Markers + reference

Ananas

2 species · Bromeliaceae · Poales

Back to catalogue

Species 2
Genome length 160–160 kb
Candidate markers 282
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 282 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA Genome 1062 0.0000 1.00 29.0 yes View details
rpoC1 Genome 2757 0.0011 1.00 56.8 yes View details
psbC Genome 1422 0.0000 1.00 28.9 yes View details
rbcL-accD Genome 741 0.0027 1.00 49.2 yes View details
accD-psaI Genome 986 0.0031 0.99 61.1 yes View details
petA-psbJ Genome 802 0.0075 1.00 63.1 yes View details
rpl14 Genome 369 0.0027 1.00 43.3 yes View details
rrn16-trnI Genome 316 0.0443 1.00 78.3 yes View details
rpl32-trnL Genome 764 0.0052 1.00 62.0 yes View details
trnI-rrn16 Genome 316 0.0443 1.00 78.3 yes View details
psbC-trnS Genome 137 0.0511 1.00 81.4 yes View details
rps19-psbA Genome 116 0.0259 1.00 67.4 no View details
clpP-clpP Genome 876 0.0000 0.98 61.0 yes View details
rps12-clpP Genome 140 0.0143 1.00 60.7 yes View details
atpB-rbcL Genome 798 0.0025 1.00 60.3 yes View details
ndhA-ndhA Genome 1068 0.0009 0.99 60.0 yes View details
ndhC-trnV Genome 1027 0.0019 1.00 59.9 yes View details
ccsA Genome 960 0.0021 1.00 59.9 yes View details
trnW-trnP Genome 147 0.0070 0.97 59.8 yes View details
ycf3-trnS Genome 617 0.0016 1.00 59.7 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TGGGTATTTTTCCTTCAGCA GTGCTTGGGAGTCCTTGAAA 1150 0.500 34.4
psbA_p2 psbA TGGGTATTTTTCCTTCAGCA AATACGTGTGCTTGGGAGTC 1157 0.500 33.8
psbA_p3 psbA TGGGTATTTTTCCTTCAGCAA GTGCTTGGGAGTCCTTGAAA 1150 0.500 33.1
psbA_p4 psbA TTGGGTATTTTTCCTTCAGCA GTGCTTGGGAGTCCTTGAAA 1151 0.500 33.1
psbA_p5 psbA TGGGTATTTTTCCTTCAGCAA AATACGTGTGCTTGGGAGTC 1157 0.500 32.5
rpoC1_p1 rpoC1 AAAACCCGAATTCCAGGCAT TTGCTCGTTCGAGAACTACG 2917–2927 1.000 79.3
rpoC1_p2 rpoC1 AAAAACCCGAATTCCAGGCA TTGCTCGTTCGAGAACTACG 2918–2928 1.000 77.4
rpoC1_p3 rpoC1 GAAAAACCCGAATTCCAGGC TTGCTCGTTCGAGAACTACG 2919–2929 1.000 76.8
rpoC1_p4 rpoC1 AAAACCCGAATTCCAGGCAT GCTCGTTCGAGAACTACGAT 2915–2925 1.000 75.9
rpoC1_p5 rpoC1 AAACCCGAATTCCAGGCATC TTGCTCGTTCGAGAACTACG 2916–2926 1.000 75.6
psbC_p1 psbC TTTCCCAAGAAATCCGTGCA CCGAGCCAGAACAGAAAAGA 1582 1.000 78.5
psbC_p2 psbC GCAGCGGAAGATCCTGAATT CCGAGCCAGAACAGAAAAGA 1565 1.000 76.0
psbC_p3 psbC AGGTATTCGTGCTTGGATGG CCGAGCCAGAACAGAAAAGA 1509 1.000 76.0
psbC_p4 psbC GTTTCCCAAGAAATCCGTGC CCGAGCCAGAACAGAAAAGA 1583 1.000 75.9
psbC_p5 psbC TTCCCAAGAAATCCGTGCAG CCGAGCCAGAACAGAAAAGA 1581 1.000 74.9
psbC-trnS_p1 psbC-trnS GCTGCAGGGTTTGAAAAAGG GGTTGATAGCTCCGGTCTTG 283 1.000 80.5
psbC-trnS_p2 psbC-trnS CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 244 1.000 80.5
psbC-trnS_p3 psbC-trnS GCTGCAGGGTTTGAAAAAGG ATTACCCCTGGGAGAGATGG 309 1.000 79.8
psbC-trnS_p4 psbC-trnS GCTGCAGGGTTTGAAAAAGG GATGGCCGAGTGGTTGATAG 294 1.000 79.8
psbC-trnS_p5 psbC-trnS CCTGTTCTTTCCATGACCCC ATTACCCCTGGGAGAGATGG 270 1.000 79.8
ycf3-trnS_p1 ycf3-trnS TTCTCCTGAAGTTGTCGGAA GTGGTCGATAACGTTGGTGA 831 1.000 66.9
ycf3-trnS_p2 ycf3-trnS TTTCTCCTGAAGTTGTCGGA GTGGTCGATAACGTTGGTGA 832 1.000 66.9
ycf3-trnS_p3 ycf3-trnS TTCTCCTGAAGTTGTCGGAA CCCTCGGTAAACAAAAGCCT 780 1.000 66.7
ycf3-trnS_p4 ycf3-trnS TTTCTCCTGAAGTTGTCGGA CCCTCGGTAAACAAAAGCCT 781 1.000 66.7
ycf3-trnS_p5 ycf3-trnS TTCTCCTGAAGTTGTCGGAA ACGGAAAGAGAGGGATTCGA 801 1.000 66.2
ndhC-trnV_p1 ndhC-trnV CTAACCGGGGCTAAAACTCC AGAAGGTCTACGGTTCGAGT 1164–1165 1.000 78.3
ndhC-trnV_p2 ndhC-trnV CTAACCGGGGCTAAAACTCC GAGCCCAATGCAACAAACAA 1251–1252 1.000 78.0
ndhC-trnV_p3 ndhC-trnV CGGGGCTAAAACTCCTGAAA AGAAGGTCTACGGTTCGAGT 1159–1160 1.000 77.0
ndhC-trnV_p4 ndhC-trnV CGGGGCTAAAACTCCTGAAA GAGCCCAATGCAACAAACAA 1246–1247 1.000 76.7
ndhC-trnV_p5 ndhC-trnV TAACCGGGGCTAAAACTCCT AGAAGGTCTACGGTTCGAGT 1163–1164 1.000 75.8

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
Ananas comosus NC_026220.1 159636 View on NCBI ↗
Ananas comosus var. erectifolius MZ457322.1 159983 View on NCBI ↗