Markers + reference

Ulota

2 species · Orthotrichaceae · Orthotrichales

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Species 2
Genome length 124–124 kb
Candidate markers 263
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-GCC-psbZ Genome 249 0.0080 1.00 48.9 yes View details
psbZ-trnS-UGA Genome 214 0.0047 1.00 49.9 yes View details
ycf2 Genome 6882 0.0036 1.00 44.2 yes View details
psbA-trnK-UUU Genome 245 0.0286 1.00 54.3 yes View details
rpoB Genome 3204 0.0042 0.82 44.0 yes View details
rpoC1-rpoB Genome 24 0.0833 1.00 85.4 yes View details
ycf12-trnG-UCC Genome 134 0.0821 1.00 85.3 yes View details
trnS-UGA-psbC Genome 94 0.0638 1.00 78.9 yes View details
trnT-UGU-rps4 Genome 298 0.0201 1.00 64.1 yes View details
trnfM-CAU-trnG-GCC Genome 113 0.0354 1.00 63.3 yes View details
rpl2-rps19 Genome 55 0.0182 1.00 63.0 yes View details
trnV-GAC-trnI-CAU Genome 1282 0.0326 0.07 62.1 no View details
psbJ-petA Genome 1024 0.0049 1.00 61.7 yes View details
petL-psbE Genome 753 0.0040 1.00 61.2 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl2-rps19_p1 rpl2-rps19 ATGGGGTCATACTGCACTTG GTCAGCTACAAAAGGGCCTT 182 1.000 76.3
rpl2-rps19_p2 rpl2-rps19 CATGGGGTCATACTGCACTT GTCAGCTACAAAAGGGCCTT 183 1.000 76.3
rpl2-rps19_p3 rpl2-rps19 GGGTCATACTGCACTTGGAA GTCAGCTACAAAAGGGCCTT 179 1.000 75.8
rpl2-rps19_p4 rpl2-rps19 ATGGGGTCATACTGCACTTG ATGGTCAGCTACAAAAGGGC 185 1.000 75.7
rpl2-rps19_p5 rpl2-rps19 CATGGGGTCATACTGCACTT ATGGTCAGCTACAAAAGGGC 186 1.000 75.7
petL-psbE_p1 petL-psbE AGCTAAAAACAAAGAGGCAAACA CAAAAGGGCGTTCTCCTGTA 837–838 1.000 52.3
petL-psbE_p2 petL-psbE AGCTAAAAACAAAGAGGCAAACA GGGCGTTCTCCTGTATTTCC 832–833 1.000 51.0
petL-psbE_p3 petL-psbE AGCTAAAAACAAAGAGGCAAACA GGCGTTCTCCTGTATTTCCA 831–832 1.000 50.5
petL-psbE_p4 petL-psbE AGCTAAAAACAAAGAGGCAAACA TATCAGCAAAAGGGCGTTCT 843–844 1.000 49.8
petL-psbE_p5 petL-psbE GCTAAAAACAAAGAGGCAAACA CAAAAGGGCGTTCTCCTGTA 836–837 1.000 49.1
psbJ-petA_p1 psbJ-petA AGGTACGGTAGCTGGTACTC TCAATTACGTGTTCAAGGTCT 1227–1241 1.000 49.5
psbJ-petA_p2 psbJ-petA GGTACGGTAGCTGGTACTCT TCAATTACGTGTTCAAGGTCT 1226–1240 1.000 49.5
psbJ-petA_p3 psbJ-petA ACGGTAGCTGGTACTCTTGT TCAATTACGTGTTCAAGGTCT 1223–1237 1.000 49.3
psbJ-petA_p4 psbJ-petA AGGTACGGTAGCTGGTACTC TGCATCTGTTATCTTAGCACA 1194–1208 1.000 48.3
psbJ-petA_p5 psbJ-petA GGTACGGTAGCTGGTACTCT TGCATCTGTTATCTTAGCACA 1193–1207 1.000 48.3
trnV-UAC_p1 trnV-UAC CCATGCGCCACTTTTAACAG GGATCCAAGCATCACCCATT 1546–1548 1.000 79.5
trnV-UAC_p2 trnV-UAC CCATGCGCCACTTTTAACAG CGTGAGCCAATTAATGACGC 1959–1961 1.000 79.3
trnV-UAC_p3 trnV-UAC CCATGCGCCACTTTTAACAG AACTGGATCCAAGCATCACC 1550–1552 1.000 79.0
trnV-UAC_p4 trnV-UAC GAAAAGAGCAAAAGCACGCT GGATCCAAGCATCACCCATT 1297–1299 1.000 78.7
trnV-UAC_p5 trnV-UAC GCGCCACTTTTAACAGCTTT GGATCCAAGCATCACCCATT 1542–1544 1.000 78.6
trnT-UGU-rps4_p1 trnT-UGU-rps4 GATGGTCATCGGTTCGACTC GAGGTCCTCGATAACGGGA 352–353 1.000 71.2
trnT-UGU-rps4_p2 trnT-UGU-rps4 TGCTTAGCTCAGAGGTCAGA GAGGTCCTCGATAACGGGA 390–391 1.000 70.6
trnT-UGU-rps4_p3 trnT-UGU-rps4 GCACTTGTAATGCGATGGTC GAGGTCCTCGATAACGGGA 365–366 1.000 68.8
trnT-UGU-rps4_p4 trnT-UGU-rps4 AGAGCACCGCACTTGTAATG GAGGTCCTCGATAACGGGA 373–374 1.000 68.0
trnT-UGU-rps4_p5 trnT-UGU-rps4 CAGAGCACCGCACTTGTAAT GAGGTCCTCGATAACGGGA 374–375 1.000 68.0
trnfM-CAU-trnG-GCC_p1 trnfM-CAU-trnG-GCC GTAGCTCGCAAGGCTCATAA AATATGCGGGTTCGATTCCC 196 1.000 79.0
trnfM-CAU-trnG-GCC_p2 trnfM-CAU-trnG-GCC TAGCTCGCAAGGCTCATAAC AATATGCGGGTTCGATTCCC 195 1.000 79.0
trnfM-CAU-trnG-GCC_p3 trnfM-CAU-trnG-GCC GTAGCTCGCAAGGCTCATAA AAGGAGAATATGCGGGTTCG 202 1.000 77.9
trnfM-CAU-trnG-GCC_p4 trnfM-CAU-trnG-GCC TAGCTCGCAAGGCTCATAAC AAGGAGAATATGCGGGTTCG 201 1.000 77.9
trnfM-CAU-trnG-GCC_p5 trnfM-CAU-trnG-GCC TAGCTCGCAAGGCTCATAAC TTGCCAAGGAGAATATGCGG 206 1.000 77.2

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
Ulota bruchii NC_042480.1 123536 View on NCBI ↗
Ulota hutchinsiae NC_058548.1 123615 View on NCBI ↗