Markers + reference

Cattleya

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 147–148 kb
Candidate markers 280
Primer pairs 85

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 7 remaining regions by MarkerSeek score (out of 280 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhC LSC 360 0.0000 1.00 31.6 yes View details
ndhC-trnV-UAC LSC 638 0.0063 1.00 62.4 yes View details
atpB-rbcL LSC 958 0.0074 0.98 64.7 yes View details
clpP LSC 2243 0.0009 1.00 51.7 yes View details
clpP-psbB LSC 960 0.0159 0.98 63.7 yes View details
rps19 LSC 279 0.0000 1.00 33.8 no View details
trnN-GUU-rpl32 SSC 956 0.0379 0.99 66.8 yes View details
ccsA-ndhD SSC 276 0.0400 1.00 61.4 yes View details
ndhD SSC 1505 0.0053 1.00 55.2 yes View details
ndhE SSC 306 0.0065 1.00 52.6 yes View details
ycf1-trnN-GUU SSC 340 0.0000 0.00 26.5 yes View details
rps19 LSC 279 0.0430 1.00 69.3 yes View details
ndhE-ndhG SSC 196 0.0217 0.94 67.6 yes View details
rps19-psbA LSC 393 0.0114 0.89 63.1 no View details
matK-trnK LSC 1046 0.0039 0.98 62.8 yes View details
rbcL-accD LSC 858 0.0012 0.97 62.1 yes View details
rps16-trnQ-UUG LSC 1875 0.0011 0.97 61.4 yes View details
petB-petD LSC 992 0.0040 1.00 61.2 yes View details
ndhK LSC 728 0.0041 1.00 61.1 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
matK-trnK_p1 matK-trnK AGGAAGTTTTGTTGCCGAAA ATCCGGGTTGCTAACTCAAC 1158–1159 1.000 67.8
matK-trnK_p2 matK-trnK AGGAAGTTTTGTTGCCGAAA AACGGTAGAGTACTCGGCTT 1141–1142 1.000 67.3
matK-trnK_p3 matK-trnK AGGAAGTTTTGTTGCCGAAA ACGGTAGAGTACTCGGCTTT 1140–1141 1.000 67.3
matK-trnK_p4 matK-trnK AGGAAGTTTTGTTGCCGAAA GATCCGGGTTGCTAACTCAA 1159–1160 1.000 65.5
matK-trnK_p5 matK-trnK AGGAAGTTTTGTTGCCGAAA TTGATCCGGGTTGCTAACTC 1161–1162 1.000 65.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTCCTTCTCTTCGGGATCGA GACCAAATCAAAATGGGGCG 2018–2070 1.000 81.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTCCTTCTCTTCGGGATCGA GAGGTTCGAATCCTTCCGTC 1957–2009 1.000 80.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GATGCCCCCGAAACGTATAG GACCAAATCAAAATGGGGCG 1945–1997 1.000 80.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GATGCCCCCGAAACGTATAG GAGGTTCGAATCCTTCCGTC 1884–1936 1.000 80.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTCCTTCTCTTCGGGATCGA CTCGGAGGTTCGAATCCTTC 1961–2013 1.000 79.4
ndhK_p1 ndhK TCTTTACGTAAAGGCCAGCC GGGGATGCTTGGGTACAATT 845 1.000 78.2
ndhK_p2 ndhK CGACACGACTCCAGATTTCA GGGGATGCTTGGGTACAATT 920 1.000 76.2
ndhK_p3 ndhK ACGACACGACTCCAGATTTC GGGGATGCTTGGGTACAATT 921 1.000 76.2
ndhK_p4 ndhK TCTTTACGTAAAGGCCAGCC TGCTTGGGTACAATTCCGAA 840 1.000 74.9
ndhK_p5 ndhK TCTTTACGTAAAGGCCAGCC GGGTACAATTCCGAATTCGC 835 1.000 73.5
ndhC_p1 ndhC TGAATTGGGGGTTGTTTGGT TTCAGCCTACTCCACATTCA 500 1.000 63.8
ndhC_p2 ndhC TGAATTGGGGGTTGTTTGGT CAGCCTACTCCACATTCATAGG 498 1.000 62.5
ndhC_p3 ndhC TGAATTGGGGGTTGTTTGGT AGCCTACTCCACATTCATAGGA 497 1.000 62.0
ndhC_p4 ndhC TGAATTGGGGGTTGTTTGGT TCAGCCTACTCCACATTCAT 499 1.000 61.9
ndhC_p5 ndhC TGAATTGGGGGTTGTTTGGT TTCAGCCTACTCCACATTCAT 500 1.000 60.2
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CGGGGCTAAAATCCCAGAAA AGAAGGTCTACGGTTCGAGT 770–776 1.000 77.7
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TCTGGACCTTCCCTAATCGG AGAAGGTCTACGGTTCGAGT 787–793 1.000 77.1
ndhC-trnV-UAC_p3 ndhC-trnV-UAC AATCGGGGCTAAAATCCCAG AGAAGGTCTACGGTTCGAGT 773–779 1.000 75.9
ndhC-trnV-UAC_p4 ndhC-trnV-UAC CGGGGCTAAAATCCCAGAAA AGCCCAATGCAACAAAATGC 852–858 1.000 75.5
ndhC-trnV-UAC_p5 ndhC-trnV-UAC CGGGGCTAAAATCCCAGAAA GAAGGTCTACGGTTCGAGTC 769–775 1.000 75.0
atpB-rbcL_p1 atpB-rbcL TGCCCGGTGGAAAAATTACA GGTGACATAAGTCCCTCCCT 1085–1102 1.000 80.8
atpB-rbcL_p2 atpB-rbcL ATCTTGCCCGGTGGAAAAAT GGTGACATAAGTCCCTCCCT 1089–1106 1.000 80.3
atpB-rbcL_p3 atpB-rbcL TGAGTGATACGCCCTAGGTT GGTGACATAAGTCCCTCCCT 1044–1061 1.000 79.6
atpB-rbcL_p4 atpB-rbcL TTGAGTGATACGCCCTAGGT GGTGACATAAGTCCCTCCCT 1045–1062 1.000 79.6
atpB-rbcL_p5 atpB-rbcL TCTTGCCCGGTGGAAAAATT GGTGACATAAGTCCCTCCCT 1088–1105 1.000 78.5

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
Cattleya crispata NC_026568.1 148343 View on NCBI ↗
Cattleya liliputana NC_032083.1 147092 View on NCBI ↗