Markers + reference

Scytosiphon

2 species · Scytosiphonaceae · Ectocarpales

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Species 2
Genome length 134–134 kb
Candidate markers 336
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 336 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rns-psbA LSC 1058 0.0378 1.00 80.6 yes View details
psbA-ccsA LSC 690 0.0101 1.00 64.6 yes View details
rpl20 LSC 363 0.0083 1.00 45.4 yes View details
dnaK LSC 1896 0.0032 1.00 44.7 yes View details
chlL LSC 870 0.0023 1.00 49.1 yes View details
trnC-psbY LSC 759 0.0105 1.00 55.2 yes View details
rps17-rpl29 SSC 55 0.0364 1.00 73.4 yes View details
psbH-ftsH SSC 134 0.0299 1.00 69.7 yes View details
trnI-rns IRa 111 0.0180 1.00 62.9 yes View details
ycf47-rpl20 LSC 649 0.0062 1.00 62.3 yes View details
chlN LSC 1368 0.0037 1.00 60.9 yes View details
chlI-psaM LSC 73 0.0137 1.00 60.4 yes View details
rpl4 SSC 771 0.0026 1.00 60.2 yes View details
petA LSC 948 0.0021 1.00 60.0 yes View details
ycf46 LSC 1476 0.0020 1.00 59.9 yes View details
atpA LSC 1506 0.0020 1.00 59.9 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
psbH-ftsH_p1 psbH-ftsH AGATTGGCAGAGCTTAGGGA AGCTGAAATACAACCAGTGGT 184 1.000 68.7
psbH-ftsH_p2 psbH-ftsH AGATTGGCAGAGCTTAGGGA GCTGAAATACAACCAGTGGT 183 1.000 64.4
psbH-ftsH_p3 psbH-ftsH GATTGGCAGAGCTTAGGGAA AGCTGAAATACAACCAGTGGT 183 1.000 63.9
psbH-ftsH_p4 psbH-ftsH AGATTGGCAGAGCTTAGGGA AAGCTGAAATACAACCAGTGGT 185 1.000 63.5
psbH-ftsH_p5 psbH-ftsH AGATTGGCAGAGCTTAGGGA AGCTGAAATACAACCAGTGG 184 1.000 62.0
rps17-rpl29_p1 rps17-rpl29 TCAACAGCAACTACAACGCT CGTTTACGACGTGGAACAAA 228 1.000 72.3
rps17-rpl29_p2 rps17-rpl29 TCAACAGCAACTACAACGCT CGTTTACGACGTGGAACAAAA 228 1.000 69.9
rps17-rpl29_p3 rps17-rpl29 TCAACAGCAACTACAACGCT ACGACGTGGAACAAAACAATC 223 1.000 69.7
rps17-rpl29_p4 rps17-rpl29 TCAACAGCAACTACAACGCT ACGACGTGGAACAAAACAAT 223 1.000 68.3
rps17-rpl29_p5 rps17-rpl29 TCAACAGCAACTACAACGCT CGACGTGGAACAAAACAATCT 222 1.000 67.5
rpl4_p1 rpl4 AGCCTAGGGTCTACTAAGAATGT AAGAAAGTGAAGAGACCGCG 905 1.000 53.3
rpl4_p2 rpl4 AGCCTAGGGTCTACTAAGAATGT GAAAGTGAAGAGACCGCGAA 903 1.000 53.2
rpl4_p3 rpl4 AGCCTAGGGTCTACTAAGAATGT AAGTGAAGAGACCGCGAATG 901 1.000 52.7
rpl4_p4 rpl4 AGCCTAGGGTCTACTAAGAATGT AAAGTGAAGAGACCGCGAAT 902 1.000 51.4
rpl4_p5 rpl4 GCCTAGGGTCTACTAAGAATGT AAGAAAGTGAAGAGACCGCG 904 1.000 49.9
trnI-rns_p1 trnI-rns GCCATCCTGGATTTGAACCA GACTGGGGTGAAGTCGTAAC 240–249 1.000 78.9
trnI-rns_p2 trnI-rns GCCATCCTGGATTTGAACCA GTAACAAGGTAGCCGTACGG 225–234 1.000 78.8
trnI-rns_p3 trnI-rns GCCATCCTGGATTTGAACCA AACCTTTTTGGAGAGAGGCG 277–286 1.000 78.6
trnI-rns_p4 trnI-rns AATGGGCCATCCTGGATTTG GACTGGGGTGAAGTCGTAAC 245–254 1.000 78.4
trnI-rns_p5 trnI-rns CAAATGGGCCATCCTGGATT GACTGGGGTGAAGTCGTAAC 247–256 1.000 78.4
rns-psbA_p1 rns-psbA CCGTACGACTTGCATGTGTA GTTGCGATTTCTGCACCTTC 1152–1166 1.000 82.5
rns-psbA_p2 rns-psbA CCGTACGACTTGCATGTGTA TTGCGATTTCTGCACCTTCT 1151–1165 1.000 81.9
rns-psbA_p3 rns-psbA GCATGTGTAAAGCATACCGC GTTGCGATTTCTGCACCTTC 1141–1155 1.000 81.8
rns-psbA_p4 rns-psbA CCGTACGACTTGCATGTGTA TGGAAGTAATGCACGAACGT 1220–1234 1.000 81.3
rns-psbA_p5 rns-psbA GCATGTGTAAAGCATACCGC TTGCGATTTCTGCACCTTCT 1140–1154 1.000 81.2
psbA-ccsA_p1 psbA-ccsA AGCAAATGTTCCCCAGTCTC GGCTGCAGTACAAAGAAAACA 858–859 1.000 65.3
psbA-ccsA_p2 psbA-ccsA GCAAATGTTCCCCAGTCTCT GGCTGCAGTACAAAGAAAACA 857–858 1.000 65.3
psbA-ccsA_p3 psbA-ccsA AGCAAATGTTCCCCAGTCTC AGGCTGCAGTACAAAGAAAAC 859–860 1.000 63.1
psbA-ccsA_p4 psbA-ccsA GCAAATGTTCCCCAGTCTCT AGGCTGCAGTACAAAGAAAAC 858–859 1.000 63.1
psbA-ccsA_p5 psbA-ccsA GCAAATGTTCCCCAGTCTCT CCAATAGGCTGCAGTACAAAG 863–864 1.000 62.6

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
Scytosiphon lomentaria NC_057081.1 134485 View on NCBI ↗
Scytosiphon promiscuus NC_046447.1 134358 View on NCBI ↗