗
Stipa borysthenica NC_037025.1 137825 View on NCBI ↗
Stipa breviflora NC_062949.1 137474 View on NCBI ↗
Stipa bungeana NC_065504.1 137759 View on NCBI ↗
Stipa capillacea NC_072323.1 137158 View on NCBI ↗
Stipa capillata NC_037026.1 137830 View on NCBI ↗
Stipa caucasica NC_037027.1 137798 View on NCBI ↗
Stipa caucasica subsp. glareosa OP681434.1 137834 View on NCBI ↗
Stipa caucasica x Stipa magnifica NC_062950.1 137801 View on NCBI ↗
Stipa ehrenbergiana NC_062951.1 137823 View on NCBI ↗
Stipa grandis NC_072324.1 137859 View on NCBI ↗
Stipa heptapotamica NC_041507.1 137829 View on NCBI ↗
Stipa hohenackeriana NC_037028.1 137753 View on NCBI ↗
Stipa hymenoides NC_027464.1 137742 View on NCBI ↗
Stipa kirghisorum NC_072316.1 137852 View on NCBI ↗
Stipa klimesii NC_062952.1 137202 View on NCBI ↗
Stipa lessingiana NC_037030.1 137829 View on NCBI ↗
Stipa lipskyi NC_028444.1 137854 View on NCBI ↗
Stipa macroglossa var. kazachstanica MT850070.1 137763 View on NCBI ↗
Stipa magnifica NC_037031.1 137848 View on NCBI ↗
Stipa narynica NC_037032.1 137854 View on NCBI ↗
Stipa orientalis NC_037033.1 137822 View on NCBI ↗
Stipa ovczinnikovii NC_037034.1 137874 View on NCBI ↗
Stipa penicillata NC_062953.1 137215 View on NCBI ↗
Stipa pennata NC_062954.1 137814 View on NCBI ↗
Stipa pennata subsp. ceynowae MG052610.1 137825 View on NCBI ↗
Stipa pennata subsp. eriocaulis PP622695.1 137860 View on NCBI ↗
Stipa pennata subsp. pennata MG052611.1 137818 View on NCBI ↗
Stipa przewalskyi NC_062955.1 137753 View on NCBI ↗
Stipa pulcherrima NC_062956.1 137832 View on NCBI ↗
Stipa purpurea NC_029390.1 137370 View on NCBI ↗
Stipa regeliana NC_072319.1 137372 View on NCBI ↗
Stipa richteriana NC_041508.1 137827 View on NCBI ↗
Stipa richteriana subsp. jagnobica NC_037029.1 137827 View on NCBI ↗
Stipa richteriana subsp. richteriana MG052612.1 137831 View on NCBI ↗
Stipa roborowskyi NC_072321.1 137214 View on NCBI ↗
Stipa sareptana NC_072317.1 137831 View on NCBI ↗
Stipa sibirica NC_062946.1 137818 View on NCBI ↗
Stipa subsessiliflora NC_072318.1 137120 View on NCBI ↗
Stipa tianschanica NC_072320.1 137620 View on NCBI ↗
Stipa tianschanica var. gobica PP234585.1 137308 View on NCBI ↗
Stipa tianschanica var. klemenzii OP681433.1 137828 View on NCBI ↗
Stipa tzveleviana NC_062957.1 137835 View on NCBI ↗
Stipa x alaica NC_037035.1 137850 View on NCBI ↗
Stipa x brevicallosa NC_037036.1 137850 View on NCBI ↗
Stipa zalesskii NC_037037.1 137836 View on NCBI ↗