Markers + reference

Ribes

15 species · Grossulariaceae · Saxifragales

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Species 15
Genome length 157–158 kb
Candidate markers 268
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1626 0.0230 0.97 67.6 yes View details
petN-psbM LSC 1188 0.0163 1.00 60.4 yes View details
trnT-GGU-psbD LSC 1256 0.0172 1.00 65.3 yes View details
psbZ-trnG-UCC LSC 567 0.0224 0.98 66.5 yes View details
ycf3-trnS-GGA LSC 835 0.0187 1.00 66.9 yes View details
trnT-UGU-trnL-UAA LSC 1124 0.0148 0.94 60.3 yes View details
accD-psaI LSC 679 0.0186 1.00 62.3 yes View details
ycf1 SSC 1209 0.0046 1.00 39.0 no View details
ndhF-rpl32 SSC 1122 0.0200 0.98 64.3 yes View details
rpl32-trnL-UAG SSC 884 0.0265 0.99 68.5 yes View details
ccsA-ndhD SSC 227 0.0315 1.00 52.2 yes View details
ycf1 SSC 5499 0.0124 1.00 51.0 yes View details
ndhC-trnV-UAC LSC 891 0.0139 1.00 72.8 yes View details
trnS-GCU-trnG-GCC LSC 880 0.0189 0.99 65.5 yes View details
psbM-trnD-GUC LSC 1156 0.0171 1.00 65.3 yes View details
atpH-atpI LSC 1111 0.0161 0.99 64.7 yes View details
trnK-UUU-rps16 LSC 847 0.0186 0.97 64.3 yes View details
trnF-GAA-ndhJ LSC 670 0.0179 1.00 64.1 yes View details
trnH-GUG-psbA LSC 349 0.0233 1.00 63.8 yes View details
ycf4-cemA LSC 593 0.0114 1.00 61.1 yes View details
psbE-petL LSC 1308 0.0132 0.99 57.8 yes View details
rps8-rpl14 LSC 148 0.0274 1.00 57.5 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAAGCTCCATCTACAAATGG 395–419 0.867 49.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAAGCTCCATCTACAAATGG 409–433 0.867 48.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GAAGCTCCATCTACAAATGG 408–432 0.867 48.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GAAGCTCCATCTACAAATGG 410–434 0.867 48.9
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC GAAGCTCCATCTACAAATGG 424–448 0.867 45.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAAAGGGTATGTTGCTGCCA 1594–1672 0.933 84.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGGTATGTTGCTGCCA 1593–1671 0.933 84.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AAAAGGGTATGTTGCTGCCA 1546–1624 0.933 84.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC AAAAGGGTATGTTGCTGCCA 1547–1625 0.933 84.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT AAAAGGGTATGTTGCTGCCA 1549–1627 0.933 84.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1281–1710 1.000 89.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1292–1721 1.000 88.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1302–1731 1.000 86.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1303–1732 1.000 86.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 1304–1733 1.000 84.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GGACCCCTTAACTATTAAAGGGG 721–1006 1.000 65.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GGACCCCTTAACTATTAAAGGGG 720–1005 1.000 65.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA GGACCCCTTAACTATTAAAGGGG 775–1060 1.000 63.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGCAATCCGACGCTTTAGTC GGACCCCTTAACTATTAAAGGGG 723–1008 1.000 62.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CGACGCTTTAGTCCACTCAG GGACCCCTTAACTATTAAAGGGG 716–1001 1.000 62.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTGCAACTTTAGCTGCAGC 1175–1206 1.000 87.4
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TTTGCAACTTTAGCTGCAGC 1176–1207 1.000 86.2
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TTTGCAACTTTAGCTGCAGC 1190–1221 1.000 85.9
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TTTGCAACTTTAGCTGCAGC 1185–1216 1.000 85.5
atpH-atpI_p5 atpH-atpI ATCCAGCAGCAATAACGGAA TTTGCAACTTTAGCTGCAGC 1186–1217 1.000 84.3
petN-psbM_p1 petN-psbM GCGAGTCTCTGAATGCTTGA AGGATCCTGCCCCTCTTATC 2260–2535 1.000 88.0
petN-psbM_p2 petN-psbM GCGAGTCTCTGAATGCTTGA CCGTCCTTTTGTCCACTTCA 2052–2338 1.000 87.9
petN-psbM_p3 petN-psbM TCCAAGGGTGTTACTGCCTA AGGATCCTGCCCCTCTTATC 1950–2223 1.000 87.8
petN-psbM_p4 petN-psbM TCCAAGGGTGTTACTGCCTA CCGTCCTTTTGTCCACTTCA 1742–2026 1.000 87.7
petN-psbM_p5 petN-psbM GCGAGTCTCTGAATGCTTGA ACGGAAGGCGGTAGGTTATA 1952–2238 1.000 87.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Ribes alpinum PP657412.1 157351 View on NCBI ↗
Ribes fasciculatum PP078696.1 157536 View on NCBI ↗
Ribes fasciculatum var. chinense MH191388.1 157298 View on NCBI ↗
Ribes glaciale NC_062156.1 157848 View on NCBI ↗
Ribes meyeri PQ124743.1 157919 View on NCBI ↗
Ribes nevadense MN496075.1 157715 View on NCBI ↗
Ribes nigrum NC_080517.1 157450 View on NCBI ↗
Ribes odoratum PQ124744.1 157143 View on NCBI ↗
Ribes petraeum PP203133.1 157449 View on NCBI ↗
Ribes roezlii MN496076.1 157781 View on NCBI ↗
Ribes rubrum NC_080516.1 157802 View on NCBI ↗
Ribes rubrum var. alba OP888486.1 157802 View on NCBI ↗
Ribes stenocarpum PQ124745.1 157396 View on NCBI ↗
Ribes tenue PP861178.1 157316 View on NCBI ↗
Ribes uva-crispa NC_080515.1 157659 View on NCBI ↗