Markers + reference

Triglochin

2 species · Juncaginaceae · Alismatales

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Species 2
Genome length 156–156 kb
Candidate markers 270
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1068 0.0282 0.96 67.8 yes View details
trnE-UUC-trnT-GGU LSC 531 0.0283 1.00 65.8 yes View details
rbcL-psbE LSC 1167 0.0182 0.99 70.2 yes View details
rpl16 LSC 1474 0.0183 1.00 57.7 yes View details
rps19 LSC 279 0.0072 1.00 43.3 yes View details
ycf1 SSC 5526 0.0201 0.99 57.8 yes View details
trnL-UAG-rpl32 SSC 694 0.0220 0.13 51.5 yes View details
psbT-pbf1 LSC 75 0.0533 1.00 81.7 yes View details
atpH-atpI LSC 817 0.0202 0.91 73.8 yes View details
rpl22-rps19 LSC 205 0.0700 0.98 73.7 yes View details
psbI-trnS-GCU LSC 112 0.0561 0.96 73.3 yes View details
trnM-CAU-atpE LSC 146 0.0345 0.99 68.3 yes View details
trnH-GUG-psbA LSC 254 0.0315 1.00 66.6 yes View details
trnR-ACG-trnN-GUU IRb 603 0.0054 0.92 65.8 yes View details
pafI-trnS-UCC LSC 468 0.0237 0.99 65.1 yes View details
rps19-rpl2 LSC 126 0.0370 0.86 64.6 yes View details
rps4-trnT-ACA LSC 392 0.0204 1.00 64.2 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 85 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 TTAGCTGGTGTTGAAGCTCC 311–323 1.000 79.5
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CTGGTGTTGAAGCTCCTTCT 307–319 1.000 76.6
trnH-GUG-psbA_p3 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTAGCTGGTGTTGAAGCTCC 340–352 1.000 76.5
trnH-GUG-psbA_p4 trnH-GUG-psbA GATTCACAATCCACCGCCTT TTAGCTGGTGTTGAAGCTCC 331–343 1.000 76.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TAGCTGGTGTTGAAGCTCCT 310–322 1.000 75.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGGTCCTGTTATTCGGAGGT 1156–1157 1.000 83.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1141–1142 1.000 83.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1145–1146 1.000 78.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACCGGTTTTGGTC 1171–1172 1.000 78.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TGGTCCTGTTATTCGGAGGT 1148–1149 1.000 77.9
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCTGGGCGTGATGAA TGGACTAAAGCGTCGGATTG 203–208 1.000 81.6
psbI-trnS-GCU_p2 psbI-trnS-GCU GTAATCCTGGGCGTGATGAA GTGGACTAAAGCGTCGGATT 204–209 1.000 81.6
psbI-trnS-GCU_p3 psbI-trnS-GCU GTAATCCTGGGCGTGATGAA GGGTTCGAATCCCTCTCTCT 153–158 1.000 81.3
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGGCGTGATGAA TTCGAATCCCTCTCTCTCCG 150–155 1.000 80.6
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCTGGGCGTGATGAA ATTGGGAGAGATGGCTGAGT 222–227 1.000 80.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 864–905 1.000 80.9
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 920–961 1.000 80.2
atpH-atpI_p3 atpH-atpI AACGGAAGCGGCAGAAATAA TTTTTGCAACTTTAGCCGCG 862–903 1.000 79.7
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 865–906 1.000 79.7
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC TTTTTGCAACTTTAGCCGCG 924–965 1.000 79.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 618–619 1.000 80.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 616–617 1.000 80.9
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 597–598 1.000 80.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 595–596 1.000 80.5
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 615–616 1.000 80.3
pafI-trnS-UCC_p1 pafI-trnS-UCC TCTCCTGAGGTTGTGGGAAT CCCTCGGTAAACAAAAGCCT 628–631 1.000 80.7
pafI-trnS-UCC_p2 pafI-trnS-UCC TCTCCTGAGGTTGTGGGAAT ACGGAAAGAGAGGGATTCGA 649–652 1.000 80.2
pafI-trnS-UCC_p3 pafI-trnS-UCC TCTCCTGAGGTTGTGGGAAT TTCCAATGCTACGCCTTGAA 599–602 1.000 80.0
pafI-trnS-UCC_p4 pafI-trnS-UCC TTCTCCTGAGGTTGTGGGAA CCCTCGGTAAACAAAAGCCT 629–632 1.000 79.5
pafI-trnS-UCC_p5 pafI-trnS-UCC TTTCTCCTGAGGTTGTGGGA CCCTCGGTAAACAAAAGCCT 630–633 1.000 79.5

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
Triglochin maritima PQ451111.1 155881 View on NCBI ↗
Triglochin palustris PQ451110.1 155803 View on NCBI ↗