Markers + reference

Suaeda

10 species · Amaranthaceae · Caryophyllales

Back to catalogue

Species 10
Genome length 145–153 kb
Candidate markers 263
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbM-trnD-GUC LSC 713 0.1196 0.98 79.2 yes View details
trnN-GUU-ndhF IRb 2238 0.1441 0.64 72.7 yes View details
rpl32-trnL-UAG SSC 697 0.1341 0.98 80.5 yes View details
ycf1 SSC 6276 0.1045 0.85 73.1 yes View details
trnH-GUG-trnK-UUU LSC 1608 0.0545 0.86 75.8 no View details
trnT-UGU-trnL-UAA LSC 593 0.0963 0.99 84.4 yes View details
trnS-GCU-trnG-UCC LSC 750 0.1116 0.98 83.6 yes View details
trnC-GCA-petN LSC 492 0.0945 0.99 83.4 yes View details
trnF-GAA-ndhJ LSC 712 0.0881 0.97 82.2 yes View details
matK-trnK-UUU LSC 734 0.0695 0.97 81.7 yes View details
rps16-trnQ-UUG LSC 469 0.1122 0.99 81.5 yes View details
psbE-petL LSC 857 0.0628 0.98 81.3 yes View details
rps16 LSC 1126 0.0640 1.00 81.1 yes View details
petA-psbJ LSC 849 0.0873 0.98 80.4 yes View details
atpH-atpI LSC 734 0.0872 0.97 80.3 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
matK-trnK-UUU_p1 matK-trnK-UUU AGTTCTATATGTCTTTGGAATTCT GGTAGAGTACTCGGCTTTTA 751–784 1.000 52.0
matK-trnK-UUU_p2 matK-trnK-UUU AGTTCTATATGTCTTTGGAATTCTTC GGTAGAGTACTCGGCTTTTA 751–784 1.000 52.0
matK-trnK-UUU_p3 matK-trnK-UUU AGTTCTATATGTCTTTGGAATTCT GGTAGAGTACTCGGCTTTTAA 751–784 1.000 52.0
matK-trnK-UUU_p4 matK-trnK-UUU AGTTCTATATGTCTTTGGAATTCTT GGTAGAGTACTCGGCTTTTA 751–784 1.000 52.0
matK-trnK-UUU_p5 matK-trnK-UUU AGTTCTATATGTCTTTGGAATTCTTC GGTAGAGTACTCGGCTTTTAA 751–784 1.000 52.0
rps16_p1 rps16 CCATTGAGTTAGCAACCCGA GAGGTTCGAATCCTTCCGTC 2269–2454 0.900 86.5
rps16_p2 rps16 CCATTGAGTTAGCAACCCGA TGGGCTGAAATTGACGAACA 2383–2568 0.800 82.9
rps16_p3 rps16 CCATTGAGTTAGCAACCCGA ATAGCAATTTAGGTGGGGCG 2330–2515 0.700 79.0
rps16_p4 rps16 ACCATTGAGTTAGCAACCCG ATAGCAATTTAGGTGGGGCG 2331–2516 0.700 78.4
rps16_p5 rps16 CCATTGAGTTAGCAACCCGA GAATCCTTCCGTCCCAGAAC 2262–2367 0.500 70.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 487–682 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 498–693 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 572–712 0.900 85.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TAAGGCATCGGGTTTTGGTC 583–723 0.900 85.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTAAGGCATCGGGTTTTGGT 573–713 0.900 83.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC ACGAATCACACTTTTACCACT 809–966 1.000 58.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC AGAACGAATCACACTTTTACCAC 812–969 1.000 57.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC GAACGAATCACACTTTTACCACT 811–968 1.000 57.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC AACGAATCACACTTTTACCACT 810–967 1.000 56.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TTTCGTCCACTCAGCCATCT ACGAATCACACTTTTACCACT 808–965 1.000 55.5
atpH-atpI_p1 atpH-atpI GCCAGTGAACGAAGAAAACG GGGGCACTTTTACCTTGGAA 1837–1879 0.900 87.8
atpH-atpI_p2 atpH-atpI GCCAGTGAACGAAGAAAACG TTGGTCAGGGGCACTTTTAC 1844–1886 0.900 87.8
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT GGGGCACTTTTACCTTGGAA 1137–1178 0.900 87.7
atpH-atpI_p4 atpH-atpI CCAGTGAACGAAGAAAACGC GGGGCACTTTTACCTTGGAA 1836–1878 0.800 83.6
atpH-atpI_p5 atpH-atpI CCAGTGAACGAAGAAAACGC TTGGTCAGGGGCACTTTTAC 1843–1885 0.800 83.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 571–622 1.000 88.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACAAT 509–558 0.900 85.3
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 518–569 1.000 84.1
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GACTACCATTAAAGCAGCCCA 525–576 1.000 83.3
trnC-GCA-petN_p5 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC GCCCAAGCGAGACTTACAAT 504–553 0.900 79.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Suaeda acuminata ON929880.1 145494 View on NCBI ↗
Suaeda aralocaspica ON929882.1 146654 View on NCBI ↗
Suaeda corniculata PP234587.1 152739 View on NCBI ↗
Suaeda glauca NC_045303.1 149807 View on NCBI ↗
Suaeda japonica NC_042675.1 152109 View on NCBI ↗
Suaeda linifolia ON929878.1 149302 View on NCBI ↗
Suaeda malacosperma NC_039180.1 151989 View on NCBI ↗
Suaeda microphylla ON929881.1 149701 View on NCBI ↗
Suaeda paradoxa ON929879.1 145543 View on NCBI ↗
Suaeda salsa NC_045302.1 151642 View on NCBI ↗