Markers + reference

Iochroma

8 species · Solanaceae · Solanales

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Species 8
Genome length 157–157 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 444 0.0056 1.00 48.2 yes View details
atpH-atpI LSC 1216 0.0038 1.00 67.3 yes View details
trnY-GUA-trnT-GGU LSC 1002 0.0044 1.00 59.1 yes View details
petA-psbJ LSC 1073 0.0028 1.00 40.5 yes View details
psbE-petL LSC 1157 0.0033 1.00 46.1 yes View details
rpl16 LSC 1447 0.0030 1.00 51.4 yes View details
ycf1 IRb 1119 0.0006 1.00 33.7 no View details
ndhF SSC 2223 0.0021 1.00 43.0 yes View details
ndhF-rpl32 SSC 784 0.0046 1.00 34.8 yes View details
rpl32-trnL-UAG SSC 825 0.0033 1.00 49.7 yes View details
ndhD SSC 1503 0.0007 1.00 28.2 yes View details
ycf1 SSC 5670 0.0022 1.00 37.1 yes View details
ycf1-ndhF SSC 20 0.0762 0.75 57.0 yes View details
rps16-trnQ-UUG LSC 1224 0.0028 1.00 55.5 yes View details
trnL-CAA-ycf15 IRa 348 0.0062 1.00 54.0 yes View details
accD-psaI LSC 750 0.0028 0.99 52.4 yes View details
ycf15-trnL-CAA IRb 348 0.0058 1.00 51.1 yes View details
psbM-trnD-GUC LSC 1073 0.0017 1.00 51.0 yes View details
petN-psbM LSC 1102 0.0024 1.00 50.1 yes View details
trnT-GGU-psbD LSC 1191 0.0009 1.00 50.0 yes View details
clpP-psbT LSC 2180 0.0009 1.00 48.7 yes View details
rpl23-trnH-GUG IRa 1649 0.0005 0.98 47.7 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 100 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 TTCCCTCTAGACCTAGCTGC 513–535 1.000 79.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 527–549 1.000 79.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 526–548 1.000 79.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 528–550 1.000 79.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 562–584 1.000 77.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1305–1361 1.000 80.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1288–1344 1.000 80.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1306–1362 1.000 79.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1303–1359 1.000 78.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1302–1358 1.000 78.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TACCTGTCATGCTCCTTGGA 1307–1353 1.000 83.3
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TACCTGTCATGCTCCTTGGA 1390–1436 1.000 82.3
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TACCTGTCATGCTCCTTGGA 1394–1440 1.000 82.3
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TACCTGTCATGCTCCTTGGA 1308–1354 1.000 82.2
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TACCTGTCATGCTCCTTGGA 1322–1368 1.000 81.9
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA AGTTCCTACCGCTTTTCTACT 1236 1.000 59.5
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG AGTTCCTACCGCTTTTCTACT 1242 1.000 58.0
petN-psbM_p3 petN-psbM GGGGAAGGAGTGGACTCTAG AGTTCCTACCGCTTTTCTACT 1180 1.000 57.9
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA AGTTCCTACCGCTTTTCTACTT 1236 1.000 57.3
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA TCTAGTTCCTACCGCTTTTCT 1239 1.000 57.3
psbM-trnD-GUC_p1 psbM-trnD-GUC AGTAGAAAAGCGGTAGGAACT CCCGTATTTCCCTGGGATTG 1225–1228 1.000 59.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AGTAGAAAAGCGGTAGGAACT TCCCGTATTTCCCTGGGATT 1226–1229 1.000 58.8
psbM-trnD-GUC_p3 psbM-trnD-GUC AAGTAGAAAAGCGGTAGGAACT CCCGTATTTCCCTGGGATTG 1226–1229 1.000 57.3
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAAAAGCGGTAGGAACTAGA CCCGTATTTCCCTGGGATTG 1222–1225 1.000 57.3
psbM-trnD-GUC_p5 psbM-trnD-GUC AAGTAGAAAAGCGGTAGGAACT TCCCGTATTTCCCTGGGATT 1227–1230 1.000 56.6
trnY-GUA-trnT-GGU_p1 trnY-GUA-trnT-GGU GCGGATTGGCGAATTATTGG GAACCGATGACTTACGCCTT 1156–1160 1.000 82.6
trnY-GUA-trnT-GGU_p2 trnY-GUA-trnT-GGU GGCGGATTGGCGAATTATTG GAACCGATGACTTACGCCTT 1157–1161 1.000 82.6
trnY-GUA-trnT-GGU_p3 trnY-GUA-trnT-GGU GCGGATTGGCGAATTATTGG CCATGGCGTTACTCTACCAC 1135–1139 1.000 82.2
trnY-GUA-trnT-GGU_p4 trnY-GUA-trnT-GGU GGCGGATTGGCGAATTATTG CCATGGCGTTACTCTACCAC 1136–1140 1.000 82.2
trnY-GUA-trnT-GGU_p5 trnY-GUA-trnT-GGU GCGGATTGGCGAATTATTGG TGGCGTTACTCTACCACTGA 1132–1136 1.000 82.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Iochroma arborescens NC_030185.1 156898 View on NCBI ↗
Iochroma cyaneum NC_030178.1 156791 View on NCBI ↗
Iochroma ellipticum NC_030177.1 157052 View on NCBI ↗
Iochroma lehmannii NC_030167.1 156835 View on NCBI ↗
Iochroma nitidum NC_026567.1 156574 View on NCBI ↗
Iochroma stenanthum NC_026574.1 156858 View on NCBI ↗
Iochroma tingoanum NC_027177.1 156823 View on NCBI ↗
Iochroma umbellatum NC_030044.1 156730 View on NCBI ↗