Markers + reference

Saccharum

12 species · Poaceae · Poales

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Species 12
Genome length 141–141 kb
Candidate markers 290
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 290 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
orf1_sac LSC 390 0.0014 1.00 47.0 yes View details
trnG-GCC-trnM-CAU LSC 491 0.0052 1.00 41.4 yes View details
trnY-GUA-trnD-GUC LSC 349 0.0033 1.00 37.5 yes View details
psbM-petN LSC 810 0.0018 1.00 48.4 yes View details
trnT-UGU-trnL-UAA LSC 799 0.0030 1.00 48.5 yes View details
ndhC-trnV-UAC LSC 928 0.0021 1.00 48.4 yes View details
petA-psbJ LSC 899 0.0049 1.00 43.5 yes View details
ndhF-rpl32 SSC 855 0.0035 1.00 50.3 yes View details
rpl32-trnL-UAG SSC 522 0.0027 1.00 46.5 yes View details
ccsA SSC 966 0.0010 1.00 31.6 yes View details
ndhH SSC 1182 0.0013 1.00 50.2 yes View details
rps11-rpl36 LSC 185 0.0027 1.00 49.2 yes View details
orf1_sac-trnQ-UUG LSC 438 0.0011 1.00 48.5 yes View details
rpl16 LSC 1491 0.0013 1.00 48.5 yes View details
petN-trnC-GCA LSC 961 0.0009 1.00 48.3 yes View details
trnC-GCA-rpoB LSC 1212 0.0010 1.00 47.1 yes View details
atpF LSC 1384 0.0005 1.00 46.9 yes View details
matK-trnK-UUU LSC 653 0.0011 1.00 46.7 yes View details
rpl33-rps18 LSC 312 0.0021 1.00 46.5 yes View details
atpI-atpH LSC 819 0.0013 1.00 46.3 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
matK-trnK-UUU_p1 matK-trnK-UUU ACGAAGTAGTGTTGACGAGA GAGCGTCCGGTGTAATTTCA 841–845 1.000 64.8
matK-trnK-UUU_p2 matK-trnK-UUU ACGAAGTAGTGTTGACGAGA AGCGTCCGGTGTAATTTCAT 840–844 1.000 63.9
matK-trnK-UUU_p3 matK-trnK-UUU ACGAAGTAGTGTTGACGAGA ATGTTTTGACAGGAGCGTCC 853–857 1.000 63.3
matK-trnK-UUU_p4 matK-trnK-UUU TGAAAGAGAAGTGGGTAGACG GAGCGTCCGGTGTAATTTCA 859–863 1.000 63.1
matK-trnK-UUU_p5 matK-trnK-UUU AGAGAAGTGGGTAGACGAAG GAGCGTCCGGTGTAATTTCA 855–859 1.000 62.7
orf1_sac_p1 orf1_sac ACCAACGAACAGTTCTTACCT CAGGATCCATTTGACACCCA 457–570 1.000 65.7
orf1_sac_p2 orf1_sac ACCAACGAACAGTTCTTACCT ACAGGATCCATTTGACACCC 458–571 1.000 65.7
orf1_sac_p3 orf1_sac AACCAACGAACAGTTCTTACCT CAGGATCCATTTGACACCCA 458–571 1.000 63.2
orf1_sac_p4 orf1_sac ACCAACGAACAGTTCTTACCTT CAGGATCCATTTGACACCCA 457–570 1.000 63.2
orf1_sac_p5 orf1_sac ACCAACGAACAGTTCTTACCTT ACAGGATCCATTTGACACCC 458–571 1.000 63.1
orf1_sac-trnQ-UUG_p1 orf1_sac-trnQ-UUG AAGGCCTGTGCTGAAACTAA GAGGTTCGAATCCTTCCGTC 509–514 0.917 71.3
orf1_sac-trnQ-UUG_p2 orf1_sac-trnQ-UUG AGGCCTGTGCTGAAACTAAA GAGGTTCGAATCCTTCCGTC 508–513 0.917 71.3
orf1_sac-trnQ-UUG_p3 orf1_sac-trnQ-UUG AGTTTTAAGGCCTGTGCTGA GAGGTTCGAATCCTTCCGTC 515–520 0.917 71.3
orf1_sac-trnQ-UUG_p4 orf1_sac-trnQ-UUG TTAAGGCCTGTGCTGAAACT GAGGTTCGAATCCTTCCGTC 511–516 0.917 71.3
orf1_sac-trnQ-UUG_p5 orf1_sac-trnQ-UUG AGGCCTGTGCTGAAACTAAA CTCGGAGGTTCGAATCCTTC 512–517 0.917 70.2
trnG-GCC-trnM-CAU_p1 trnG-GCC-trnM-CAU AATATAGGCCGTAGCAAGCG CGAGGCTCATAACCTTGAGG 637–665 1.000 79.1
trnG-GCC-trnM-CAU_p2 trnG-GCC-trnM-CAU AATATAGGCCGTAGCAAGCG CAGTTTTCGGCCCTACAGAG 682–710 1.000 78.7
trnG-GCC-trnM-CAU_p3 trnG-GCC-trnM-CAU AATATAGGCCGTAGCAAGCG CAGTTTGGTAGCTCACGAGG 652–680 1.000 78.7
trnG-GCC-trnM-CAU_p4 trnG-GCC-trnM-CAU AATATAGGCCGTAGCAAGCG TACAGAGCGGAGTAGAGCAG 669–697 1.000 78.3
trnG-GCC-trnM-CAU_p5 trnG-GCC-trnM-CAU AATATAGGCCGTAGCAAGCG CTACAGAGCGGAGTAGAGCA 670–698 1.000 78.2
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 473–474 1.000 76.7
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 440–441 1.000 74.3
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 439–440 1.000 74.1
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 472–473 1.000 72.5
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 441–442 1.000 70.9
psbM-petN_p1 psbM-petN TGTTCATTCTAGTTCCTACTGCC TAGTAAGTCTCGCTTGGGCT 960–962 1.000 54.8
psbM-petN_p2 psbM-petN TGTTCATTCTAGTTCCTACTGCC GTAGTATGGGGGAGGAGTGG 904–906 1.000 53.9
psbM-petN_p3 psbM-petN TGTTCATTCTAGTTCCTACTGCC TAGTATGGGGGAGGAGTGGA 903–905 1.000 53.1
psbM-petN_p4 psbM-petN GTTCATTCTAGTTCCTACTGCCT TAGTAAGTCTCGCTTGGGCT 959–961 1.000 52.8
psbM-petN_p5 psbM-petN TGTTCATTCTAGTTCCTACTGCC CGCTAGTAGTATGGGGGAGG 909–911 1.000 52.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Saccharum barberi NC_072524.1 141174 View on NCBI ↗
Saccharum fulvum NC_082231.1 141151 View on NCBI ↗
Saccharum hybrid cultivar B4362 BK010677.1 141172 View on NCBI ↗
Saccharum hybrid cultivar NC_029221.1 141181 View on NCBI ↗
Saccharum hybrid cultivar NCo 310 NC_006084.1 141182 View on NCBI ↗
Saccharum hybrid cultivar RB867515 KX507245.1 141181 View on NCBI ↗
Saccharum hybrid cultivar SP80-3280 NC_005878.2 141182 View on NCBI ↗
Saccharum longisetosum PV091122.1 141133 View on NCBI ↗
Saccharum narenga NC_070069.1 141218 View on NCBI ↗
Saccharum officinarum NC_035224.1 141176 View on NCBI ↗
Saccharum sinense NC_072525.1 141174 View on NCBI ↗
Saccharum spontaneum NC_034802.1 141168 View on NCBI ↗