Markers + reference

Schizachne

2 species · Poaceae · Poales

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Species 2
Genome length 136–136 kb
Candidate markers 257
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 399 0.0251 1.00 69.0 yes View details
trnG-trnT LSC 1569 0.0051 1.00 60.7 yes View details
psbM-petN LSC 766 0.0081 0.96 61.4 yes View details
rpoB LSC 3231 0.0022 1.00 41.5 yes View details
psaA-ycf3 LSC 631 0.0111 1.00 65.5 yes View details
trnT-trnL LSC 762 0.0079 1.00 63.3 yes View details
ndhC-trnV LSC 860 0.0058 1.00 57.0 yes View details
rps15-ndhF IRb 460 0.0109 1.00 62.5 yes View details
ndhF SSC 2220 0.0018 1.00 45.5 yes View details
ndhF-rpl32 SSC 840 0.0072 0.99 59.7 yes View details
ndhG SSC 531 0.0056 1.00 47.6 yes View details
rps3-rpl22 LSC 57 0.0351 1.00 72.7 yes View details
rpl22-rps19 IRb 84 0.0238 1.00 66.2 yes View details
rps19-psbA LSC 128 0.0234 1.00 66.0 no View details
ycf3-trnS LSC 593 0.0067 1.00 62.5 yes View details
petA-psbJ LSC 824 0.0049 1.00 61.6 yes View details
trnG-trnfM LSC 494 0.0081 1.00 61.4 yes View details
trnC-rpoB LSC 1106 0.0045 1.00 61.3 yes View details
rbcL-psaI LSC 960 0.0042 1.00 61.1 yes View details
psbH-petB LSC 869 0.0035 1.00 60.7 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_p1 trnK CCAAGGTCAGCCCAAAGATT GGCGTGCGGTGTAATTCTAT 2739 1.000 76.1
trnK_p2 trnK CCAAGGTCAGCCCAAAGATT AATGTTTTGATAGGGCGTGC 2752 1.000 71.9
trnK_p3 trnK CCAAGGTCAGCCCAAAGATT GCGTGCGGTGTAATTCTATTG 2738 1.000 71.2
trnK_p4 trnK CCAAGGTCAGCCCAAAGATT GGCGTGCGGTGTAATTCTA 2739 1.000 71.0
trnK_p5 trnK CCAAGGTCAGCCCAAAGATT ATGTTTTGATAGGGCGTGCG 2751 1.000 69.3
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT ACGTCCTGGGTCATTGGATA 524 1.000 80.1
psbK-psbI_p2 psbK-psbI CTTTTGTTTGGCAAGCTGCT TACGTCCTGGGTCATTGGAT 525 1.000 80.1
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGTCCTGGGTCATTGGATA 519 1.000 80.1
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGTCCTGGGTCATTGGAT 520 1.000 80.1
psbK-psbI_p5 psbK-psbI CTTTTGTTTGGCAAGCTGCT TTTTTACTCCTCACGCCCAG 548 1.000 79.6
trnG-trnfM_p1 trnG-trnfM GTCGACCCAAGCGGATATAC CGAGGCTCATAACCTTGAGG 651–652 1.000 78.3
trnG-trnfM_p2 trnG-trnfM GCGAGCGTAGTTCAATGGTA CGAGGCTCATAACCTTGAGG 611–612 1.000 78.1
trnG-trnfM_p3 trnG-trnfM GTCGACCCAAGCGGATATAC CAGTTTGGTAGCTCACGAGG 666–667 1.000 77.8
trnG-trnfM_p4 trnG-trnfM GCGAGCGTAGTTCAATGGTA CAGTTTGGTAGCTCACGAGG 626–627 1.000 77.7
trnG-trnfM_p5 trnG-trnfM GTCGACCCAAGCGGATATAC TTTTTCGTCCACCAGTTCCC 708–709 1.000 77.5
trnG-trnT_p1 trnG-trnT ACGAATCACACTTTTACCACT ACGTCTTACCACGGCATTAC 1711–1713 1.000 52.2
trnG-trnT_p2 trnG-trnT AGAACGAATCACACTTTTACCAC ACGTCTTACCACGGCATTAC 1714–1716 1.000 51.1
trnG-trnT_p3 trnG-trnT GAACGAATCACACTTTTACCACT ACGTCTTACCACGGCATTAC 1713–1715 1.000 51.1
trnG-trnT_p4 trnG-trnT AACGAATCACACTTTTACCACT ACGTCTTACCACGGCATTAC 1712–1714 1.000 50.3
trnG-trnT_p5 trnG-trnT ACGAATCACACTTTTACCACT CGTCTTACCACGGCATTACT 1710–1712 1.000 49.9
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 906–928 1.000 70.6
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT GTAGTATGGGGGAGGAGTGG 850–872 1.000 69.7
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTCT TAGTATGGGGGAGGAGTGGA 849–871 1.000 69.0
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTC TAGTAAGTCTCGCTTGGGCT 906–928 1.000 66.4
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT AGTAGTATGGGGGAGGAGTG 851–873 1.000 65.8
trnC-rpoB_p1 trnC-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1190–1202 1.000 77.2
trnC-rpoB_p2 trnC-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1189–1201 1.000 77.2
trnC-rpoB_p3 trnC-rpoB AAAGGATTTGCAGTCCCCTG AAGTTCTTCTGCCAAGCCTT 1254–1266 1.000 76.8
trnC-rpoB_p4 trnC-rpoB AAAGGATTTGCAGTCCCCTG AGTTCTTCTGCCAAGCCTTG 1253–1265 1.000 76.7
trnC-rpoB_p5 trnC-rpoB AAAGGATTTGCAGTCCCCTG CAAGTTCTTCTGCCAAGCCT 1255–1267 1.000 76.7

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
Schizachne purpurascens NC_050410.1 135671 View on NCBI ↗
Schizachne purpurascens subsp. callosa PZ098273.1 135621 View on NCBI ↗