Markers + reference

Pseudotsuga

3 species · Pinaceae · Pinales

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Species 3
Genome length 122–123 kb
Candidate markers 229
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 14 remaining regions by MarkerSeek score (out of 229 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf12-clpP Genome 419 0.0064 1.00 45.1 yes View details
ycf4-psaI Genome 543 0.0148 0.99 53.4 yes View details
tRNA-Thr-tRNA-Ser Genome 1180 0.0119 1.00 61.7 yes View details
tRNA-Tyr-tRNA-Ser Genome 297 0.0470 0.98 68.8 yes View details
tRNA-Ile-tRNA-Phe Genome 1941 0.0100 1.00 57.1 yes View details
chlN-rps15 Genome 6513 0.0049 1.00 41.3 yes View details
rps7-tRNA-Leu Genome 1396 0.0149 0.99 60.0 yes View details
tRNA-His-tRNA-Ile Genome 293 0.0614 1.00 77.6 yes View details
tRNA-Ile-psaA Genome 145 0.0069 0.99 68.8 no View details
tRNA-Met-tRNA-Gly Genome 165 0.0218 0.93 67.7 yes View details
infA-rps8 Genome 142 0.0146 0.96 64.9 yes View details
psbJ-petA Genome 1048 0.0070 1.00 63.7 yes View details
matK-tRNA-Lys Genome 784 0.0068 1.00 63.1 yes View details
tRNA-Ser Genome 85 0.0583 0.94 62.1 yes View details
rps12 Genome 801 0.0058 1.00 62.1 yes View details
petL-psbE Genome 1209 0.0040 0.82 61.6 yes View details
tRNA-Asp-psbM Genome 732 0.0091 1.00 61.6 yes View details
rps15-psaC Genome 1335 0.0070 1.00 61.6 yes View details
tRNA-Ser Genome 88 0.0000 1.00 21.3 no View details
tRNA-Ser Genome 88 0.0000 1.00 21.3 no View details
tRNA-Ser Genome 88 0.0000 1.00 20.4 no View details
tRNA-Ser Genome 87 0.0000 1.00 20.2 no 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
matK-tRNA-Lys_p1 matK-tRNA-Lys TGTTGCCAAGAGCTATCTTCC TAACCTCGCATTCCACTTCG 921 1.000 72.6
matK-tRNA-Lys_p2 matK-tRNA-Lys GCATTGTTGCCAAGAGCTATC TAACCTCGCATTCCACTTCG 925 1.000 72.0
matK-tRNA-Lys_p3 matK-tRNA-Lys TGTTGCCAAGAGCTATCTTCC CGCATTCCACTTCGATCGTA 915 1.000 71.3
matK-tRNA-Lys_p4 matK-tRNA-Lys GCATTGTTGCCAAGAGCTATC CGCATTCCACTTCGATCGTA 919 1.000 70.8
matK-tRNA-Lys_p5 matK-tRNA-Lys GCATTGTTGCCAAGAGCTAT TAACCTCGCATTCCACTTCG 925 1.000 70.7
ycf12-clpP_p1 ycf12-clpP AGTCGATGGGATCATAGGGG AGCATCGTTACGTGTTTCGA 1004–1092 1.000 81.5
ycf12-clpP_p2 ycf12-clpP AGTCGATGGGATCATAGGGG CTCGTTGAATGACCTCTCCG 1069–1157 1.000 81.2
ycf12-clpP_p3 ycf12-clpP AGTCGATGGGATCATAGGGG CGTTATGAAAATCTGCGGCC 982–1070 1.000 81.1
ycf12-clpP_p4 ycf12-clpP AGTCGATGGGATCATAGGGG GTTATGAAAATCTGCGGCCG 981–1069 1.000 81.1
ycf12-clpP_p5 ycf12-clpP GGTTGTATCGGGCCCATTAG AGCATCGTTACGTGTTTCGA 926 0.333 52.0
petL-psbE_p1 petL-psbE GCGTGGAAGGACTGAATGAA AATGTCAGCAAAGGAGCGTT 1091–1303 1.000 79.8
petL-psbE_p2 petL-psbE GCGTGGAAGGACTGAATGAA GTATTCCCAGCCATGCTCAG 1066–1278 1.000 79.7
petL-psbE_p3 petL-psbE GCGTGGAAGGACTGAATGAA TAATGTCAGCAAAGGAGCGT 1092–1304 1.000 79.1
petL-psbE_p4 petL-psbE TAGGCGTGGAAGGACTGAAT AATGTCAGCAAAGGAGCGTT 1094–1306 1.000 77.8
petL-psbE_p5 petL-psbE TAGGCGTGGAAGGACTGAAT GTATTCCCAGCCATGCTCAG 1069–1281 1.000 77.8
psbJ-petA_p1 psbJ-petA TGGAAGGATCCCTCTTTGGT AGCATCTGTCATTCTGGCAC 1242–1288 1.000 78.5
psbJ-petA_p2 psbJ-petA TACCACTGGAAGGATCCCTC AGCATCTGTCATTCTGGCAC 1248–1294 1.000 77.6
psbJ-petA_p3 psbJ-petA TGGAAGGATCCCTCTTTGGT GCATCTGTCATTCTGGCACA 1241–1287 1.000 76.2
psbJ-petA_p4 psbJ-petA CCACTGGAAGGATCCCTCTT AGCATCTGTCATTCTGGCAC 1246–1292 1.000 75.7
psbJ-petA_p5 psbJ-petA TACCACTGGAAGGATCCCTC GCATCTGTCATTCTGGCACA 1247–1293 1.000 75.2
ycf4-psaI_p1 ycf4-psaI GAGCCATTTGGATCGACGAT TTTCCGCTCTCCGAAATCAG 1022–1025 1.000 80.5
ycf4-psaI_p2 ycf4-psaI AGGGGTATCAGGTTCTCACC TTTCCGCTCTCCGAAATCAG 1150–1153 1.000 80.4
ycf4-psaI_p3 ycf4-psaI ACTCGAAATACCGACCAGGA TTTCCGCTCTCCGAAATCAG 1124–1127 1.000 80.2
ycf4-psaI_p4 ycf4-psaI CGACGAGGGGAAATACCTTC TTTCCGCTCTCCGAAATCAG 1417–1420 1.000 79.5
ycf4-psaI_p5 ycf4-psaI TTCAGCAGCTTTCTGTTCGA TTTCCGCTCTCCGAAATCAG 1514–1517 1.000 79.3
tRNA-Thr-tRNA-Ser_p1 tRNA-Thr-tRNA-Ser GAACCGATGACTTACGCCTT TAGTGACCGAACGGAGAGAG 1334–1347 1.000 79.2
tRNA-Thr-tRNA-Ser_p2 tRNA-Thr-tRNA-Ser GAACCGATGACTTACGCCTT CGGAGAGAGAGGGATTCGAA 1323–1336 1.000 78.8
tRNA-Thr-tRNA-Ser_p3 tRNA-Thr-tRNA-Ser CCATGGCGTTACTCTACCAC TAGTGACCGAACGGAGAGAG 1313–1326 1.000 78.8
tRNA-Thr-tRNA-Ser_p4 tRNA-Thr-tRNA-Ser TGGCGTTACTCTACCACTGA TAGTGACCGAACGGAGAGAG 1310–1323 1.000 78.6
tRNA-Thr-tRNA-Ser_p5 tRNA-Thr-tRNA-Ser CGTGTAAGACGGACATCCAG TAGTGACCGAACGGAGAGAG 1399–1412 1.000 78.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Pseudotsuga menziesii var. glauca MH612867.1 121631 View on NCBI ↗
Pseudotsuga sinensis var. brevifolia NC_058308.1 122348 View on NCBI ↗
Pseudotsuga sinensis var. wilsoniana NC_016064.1 122513 View on NCBI ↗