Markers + reference

Aphanochaete

2 species · Aphanochaetaceae · Chaetophorales

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Species 2
Genome length 150–158 kb
Candidate markers 205
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 205 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC1 Genome 6591 0.4116 0.81 73.5 yes View details
trnH(gug)-trnV(uac) Genome 343 0.4839 0.81 75.8 yes View details
trnM(cau)-trnfM(cau) Genome 1345 0.4116 0.76 78.2 yes View details
ftsH Genome 10953 0.2934 0.94 77.0 yes View details
petB-psbI Genome 662 0.3415 0.93 83.4 yes View details
petL-rpoC2 Genome 656 0.3377 0.94 83.3 yes View details
psbK-psbL Genome 735 0.3318 0.89 83.1 yes View details
chlN Genome 1518 0.1695 0.96 83.0 yes View details
rpoBb-rpl32 Genome 603 0.3261 0.92 83.0 yes View details
rpoA Genome 1656 0.2682 0.94 83.0 yes View details
rbcL-rps14 Genome 572 0.3792 0.89 82.7 yes View details
petD-rps4 Genome 1493 0.3363 0.90 82.6 yes View details
psbB-psbT Genome 865 0.3573 0.92 82.6 yes View details
trnS(gga)-rrs Genome 608 0.3390 0.97 82.3 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
petD-rps4_p1 petD-rps4 TTCTCCAATTGCTGCTGGTT ATTGTTCGTGATATGGCCCC 1763 0.500 59.8
petD-rps4_p2 petD-rps4 ACAGTTGTTGCGATTGGTCT ATTGTTCGTGATATGGCCCC 1966 0.500 59.6
petD-rps4_p3 petD-rps4 TTCTCCAATTGCTGCTGGTT ACGTCGTAGTGTAGGTTTGC 1743 0.500 59.5
petD-rps4_p4 petD-rps4 ACAGTTGTTGCGATTGGTCT ACGTCGTAGTGTAGGTTTGC 1946 0.500 59.3
petD-rps4_p5 petD-rps4 CTGTTAAAAGCCCTGCTGGA ATTGTTCGTGATATGGCCCC 1902 0.500 59.1
rpoC1_p1 rpoC1 GCTATTTGCGTTTTATGCCGA GAACGCATTTTTGGCCCTAC 725 0.500 51.4
rpoC1_p2 rpoC1 GCTATTTGCGTTTTATGCCGA AATGCCAATACCTTGCACCA 782 0.500 51.0
rpoC1_p3 rpoC1 GCTATTTGCGTTTTATGCCGA AACGCGTCCAGATTTGATGA 899 0.500 50.8
rpoC1_p4 rpoC1 GCTATTTGCGTTTTATGCCGA ACGCGTCCAGATTTGATGAA 898 0.500 50.8
rpoC1_p5 rpoC1 GCTATTTGCGTTTTATGCCGA TCTGTGAACGCATTTTTGGC 730 0.500 50.5
trnH(gug)-trnV(uac)_p1 trnH(gug)-trnV(uac) ACCCATTGCCTTACCACTTG CCAACTGAGTTATGGGCCT 393 0.500 41.0
trnH(gug)-trnV(uac)_p2 trnH(gug)-trnV(uac) CAACCCATTGCCTTACCACT CCAACTGAGTTATGGGCCT 395 0.500 41.0
trnH(gug)-trnV(uac)_p3 trnH(gug)-trnV(uac) CATGATGGAACCACAACCCA CCAACTGAGTTATGGGCCT 408 0.500 41.0
trnH(gug)-trnV(uac)_p4 trnH(gug)-trnV(uac) TTGCCTTACCACTTGGCTAC CCAACTGAGTTATGGGCCT 388 0.500 40.1
trnH(gug)-trnV(uac)_p5 trnH(gug)-trnV(uac) ACAACCCATTGCCTTACCAC CCAACTGAGTTATGGGCCT 396 0.500 38.7
trnM(cau)-trnfM(cau)_p1 trnM(cau)-trnfM(cau) CGGTTTAGGCAATCGACTCA ATATCGCTGGGTAGAGCAGT 1481 0.500 59.9
trnM(cau)-trnfM(cau)_p2 trnM(cau)-trnfM(cau) CGGTTTAGGCAATCGACTCA AGCCTGCTTAACTCAATCGG 1714 0.500 59.7
trnM(cau)-trnfM(cau)_p3 trnM(cau)-trnfM(cau) CGGTTTAGGCAATCGACTCA TTTCCAAAACCGGATGTCGT 2026 0.500 59.7
trnM(cau)-trnfM(cau)_p4 trnM(cau)-trnfM(cau) CGGTTTAGGCAATCGACTCA TAGAACGCCGGTTTCCAAAA 2037 0.500 59.7
trnM(cau)-trnfM(cau)_p5 trnM(cau)-trnfM(cau) ACCCATTGCCTTACCACTTG ATATCGCTGGGTAGAGCAGT 2119 0.500 59.4
trnS(gga)-rrs_p1 trnS(gga)-rrs TCGAACCCTCGGTAGTTCTT CTCTCAGTGTCAGTAACGGC 1419 0.500 59.2
trnS(gga)-rrs_p2 trnS(gga)-rrs TTCGAACCCTCGGTAGTTCT CTCTCAGTGTCAGTAACGGC 1420 0.500 59.2
trnS(gga)-rrs_p3 trnS(gga)-rrs TTCAAAGCGAGCTTCCCATT CTCTCAGTGTCAGTAACGGC 2063 0.500 59.1
trnS(gga)-rrs_p4 trnS(gga)-rrs TTTCAAAGCGAGCTTCCCAT CTCTCAGTGTCAGTAACGGC 2064 0.500 59.1
trnS(gga)-rrs_p5 trnS(gga)-rrs TCGAACCCTCGGTAGTTCTT TACGTCGTCTGACTTGCATG 749 0.500 59.1
psbK-psbL_p1 psbK-psbL CGGAGGCTTATGCTCCTTTT TGGGCGTGAAACTACTTCTG 902 0.500 58.3
psbK-psbL_p2 psbK-psbL CGGAGGCTTATGCTCCTTTT GGCGTGAAACTACTTCTGCT 900 0.500 58.0
psbK-psbL_p3 psbK-psbL CGGAGGCTTATGCTCCTTTT TGTTTGTTTGGATTTGGGCG 916 0.500 57.8
psbK-psbL_p4 psbK-psbL CGGAGGCTTATGCTCCTTTT TTTGTTTGGATTTGGGCGTG 914 0.500 57.8
psbK-psbL_p5 psbK-psbL CGGAGGCTTATGCTCCTTTT GTTTGTTTGGATTTGGGCGT 915 0.500 57.8

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
Aphanochaete confervicola NC_047441.1 157920 View on NCBI ↗
Aphanochaete elegans NC_047440.1 150157 View on NCBI ↗