Markers + reference

Stigmatodon

2 species · Bromeliaceae · Poales

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Species 2
Genome length 157–157 kb
Candidate markers 279
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 9 remaining regions by MarkerSeek score (out of 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5601 0.0016 1.00 53.4 yes View details
trnI-GAU-rrn16S IRb 316 0.0443 1.00 78.3 yes View details
atpH-atpI LSC 672 0.0060 1.00 62.2 yes View details
rpoB LSC 3219 0.0016 1.00 55.9 yes View details
trnC-GCA-petN LSC 794 0.0063 1.00 53.6 yes View details
rbcL-atpB LSC 776 0.0064 1.00 55.5 yes View details
trnV-UAC-ndhC LSC 796 0.0051 0.99 62.3 yes View details
psbC LSC 1422 0.0007 1.00 48.1 yes View details
trnW-CCA-trnP-UGG LSC 138 0.0000 0.99 50.7 yes View details
clpP LSC 2154 0.0033 1.00 59.3 yes View details
rrn16S-trnI-GAU IRa 316 0.0443 1.00 78.3 yes View details
ycf1 IRa 1078 0.0000 1.00 40.0 no View details
ndhF-rpl32 SSC 999 0.0000 1.00 77.4 no View details
petG-trnW-CCA LSC 122 0.0328 1.00 71.4 yes View details
trnS-UGA-psbC LSC 137 0.0511 1.00 67.1 yes View details
psbE-petL LSC 1524 0.0007 0.97 62.0 yes View details
trnV-GAC-rps12 IRb 1713 0.0000 0.86 60.6 yes View details
ndhJ-trnF-GAA LSC 779 0.0013 0.99 60.6 yes View details
rps12-trnV-GAC IRa 1713 0.0000 0.86 60.6 yes View details
matK-trnK-UUU LSC 824 0.0012 0.99 60.3 yes View details
psbI-trnS-GCU LSC 124 0.0161 1.00 60.3 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
ycf1_p1 ycf1 TGGAAATAGATCCTGTGAATGGT TCAACCATTCAAATCCAATCCA 305 1.000 40.5
ycf1_p2 ycf1 TGGAAATAGATCCTGTGAATGGT ACCATTCAAATCCAATCCATGA 302 1.000 40.5
ycf1_p3 ycf1 TGGAAATAGATCCTGTGAATGGT CAACCATTCAAATCCAATCCATGA 304 1.000 40.5
ycf1_p4 ycf1 TGGAAATAGATCCTGTGAATGGT TCAACCATTCAAATCCAATCCATG 305 1.000 40.5
ycf1_p5 ycf1 TTGGAAATAGATCCTGTGAATGGT TCAACCATTCAAATCCAATCCA 306 1.000 40.5
trnI-GAU_p1 trnI-GAU TCTATTCTTTTCCCTGGCGC GGGGTTTTTCTCGCTTTTGG 1090 1.000 78.5
trnI-GAU_p2 trnI-GAU GCCAAGTGGAGTATGCATGA GGGGTTTTTCTCGCTTTTGG 1127 1.000 78.5
trnI-GAU_p3 trnI-GAU AGCCAAGTGGAGTATGCATG GGGGTTTTTCTCGCTTTTGG 1128 1.000 78.4
trnI-GAU_p4 trnI-GAU TCTATTCTTTTCCCTGGCGC TTCTCGCTTTTGGCATAGCA 1083 1.000 78.3
trnI-GAU_p5 trnI-GAU GCCAAGTGGAGTATGCATGA TTCTCGCTTTTGGCATAGCA 1120 1.000 78.2
trnI-GAU-rrn16S_p1 trnI-GAU-rrn16S GGCACAACGACGCAATTATC CAAGGTAGCCGTACTGGAAG 410 1.000 78.9
trnI-GAU-rrn16S_p2 trnI-GAU-rrn16S CTATCCATGTGGCTGAGAGC CAAGGTAGCCGTACTGGAAG 442 1.000 78.8
trnI-GAU-rrn16S_p3 trnI-GAU-rrn16S CGCTGATGAGCACATTGAAC CAAGGTAGCCGTACTGGAAG 461 1.000 78.7
trnI-GAU-rrn16S_p4 trnI-GAU-rrn16S CTATCCATGTGGCTGAGAGC AGTGACTGGAGTGAAGTCGT 464 1.000 78.6
trnI-GAU-rrn16S_p5 trnI-GAU-rrn16S CGCTGATGAGCACATTGAAC AGTGACTGGAGTGAAGTCGT 483 1.000 78.5
trnV-GAC-rps12_p1 trnV-GAC-rps12 CGGGGGAGCAAGTCAAAATA TGGCAACTTTACGTAAGGCA 1631–1870 1.000 81.0
trnV-GAC-rps12_p2 trnV-GAC-rps12 GATGACTTCCACCACGTCAA TGGCAACTTTACGTAAGGCA 1570–1809 1.000 80.6
trnV-GAC-rps12_p3 trnV-GAC-rps12 AACTGATGACTTCCACCACG TGGCAACTTTACGTAAGGCA 1574–1813 1.000 80.6
trnV-GAC-rps12_p4 trnV-GAC-rps12 ATGACTTCCACCACGTCAAG TGGCAACTTTACGTAAGGCA 1569–1808 1.000 80.6
trnV-GAC-rps12_p5 trnV-GAC-rps12 CTGATGACTTCCACCACGTC TGGCAACTTTACGTAAGGCA 1572–1811 1.000 79.7
matK-trnK-UUU_p1 matK-trnK-UUU CCATGATCATGAGCAAACGC TTTGATAGGGTCGTGCAGTG 1032–1039 1.000 78.9
matK-trnK-UUU_p2 matK-trnK-UUU CCATGATCATGAGCAAACGC ATCCGGGTTGCTAACTCAAC 965–972 1.000 78.9
matK-trnK-UUU_p3 matK-trnK-UUU TAGGAAGTGTTGTTGCCGAG TTTGATAGGGTCGTGCAGTG 982–989 1.000 78.6
matK-trnK-UUU_p4 matK-trnK-UUU TAGGAAGTGTTGTTGCCGAG ATCCGGGTTGCTAACTCAAC 915–922 1.000 78.5
matK-trnK-UUU_p5 matK-trnK-UUU CCATGATCATGAGCAAACGC ACGGTAGAGTACTCGGCTTT 947–954 1.000 78.4
psbI-trnS-GCU_p1 psbI-trnS-GCU CAATCCTGGACGTGAGGAAT TAAAGCGGCGGATTGCTAAT 214 1.000 74.9
psbI-trnS-GCU_p2 psbI-trnS-GCU CAATCCTGGACGTGAGGAAT TAGGAGAGATGGCTGAGTGG 236 1.000 74.5
psbI-trnS-GCU_p3 psbI-trnS-GCU CAATCCTGGACGTGAGGAAT ATGGCTGAGTGGACTAAAGC 228 1.000 71.8
psbI-trnS-GCU_p4 psbI-trnS-GCU CAATCCTGGACGTGAGGAAT GAGAGATGGCTGAGTGGACT 233 1.000 71.0
psbI-trnS-GCU_p5 psbI-trnS-GCU CAATCCTGGACGTGAGGAAT CTAAAGCGGCGGATTGCTAA 215 1.000 69.5

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
Stigmatodon gastinianus NC_081608.1 156979 View on NCBI ↗
Stigmatodon plurifolius NC_081609.1 157146 View on NCBI ↗