Markers + reference

Dystaenia

2 species · Apiaceae · Apiales

Back to catalogue

Species 2
Genome length 148–153 kb
Candidate markers 262
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf2 Genome 2725 0.2821 0.01 66.9 yes View details
rpl16 Genome 1357 0.2000 0.01 69.0 yes View details
rpoA Genome 1062 0.1429 0.01 69.2 yes View details
psbH Genome 222 NA 0.00 35.4 yes View details
psbB-trnH-GUG Genome 2887 0.0870 0.01 57.5 yes View details
trnH-GUG-psbA Genome 189 0.0370 1.00 65.5 yes View details
rpl32-trnL-UAG Genome 938 0.0098 0.98 58.1 yes View details
psbN Genome 132 0.2143 0.11 66.7 yes View details
petN-psbM Genome 1158 0.0052 0.99 62.8 yes View details
matK-trnK Genome 746 0.0067 1.00 62.5 yes View details
clpP Genome 2089 0.0044 0.98 62.0 yes View details
psaA-ycf3 Genome 696 0.0043 1.00 61.4 yes View details
petA-psbJ Genome 1021 0.0063 0.94 61.4 yes View details
cemA Genome 690 0.0043 1.00 61.2 yes View details
trnC-GCA-petN Genome 719 0.0000 0.98 60.8 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf2_p1 ycf2 GGAACCATATCACATCCCGG ACTGTCTACGGTTCGATTGC 1793 0.500 58.5
ycf2_p2 ycf2 GGAACCATATCACATCCCGG GTTGGGCGCTTTAACCATTC 1226 0.500 58.4
ycf2_p3 ycf2 CGGAACCATATCACATCCCG ACTGTCTACGGTTCGATTGC 1794 0.500 58.3
ycf2_p4 ycf2 CGGAACCATATCACATCCCG GTTGGGCGCTTTAACCATTC 1227 0.500 58.3
ycf2_p5 ycf2 GGAACCATATCACATCCCGG TTCTACCCTTTCCCGGAAGT 1614 0.500 58.2
rpl16_p1 rpl16 TGTTCAATCAAAACAAAACCA AAACCGGCACCTGTTATTGT 1492 0.500 20.0
rpl16_p2 rpl16 TGTTCAATCAAAACAAAACCA AACCGGCACCTGTTATTGTT 1491 0.500 20.0
rpl16_p3 rpl16 TGTTCAATCAAAACAAAACCA ACCGGCACCTGTTATTGTTT 1490 0.500 20.0
rpl16_p4 rpl16 TGTTCAATCAAAACAAAACCA TCCAAAGAAAGAAACCGGCA 1503 0.500 20.0
rpl16_p5 rpl16 TGTTCAATCAAAACAAAACCA AAAGAAAGAAACCGGCACCT 1500 0.500 20.0
rpoA_p1 rpoA TGTAGACCTCCGAAAAAGCG ACGACCTGTGTATCTAGGGA 1252 0.500 50.5
rpoA_p2 rpoA TGTAGACCTCCGAAAAAGCG CACGACCTGTGTATCTAGGG 1253 0.500 50.1
rpoA_p3 rpoA CGAAAAAGCGACGTGTGTAG ACGACCTGTGTATCTAGGGA 1242 0.500 49.5
rpoA_p4 rpoA CGAAAAAGCGACGTGTGTAG CACGACCTGTGTATCTAGGG 1243 0.500 49.2
rpoA_p5 rpoA TGTAGACCTCCGAAAAAGCG CACGACCTGTGTATCTAGGGA 1253 0.500 48.6
psbH_p1 psbH CGCGGTCGAACTACCAAAAT ACAAAGTCAACAGCTCTCAATG 360 0.500 30.0
psbH_p2 psbH CGCGGTCGAACTACCAAAAT ACAAAGTCAACAGCTCTCAA 360 0.500 29.6
psbH_p3 psbH CGCGGTCGAACTACCAAAAT CAAAGTCAACAGCTCTCAATGA 359 0.500 27.9
psbH_p4 psbH CGCGGTCGAACTACCAAAAT AGGGTTGCTGTTTCCATTAT 442 0.500 27.6
psbH_p5 psbH CGCGGTCGAACTACCAAAAT ACAAAGTCAACAGCTCTCAAT 360 0.500 26.4
psbN_p1 psbN CATTGAGAGCTGTTGACTTTGT GAGAACCGCCTAAAGTTCCA 337 0.500 33.7
psbN_p2 psbN TTGAGAGCTGTTGACTTTGT GAGAACCGCCTAAAGTTCCA 335 0.500 33.3
psbN_p3 psbN CATTGAGAGCTGTTGACTTTGT AACCGCCTAAAGTTCCAACT 334 0.500 32.2
psbN_p4 psbN TTGAGAGCTGTTGACTTTGT AACCGCCTAAAGTTCCAACT 332 0.500 31.9
psbN_p5 psbN TCATTGAGAGCTGTTGACTTTG GAGAACCGCCTAAAGTTCCA 338 0.500 31.6
psbB-trnH-GUG_p1 psbB-trnH-GUG CGATACCAAGGCAAACCCAT CGGATGTAGCCAAGTGGATC 2980 0.500 57.1
psbB-trnH-GUG_p2 psbB-trnH-GUG CGATACCAAGGCAAACCCAT TGGATCAAGGCAGTGGATTG 2966 0.500 57.0
psbB-trnH-GUG_p3 psbB-trnH-GUG CGATACCAAGGCAAACCCAT GGATCAAGGCAGTGGATTGT 2965 0.500 57.0
psbB-trnH-GUG_p4 psbB-trnH-GUG CGATACCAAGGCAAACCCAT GTGGATCAAGGCAGTGGATT 2967 0.500 57.0
psbB-trnH-GUG_p5 psbB-trnH-GUG ACACGATACCAAGGCAAACC CGGATGTAGCCAAGTGGATC 2983 0.500 55.2

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
Dystaenia ibukiensis OR231236.1 153487 View on NCBI ↗
Dystaenia takeshimana OR231235.1 147706 View on NCBI ↗