Markers + reference

Kalidium

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 154–154 kb
Candidate markers 271
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 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
trnK-UUU-rps16 LSC 706 0.0115 0.98 66.9 yes View details
trnS-GCU-trnG-GCC LSC 938 0.0107 0.99 54.3 yes View details
atpH-atpI LSC 738 0.0136 1.00 66.7 yes View details
trnS-UGA-psbZ LSC 368 0.0083 0.98 52.4 yes View details
psaA-ycf3 LSC 784 0.0128 1.00 66.1 yes View details
trnP-UGG-psaJ LSC 430 0.0209 1.00 67.2 yes View details
rpl16 LSC 1458 0.0174 0.98 56.5 yes View details
rpl22 LSC 594 0.0168 1.00 53.4 yes View details
trnN-GUU-ndhF IRb 1851 0.0103 1.00 56.2 yes View details
ndhF-rpl32 SSC 1145 0.0210 1.00 71.2 yes View details
ccsA-ndhD SSC 250 0.0245 0.98 56.8 yes View details
psbC-trnS-UGA LSC 197 0.0355 1.00 72.9 yes View details
rpl2-trnH-GUG IRa 214 0.0000 1.00 69.1 no View details
trnH-GUG-psbA LSC 366 0.0223 0.98 68.5 yes View details
rps3-rpl22 LSC 20 0.0500 1.00 68.1 yes View details
ndhC-trnV-UAC LSC 709 0.0087 0.97 66.5 yes View details
rps12-clpP LSC 135 0.0224 0.99 66.1 yes View details
rpl32-trnL-UAG SSC 813 0.0066 0.93 64.6 yes View details
rpoC1-rpoB LSC 26 0.0385 1.00 64.3 yes View details
trnM-CAU-atpE LSC 290 0.0186 0.93 64.2 yes View details
atpF-atpH LSC 449 0.0134 1.00 63.3 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 435–436 1.000 81.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 449–450 1.000 81.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 448–449 1.000 81.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 450–451 1.000 81.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 484–485 1.000 78.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGAAACT 799–800 1.000 71.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGAAACT 798–799 1.000 71.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGAAACT 785–786 1.000 69.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAGAAACT 810–811 1.000 68.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGAAAC 798–799 1.000 67.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 1061–1064 1.000 51.6
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC TGGAAACGGAAAGAGAGGGA ACGAATCACACTTTTACCACT 1066–1069 1.000 50.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA AGAACGAATCACACTTTTACCAC 1064–1067 1.000 50.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA GAACGAATCACACTTTTACCACT 1063–1066 1.000 50.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA AACGAATCACACTTTTACCACT 1062–1065 1.000 49.7
atpF-atpH_p1 atpF-atpH CCAGTGACCCAAGAAAACGA CCCGAGGCAGAAGGAAAAAT 611–617 1.000 79.2
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG CCCGAGGCAGAAGGAAAAAT 638–644 1.000 78.5
atpF-atpH_p3 atpF-atpH CCAGTGACCCAAGAAAACGA CCCGAGGCAGAAGGAAAAATA 611–617 1.000 72.5
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG CCCGAGGCAGAAGGAAAAATA 638–644 1.000 71.8
atpF-atpH_p5 atpF-atpH GGCCAGTGACCCAAGAAAA CCCGAGGCAGAAGGAAAAAT 613–619 1.000 70.5
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA GCGAATCCATGGAAGGTCAT 794–801 1.000 80.1
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT GCGAATCCATGGAAGGTCAT 852–859 1.000 79.9
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA GCGAATCCATGGAAGGTCAT 812–819 1.000 79.7
atpH-atpI_p4 atpH-atpI CAGCAGCAATAACAGAAGCG GCGAATCCATGGAAGGTCAT 804–811 1.000 79.5
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC GCGAATCCATGGAAGGTCAT 856–863 1.000 79.3
rpoC1-rpoB_p1 rpoC1-rpoB GCGAAACTGATCCAATTCGG ACGATCTTTGGCTCTGGAAC 151 1.000 76.1
rpoC1-rpoB_p2 rpoC1-rpoB GGCGAAACTGATCCAATTCG ACGATCTTTGGCTCTGGAAC 152 1.000 76.1
rpoC1-rpoB_p3 rpoC1-rpoB GCGAAACTGATCCAATTCGG CCCGAAGATGCTCCAGAATC 195 1.000 75.8
rpoC1-rpoB_p4 rpoC1-rpoB GGCGAAACTGATCCAATTCG CCCGAAGATGCTCCAGAATC 196 1.000 75.8
rpoC1-rpoB_p5 rpoC1-rpoB TTGAGGCGAAACTGATCCAA ACGATCTTTGGCTCTGGAAC 156 1.000 75.2

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
Kalidium caspicum ON929871.1 153693 View on NCBI ↗
Kalidium gracile ON149858.1 153646 View on NCBI ↗