Markers + reference

Caloglossa

3 species · Delesseriaceae · Ceramiales

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Species 3
Genome length 165–166 kb
Candidate markers 463
Primer pairs 120

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 463 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbY-rpl32 Genome 253 0.3981 0.85 72.2 yes View details
dsbD Genome 756 0.3098 0.98 81.8 yes View details
ycf21 Genome 546 0.2692 1.00 77.6 yes View details
ycf23 Genome 837 0.2942 0.97 82.6 yes View details
ycf80 Genome 1419 0.2819 1.00 79.6 yes View details
ConsOrf4 Genome 786 0.3555 1.00 80.0 yes View details
infB Genome 2172 0.2660 1.00 77.9 yes View details
ycf45 Genome 1713 0.2371 1.00 79.0 yes View details
accB Genome 495 0.2687 1.00 77.4 yes View details
dnaB Genome 1764 0.2742 1.00 80.7 yes View details
syfB Genome 1992 0.2924 1.00 78.0 yes View details
ConsOrf3 Genome 486 0.3519 0.92 79.9 yes View details
upp Genome 570 0.2807 1.00 78.2 yes View details
ConsOrf5 Genome 969 0.3264 0.94 82.9 yes View details
rps2 Genome 702 0.1608 0.97 81.5 yes View details
carA Genome 1182 0.2580 0.98 81.2 yes View details
moeB Genome 1080 0.2834 0.98 80.4 yes View details
sufC Genome 768 0.2263 0.99 80.2 yes View details
ycf29 Genome 621 0.2358 0.99 80.2 yes View details
tilS Genome 978 0.2557 0.99 80.1 yes View details
ntcA Genome 645 0.2764 0.99 79.9 yes View details
ycf63 Genome 768 0.2297 0.99 79.8 yes View details
rnz Genome 681 0.2810 0.99 79.6 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 120 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
carA_p1 carA TTTGGAAGCTATTGCCGGTT AGGCTGGAGTCATCAAGGAA 1974 0.333 50.0
carA_p2 carA ACGCAATGCCTAGTTTTGGA AGGCTGGAGTCATCAAGGAA 1563 0.333 49.9
carA_p3 carA ATTTGGAAGCTATTGCCGGT AGGCTGGAGTCATCAAGGAA 1975 0.333 49.5
carA_p4 carA GCCTAGTTTTGGAGGTCGTT AGGCTGGAGTCATCAAGGAA 1556 0.333 49.2
carA_p5 carA TTTGGAAGCTATTGCCGGTT GGCTGGAGTCATCAAGGAAA 1973 0.333 48.7
psbY-rpl32_p1 psbY-rpl32 TGCCCGCTTCTGTTAAAGTT ACCCTGTGCTTAAAACATGA 1304 0.333 30.4
psbY-rpl32_p2 psbY-rpl32 TTGCCCGCTTCTGTTAAAGT ACCCTGTGCTTAAAACATGA 1305 0.333 30.4
psbY-rpl32_p3 psbY-rpl32 AGTTCCCGTAGTTTGGCTTG ACCCTGTGCTTAAAACATGA 1429 0.333 29.7
psbY-rpl32_p4 psbY-rpl32 TGCCCGCTTCTGTTAAAGTT AACCCTGTGCTTAAAACATGA 1305 0.333 28.9
psbY-rpl32_p5 psbY-rpl32 TGCCCGCTTCTGTTAAAGTT ACCCTGTGCTTAAAACATGAA 1304 0.333 28.9
rnz_p1 rnz CAGCTGGATCATGGGCTATA TCACGACCGTTTTTAGTGCT 1690 0.333 39.8
rnz_p2 rnz TATAGCAGCTGGATCATGGG TCACGACCGTTTTTAGTGCT 1695 0.333 39.8
rnz_p3 rnz AACGTAAAGGTGGCAAACAA TCACGACCGTTTTTAGTGCT 1889 0.333 38.6
rnz_p4 rnz ACGTAAAGGTGGCAAACAAA TCACGACCGTTTTTAGTGCT 1888 0.333 38.6
rnz_p5 rnz TTATAGCAGCTGGATCATGGG TCACGACCGTTTTTAGTGCT 1696 0.333 37.8
dsbD_p1 dsbD TGGTCGTAGGTTCAAGTCCT CGAGAAAACTTCCAGCGTCT 1244 0.333 51.6
dsbD_p2 dsbD TGGTCGTAGGTTCAAGTCCT GCCAAACGACCAAACAATCC 1409 0.333 51.5
dsbD_p3 dsbD TGGTCGTAGGTTCAAGTCCT GGCCAAACGACCAAACAATC 1410 0.333 51.5
dsbD_p4 dsbD AATCGTTTTATGCGGACGGA CGAGAAAACTTCCAGCGTCT 1504 0.333 51.5
dsbD_p5 dsbD AATCGTTTTATGCGGACGGA GCCAAACGACCAAACAATCC 1669 0.333 51.5
ycf63_p1 ycf63 AACCAGTGACCATCTGCTTG ACCTGTTGATCCTCCTGACA 1102–1168 1.000 91.0
ycf63_p2 ycf63 AACGGGACTGATGAAGTTCG ACCTGTTGATCCTCCTGACA 1463 0.333 52.5
ycf63_p3 ycf63 CGGGACTGATGAAGTTCGTT ACCTGTTGATCCTCCTGACA 1461 0.333 52.5
ycf63_p4 ycf63 TGAGCTAACCGCCCCTAATA ACCTGTTGATCCTCCTGACA 1128 0.333 52.4
ycf63_p5 ycf63 CGGGACTGATGAAGTTCGTT AAAAAGGACGCTCACCTGTT 1474 0.333 52.3
tilS_p1 tilS GAGTGTTACCGCTGTTGTGA TCAAGGCATAAGTCGTCTGC 2155 0.333 52.1
tilS_p2 tilS GAGTGTTACCGCTGTTGTGA CAAGGCATAAGTCGTCTGCT 2154 0.333 52.1
tilS_p3 tilS GCGCTCCTTTATGTCCTTGT TCAAGGCATAAGTCGTCTGC 2102 0.333 51.2
tilS_p4 tilS GCGCTCCTTTATGTCCTTGT CAAGGCATAAGTCGTCTGCT 2101 0.333 51.1
tilS_p5 tilS TGGAATTGTCCTTGTGTCCC TCAAGGCATAAGTCGTCTGC 2040 0.333 51.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Caloglossa beccarii NC_035269.1 165038 View on NCBI ↗
Caloglossa intermedia NC_035265.1 166397 View on NCBI ↗
Caloglossa monosticha NC_035263.1 165111 View on NCBI ↗