Markers + reference

Haloragis

2 species · Haloragaceae · Saxifragales

Back to catalogue

Species 2
Genome length 159–159 kb
Candidate markers 260
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 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1585 0.0152 1.00 64.6 yes View details
trnR-UCU-atpA LSC 545 0.0326 0.68 61.6 yes View details
psbM-petN LSC 923 0.0220 0.99 72.7 yes View details
trnC-GCA-trnT-GGU LSC 1105 0.0275 0.95 77.0 yes View details
trnT-GGU-psbD LSC 1528 0.0134 0.98 64.2 yes View details
psbZ-trnG-UCC LSC 949 0.0312 0.95 73.2 yes View details
trnT-UGU-trnL-UAA LSC 1455 0.0188 0.95 70.0 yes View details
psbE-petL LSC 1238 0.0170 0.95 73.2 yes View details
rpl16 LSC 1637 0.0092 0.99 56.0 yes View details
petD-rpoA LSC 118 0.0424 1.00 76.9 yes View details
ndhC-trnV-UAC LSC 958 0.0123 0.94 70.2 yes View details
rps4-trnT-UGU LSC 309 0.0324 1.00 68.9 yes View details
rpoB-trnE-UUC LSC 642 0.0066 0.95 67.3 yes View details
trnK-UUU-rps16 LSC 971 0.0096 0.96 65.2 yes View details
atpB-rbcL LSC 827 0.0061 1.00 62.6 yes View details
atpH-atpI LSC 1167 0.0043 0.99 61.8 yes View details
trnG-UCC-trnfM-CAU LSC 184 0.0223 0.97 61.8 yes View details
trnF-GAA-ndhJ LSC 670 0.0030 0.99 61.6 yes View details
rbcL LSC 1428 0.0042 1.00 61.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGAGGGCGGAGGTTTTTAC 1050–1065 1.000 80.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGAGGGCGGAGGTTTTTAC 1049–1064 1.000 80.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CCCAACCAACAGGAACAGTT 1082–1097 1.000 80.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCCAACCAACAGGAACAGTT 1081–1096 1.000 80.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC AAGAGGGCGGAGGTTTTTAC 1065–1080 1.000 79.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1658–1725 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1669–1736 1.000 79.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1679–1746 1.000 77.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1680–1747 1.000 77.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCAAGAGCACCTTCATCACT GAGGTTCGAATCCTTCCGTC 1724–1791 1.000 76.7
trnR-UCU-atpA_p1 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT GAACAGATGGAGCGCTTTCT 493–666 1.000 70.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT ACAGATGGAGCGCTTTCTAC 491–664 1.000 70.6
trnR-UCU-atpA_p3 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT ATTCAGGAACAGATGGAGCG 499–672 1.000 70.5
trnR-UCU-atpA_p4 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT GGAGCGCTTTCTACTTCAGG 485–658 1.000 70.2
trnR-UCU-atpA_p5 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT TGGAGCGCTTTCTACTTCAG 486–659 1.000 70.1
atpH-atpI_p1 atpH-atpI GCAAGTCCTACGGCTAATCC TTTTTGCAACTTTAGCCGCG 1275–1282 1.000 75.5
atpH-atpI_p2 atpH-atpI CAGGGCCAATAGAAGCAAGT TTTTTGCAACTTTAGCCGCG 1289–1296 1.000 75.5
atpH-atpI_p3 atpH-atpI AGAAGCAAGTCCTACGGCTA TTTTTGCAACTTTAGCCGCG 1279–1286 1.000 75.4
atpH-atpI_p4 atpH-atpI TAGAAGCAAGTCCTACGGCT TTTTTGCAACTTTAGCCGCG 1280–1287 1.000 75.4
atpH-atpI_p5 atpH-atpI ATCCAGCAGCAATAACGGAC TTTTTGCAACTTTAGCCGCG 1259–1266 1.000 74.0
rpoB-trnE-UUC_p1 rpoB-trnE-UUC CGTCAAGCCCTGATCAAGAA GCTGCCTCCTTGAAAGAGAG 729–761 1.000 81.0
rpoB-trnE-UUC_p2 rpoB-trnE-UUC CGTCAAGCCCTGATCAAGAA TTTCTTTCGCCGGATCTCAC 771–803 1.000 80.6
rpoB-trnE-UUC_p3 rpoB-trnE-UUC AAAGTTCTTCCGTCAAGCCC GCTGCCTCCTTGAAAGAGAG 739–771 1.000 78.6
rpoB-trnE-UUC_p4 rpoB-trnE-UUC CGTCAAGCCCTGATCAAGAA CGGGAAGGCGAATTTCTTTC 783–815 1.000 78.5
rpoB-trnE-UUC_p5 rpoB-trnE-UUC AAAGTTCTTCCGTCAAGCCC TTTCTTTCGCCGGATCTCAC 781–813 1.000 78.2
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTTATTCT TAGTAAGTCTCGCTTGGGCT 1091–1093 1.000 51.1
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTTATTCT ATGGGGAAGAAGTGGACTCT 1030–1032 1.000 49.7
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTTATTC TAGTAAGTCTCGCTTGGGCT 1091–1093 1.000 46.3
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTTATTCT ATAGTAAGTCTCGCTTGGGC 1092–1094 1.000 45.2
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTTATTCT CTCGCTTGGGCTGCTTTAAT 1083–1085 1.000 45.2

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
Haloragis aspera MW971557.1 159395 View on NCBI ↗
Haloragis erecta MW971558.1 159414 View on NCBI ↗