Markers + reference

Triniochloa

2 species · Poaceae · Poales

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Species 2
Genome length 133–133 kb
Candidate markers 251
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 251 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ LSC 1104 0.0064 1.00 62.8 yes View details
trnQ-psbI LSC 930 0.0129 1.00 57.6 yes View details
trnS-psbD LSC 987 0.0072 0.99 63.6 yes View details
trnG-trnT LSC 1297 0.0070 1.00 63.2 yes View details
ndhC-trnV LSC 883 0.0083 0.96 67.5 yes View details
rbcL-psaI LSC 965 0.0083 1.00 50.7 yes View details
ndhF-trnL SSC 1469 0.0171 0.99 69.3 yes View details
psaC-ndhE SSC 496 0.0202 1.00 66.6 yes View details
psbL-psbF LSC 22 0.0455 1.00 69.7 yes View details
rps19-psbA LSC 125 0.0240 1.00 66.3 no View details
trnR-rps14 LSC 387 0.0110 0.94 65.1 yes View details
atpI-atpH LSC 607 0.0036 0.92 64.7 yes View details
ycf3-trnS LSC 599 0.0100 1.00 64.5 yes View details
trnH-rpl2 IRb 55 0.0182 1.00 63.0 yes View details
rpl16 LSC 1435 0.0049 0.99 62.6 yes View details
psaA-ycf3 LSC 597 0.0067 1.00 62.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA TAAAACCTGAAATGGGGCGT 1237–1250 1.000 77.3
rps16-trnQ_p2 rps16-trnQ TCATGTCCTTCAAGTCGCAC TAAAACCTGAAATGGGGCGT 1248–1261 1.000 76.8
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA CGTTACTCGGAGGTTCGAAC 1186–1199 1.000 76.6
rps16-trnQ_p4 rps16-trnQ TCATGTCCTTCAAGTCGCAC CGTTACTCGGAGGTTCGAAC 1197–1210 1.000 76.1
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA TAAGGCAGCGGGTTTTGATC 1207–1220 1.000 75.4
trnQ-psbI_p1 trnQ-psbI GGTTCGAACCTCCGAGTAAC CCTGGGTCATTGGATAAGAA 1076–1089 1.000 51.9
trnQ-psbI_p2 trnQ-psbI GGTTCGAACCTCCGAGTAAC CCTGGGTCATTGGATAAGAATC 1076–1089 1.000 51.0
trnQ-psbI_p3 trnQ-psbI GGTTCGAACCTCCGAGTAAC CCTGGGTCATTGGATAAGAAT 1076–1089 1.000 49.0
trnQ-psbI_p4 trnQ-psbI GTTCGAACCTCCGAGTAACG CCTGGGTCATTGGATAAGAA 1075–1088 1.000 48.9
trnQ-psbI_p5 trnQ-psbI GTTCGAACCTCCGAGTAACG CCTGGGTCATTGGATAAGAATC 1075–1088 1.000 47.9
trnS-psbD_p1 trnS-psbD ATTAGCAATCCGCCGCTTTA GACAAAAACGAAACGGTCCC 1120–1136 1.000 79.9
trnS-psbD_p2 trnS-psbD ATTAGCAATCCGCCGCTTTA GAGCAATAGGCCAGACCATC 1141–1157 1.000 79.9
trnS-psbD_p3 trnS-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1119–1135 1.000 78.8
trnS-psbD_p4 trnS-psbD ATTAGCAATCCGCCGCTTTA CCGACAAAAACGAAACGGTC 1122–1138 1.000 78.6
trnS-psbD_p5 trnS-psbD ATTAGCAATCCGCCGCTTTA CGACAAAAACGAAACGGTCC 1121–1137 1.000 78.6
trnG-trnT_p1 trnG-trnT ACGAATCACACTTTTACCACT ACCATGGCATTACTCTAGCAC 1431–1434 1.000 43.0
trnG-trnT_p2 trnG-trnT ACGAATCACACTTTTACCACT GACTTACGTCTTACCATGGCA 1443–1446 1.000 42.6
trnG-trnT_p3 trnG-trnT ACGAATCACACTTTTACCACT TGACTTACGTCTTACCATGGC 1444–1447 1.000 42.6
trnG-trnT_p4 trnG-trnT AGAACGAATCACACTTTTACCAC ACCATGGCATTACTCTAGCAC 1434–1437 1.000 41.9
trnG-trnT_p5 trnG-trnT GAACGAATCACACTTTTACCACT ACCATGGCATTACTCTAGCAC 1433–1436 1.000 41.9
atpI-atpH_p1 atpI-atpH TTTTGCAACATTAGCCGCAG GCAATAACAGAAGCAGCAGC 646–697 1.000 83.0
atpI-atpH_p2 atpI-atpH TTTTGCAACATTAGCCGCAG GCAGCAATAACAGAAGCAGC 649–700 1.000 83.0
atpI-atpH_p3 atpI-atpH TTTTGCAACATTAGCCGCAG AGCCAATCCAGCAGCAATAA 659–710 1.000 82.5
atpI-atpH_p4 atpI-atpH TTTTGCAACATTAGCCGCAG GCAGTACCTTGACCAACTCC 703–754 1.000 82.2
atpI-atpH_p5 atpI-atpH TTTTGCAACATTAGCCGCAG AAGCAGCAGCAATTAGTGGA 636–687 1.000 82.1
trnR-rps14_p1 trnR-rps14 AGAAGACCTCTGTCCTATCCA TATCCGGACACGTACTTCGA 471–494 1.000 67.9
trnR-rps14_p2 trnR-rps14 AGGTTTAGAAGACCTCTGTCCT TATCCGGACACGTACTTCGA 477–500 1.000 67.2
trnR-rps14_p3 trnR-rps14 AGAAGACCTCTGTCCTATCCA GCTATCCGGACACGTACTTC 473–496 1.000 67.1
trnR-rps14_p4 trnR-rps14 AGAAGACCTCTGTCCTATCCA TTACCGGGTGCAACAAGATC 430–453 1.000 66.8
trnR-rps14_p5 trnR-rps14 AGGTTTAGAAGACCTCTGTCCT GCTATCCGGACACGTACTTC 479–502 1.000 66.4

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
Triniochloa micrantha PZ098270.1 133074 View on NCBI ↗
Triniochloa stipoides PZ098609.1 132947 View on NCBI ↗