Markers + reference

Siphocranion

2 species · Lamiaceae · Lamiales

Back to catalogue

Species 2
Genome length 152–152 kb
Candidate markers 272
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1059 0.0019 1.00 49.9 yes View details
rps16-trnQ-UUG LSC 843 0.0261 1.00 62.1 yes View details
psbI-trnS-GCU LSC 244 0.0383 0.75 60.0 yes View details
trnT-GGU-psbD LSC 1322 0.0146 0.98 68.9 yes View details
petA-psbJ LSC 924 0.0162 1.00 54.6 yes View details
ycf1 IRb 1131 0.0018 1.00 58.0 no View details
rpl32-trnL-UAG SSC 667 0.0255 1.00 65.5 yes View details
ccsA SSC 978 0.0082 1.00 49.7 yes View details
ccsA-ndhD SSC 213 0.0377 1.00 62.6 yes View details
rps15-ycf1 SSC 425 0.0223 0.95 57.9 yes View details
ycf1 SSC 5511 0.0131 1.00 46.5 yes View details
rps18-rpl20 LSC 241 0.0339 0.98 73.9 yes View details
trnH-GUG-psbA LSC 234 0.0858 1.00 72.7 yes View details
trnL-UAG-ccsA SSC 102 0.0392 1.00 70.8 yes View details
rpoB-trnC-GCA LSC 1159 0.0156 0.99 67.8 yes View details
rbcL-accD LSC 697 0.0131 0.99 66.5 yes View details
trnF-GAA-ndhJ LSC 634 0.0095 1.00 64.2 yes View details
trnY-GUA-trnE-UUC LSC 86 0.0123 0.94 63.4 yes View details
trnS-UGA-psbZ LSC 353 0.0129 0.88 63.3 yes View details
ycf3-trnS-GGA LSC 850 0.0095 0.99 63.3 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 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 TCAGTGCTATGCATGGTTCC 683–684 1.000 81.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGTGGGAGCTTAGTTTCCG 927–928 1.000 80.8
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGTGGGAGCTTAGTTTCCG 941–942 1.000 80.7
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GAGTGGGAGCTTAGTTTCCG 940–941 1.000 80.7
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GAGTGGGAGCTTAGTTTCCG 942–943 1.000 80.7
psbA_p1 psbA ACTCCTACACACTAAAAACAAGTC AAATTGGTGTGCTTGGGAGT 1134 1.000 40.1
psbA_p2 psbA ACTCCTACACACTAAAAACAAGT AAATTGGTGTGCTTGGGAGT 1134 1.000 40.1
psbA_p3 psbA AGGGGTTTATTGCTCCTTAT AAATTGGTGTGCTTGGGAGT 1177 0.500 24.3
psbA_p4 psbA AGGGGTTTATTGCTCCTTAT AATTGGTGTGCTTGGGAGTC 1176 0.500 21.9
psbA_p5 psbA AGGGGTTTATTGCTCCTTAT GAAAATTGGTGTGCTTGGGAG 1179 0.500 20.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 908–911 1.000 75.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 911–914 1.000 72.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GGGTTTTGGTCCCGGTATTC 929–932 1.000 71.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 912–915 1.000 70.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TAAGGCAACGGGTTTTGGTC 938–941 1.000 70.1
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCCGGACGTGAAGAA TGGACTAAAGCGTCGGATTG 287–340 1.000 80.5
psbI-trnS-GCU_p2 psbI-trnS-GCU GTAATCCCGGACGTGAAGAA GTGGACTAAAGCGTCGGATT 288–341 1.000 80.5
psbI-trnS-GCU_p3 psbI-trnS-GCU GTAATCCCGGACGTGAAGAA GACTAAAGCGTCGGATTGCT 285–338 1.000 77.6
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCCGGACGTGAAGAA CTGAGTGGACTAAAGCGTCG 292–345 1.000 77.4
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCCGGACGTGAAG TGGACTAAAGCGTCGGATTG 288–341 1.000 77.4
trnG-UCC_p1 trnG-UCC CCCTTCTTATTCTCACGGCC CGGACCGGTTTCTACTTCAG 1653–1681 1.000 81.0
trnG-UCC_p2 trnG-UCC CCTTCTTATTCTCACGGCCC CGGACCGGTTTCTACTTCAG 1652–1680 1.000 81.0
trnG-UCC_p3 trnG-UCC GGCCCTTCTTATTCTCACGG CGGACCGGTTTCTACTTCAG 1655–1683 1.000 81.0
trnG-UCC_p4 trnG-UCC CCCTTCTTATTCTCACGGCC CCGGTTTCTACTTCAGGAGC 1649–1677 1.000 81.0
trnG-UCC_p5 trnG-UCC CCTTCTTATTCTCACGGCCC CCGGTTTCTACTTCAGGAGC 1648–1676 1.000 81.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GACATTGCCTCGTTTGCATC TTTTGGTGATTCAGGCGACA 1265–1271 1.000 80.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GACATTGCCTCGTTTGCATC CCGGATTTGAACTGGGGAAA 1244–1250 1.000 80.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TAGACATTGCCTCGTTTGCA TTTTGGTGATTCAGGCGACA 1267–1273 1.000 79.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TAGACATTGCCTCGTTTGCA CCGGATTTGAACTGGGGAAA 1246–1252 1.000 79.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCAAACCCTGATCGATGAA TTTTGGTGATTCAGGCGACA 1331–1337 1.000 79.2

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
Siphocranion flavidum MT473778.1 152039 View on NCBI ↗
Siphocranion macranthum MT473779.1 152126 View on NCBI ↗