Markers + reference

Erycibe

2 species · Convolvulaceae · Solanales

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Species 2
Genome length 150–156 kb
Candidate markers 283
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 Genome 5748 0.0231 0.98 56.7 no View details
ccsA Genome 942 0.4617 0.68 76.0 yes View details
ndhD Genome 1539 0.4852 0.75 77.9 yes View details
psaC Genome 246 0.5195 0.94 77.0 yes View details
ndhG Genome 531 0.4626 0.40 70.0 yes View details
ndhI Genome 504 0.4421 0.65 74.0 yes View details
ndhA Genome 553 0.4665 0.62 73.4 yes View details
rps15-ycf1 Genome 358 0.4507 0.59 69.2 yes View details
ycf1 Genome 5748 0.3336 0.66 72.1 yes View details
clpP Genome 237 0.0717 1.00 80.7 yes View details
4.5S ribosomal RNA-5S ribosomal RNA Genome 213 0.0704 1.00 79.1 yes View details
5S ribosomal RNA-4.5S ribosomal RNA Genome 213 0.0704 1.00 79.1 yes View details
trnH-GUG-psbA Genome 297 0.3547 0.94 77.1 no View details
ndhD-psaC Genome 88 0.5405 0.84 74.5 yes View details
ndhF-rpl32 Genome 724 0.4251 0.62 74.2 yes View details
ndhH Genome 1182 0.4470 0.59 73.6 yes View details
rpl32-trnL-UAG Genome 1018 0.4262 0.53 72.8 yes View details
ndhH Genome 1182 0.0000 1.00 29.0 no 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
clpP_p1 clpP CACGTATTTGAGCGAAATCCA CAATGCCCAAAAGATGCCTG 406 1.000 67.1
clpP_p2 clpP CACGTATTTGAGCGAAATCCA AGATGCCTGTACGGTTGTTC 395 1.000 66.6
clpP_p3 clpP CACGTATTTGAGCGAAATCCA CCAAAAGATGCCTGTACGGT 400 1.000 65.9
clpP_p4 clpP CACGTATTTGAGCGAAATCCA GATGCCTGTACGGTTGTTCA 394 1.000 65.8
clpP_p5 clpP ACAATCCCTACAAGATCAACCC CAATGCCCAAAAGATGCCTG 378 1.000 65.6
4.5S ribosomal RNA-5S ribosomal RNA_p1 4.5S ribosomal RNA-5S ribosomal RNA AGGCATCCTAACAGACCAGT AGTATCGTCACCGCAGTAGA 324–329 1.000 83.1
4.5S ribosomal RNA-5S ribosomal RNA_p2 4.5S ribosomal RNA-5S ribosomal RNA AGGCATCCTAACAGACCAGT TATCGTCACCGCAGTAGAGT 322–327 1.000 83.1
4.5S ribosomal RNA-5S ribosomal RNA_p3 4.5S ribosomal RNA-5S ribosomal RNA TGAGGCATCCTAACAGACCA TATCGTCACCGCAGTAGAGT 324–329 1.000 83.0
4.5S ribosomal RNA-5S ribosomal RNA_p4 4.5S ribosomal RNA-5S ribosomal RNA GTCAAGTGGAAGTGCAGTGA AGTATCGTCACCGCAGTAGA 356–361 1.000 82.7
4.5S ribosomal RNA-5S ribosomal RNA_p5 4.5S ribosomal RNA-5S ribosomal RNA GTCAAGTGGAAGTGCAGTGA TATCGTCACCGCAGTAGAGT 354–359 1.000 82.7
ndhF-rpl32_p1 ndhF-rpl32 GCACCGACAAATAATAGCGC TAAGAGCGAGGCGAGTTCTA 1720 0.500 59.6
ndhF-rpl32_p2 ndhF-rpl32 GCACCGACAAATAATAGCGC GAAGAGATAAGAGCGAGGCG 1727 0.500 59.5
ndhF-rpl32_p3 ndhF-rpl32 ATCCTAACATGGCAGCACTG TAAGAGCGAGGCGAGTTCTA 1422 0.500 59.3
ndhF-rpl32_p4 ndhF-rpl32 ATCCTAACATGGCAGCACTG GAAGAGATAAGAGCGAGGCG 1429 0.500 59.3
ndhF-rpl32_p5 ndhF-rpl32 AGAAGTCAGTGGGTCGATCA TAAGAGCGAGGCGAGTTCTA 1292 0.500 59.1
rpl32-trnL-UAG_p1 rpl32-trnL-UAG AGGAAGAGCTTTTGGACAGC CCCTGGGTAAAAATAGCGCT 1669 0.500 58.8
rpl32-trnL-UAG_p2 rpl32-trnL-UAG AGGAAAATCCCTTTCGACCG CCCTGGGTAAAAATAGCGCT 1631 0.500 58.7
rpl32-trnL-UAG_p3 rpl32-trnL-UAG AGGAAGAGCTTTTGGACAGC TCCTAAGAGCAGCGTGTCTA 1168 0.500 58.2
rpl32-trnL-UAG_p4 rpl32-trnL-UAG AGGAAGAGCTTTTGGACAGC GAGAAGAGTCTAGCCCCCAA 1316 0.500 58.2
rpl32-trnL-UAG_p5 rpl32-trnL-UAG AGGAAAATCCCTTTCGACCG TCCTAAGAGCAGCGTGTCTA 1130 0.500 58.1
ccsA_p1 ccsA TAGACACGCTGCTCTTAGGA TGCTGCAACCTCTTGGATTT 1170 0.500 59.0
ccsA_p2 ccsA TTGGGGGCTAGACTCTTCTC TGCTGCAACCTCTTGGATTT 1022 0.500 58.9
ccsA_p3 ccsA TAGACACGCTGCTCTTAGGA GGTATGAGCGGTTTTGTTGC 1721 0.500 58.8
ccsA_p4 ccsA TAGACACGCTGCTCTTAGGA GTATGAGCGGTTTTGTTGCC 1720 0.500 58.8
ccsA_p5 ccsA TTGGGGGCTAGACTCTTCTC GTATGAGCGGTTTTGTTGCC 1572 0.500 58.8
ndhD_p1 ndhD AAATCCAAGAGGTTGCAGCA GCTATTGGGCTGGCTATTGT 2442 0.500 59.9
ndhD_p2 ndhD AAATCCAAGAGGTTGCAGCA CAAATTGCTTCCGCTCCAAG 1988 0.500 59.9
ndhD_p3 ndhD AAATCCAAGAGGTTGCAGCA AGATGTGAATCCGCTTGTCC 1943 0.500 59.8
ndhD_p4 ndhD AAATCCAAGAGGTTGCAGCA AAATTGCTTCCGCTCCAAGA 1987 0.500 59.3
ndhD_p5 ndhD AAATCCAAGAGGTTGCAGCA AATTGCTTCCGCTCCAAGAA 1986 0.500 59.3

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
Erycibe henryi LC729544.1 155683 View on NCBI ↗
Erycibe obtusifolia NC_060792.1 150333 View on NCBI ↗