Markers + reference

Spodiopogon

5 species · Poaceae · Poales

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Species 5
Genome length 139–140 kb
Candidate markers 279
Primer pairs 105

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 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps8 LSC 411 0.0000 1.00 21.4 yes View details
petL-psbE LSC 1282 0.0064 1.00 52.9 yes View details
trnfM-CAU-trnR-UCU LSC 165 0.0255 1.00 57.8 yes View details
rps2 LSC 711 0.0028 1.00 39.3 yes View details
rps2-rpoC2 LSC 305 0.0193 1.00 51.7 yes View details
rpoB-trnC-GCA LSC 1169 0.0051 1.00 41.6 yes View details
trnD-GUC-trnY-GUA LSC 351 0.0182 1.00 59.8 yes View details
trnT-GGU-trnfM-CAU LSC 2848 0.0058 1.00 51.7 yes View details
trnL-UAG-rpl32 SSC 531 0.0087 1.00 42.7 yes View details
rpl32-ndhF SSC 840 0.0090 1.00 44.2 yes View details
ndhF SSC 2217 0.0058 1.00 40.2 yes View details
rps8-infA LSC 172 0.0500 1.00 83.3 yes View details
rpl22-rps3 LSC 63 0.0286 1.00 59.4 yes View details
psbZ-trnS-UGA LSC 377 0.0069 1.00 56.5 yes View details
rps16 LSC 1106 0.0058 1.00 56.2 yes View details
psbJ-petA LSC 890 0.0052 1.00 55.8 yes View details
rpl36-rps11 LSC 179 0.0145 1.00 55.0 yes View details
rbcL-atpB LSC 788 0.0046 1.00 54.7 yes View details
ycf3-psaA LSC 604 0.0036 1.00 54.1 yes View details
atpH-atpI LSC 821 0.0027 1.00 53.5 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl22-rps3_p1 rpl22-rps3 CGAGCTCGAGGACGTAGTTA GTGCGAACCAAAAGGAATGG 220–239 1.000 75.5
rpl22-rps3_p2 rpl22-rps3 CGAGCTCGAGGACGTAGTTA ACCAAGTCTGAAACCGAGTG 186–205 1.000 74.4
rpl22-rps3_p3 rpl22-rps3 CGAGCTCGAGGACGTAGTTA CCAAGTCTGAAACCGAGTGG 185–204 1.000 72.5
rpl22-rps3_p4 rpl22-rps3 CGAGCTCGAGGACGTAGTTA CAAGTCTGAAACCGAGTGGA 184–203 1.000 72.2
rpl22-rps3_p5 rpl22-rps3 CGAGCTCGAGGACGTAGTTA GTTGTGCGAACCAAAAGGAA 223–242 1.000 71.5
rps8_p1 rps8 CAAAGGCGACGACGGTATAA TTGACCCTATCCCCCATCAG 968–986 1.000 80.9
rps8_p2 rps8 CATAGGAGCCGCTGGTAATC TTGACCCTATCCCCCATCAG 1106–1124 1.000 80.7
rps8_p3 rps8 CATAGGAGCCGCTGGTAATC GGGTAGGGCTTCCGTAACTA 999–1017 1.000 80.6
rps8_p4 rps8 CAAAGGCGACGACGGTATAA TTGGACATTTCCGTGGGTAC 1387–1400 1.000 79.9
rps8_p5 rps8 CATAGGAGCCGCTGGTAATC TTGGACATTTCCGTGGGTAC 1525–1538 1.000 79.8
rps8-infA_p1 rps8-infA ATTCCTAAGGTTTTGGGCGG TCGTGTCATTCTCTAGGCGA 305–323 1.000 84.6
rps8-infA_p2 rps8-infA CCTAAGGTTTTGGGCGGAAT TCGTGTCATTCTCTAGGCGA 302–320 1.000 84.6
rps8-infA_p3 rps8-infA ATTCCTAAGGTTTTGGGCGG TTGACCCTATCCCCCATCAG 375–393 1.000 84.2
rps8-infA_p4 rps8-infA CCTAAGGTTTTGGGCGGAAT TTGACCCTATCCCCCATCAG 372–390 1.000 84.2
rps8-infA_p5 rps8-infA CCTAAGGTTTTGGGCGGAAT ATAGCCCAGGATGATCGTGT 316–334 1.000 84.2
rpl36-rps11_p1 rpl36-rps11 CGTGGGCGAATTAGAGTCAT CGCAAACCAATACGCACTTT 292–298 1.000 79.2
rpl36-rps11_p2 rpl36-rps11 CGTGGGCGAATTAGAGTCAT CTACGCAAACCAATACGCAC 295–301 1.000 78.3
rpl36-rps11_p3 rpl36-rps11 CGTGGGCGAATTAGAGTCAT TCTACGTGCACTCTTCCGTA 332–338 1.000 77.9
rpl36-rps11_p4 rpl36-rps11 CGTGGGCGAATTAGAGTCAT TACGCAAACCAATACGCACT 294–300 1.000 77.9
rpl36-rps11_p5 rpl36-rps11 CGTGGGCGAATTAGAGTCAT CGTGCACTCTTCCGTAAACT 328–334 1.000 77.6
petL-psbE_p1 petL-psbE AAGCAGCCAGTAGAAAACCG TGACAAATAACCAACCCGCA 1440–1469 1.000 77.5
petL-psbE_p2 petL-psbE GCAGCCAGTAGAAAACCGAA TGACAAATAACCAACCCGCA 1438–1467 1.000 77.5
petL-psbE_p3 petL-psbE AAGCAGCCAGTAGAAAACCG CAACCCGCAATGAATAGGGA 1429–1458 1.000 77.3
petL-psbE_p4 petL-psbE GCAGCCAGTAGAAAACCGAA CAACCCGCAATGAATAGGGA 1427–1456 1.000 77.2
petL-psbE_p5 petL-psbE AAGCAGCCAGTAGAAAACCG ACCAACCCGCAATGAATAGG 1431–1460 1.000 75.8
psbJ-petA_p1 psbJ-petA TGGTTCGTATTCTGGATTGGG GGCCTTTTGTTCTTCTTCGC 1025–1032 1.000 70.6
psbJ-petA_p2 psbJ-petA GGTTCGTATTCTGGATTGGGT GGCCTTTTGTTCTTCTTCGC 1024–1031 1.000 70.6
psbJ-petA_p3 psbJ-petA TGGTTCGTATTCTGGATTGGG CGTCCAAGGCCTTTTGTTCT 1032–1039 1.000 65.6
psbJ-petA_p4 psbJ-petA GGTTCGTATTCTGGATTGGGT CGTCCAAGGCCTTTTGTTCT 1031–1038 1.000 65.6
psbJ-petA_p5 psbJ-petA TGGTTCGTATTCTGGATTGGG GCCTTTTGTTCTTCTTCGCA 1024–1031 1.000 64.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Spodiopogon cotulifer PQ469702.1 139335 View on NCBI ↗
Spodiopogon duclouxii PQ469704.1 139512 View on NCBI ↗
Spodiopogon formosanus PQ550994.1 139336 View on NCBI ↗
Spodiopogon sagittifolius NC_064989.1 139401 View on NCBI ↗
Spodiopogon sibiricus PQ469703.1 139486 View on NCBI ↗