Markers + reference

Sorghum

6 species · Poaceae · Poales

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Species 6
Genome length 141–141 kb
Candidate markers 281
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 281 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps19 LSC 282 0.0000 0.00 27.5 yes View details
matK-trnK-UUU LSC 692 0.0031 1.00 46.9 yes View details
trnS-GCU-psbD LSC 993 0.0005 1.00 36.2 yes View details
trnG-UCC-trnM-CAU LSC 1948 0.0010 1.00 39.2 yes View details
trnY-GUA-trnD-GUC LSC 349 0.0061 1.00 34.4 yes View details
trnD-GUC-psbM LSC 1058 0.0010 1.00 40.9 yes View details
psbM-petN LSC 807 0.0020 1.00 41.5 yes View details
rpoC2 LSC 4563 0.0008 1.00 35.3 yes View details
trnS-GGA-rps4 LSC 280 0.0057 1.00 37.7 yes View details
rps19 LSC 282 0.0000 1.00 33.8 no View details
rps15 IRb 237 0.0000 1.00 28.9 yes View details
ndhF SSC 2217 0.0014 1.00 45.8 yes View details
ccsA SSC 966 0.0025 1.00 38.5 yes View details
rps15 IRa 237 0.0000 1.00 33.8 no View details
rpl2-trnH-GUG IRa 55 0.0182 0.96 53.8 no View details
trnC-GCA-rpoB LSC 1203 0.0009 1.00 47.1 yes View details
rpl16 LSC 1482 0.0000 1.00 43.7 yes View details
psbE-petL LSC 1264 0.0005 1.00 43.6 yes View details
SobiCr001 IRb 1492 0.0002 1.00 43.3 yes View details
SobiCr008 IRa 1492 0.0002 1.00 43.3 yes View details
ndhG SSC 531 0.0006 1.00 42.2 yes View details
rpl33-rps18 LSC 296 0.0018 1.00 41.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps19_p1 rps19 TGGACATAGGATGCCACTCT GAAGGAAGGAAAGCCGGAAA 423 0.167 44.5
rps19_p2 rps19 TGGACATAGGATGCCACTCT AAGGAAAGCCGGAAATACCC 418 0.167 44.1
rps19_p3 rps19 TGGACATAGGATGCCACTCT GGAAAGCCGGAAATACCCAA 416 0.167 44.0
rps19_p4 rps19 GTGGACATAGGATGCCACTC GAAGGAAGGAAAGCCGGAAA 424 0.167 43.9
rps19_p5 rps19 GTGGACATAGGATGCCACTC AAGGAAAGCCGGAAATACCC 419 0.167 43.6
matK-trnK-UUU_p1 matK-trnK-UUU ACGAAGTAGTGTTGACGAGA GAGCGTCCGGTGTAATTTCA 841–844 1.000 64.5
matK-trnK-UUU_p2 matK-trnK-UUU ACGAAGTAGTGTTGACGAGA AGCGTCCGGTGTAATTTCAT 840–843 1.000 63.6
matK-trnK-UUU_p3 matK-trnK-UUU ACGAAGTAGTGTTGACGAGA ATGTTTTGACAGGAGCGTCC 853–856 1.000 63.0
matK-trnK-UUU_p4 matK-trnK-UUU TGAAAGAGAAGTGGGTAGACG GAGCGTCCGGTGTAATTTCA 859–862 1.000 62.8
matK-trnK-UUU_p5 matK-trnK-UUU AGAGAAGTGGGTAGACGAAG GAGCGTCCGGTGTAATTTCA 855–858 1.000 62.4
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ATAAGCCGGACCATCCTACA 1142 1.000 79.0
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA AAAACGGTCCCTTCGTAACC 1117 1.000 78.8
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA TAAGCCGGACCATCCTACAA 1141 1.000 78.7
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1138 1.000 78.4
trnS-GCU-psbD_p5 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA AAACAAAACGGTCCCTTCGT 1121 1.000 77.8
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2062–2063 1.000 41.1
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 2032–2033 1.000 40.9
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 2028–2029 1.000 40.2
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 2029–2030 1.000 40.2
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2064–2065 1.000 40.2
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 473 1.000 76.5
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 440 1.000 74.1
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 439 1.000 73.9
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 472 1.000 72.3
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 441 1.000 70.7
trnD-GUC-psbM_p1 trnD-GUC-psbM AATAGGCATGCCATACACCC GGCAGTAGGAACTAGAATGAACA 1215–1220 1.000 53.2
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG GGCAGTAGGAACTAGAATGAACA 1181–1186 1.000 51.8
trnD-GUC-psbM_p3 trnD-GUC-psbM AATAGGCATGCCATACACCC AGGCAGTAGGAACTAGAATGAAC 1216–1221 1.000 51.2
trnD-GUC-psbM_p4 trnD-GUC-psbM AATAGGCATGCCATACACCC AGGCAGTAGGAACTAGAATGA 1216–1221 1.000 49.9
trnD-GUC-psbM_p5 trnD-GUC-psbM AATAGGCATGCCATACACCC TGCGAGAATATTGACTTCCA 1176–1181 1.000 49.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Sorghum bicolor NC_008602.1 140754 View on NCBI ↗
Sorghum bicolor x Sorghum x drummondii NC_082845.1 140643 View on NCBI ↗
Sorghum halepense NC_084351.1 140812 View on NCBI ↗
Sorghum mekongense NC_035022.1 140765 View on NCBI ↗
Sorghum propinquum NC_042789.1 140642 View on NCBI ↗
Sorghum x drummondii NC_042790.1 140755 View on NCBI ↗