Markers + reference

Chenopodiastrum

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 152–153 kb
Candidate markers 271
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 601 0.0662 0.98 83.0 yes View details
trnS-GCU-trnG-UCC LSC 726 0.0862 0.99 79.8 yes View details
petN-psbM LSC 869 0.0558 0.89 76.2 yes View details
ndhC-rbcL LSC 734 0.0589 0.97 81.0 yes View details
accD-psaI LSC 444 0.1170 0.89 79.3 yes View details
petA-psbJ LSC 863 0.0615 1.00 78.3 yes View details
psbE-petL LSC 1092 0.0723 0.99 78.3 yes View details
ndhF-rpl32 SSC 986 0.0827 0.96 82.5 yes View details
rpl32-trnL-UAG SSC 1076 0.0790 0.98 79.4 yes View details
psbI-trnS-GCU LSC 199 0.0909 0.99 82.0 yes View details
trnE-UUC-trnT-GGU LSC 490 0.0637 0.93 81.2 yes View details
trnT-UGU-trnL-UAA LSC 789 0.0639 0.99 80.9 yes View details
rrn23-rrn4.5 IRb 144 0.0928 0.67 79.9 yes View details
rrn4.5-rrn23 IRa 144 0.0928 0.67 79.9 yes View details
trnT-GGU-psbD LSC 1212 0.0506 0.82 78.5 yes View details
trnP-UGG-psaJ LSC 433 0.0636 0.94 77.8 yes View details
rps4-trnT-UGU LSC 385 0.0688 0.98 77.7 yes View details
atpA-atpF LSC 69 0.0833 0.87 77.6 yes View details
trnG-GCC-trnfM-CAU LSC 225 0.0648 0.96 77.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACGGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 690–695 1.000 84.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 669–674 1.000 84.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 680–685 1.000 83.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACGGATCATGTCCTT TAAGGCATCGGGTTTTGGTC 720–725 1.000 83.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 699–704 1.000 83.3
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA GTCATTCGTACCGAGGGTTC 259–260 1.000 82.9
psbI-trnS-GCU_p2 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA AGTCATTCGTACCGAGGGTT 260–261 1.000 80.0
psbI-trnS-GCU_p3 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA TTTTCAACGGGGAGAGATGG 320–321 1.000 78.5
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA GATGGCTGAGTGGACGAAAG 305–306 1.000 77.6
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA GAGTCATTCGTACCGAGGGT 261–262 1.000 76.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 835–912 1.000 53.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CGAATGACTCGTACAACGGA TACCACTAAACTATACCCGC 805–882 1.000 52.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TTACCACTAAACTATACCCGC 836–913 1.000 51.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGAATGACTCGTACAACGGA TTACCACTAAACTATACCCGC 806–883 1.000 51.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TTTACCACTAAACTATACCCGC 837–914 1.000 50.2
atpA-atpF_p1 atpA-atpF TTTCGTCTGCTCGAATGGTT GTTTGGTGCGATGAACGAAA 116–125 1.000 82.9
atpA-atpF_p2 atpA-atpF TTTCGTCTGCTCGAATGGTT CATGTTTGGTGCGATGAACG 119–128 1.000 82.8
atpA-atpF_p3 atpA-atpF TTTCGTCTGCTCGAATGGTT TATTGGCATGTTTGGTGCGA 125–134 1.000 82.1
atpA-atpF_p4 atpA-atpF TTTCGTCTGCTCGAATGGTT ATGTTTGGTGCGATGAACGA 118–127 1.000 82.1
atpA-atpF_p5 atpA-atpF TTTCGTCTGCTCGAATGGTT ATATTGGCATGTTTGGTGCG 126–135 1.000 81.1
petN-psbM_p1 petN-psbM GGGGAAGGAGAAGAAGAGGT TCCAGATGTTTCTCGGGAGT 1952 0.500 59.2
petN-psbM_p2 petN-psbM TTTTGTATCGTTTTGGCGGC TCCAGATGTTTCTCGGGAGT 2114 0.500 59.1
petN-psbM_p3 petN-psbM GGTACGTACTTGTGGGGTTC TCCAGATGTTTCTCGGGAGT 1927 0.500 58.8
petN-psbM_p4 petN-psbM CTTGGTACGTACTTGTGGGG TCCAGATGTTTCTCGGGAGT 1930 0.500 58.8
petN-psbM_p5 petN-psbM TGTTCCCCAGTTCAAATCCG TCCAGATGTTTCTCGGGAGT 2059 0.500 58.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 577–589 1.000 86.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 575–587 1.000 86.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 556–568 1.000 86.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 554–566 1.000 86.5
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 574–586 1.000 86.3

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
Chenopodiastrum gracilispicum PP056262.1 152437 View on NCBI ↗
Chenopodiastrum hybridum OR884981.1 152908 View on NCBI ↗