Markers + reference

Krameria

2 species · Krameriaceae · Zygophyllales

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Species 2
Genome length 172–173 kb
Candidate markers 266
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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps19-trnH-GUG LSC 1101 0.0338 0.78 63.4 yes View details
trnH-GUG-psbA LSC 667 0.0370 0.97 72.1 yes View details
FNM16_pgt002-rps16 LSC 746 0.0255 1.00 59.1 yes View details
rps16 LSC 1822 0.0174 0.95 61.7 yes View details
rps16-trnQ-UUG LSC 1089 0.0393 0.93 77.3 yes View details
trnQ-UUG-psbK LSC 3353 0.0160 0.67 47.1 yes View details
trnS-GCU-FNM16_pgt005 LSC 958 0.0315 0.99 73.7 yes View details
FNM16_pgt005-trnR-UCU LSC 730 0.0404 0.95 82.5 yes View details
psaJ-rpl33 LSC 1336 0.0228 0.98 73.5 yes View details
ndhF-rpl32 SSC 1663 0.0276 0.98 76.1 yes View details
trnR-UCU-atpA LSC 752 0.0280 0.95 77.5 yes View details
psbZ-trnG-GCC LSC 638 0.0242 0.97 75.1 yes View details
petD-rpoA LSC 238 0.0672 1.00 73.1 yes View details
rpl33-rps18 LSC 898 0.0215 0.98 72.6 yes View details
FNM16_pgt002 LSC 35 0.0588 0.97 72.2 yes View details
trnT-GGU-psbD LSC 2382 0.0131 0.96 68.1 yes View details
atpF-atpH LSC 455 0.0117 0.94 67.0 yes View details
accD-psaI LSC 871 0.0134 0.94 64.9 yes View details
atpH-atpI LSC 859 0.0081 1.00 63.4 yes View details
rps4-trnT-UGU LSC 417 0.0121 0.99 62.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps19-trnH-GUG_p1 rps19-trnH-GUG GAAAGGAGCACGTACCGATT GTAGAGTTAGAGGGGCGGAT 1135–1309 1.000 85.9
rps19-trnH-GUG_p2 rps19-trnH-GUG GAAAGGAGCACGTACCGATT TAGAGTTAGAGGGGCGGATG 1134–1308 1.000 85.9
rps19-trnH-GUG_p3 rps19-trnH-GUG TAGTTACTTGGTCTCGGGCA GTAGAGTTAGAGGGGCGGAT 1204–1378 1.000 85.3
rps19-trnH-GUG_p4 rps19-trnH-GUG TAGTTACTTGGTCTCGGGCA TAGAGTTAGAGGGGCGGATG 1203–1377 1.000 85.3
rps19-trnH-GUG_p5 rps19-trnH-GUG AATGGAAAGGAGCACGTACC GTAGAGTTAGAGGGGCGGAT 1139–1313 1.000 85.1
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCTGTTGCCGAAGTTTCATC 722–814 1.000 83.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCTGTTGCCGAAGTTTCATC 736–828 1.000 83.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCTGTTGCCGAAGTTTCATC 735–827 1.000 83.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCTGTTGCCGAAGTTTCATC 737–829 1.000 83.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGACTTAGCTGTTGCCGAAG 729–821 1.000 82.6
FNM16_pgt002_p1 FNM16_pgt002 GGACTCCCAAGCACACAAAT TTATCGACCGATTTGTGCGT 1329–1335 1.000 78.9
FNM16_pgt002_p2 FNM16_pgt002 GGACTCCCAAGCACACAAAT ACAAAAGTACTGTACGCGCT 1200–1206 1.000 77.9
FNM16_pgt002_p3 FNM16_pgt002 GGACTCCCAAGCACACAAAT CACAAAAGTACTGTACGCGC 1201–1207 1.000 77.4
FNM16_pgt002_p4 FNM16_pgt002 GGACTCCCAAGCACACAAAT ATCGACCGATTTGTGCGTAT 1327–1333 1.000 77.1
FNM16_pgt002_p5 FNM16_pgt002 GGACTCCCAAGCACACAAAT CGGTTTGGGGAGGGATTTTT 758–764 1.000 76.7
FNM16_pgt002-rps16_p1 FNM16_pgt002-rps16 TCAGGATCAGTCGTGGTCTT TTTCCTTGAAAGGGGTGCTC 974–977 1.000 81.4
FNM16_pgt002-rps16_p2 FNM16_pgt002-rps16 TTCAGGATCAGTCGTGGTCT TTTCCTTGAAAGGGGTGCTC 975–978 1.000 81.4
FNM16_pgt002-rps16_p3 FNM16_pgt002-rps16 TCAGGATCAGTCGTGGTCTT CGTTGCAATTGATGTTCGCT 1082–1085 1.000 81.0
FNM16_pgt002-rps16_p4 FNM16_pgt002-rps16 TTCAGGATCAGTCGTGGTCT CGTTGCAATTGATGTTCGCT 1083–1086 1.000 81.0
FNM16_pgt002-rps16_p5 FNM16_pgt002-rps16 TCAGGATCAGTCGTGGTCTT TCGTTGCAATTGATGTTCGC 1083–1086 1.000 80.9
rps16_p1 rps16 AGTAATCCACACCCTCTTTT ACTGGTTAAAAAGAAAGGAATGT 1843–1886 1.000 45.3
rps16_p2 rps16 AAAAGTAATCCACACCCTCT TGTATCAAATGAACCAATGACT 1899–1942 1.000 45.2
rps16_p3 rps16 AAAGTAATCCACACCCTCTT TGTATCAAATGAACCAATGACT 1898–1941 1.000 45.2
rps16_p4 rps16 AAGTAATCCACACCCTCTTT TGTATCAAATGAACCAATGACT 1897–1940 1.000 45.2
rps16_p5 rps16 AGTAATCCACACCCTCTTTT TGTATCAAATGAACCAATGACT 1896–1939 1.000 45.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACGGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1135–1183 1.000 85.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ACACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1109–1157 1.000 83.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCACACGTTGCTTTCTACCA GAGGTTCGAATCCTTCCGTC 1111–1159 1.000 81.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CACACGTTGCTTTCTACCAC GAGGTTCGAATCCTTCCGTC 1110–1158 1.000 80.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCCTTCAAGTCACACGTT GAGGTTCGAATCCTTCCGTC 1122–1170 1.000 80.7

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
Krameria bicolor NC_043800.1 172606 View on NCBI ↗
Krameria lanceolata NC_043801.1 171851 View on NCBI ↗