Markers + reference

Jovibarba

2 species · Crassulaceae · Saxifragales

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Species 2
Genome length 151–151 kb
Candidate markers 269
Primer pairs 55

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 40.0 yes View details
trnK-UUU-rps16 LSC 657 0.0000 1.00 40.0 yes View details
rps16 LSC 1057 0.0000 1.00 40.0 yes View details
matK LSC 1503 0.0000 1.00 40.0 yes View details
matK-trnK-UUU LSC 688 0.0000 1.00 40.0 yes View details
atpA LSC 1524 0.0000 1.00 40.0 yes View details
atpF LSC 1285 0.0000 1.00 40.0 yes View details
atpH-atpI LSC 680 0.0000 1.00 40.0 yes View details
atpI LSC 735 0.0000 1.00 40.0 yes View details
rps2 LSC 711 0.0000 1.00 40.0 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 55 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA ACCCATTTCTTGGTTATTTCTCCT ATTTGGTTGCTTGGGAGTCC 1172 1.000 44.3
psbA_p2 psbA ACCCATTTCTTGGTTATTTCTCC ATTTGGTTGCTTGGGAGTCC 1172 1.000 43.0
psbA_p3 psbA CCCATTTCTTGGTTATTTCTCCT ATTTGGTTGCTTGGGAGTCC 1171 1.000 40.9
psbA_p4 psbA AACCCATTTCTTGGTTATTTCTCC ATTTGGTTGCTTGGGAGTCC 1173 1.000 40.2
psbA_p5 psbA ACCCATTTCTTGGTTATTTCTCCT TTTGGTTGCTTGGGAGTCC 1171 1.000 40.0
matK_p1 matK AGTGATTTGATTCAACACCAATGT ACCTATCTCCGGGGTATTTT 1720 1.000 40.0
matK_p2 matK AGTGATTTGATTCAACACCAATGT ACCTATCTCCGGGGTATTTTT 1720 1.000 40.0
matK_p3 matK GTGATTTGATTCAACACCAATGT ACCTATCTCCGGGGTATTTT 1719 1.000 40.0
matK_p4 matK GTGATTTGATTCAACACCAATGT ACCTATCTCCGGGGTATTTTT 1719 1.000 40.0
matK_p5 matK AGTGATTTGATTCAACACCAATG ACCTATCTCCGGGGTATTTT 1720 1.000 40.0
matK-trnK-UUU_p1 matK-trnK-UUU CGCACCTATGATCATGAGCA AACGGTAGAGTACTCGGCTT 824 1.000 77.4
matK-trnK-UUU_p2 matK-trnK-UUU CGCACCTATGATCATGAGCA ACGGTAGAGTACTCGGCTTT 823 1.000 77.4
matK-trnK-UUU_p3 matK-trnK-UUU ACGCACCTATGATCATGAGC AACGGTAGAGTACTCGGCTT 825 1.000 77.4
matK-trnK-UUU_p4 matK-trnK-UUU ACGCACCTATGATCATGAGC ACGGTAGAGTACTCGGCTTT 824 1.000 77.4
matK-trnK-UUU_p5 matK-trnK-UUU CGCACCTATGATCATGAGCA TTTTGGCTTGGGGTTGCTAA 847 1.000 77.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA TTGAAAAGGGGGCTAAACCG 840 1.000 76.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC TTGAAAAGGGGGCTAAACCG 841 1.000 76.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT TTGAAAAGGGGGCTAAACCG 843 1.000 76.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGTACAAACTCTACCGACGG TTGAAAAGGGGGCTAAACCG 866 1.000 76.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCGTACAAAC TTGAAAAGGGGGCTAAACCG 877 1.000 76.0
rps16_p1 rps16 TAGATCCCAGCCATACCCAC CACCACCCATATGCACGTAA 1190 1.000 77.6
rps16_p2 rps16 CAGCCATACCCACACTCTTT CACCACCCATATGCACGTAA 1183 1.000 75.8
rps16_p3 rps16 TTAGATCCCAGCCATACCCA CACCACCCATATGCACGTAA 1191 1.000 75.7
rps16_p4 rps16 TAGATCCCAGCCATACCCAC CGGAGTACTGACCAAACCAA 1150 1.000 73.5
rps16_p5 rps16 TAGATCCCAGCCATACCCAC TTTCACCACCCATATGCACG 1193 1.000 73.5
trnG-GCC_p1 trnG-GCC TCACCTGACAAAAGGCATCA TGCATTCATTCTGCATTCTA 980 1.000 40.0
trnG-GCC_p2 trnG-GCC TCACCTGACAAAAGGCATCA TGCATTCATTCTGCATTCTATTTCT 980 1.000 40.0
trnG-GCC_p3 trnG-GCC TCACCTGACAAAAGGCATCA TGCATTCATTCTGCATTCTAT 980 1.000 40.0
trnG-GCC_p4 trnG-GCC GTCACCTGACAAAAGGCATC TGCATTCATTCTGCATTCTA 981 1.000 40.0
trnG-GCC_p5 trnG-GCC CCTGACAAAAGGCATCAACAC TGCATTCATTCTGCATTCTA 977 1.000 40.0

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
Jovibarba globifera PP262172.1 151182 View on NCBI ↗
Jovibarba globifera subsp. hirta PP262175.1 151182 View on NCBI ↗