Markers + reference

Diocirea

3 species · Scrophulariaceae · Lamiales

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Species 3
Genome length 152–152 kb
Candidate markers 264
Primer pairs 110

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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 991 0.0044 1.00 61.8 yes View details
rps16 LSC 1099 0.0030 1.00 52.1 yes View details
psbK-psbI LSC 374 0.0036 1.00 45.1 yes View details
rps2-rpoC2 LSC 219 0.0107 1.00 47.4 yes View details
petN-psbM LSC 984 0.0041 1.00 61.8 yes View details
trnT-GGU-psbD LSC 1332 0.0043 1.00 60.0 yes View details
petD LSC 1227 0.0114 1.00 44.7 yes View details
rpl23 LSC 282 0.0024 1.00 32.6 yes View details
ndhF SSC 2232 0.0024 1.00 53.7 yes View details
rpl32-trnL-UAG SSC 881 0.0083 1.00 64.1 yes View details
psaC-ndhE SSC 256 0.0052 1.00 45.9 yes View details
petA-psbJ LSC 1075 0.0006 0.98 61.1 yes View details
psbE-petL LSC 922 0.0036 1.00 61.1 yes View details
rps16-trnQ-UUG LSC 1148 0.0035 1.00 61.0 yes View details
atpB-rbcL LSC 784 0.0034 1.00 60.9 yes View details
psbN-psbH LSC 105 0.0127 1.00 60.6 yes View details
rps12-trnV-GAC IRb 1679 0.0018 1.00 60.6 yes View details
trnV-GAC-rps12 IRa 1679 0.0016 1.00 60.5 yes View details
rpl20-rps12 LSC 796 0.0025 1.00 60.4 yes View details
ycf4-cemA LSC 719 0.0009 1.00 59.5 yes View details
trnP-UGG-psaJ LSC 439 0.0000 0.95 59.5 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 110 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 GTGCTCAACCCACAGGAAC 1084–1103 1.000 66.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGGAAC 1083–1102 1.000 66.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CAGTCGCGGTCTTACAAACT GTGCTCAACCCACAGGAAC 1168–1187 1.000 65.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAC GTGCTCAACCCACAGGAAC 1169–1188 1.000 65.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GTGCTCAACCCACAGGAAC 1098–1117 1.000 65.2
rps16_p1 rps16 TGAATTTCGTTTGATTAGACGGA TCAATTCCATACCGGTTCCA 1159 1.000 40.3
rps16_p2 rps16 TTCGTTTGATTAGACGGAAG TCAATTCCATACCGGTTCCA 1154 1.000 40.3
rps16_p3 rps16 TGAATTTCGTTTGATTAGACGGA TCAATTCCATACCGGTTCCAA 1159 1.000 40.3
rps16_p4 rps16 TTTCGTTTGATTAGACGGAAG TCAATTCCATACCGGTTCCA 1155 1.000 40.3
rps16_p5 rps16 TGAATTTCGTTTGATTAGACGGAA TCAATTCCATACCGGTTCCA 1159 1.000 40.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 1296 1.000 79.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1279 1.000 79.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1238 1.000 79.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1221 1.000 78.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 1297 1.000 78.6
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT ACGCCCCGGATCATTAGATA 499 1.000 79.3
psbK-psbI_p2 psbK-psbI CTTTTGTTTGGCAAGCTGCT TACGCCCCGGATCATTAGAT 500 1.000 79.3
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 494 1.000 79.3
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 495 1.000 79.3
psbK-psbI_p5 psbK-psbI CTTTTGTTTGGCAAGCTGCT TTACGCCCCGGATCATTAGA 501 1.000 77.5
rps2-rpoC2_p1 rps2-rpoC2 CCGCATCTCTTTTCGGAAGA GGGTCGAATCGATTGGTTGA 890–893 1.000 80.4
rps2-rpoC2_p2 rps2-rpoC2 CCGCATCTCTTTTCGGAAGA TATAACCCAGGGGCTTCCAA 1376–1379 1.000 80.2
rps2-rpoC2_p3 rps2-rpoC2 CACCATAGCCGCATCTCTTT GGGTCGAATCGATTGGTTGA 898–901 1.000 80.1
rps2-rpoC2_p4 rps2-rpoC2 CACCATAGCCGCATCTCTTT TATAACCCAGGGGCTTCCAA 1384–1387 1.000 80.0
rps2-rpoC2_p5 rps2-rpoC2 TTTCACCATAGCCGCATCTC TATAACCCAGGGGCTTCCAA 1387–1390 1.000 79.9
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA TGCTACTGCGCTATTCATTCT 1090–1094 1.000 69.0
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT TGCTACTGCGCTATTCATTCT 1088–1092 1.000 69.0
petN-psbM_p3 petN-psbM CGTAGTGTGGGGAAGAAGTG TGCTACTGCGCTATTCATTCT 1087–1091 1.000 68.4
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGCTATTCATTCT 1142–1146 1.000 67.8
petN-psbM_p5 petN-psbM GTAGTGTGGGGAAGAAGTGG TGCTACTGCGCTATTCATTCT 1086–1090 1.000 65.3

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
Diocirea acutifolia NC_077272.1 151728 View on NCBI ↗
Diocirea microphylla NC_077301.1 151655 View on NCBI ↗
Diocirea violacea NC_050957.1 151900 View on NCBI ↗