Markers + reference

Xyris

2 species · Xyridaceae · Poales

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Species 2
Genome length 140–141 kb
Candidate markers 255
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbD-psbE LSC 2440 0.1281 0.82 82.0 yes View details
accD LSC 2172 0.2397 0.87 79.9 yes View details
trnT-UGU-petL LSC 1316 0.1824 0.77 80.7 yes View details
clpP-psbB LSC 1242 0.2255 0.95 84.1 yes View details
trnC-GCA-rpoB LSC 1339 0.1128 0.96 89.0 yes View details
trnE-UUC-trnT-GGU LSC 901 0.1164 0.89 88.6 yes View details
trnK-UUU-trnQ-UUG LSC 963 0.1565 0.90 87.9 yes View details
petN-trnC-GCA LSC 468 0.0995 0.94 85.8 yes View details
ycf3-trnS-GGA LSC 641 0.0777 0.98 85.3 yes View details
psbK-psbI LSC 537 0.0927 0.92 84.6 yes View details
psaI-trnV-UAC LSC 869 0.1142 0.86 84.4 yes View details
trnG-GCC-trnfM-CAU LSC 313 0.1438 0.93 84.1 yes View details
rps15-trnN-GUU SSC 1391 0.1830 0.90 83.6 yes View details
psbM-trnD-GUC LSC 936 0.1095 0.96 83.4 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AGTCGCACTTAAAAGCCGAG GAGGTTCGAATCCTTCCGTC 1032–1089 1.000 86.8
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG TAGTCGCACTTAAAAGCCGA GAGGTTCGAATCCTTCCGTC 1033–1090 1.000 85.6
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG TCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 1030–1087 1.000 85.6
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG CGCACTTAAAAGCCGAGTAC GAGGTTCGAATCCTTCCGTC 1029–1086 1.000 85.1
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG GTCGCACTTAAAAGCCGAGT GAGGTTCGAATCCTTCCGTC 1031–1088 1.000 84.6
psbK-psbI_p1 psbK-psbI CGTGGATGTTATGCCTGTCA TCACTACTGTGTAAACAAAAAGT 644–653 1.000 49.7
psbK-psbI_p2 psbK-psbI CGTGGATGTTATGCCTGTCA TCACTACTGTGTAAACAAAAAGTT 644–653 1.000 49.7
psbK-psbI_p3 psbK-psbI TCGTGGATGTTATGCCTGTC TCACTACTGTGTAAACAAAAAGT 645–654 1.000 49.7
psbK-psbI_p4 psbK-psbI CGTGGATGTTATGCCTGTCA ATCACTACTGTGTAAACAAAAAGT 645–654 1.000 49.7
psbK-psbI_p5 psbK-psbI CGTGGATGTTATGCCTGTCA CACTACTGTGTAAACAAAAAGT 643–652 1.000 49.7
petN-trnC-GCA_p1 petN-trnC-GCA ACTACCATTAGAGCAGCCCA CTGCAAATCCTTTACCCCCA 550–556 1.000 87.3
petN-trnC-GCA_p2 petN-trnC-GCA ACTACCATTAGAGCAGCCCA TGCAAATCCTTTACCCCCAG 549–555 1.000 87.3
petN-trnC-GCA_p3 petN-trnC-GCA ACTACCATTAGAGCAGCCCA ACTGCAAATCCTTTACCCCC 551–557 1.000 87.3
petN-trnC-GCA_p4 petN-trnC-GCA ACTACCATTAGAGCAGCCCA GCAAATCCTTTACCCCCAGT 548–554 1.000 87.3
petN-trnC-GCA_p5 petN-trnC-GCA CAGCCCAAGCAAGACTTACT TGCAAATCCTTTACCCCCAG 536–542 1.000 87.0
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCTCATTCTCATTCCGGAGC 1404–1414 1.000 89.5
trnC-GCA-rpoB_p2 trnC-GCA-rpoB TTAGGCGACACCCAGATTTG CCTCATTCTCATTCCGGAGC 1434–1444 1.000 89.1
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG TCCCTCATTCTCATTCCGGA 1406–1416 1.000 89.1
trnC-GCA-rpoB_p4 trnC-GCA-rpoB TTAGGCGACACCCAGATTTG TCCCTCATTCTCATTCCGGA 1436–1446 1.000 88.7
trnC-GCA-rpoB_p5 trnC-GCA-rpoB TTGTTGATTAGGCGACACCC CCTCATTCTCATTCCGGAGC 1441–1451 1.000 88.5
psbM-trnD-GUC_p1 psbM-trnD-GUC TCGTTTTGGCTGACTGTTTT ATGCATGTTTGTTACCGGGT 1286–1462 1.000 75.6
psbM-trnD-GUC_p2 psbM-trnD-GUC TCGTTTTGGCTGACTGTTTT GGGCTATCCGGACGTATACT 1320–1496 1.000 74.7
psbM-trnD-GUC_p3 psbM-trnD-GUC TCGTTTTGGCTGACTGTTTT AGATCACAGAAAGGCCCTCT 1193 0.500 46.9
psbM-trnD-GUC_p4 psbM-trnD-GUC TCTGGAACTGGAAACTGGAA AGATCACAGAAAGGCCCTCT 1400 0.500 46.0
psbM-trnD-GUC_p5 psbM-trnD-GUC TTCTGGAACTGGAAACTGGA AGATCACAGAAAGGCCCTCT 1401 0.500 46.0
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TCTCCTGAGGTTGTCGGAAT CTACACCTTCAACCACTCGG 766–771 1.000 85.0
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TCTCCTGAGGTTGTCGGAAT GCAGTTCCAATGCTACACCT 778–783 1.000 84.2
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTCTCCTGAGGTTGTCGGAA CTACACCTTCAACCACTCGG 767–772 1.000 83.2
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTCTCCTGAGGTTGTCGGA CTACACCTTCAACCACTCGG 768–773 1.000 83.2
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TCTCCTGAGGTTGTCGGAAT AGCAAAAGGAGAGAGAGGGA 829–834 1.000 82.5

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
Xyris indica NC_061356.1 140302 View on NCBI ↗
Xyris pauciflora NC_061357.1 141159 View on NCBI ↗