Markers + reference

Cryptotaenia

2 species · Apiaceae · Apiales

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Species 2
Genome length 153–154 kb
Candidate markers 273
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0028 1.00 49.6 yes View details
rps16 LSC 1094 0.0101 1.00 51.9 yes View details
petN-psbM LSC 909 0.0142 0.93 59.9 yes View details
trnT-UGU-trnL-UAA LSC 798 0.0125 1.00 62.0 yes View details
psbE-petL LSC 1119 0.0170 1.00 62.5 yes View details
trnP-UGG-psaJ LSC 387 0.0160 0.97 60.9 yes View details
petB LSC 1396 0.0086 1.00 61.4 yes View details
rpl16 LSC 1334 0.0106 0.99 55.0 yes View details
ycf1 IRb 2031 0.0015 1.00 58.5 no View details
ndhF SSC 2232 0.0076 1.00 61.6 yes View details
ndhF-rpl32 SSC 1107 0.0234 0.77 62.1 yes View details
ycf1 SSC 5397 0.0089 1.00 42.9 yes View details
trnH-GUG-psbA LSC 143 0.0845 0.99 76.1 yes View details
rpl16-rps3 LSC 154 0.0390 1.00 74.9 yes View details
trnL-UAG-ccsA SSC 102 0.0392 1.00 70.8 yes View details
ndhI-ndhA SSC 93 0.0323 1.00 68.1 yes View details
rps15-ycf1 SSC 465 0.0224 0.86 67.1 yes View details
trnG-UCC-trnR-UCU LSC 138 0.0221 0.99 66.5 yes View details
trnW-CCA-trnP-UGG LSC 155 0.0333 0.97 66.5 yes View details
atpH-atpI LSC 840 0.0119 1.00 65.6 yes View details
ndhC-trnV-UAC LSC 722 0.0098 0.99 65.6 yes View details
petA-psbJ LSC 727 0.0083 1.00 63.5 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 105 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 CCTCTAGACCTAGCTGCTGT 211–267 1.000 82.8
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 214–270 1.000 82.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 225–281 1.000 82.5
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 224–280 1.000 82.5
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 226–282 1.000 82.5
psbA_p1 psbA ACTCGTATATACTAAGACACGGTC AAATTCGTGTGCTTGGGAGT 1137 1.000 41.8
psbA_p2 psbA ACTCGTATATACTAAGACACGGT AAATTCGTGTGCTTGGGAGT 1137 1.000 41.3
psbA_p3 psbA AACTCGTATATACTAAGACACGGT AAATTCGTGTGCTTGGGAGT 1138 1.000 40.2
psbA_p4 psbA AACTCGTATATACTAAGACACGGTC AAATTCGTGTGCTTGGGAGT 1138 1.000 40.2
psbA_p5 psbA ACTCGTATATACTAAGACACGGTC AATTCGTGTGCTTGGGAGTC 1136 1.000 40.2
rps16_p1 rps16 TTTTGTTTGATTAGGACCAAG TGTATCGACGGAACCAATGAC 1198–1202 1.000 40.7
rps16_p2 rps16 TTTTGTTTGATTAGGACCAAG GTATCGACGGAACCAATGACT 1197–1201 1.000 40.7
rps16_p3 rps16 TTTTGTTTGATTAGGACCAAG TGTATCGACGGAACCAATGA 1198–1202 1.000 40.7
rps16_p4 rps16 ATTTTGTTTGATTAGGACCAAG TGTATCGACGGAACCAATGAC 1199–1203 1.000 40.7
rps16_p5 rps16 ATTTTGTTTGATTAGGACCAAG GTATCGACGGAACCAATGACT 1198–1202 1.000 40.7
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 218–223 1.000 65.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 221–226 1.000 64.9
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 224–229 1.000 64.4
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 227–232 1.000 64.2
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 222–227 1.000 62.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 902–960 1.000 80.0
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 958–1016 1.000 79.4
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 918–976 1.000 79.1
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 903–961 1.000 78.9
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 962–1020 1.000 78.8
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGTAAAAACAGAAAGTCAAAATCA 962–1025 1.000 45.0
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGTAAAAACAGAAAGTCAAAATCA 968–1031 1.000 45.0
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGTAAAAACAGAAAGTCAAAATCA 908–971 1.000 45.0
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA GTAAAAACAGAAAGTCAAAATCA 961–1024 1.000 45.0
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA TGTAAAAACAGAAAGTCAAAATC 962–1025 1.000 45.0

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
Cryptotaenia canadensis PQ283864.1 154101 View on NCBI ↗
Cryptotaenia japonica NC_046737.1 153259 View on NCBI ↗