Markers + reference

Stenocoelium

2 species · Apiaceae · Apiales

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Species 2
Genome length 148–154 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

11 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
petN-psbM Genome 951 0.0074 1.00 61.5 yes View details
trnE-UUC-trnT-GGU Genome 793 0.0053 0.96 65.8 yes View details
petA-psbJ Genome 982 0.0085 0.96 67.2 yes View details
clpP-psbB Genome 459 0.0088 0.99 61.7 yes View details
ycf2 Genome 6270 0.0037 1.00 48.2 yes View details
trnL-CAA-ndhB Genome 573 0.0087 1.00 63.2 yes View details
ycf1 Genome 1935 0.0005 1.00 44.9 no View details
ndhF-rpl32 Genome 1058 0.0086 0.98 65.2 yes View details
ycf1 Genome 5487 0.0033 1.00 47.2 yes View details
ndhB-trnL-CAA Genome 573 0.0087 1.00 63.2 yes View details
trnL-CAA-trnH-GUG Genome 2268 0.0020 0.65 47.1 no View details
rpoB-trnC-GCA Genome 1241 0.0034 0.96 64.8 yes View details
psaJ-rpl33 Genome 471 0.0066 0.96 63.3 yes View details
rpl32-trnL-UAG Genome 980 0.0033 0.94 62.9 yes View details
trnH-GUG-psbA Genome 193 0.0156 0.99 62.0 yes View details
trnG-GCC-trnR-UCU Genome 134 0.0079 0.95 61.8 yes View details
ndhC-trnV-UAC Genome 1071 0.0019 0.98 61.5 yes View details
trnK-UUU-rps16 Genome 713 0.0029 0.98 61.3 yes View details
ndhI Genome 504 0.0079 1.00 61.3 yes View details
rbcL-accD Genome 613 0.0017 0.99 61.0 yes View details
rpl2 Genome 1476 0.0034 1.00 60.7 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 310–314 1.000 79.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 324–328 1.000 79.7
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 260–264 1.000 79.7
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 323–327 1.000 79.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 325–329 1.000 79.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AGGAACTGTTCGGGATCTTT 826–837 1.000 68.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGGAACTGTTCGGGATCTTT 843–854 1.000 68.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AGGAACTGTTCGGGATCTTT 842–853 1.000 68.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGAACTGTTCGGGATCTTT 782–793 1.000 67.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTGTTCGGGATCTTT 781–792 1.000 67.7
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 213–214 1.000 66.7
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 216–217 1.000 66.4
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 219–220 1.000 66.0
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 222–223 1.000 65.7
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 217–218 1.000 64.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT CCGGATTTGAACTGGGGAAA 1334–1385 1.000 81.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCACGAACCTACAAAAGCC CCGGATTTGAACTGGGGAAA 1335–1386 1.000 81.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT AAAAGGATTTGCAGTCCCCC 1316–1367 1.000 79.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT TATTGAATCAGGCGACACCC 1403 0.500 56.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCCACGAACCTACAAAAGCC TATTGAATCAGGCGACACCC 1404 0.500 56.5
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATCC 1125–1311 1.000 78.6
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATCC 1064–1250 1.000 77.0
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT GCTACTGCACTGTTCATCCT 1124–1310 1.000 76.2
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT GCTACTGCACTGTTCATCCT 1063–1249 1.000 74.7
petN-psbM_p5 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATCC 1126–1312 1.000 72.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 870–897 1.000 81.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GTGTAGTACCCTACCCCCAG GAACCGATGACTTACGCCTT 905–932 1.000 81.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 835–862 1.000 81.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GTGTAGTACCCTACCCCCAG TACCGCTGAGTTAAAAGGGC 870–897 1.000 80.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 867–894 1.000 80.8

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
Stenocoelium popovii NC_087716.1 147519 View on NCBI ↗
Stenocoelium trichocarpum PP078861.1 154227 View on NCBI ↗