Markers + reference

Orthotrichum

2 species · Orthotrichaceae · Orthotrichales

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Species 2
Genome length 123–123 kb
Candidate markers 257
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
chlL Genome 876 0.4673 0.91 82.4 yes View details
chlN Genome 1410 0.4506 0.72 77.1 yes View details
ycf1 Genome 4824 0.4299 0.82 74.1 yes View details
ndhH Genome 1176 0.4803 0.80 79.3 yes View details
ndhA Genome 1831 0.4411 0.90 81.4 yes View details
ndhI Genome 552 0.4342 0.96 81.3 yes View details
rpl21 Genome 351 0.4911 0.96 77.3 yes View details
ndhF Genome 2109 0.4541 0.87 80.2 yes View details
ndhG Genome 576 0.4147 0.97 81.5 yes View details
ndhD Genome 1500 0.4390 0.85 80.9 yes View details
rps19-rpl22 Genome 17 0.1176 1.00 79.4 yes View details
rpl21-ndhF Genome 408 0.4063 0.93 79.0 yes View details
psbN-psbT Genome 87 0.1149 1.00 78.1 yes View details
psbD-trnT-GGU Genome 513 0.0371 1.00 77.6 yes View details
ndhE Genome 303 0.3718 0.91 77.3 yes View details
trnfM-CAU-trnG-GCC Genome 113 0.0811 0.98 77.1 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps19-rpl22_p1 rps19-rpl22 TCGAGGACATGCAAAAAGTGA TGTTTGGCTAAAGCTTTGGC 104 1.000 68.1
rps19-rpl22_p2 rps19-rpl22 GGAGAATTTGCACCTACACG TGTTTGGCTAAAGCTTTGGC 130 1.000 67.6
rps19-rpl22_p3 rps19-rpl22 AGGAGAATTTGCACCTACACG TGTTTGGCTAAAGCTTTGGC 131 1.000 66.6
rps19-rpl22_p4 rps19-rpl22 GGAGAATTTGCACCTACACGA TGTTTGGCTAAAGCTTTGGC 130 1.000 66.6
rps19-rpl22_p5 rps19-rpl22 CGAGGACATGCAAAAAGTGA TGTTTGGCTAAAGCTTTGGC 103 1.000 66.6
psbN-psbT_p1 psbN-psbT ACAGCTTTTGGACAACCTTCT TCGTGAAACACCTAAAATTCAAACT 187 1.000 44.3
psbN-psbT_p2 psbN-psbT ACAGCTTTTGGACAACCTTCT TCGTGAAACACCTAAAATTCA 187 1.000 44.3
psbN-psbT_p3 psbN-psbT ACAGCTTTTGGACAACCTTCT TCGTGAAACACCTAAAATTCAAAC 187 1.000 44.3
psbN-psbT_p4 psbN-psbT ACAGCTTTTGGACAACCTTCT CGTGAAACACCTAAAATTCAAACT 186 1.000 44.3
psbN-psbT_p5 psbN-psbT ACAGCTTTTGGACAACCTTCT TCGTGAAACACCTAAAATTCAA 187 1.000 44.3
trnL-UAA_p1 trnL-UAA TGGATTTGGAAAAGTGCGGA GAGTCGAACCGATGACCATC 1207 1.000 86.1
trnL-UAA_p2 trnL-UAA ACTTGGATTGGTTGGCCTTT GAGTCGAACCGATGACCATC 1105 1.000 86.0
trnL-UAA_p3 trnL-UAA TGGATTTGGAAAAGTGCGGA TCTGACCTCTGAGCTAAGCA 1169 1.000 85.9
trnL-UAA_p4 trnL-UAA ACTTGGATTGGTTGGCCTTT TCTGACCTCTGAGCTAAGCA 1067 1.000 85.7
trnL-UAA_p5 trnL-UAA TCTACCAACTGAGCTACCCC GAGTCGAACCGATGACCATC 780 0.500 57.6
trnfM-CAU-trnG-GCC_p1 trnfM-CAU-trnG-GCC GTAGCTCGCAAGGCTCATAA AATATGCGGGTTCGATTCCC 196–198 1.000 81.8
trnfM-CAU-trnG-GCC_p2 trnfM-CAU-trnG-GCC TAGCTCGCAAGGCTCATAAC AATATGCGGGTTCGATTCCC 195–197 1.000 81.8
trnfM-CAU-trnG-GCC_p3 trnfM-CAU-trnG-GCC GTAGCTCGCAAGGCTCATAA AAGGAGAATATGCGGGTTCG 202–204 1.000 80.6
trnfM-CAU-trnG-GCC_p4 trnfM-CAU-trnG-GCC TAGCTCGCAAGGCTCATAAC AAGGAGAATATGCGGGTTCG 201–203 1.000 80.6
trnfM-CAU-trnG-GCC_p5 trnfM-CAU-trnG-GCC TAGCTCGCAAGGCTCATAAC TTGCCAAGGAGAATATGCGG 206–208 1.000 79.9
psbD-trnT-GGU_p1 psbD-trnT-GGU GCCAGTCATCCATGCTATCA GTGGTAGAGTAACGCCATGG 637–638 1.000 77.5
psbD-trnT-GGU_p2 psbD-trnT-GGU GCCAGTCATCCATGCTATCA TCAGTGGTAGAGTAACGCCA 640–641 1.000 77.4
psbD-trnT-GGU_p3 psbD-trnT-GGU TCTTAGCCAGTCATCCATGC GTGGTAGAGTAACGCCATGG 642–643 1.000 77.0
psbD-trnT-GGU_p4 psbD-trnT-GGU CTTAGCCAGTCATCCATGCT GTGGTAGAGTAACGCCATGG 641–642 1.000 76.9
psbD-trnT-GGU_p5 psbD-trnT-GGU TCTTAGCCAGTCATCCATGC TCAGTGGTAGAGTAACGCCA 645–646 1.000 76.8
chlL_p1 chlL CGCAATCAAGCAGGAAAAGG TAGTTTTGGTGCCATGCCTT 1627 0.500 59.8
chlL_p2 chlL AGTGGGAAGTCGGGAAGTTA TAGTTTTGGTGCCATGCCTT 1505 0.500 59.8
chlL_p3 chlL TAGTGGGAAGTCGGGAAGTT TAGTTTTGGTGCCATGCCTT 1506 0.500 59.8
chlL_p4 chlL CGCAATCAAGCAGGAAAAGG CTGGACAACGATGTGCCATA 1736 0.500 59.7
chlL_p5 chlL CGCAATCAAGCAGGAAAAGG TGGACAACGATGTGCCATAG 1735 0.500 59.7

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
Orthotrichum rogeri NC_026212.1 123363 View on NCBI ↗
Orthotrichum stellatum NC_058546.1 123253 View on NCBI ↗