Markers + reference

Bangia

2 species · Bangiaceae · Bangiales

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Species 2
Genome length 194–197 kb
Candidate markers 495
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 10 remaining regions by MarkerSeek score (out of 495 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rne Genome 1536 0.2090 1.00 78.7 yes View details
orf121 Genome 366 0.3443 1.00 73.9 yes View details
orf745 Genome 2145 0.3565 0.98 78.9 yes View details
orf286 Genome 861 0.3159 1.00 78.8 yes View details
dnaB Genome 1710 0.2788 1.00 78.7 yes View details
orf382b Genome 825 0.2937 1.00 79.0 yes View details
ntcA Genome 603 0.2604 1.00 78.8 yes View details
syfB Genome 2097 0.2865 1.00 78.1 yes View details
tatC Genome 780 0.1824 0.98 81.1 yes View details
psaA Genome 2259 0.1231 1.00 80.8 yes View details
ycf37 Genome 537 0.3055 0.98 79.5 yes View details
chlN Genome 1326 0.1761 1.00 79.3 yes View details
rps2 Genome 726 0.1662 0.99 79.3 yes View details
rps1-syfB Genome 540 0.1714 0.98 79.3 yes View details
fabH Genome 981 0.1781 1.00 79.2 yes View details
atpB Genome 1428 0.1370 1.00 79.2 yes View details
rbcR Genome 954 0.1426 1.00 79.1 yes View details
sufB Genome 1464 0.1557 1.00 79.1 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
chlN_p1 chlN GCTAGGCCAGAAGGAGTAGT TTGGCGGATTAGTTGGTGAG 2143 0.500 57.4
chlN_p2 chlN TGCTAGGCCAGAAGGAGTAG TTGGCGGATTAGTTGGTGAG 2144 0.500 57.4
chlN_p3 chlN TTGCTAGGCCAGAAGGAGTA TTGGCGGATTAGTTGGTGAG 2145 0.500 57.2
chlN_p4 chlN GATTGCTAGGCCAGAAGGAG TTGGCGGATTAGTTGGTGAG 2147 0.500 57.1
chlN_p5 chlN GCTAGGCCAGAAGGAGTAGT AAGTGGCGCTAGAGCAATTT 1660 0.500 56.9
ycf37_p1 ycf37 TTTGAGCCTTCCAGTGTTCC ACGGGATATAGCGCAGTTTG 812 0.500 58.8
ycf37_p2 ycf37 TTTGAGCCTTCCAGTGTTCC ACAGTAGGCGAGAGTTCTGA 1361 0.500 58.2
ycf37_p3 ycf37 GCGTCCACTAGGTGTTTTCA ACGGGATATAGCGCAGTTTG 870 0.500 57.9
ycf37_p4 ycf37 TTTGAGCCTTCCAGTGTTCC GGGATATAGCGCAGTTTGGT 810 0.500 57.8
ycf37_p5 ycf37 AGCGTCCACTAGGTGTTTTC ACGGGATATAGCGCAGTTTG 871 0.500 57.6
fabH_p1 fabH AGTCAACTCAAGCCCGAAAG ACAGCCCCAAGGATAAGACT 1584 0.500 58.9
fabH_p2 fabH GCTGCAGGTTCACGAAAAAG ACAGCCCCAAGGATAAGACT 1904 0.500 57.9
fabH_p3 fabH AACCTTGTCAGAACCGGAAG ACAGCCCCAAGGATAAGACT 1545 0.500 57.7
fabH_p4 fabH AGTCAACTCAAGCCCGAAAG ACTCGATAAGGACGGTGTCA 1555 0.500 57.7
fabH_p5 fabH TTTACGCGATTATGGCTGGT ACAGCCCCAAGGATAAGACT 1875 0.500 57.2
rbcR_p1 rbcR TTTGACTTCTGCCCGAAACA CCAGTTAGTACGGACTTGGC 2311 0.500 59.6
rbcR_p2 rbcR TTTGACTTCTGCCCGAAACA ATGCAGCTGCTAAAACTGGT 1938 0.500 59.0
rbcR_p3 rbcR CTTCTGCCCGAAACACATCT CCAGTTAGTACGGACTTGGC 2306 0.500 58.5
rbcR_p4 rbcR CTTCTGCCCGAAACACATCT ATGCAGCTGCTAAAACTGGT 1933 0.500 57.8
rbcR_p5 rbcR CCCTGAGAGCTAGGCCAATA CCAGTTAGTACGGACTTGGC 2190 0.500 57.7
rne_p1 rne GGAGCTACAGTACAGGCAAC TTCCAAGCTGAGCACAACAT 2780 0.500 59.8
rne_p2 rne GGAGCTACAGTACAGGCAAC GCCTGTAGTTGGTATCTGGC 2502 0.500 59.5
rne_p3 rne GGAGCTACAGTACAGGCAAC TCCGGTGAATCCTTACCAGT 2303 0.500 59.5
rne_p4 rne GGAGCTACAGTACAGGCAAC CCCAATTGGCCAAGGTAGTT 2853 0.500 59.4
rne_p5 rne GGAGCTACAGTACAGGCAAC CGTGAAACAAGCGAAAACGA 2663 0.500 59.3
orf121_p1 orf121 TATCCCTAAGACACGCAGCA ATTCCTGAACAGCCACCTTG 1605 0.500 55.2
orf121_p2 orf121 TATCCCTAAGACACGCAGCA CATTCCTGAACAGCCACCTT 1606 0.500 55.2
orf121_p3 orf121 TCCCTAAGACACGCAGCATA ATTCCTGAACAGCCACCTTG 1603 0.500 55.2
orf121_p4 orf121 TCCCTAAGACACGCAGCATA CATTCCTGAACAGCCACCTT 1604 0.500 55.2
orf121_p5 orf121 CCCTAAGACACGCAGCATAT ATTCCTGAACAGCCACCTTG 1602 0.500 55.1

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
Bangia atropurpurea NC_062392.1 194293 View on NCBI ↗
Bangia fuscopurpurea NC_084208.1 196746 View on NCBI ↗