Markers + reference

Pseudalcantarea

2 species · Bromeliaceae · Poales

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Species 2
Genome length 144–144 kb
Candidate markers 265
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhG-ndhI SSC 387 0.0078 1.00 44.4 yes View details
trnI-GAU-rrn16S IRb 316 0.0443 1.00 78.3 yes View details
ycf2 LSC 6843 0.0020 1.00 53.7 yes View details
trnS-GCU-trnG-UCC LSC 1013 0.0041 0.96 65.2 yes View details
ndhC-trnV-UAC LSC 1041 0.0038 1.00 61.0 yes View details
psaJ-rpl33 LSC 524 0.0095 1.00 62.7 yes View details
rpl22 LSC 387 0.0000 1.00 22.9 yes View details
rrn16S-trnI-GAU IRa 316 0.0443 1.00 78.3 yes View details
rpl22-ndhB LSC 51 0.2292 0.94 92.1 yes View details
ycf1-ndhF SSC 5 0.0000 1.00 71.2 no View details
rps12-rps7 IRb 58 0.0172 1.00 62.4 yes View details
rps7-rps12 IRa 58 0.0172 1.00 62.4 yes View details
rpl16 LSC 1490 0.0021 0.98 61.9 yes View details
ycf4-cemA LSC 851 0.0024 0.98 61.7 yes View details
rpoB-trnC-GCA LSC 1372 0.0015 0.98 61.1 yes View details
atpB-rbcL LSC 776 0.0026 0.99 61.1 yes View details
ndhF-rpl32 SSC 998 0.0030 1.00 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhF-rpl32_p1 ndhF-rpl32 TTGTTGCTGTCGGAATAAGT GGTGGAAACCGATTTCGCTA 1218 1.000 56.6
ndhF-rpl32_p2 ndhF-rpl32 TGTTGCTGTCGGAATAAGTAGA GGTGGAAACCGATTTCGCTA 1217 1.000 55.9
ndhF-rpl32_p3 ndhF-rpl32 CTGGAAGTGGAAGAAAAGGT GGTGGAAACCGATTTCGCTA 1170 1.000 55.6
ndhF-rpl32_p4 ndhF-rpl32 TTTGTTGCTGTCGGAATAAGT GGTGGAAACCGATTTCGCTA 1219 1.000 55.0
ndhF-rpl32_p5 ndhF-rpl32 TGCTGTCGGAATAAGTAGAAGTC GGTGGAAACCGATTTCGCTA 1214 1.000 54.2
ndhG-ndhI_p1 ndhG-ndhI TCTGGTTTGACCTTGCAGTC GGGGTCGAATCCACTTTGAA 1164 1.000 78.7
ndhG-ndhI_p2 ndhG-ndhI CCCCAGACCCCCTAATACAA GGGGTCGAATCCACTTTGAA 845 1.000 78.3
ndhG-ndhI_p3 ndhG-ndhI TGTGCGGCAGCTACAAAATA GGGGTCGAATCCACTTTGAA 955 1.000 77.6
ndhG-ndhI_p4 ndhG-ndhI TCTGGTTTGACCTTGCAGTC ATCACATCAGAGCGTTTCCG 1183 1.000 77.4
ndhG-ndhI_p5 ndhG-ndhI TCAAAGTGACCCCATCTCCA GGGGTCGAATCCACTTTGAA 1074 1.000 76.9
trnI-GAU_p1 trnI-GAU TCTATTCTTTTCCCTGGCGC GGGGTTTTTCTCGCTTTTGG 1091 1.000 78.5
trnI-GAU_p2 trnI-GAU GCCAAGTGGAGTATGCATGA GGGGTTTTTCTCGCTTTTGG 1128 1.000 78.5
trnI-GAU_p3 trnI-GAU AGCCAAGTGGAGTATGCATG GGGGTTTTTCTCGCTTTTGG 1129 1.000 78.4
trnI-GAU_p4 trnI-GAU TCTATTCTTTTCCCTGGCGC TTCTCGCTTTTGGCATAGCA 1084 1.000 78.3
trnI-GAU_p5 trnI-GAU GCCAAGTGGAGTATGCATGA TTCTCGCTTTTGGCATAGCA 1121 1.000 78.2
trnI-GAU-rrn16S_p1 trnI-GAU-rrn16S GGCACAACGACGCAATTATC CAAGGTAGCCGTACTGGAAG 410 1.000 78.9
trnI-GAU-rrn16S_p2 trnI-GAU-rrn16S CTATCCATGTGGCTGAGAGC CAAGGTAGCCGTACTGGAAG 442 1.000 78.8
trnI-GAU-rrn16S_p3 trnI-GAU-rrn16S CGCTGATGAGCACATTGAAC CAAGGTAGCCGTACTGGAAG 461 1.000 78.7
trnI-GAU-rrn16S_p4 trnI-GAU-rrn16S CTATCCATGTGGCTGAGAGC AGTGACTGGAGTGAAGTCGT 464 1.000 78.6
trnI-GAU-rrn16S_p5 trnI-GAU-rrn16S CGCTGATGAGCACATTGAAC AGTGACTGGAGTGAAGTCGT 483 1.000 78.5
rps12-rps7_p1 rps12-rps7 CTGTGGAAAGCCGTATTCGA TTCTTCTGCAGTACCTCGAC 190 1.000 72.3
rps12-rps7_p2 rps12-rps7 TCTGTGGAAAGCCGTATTCG TTCTTCTGCAGTACCTCGAC 191 1.000 72.3
rps12-rps7_p3 rps12-rps7 CTGTGGAAAGCCGTATTCGA TCTTCTGCAGTACCTCGACG 189 1.000 70.8
rps12-rps7_p4 rps12-rps7 TCTGTGGAAAGCCGTATTCG TCTTCTGCAGTACCTCGACG 190 1.000 70.8
rps12-rps7_p5 rps12-rps7 CTGTGGAAAGCCGTATTCGA TTTCTTCTGCAGTACCTCGAC 191 1.000 70.0
ycf2_p1 ycf2 CCTGTGACTCGATTGGTGAA AATTGGCTGAATCCCGTGAA 283 1.000 75.5
ycf2_p2 ycf2 CCTGTGACTCGATTGGTGAA ATTGGCTGAATCCCGTGAAA 282 1.000 75.5
ycf2_p3 ycf2 CCTGTGACTCGATTGGTGAA AGACAATTGGCTGAATCCCG 287 1.000 75.2
ycf2_p4 ycf2 ACCTGTGACTCGATTGGTGA AATTGGCTGAATCCCGTGAA 284 1.000 73.8
ycf2_p5 ycf2 ACCTGTGACTCGATTGGTGA ATTGGCTGAATCCCGTGAAA 283 1.000 73.8

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
Pseudalcantarea macropetala NC_065169.1 143799 View on NCBI ↗
Pseudalcantarea viridiflora NC_065170.1 144169 View on NCBI ↗