Markers + reference

Paspalum

23 species · Poaceae · Poales

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Species 23
Genome length 136–162 kb
Candidate markers 269
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

2 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
trnI-CAU-trnL-CAA IRb 5184 0.1349 0.75 79.1 yes View details
trnL-CAA-trnI-CAU IRa 5184 0.1262 0.76 79.3 yes View details
trnC-GCA-rpoB LSC 1224 0.0163 1.00 76.8 yes View details
trnY-GUA-trnD-GUC LSC 369 0.0181 1.00 70.5 yes View details
rbcL-psaI LSC 942 0.0180 0.98 70.5 yes View details
psbM-petN LSC 819 0.0113 0.97 68.7 yes View details
trnD-GUC-psbM LSC 1078 0.0122 0.99 67.7 yes View details
rpl32-trnL-UAG SSC 536 0.0223 1.00 67.5 yes View details
ycf3-trnS-GGA LSC 604 0.0081 1.00 66.2 yes View details
ccsA-ndhD SSC 191 0.0236 0.98 66.2 yes View details
trnK-UUU-rps16 LSC 550 0.0115 1.00 65.9 yes View details
ndhG-ndhI SSC 198 0.0135 1.00 65.9 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CATTGAGTTAGCAACCCGGA TCTTGAAAAGGGGGCTCAAC 663–670 1.000 84.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACCATTGAGTTAGCAACCCG TCTTGAAAAGGGGGCTCAAC 665–672 1.000 84.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CATTGAGTTAGCAACCCGGA GAAAAGGGGGCTCAACCTAC 659–666 1.000 83.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CATTGAGTTAGCAACCCGGA GGGGCTCAACCTACAAGAAC 653–660 1.000 83.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACCATTGAGTTAGCAACCCG GAAAAGGGGGCTCAACCTAC 661–668 1.000 82.9
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 482–493 1.000 84.5
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 449–460 1.000 82.6
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 448–459 1.000 82.5
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 481–492 1.000 80.3
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 450–461 1.000 79.2
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TCATTTTGGCTGGCTGTTTT 773–1249 1.000 75.3
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AATCATTTTGGCTGGCTGTT 775–1251 1.000 73.5
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATCATTTTGGCTGGCTGTTT 774–1250 1.000 73.5
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TCATTTTGGCTGGCTGTTTTT 773–1249 1.000 73.3
trnD-GUC-psbM_p5 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TTTGGCTGGCTGTTTTTACA 769–1245 1.000 72.5
psbM-petN_p1 psbM-petN AAAACAGCCAGCCAAAATGA TAGTAAGTCTCGCTTGGGCT 881–929 1.000 78.2
psbM-petN_p2 psbM-petN AAAACAGCCAGCCAAAATGA GGCTGCTTTAATGGTGGTCT 865–913 1.000 78.2
psbM-petN_p3 psbM-petN AAAACAGCCAGCCAAAATGA GTAGTATGGGGGAGGAGTGG 825–873 1.000 77.5
psbM-petN_p4 psbM-petN AACAGCCAGCCAAAATGATT TAGTAAGTCTCGCTTGGGCT 879–927 1.000 76.3
psbM-petN_p5 psbM-petN AAAACAGCCAGCCAAAATGA TAGTATGGGGGAGGAGTGGA 824–872 0.957 74.7
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1264–1325 1.000 87.4
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1263–1324 1.000 87.4
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AGTTCTTCTGCCAAGCCTTG 1327–1388 1.000 86.9
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AAGTTCTTCTGCCAAGCCTT 1328–1387 0.957 84.9
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CAAGTTCTTCTGCCAAGCCT 1329–1388 0.957 84.7
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TTGGCTACAATCGAGGAGGT TTCCAATGCTACGCCTTGAA 681–728 1.000 82.1
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TTGGCTACAATCGAGGAGGT ACGGAAAGAGAGGGATTCGA 731–778 1.000 81.9
ycf3-trnS-GGA_p3 ycf3-trnS-GGA GGCTACAATCGAGGAGGTCT TTCCAATGCTACGCCTTGAA 679–726 1.000 80.8
ycf3-trnS-GGA_p4 ycf3-trnS-GGA GGCTACAATCGAGGAGGTCT ACGGAAAGAGAGGGATTCGA 729–776 1.000 80.6
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTGGCTACAATCGAGGAGGT AGTTCCAATGCTACGCCTTG 683–730 1.000 79.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

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

Species Accession Length (bp) Link
Paspalum atratum MT083946.1 142091 View on NCBI ↗
Paspalum dilatatum NC_030614.1 135950 View on NCBI ↗
Paspalum fimbriatum NC_030495.1 140804 View on NCBI ↗
Paspalum floridanum MT094441.1 139365 View on NCBI ↗
Paspalum glaziovii NC_030496.1 139255 View on NCBI ↗
Paspalum inaequivalve NC_039463.1 140312 View on NCBI ↗
Paspalum ionanthum NC_039464.1 162086 View on NCBI ↗
Paspalum juergensii NC_039459.1 137513 View on NCBI ↗
Paspalum laeve MT094442.1 141643 View on NCBI ↗
Paspalum lividum MT472620.1 142825 View on NCBI ↗
Paspalum millegrana MT094443.1 144079 View on NCBI ↗
Paspalum minus NC_039460.1 152184 View on NCBI ↗
Paspalum nicorae MT120331.1 142425 View on NCBI ↗
Paspalum notatum MT094444.1 152500 View on NCBI ↗
Paspalum paniculatum NC_036114.1 157507 View on NCBI ↗
Paspalum pauciciliatum MT457745.1 136016 View on NCBI ↗
Paspalum plicatulum MT732565.1 142425 View on NCBI ↗
Paspalum pubiflorum NC_039448.1 157521 View on NCBI ↗
Paspalum scrobiculatum PQ037186.1 140622 View on NCBI ↗
Paspalum setaceum MT094445.1 142955 View on NCBI ↗
Paspalum simplex NC_039461.1 143254 View on NCBI ↗
Paspalum vaginatum NC_039462.1 140451 View on NCBI ↗
Paspalum virgatum NC_039449.1 142796 View on NCBI ↗