Markers + reference

Cryptospora

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 153–154 kb
Candidate markers 266
Primer pairs 90

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 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 341 0.0402 0.95 81.0 yes View details
rps16 LSC 1112 0.0117 1.00 58.0 yes View details
trnS-AGC-trnG-GGA LSC 612 0.0229 1.00 66.2 yes View details
psbZ-trnG-GGC LSC 398 0.0176 1.00 52.4 yes View details
trnL-UUA-trnF-UUC LSC 543 0.0220 0.92 74.0 yes View details
ycf1 IRb 999 0.0000 1.00 26.1 no View details
ndhF-rpl32 SSC 845 0.0155 0.99 58.6 yes View details
rpl32-trnL-CUA SSC 787 0.0306 1.00 68.3 yes View details
ycf1 SSC 5313 0.0109 1.00 44.6 yes View details
trnL-CUA-ccsA SSC 116 0.0517 1.00 76.4 yes View details
psbT-psbN LSC 65 0.0308 1.00 68.2 yes View details
rbcL-accD LSC 671 0.0104 1.00 64.9 yes View details
psbE-petL LSC 1266 0.0095 1.00 64.7 yes View details
rpoC2-rpoC1 LSC 187 0.0214 1.00 63.0 yes View details
trnT-ACC-psbD LSC 1232 0.0065 1.00 62.9 yes View details
petA-psbJ LSC 912 0.0110 1.00 62.0 yes View details
trnL-UUG-ndhB IRb 600 0.0017 0.98 62.0 yes View details
ndhB-trnL-UUG IRa 600 0.0017 0.98 62.0 yes View details
rps16-trnQ-CAA LSC 384 0.0083 0.94 61.8 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 383–399 1.000 84.8
trnH-CAC-psbA_p2 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 384–400 1.000 84.6
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 398–414 1.000 84.5
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 401–417 1.000 84.4
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 399–415 1.000 84.3
rps16_p1 rps16 CGAGTCTTTCGCATCCTCTT ACTGACTGAACTATGACTATTCATGA 1214–1225 1.000 40.9
rps16_p2 rps16 CGAGTCTTTCGCATCCTCTT ACTGACTGAACTATGACTATTCA 1214–1225 1.000 40.9
rps16_p3 rps16 CGAGTCTTTCGCATCCTCTT TCAATTACACAAACTAGAGGAATGT 1175–1186 1.000 40.9
rps16_p4 rps16 CGAGTCTTTCGCATCCTCTT ACGATATACTGACTGAACTATGACT 1221–1232 1.000 40.8
rps16_p5 rps16 CGAGTCTTTCGCATCCTCTT ACGATATACTGACTGAACTATGAC 1221–1232 1.000 40.8
rps16-trnQ-CAA_p1 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 434–457 1.000 82.8
rps16-trnQ-CAA_p2 rps16-trnQ-CAA CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 444–467 1.000 82.1
rps16-trnQ-CAA_p3 rps16-trnQ-CAA CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 460–483 1.000 80.6
rps16-trnQ-CAA_p4 rps16-trnQ-CAA TCCACAGCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 461–484 1.000 80.5
rps16-trnQ-CAA_p5 rps16-trnQ-CAA ATCCACAGCAGATCATGTCC GAGGTTCGAATCCTTCCGTC 462–485 1.000 78.8
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TAATCAAACCGAGGGACCCT 721–743 1.000 79.9
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TAATCAAACCGAGGGACCCT 719–741 1.000 79.6
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AACCGAGGGACCCTTTAACT 715–737 1.000 78.1
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TCAAACCGAGGGACCCTTTA 718–740 1.000 78.1
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA GCTTTAGTCCACTCAGCCAT TAATCAAACCGAGGGACCCT 716–738 1.000 78.0
rpoC2-rpoC1_p1 rpoC2-rpoC1 TGAAATACCAGATTGGCCCG GGTTTTTCTCAAGCCTGTTCG 249 1.000 72.9
rpoC2-rpoC1_p2 rpoC2-rpoC1 AATACCAGATTGGCCCGTTC GGTTTTTCTCAAGCCTGTTCG 246 1.000 72.9
rpoC2-rpoC1_p3 rpoC2-rpoC1 GAAATACCAGATTGGCCCGT GGTTTTTCTCAAGCCTGTTCG 248 1.000 72.9
rpoC2-rpoC1_p4 rpoC2-rpoC1 TGCCATCCCGAAGTGATCTA GGTTTTTCTCAAGCCTGTTCG 319 1.000 71.3
rpoC2-rpoC1_p5 rpoC2-rpoC1 AAATACCAGATTGGCCCGTT GGTTTTTCTCAAGCCTGTTCG 247 1.000 69.1
trnT-ACC-psbD_p1 trnT-ACC-psbD TCAGGAATTAAACCGAGGCG CAAAAACAAAGCGGTCCCTC 1415–1422 1.000 79.5
trnT-ACC-psbD_p2 trnT-ACC-psbD GTGGTAGAGTAACGCCATGG CAAAAACAAAGCGGTCCCTC 1381–1388 1.000 79.2
trnT-ACC-psbD_p3 trnT-ACC-psbD TCAGTGGTAGAGTAACGCCA CAAAAACAAAGCGGTCCCTC 1384–1391 1.000 79.0
trnT-ACC-psbD_p4 trnT-ACC-psbD GGCGTAAGTCATCGGTTCAA CAAAAACAAAGCGGTCCCTC 1358–1365 1.000 77.4
trnT-ACC-psbD_p5 trnT-ACC-psbD GGCCCTTTTAACTCAGTGGT CAAAAACAAAGCGGTCCCTC 1396–1403 1.000 77.4

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
Cryptospora falcata NC_050791.1 153295 View on NCBI ↗
Cryptospora inconspicua NC_053333.1 153809 View on NCBI ↗