Markers + reference

Senna

13 species · Fabaceae · Fabales

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Species 13
Genome length 159–162 kb
Candidate markers 256
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 256 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 655 0.0899 0.97 77.5 yes View details
trnS-GCU-trnT-CGU LSC 898 0.0826 0.91 77.4 yes View details
atpF-atpH LSC 767 0.0811 0.59 66.3 yes View details
psbZ-trnG-GCC LSC 601 0.0866 0.94 78.6 yes View details
trnT-UGU-trnL-UAA LSC 1363 0.0616 0.92 83.8 yes View details
ndhC-trnV-UAC LSC 567 0.0777 0.98 75.3 yes View details
rps3-rps19 LSC 683 0.0652 0.95 78.1 yes View details
ycf1 IRb 762 0.0401 0.98 72.0 yes View details
ndhF SSC 2253 0.0244 1.00 57.2 yes View details
ndhG-ndhI SSC 435 0.1013 0.92 70.3 yes View details
ycf1 SSC 4611 0.0395 1.00 63.1 yes View details
trnQ-UUG-psbK LSC 615 0.0597 0.97 79.2 yes View details
ndhF-trnL-UAG SSC 1442 0.0436 0.99 78.0 yes View details
trnT-CGU-trnR-UCU LSC 365 0.0674 0.97 75.1 yes View details
trnR-UCU-atpA LSC 341 0.0807 0.99 74.5 yes View details
trnC-GCA-petN LSC 1035 0.0353 0.96 74.3 yes View details
trnG-GCC-trnM-CAU LSC 170 0.0517 0.99 73.3 yes View details
rps11-rpl36 LSC 277 0.0834 0.93 73.3 yes View details
trnK-UUU-rps16 LSC 1146 0.0463 0.97 72.8 yes View details
petA-psbJ LSC 1194 0.0427 0.96 72.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1368–1623 1.000 91.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 GGGCCCGATCCAATAACAAT CCCAATGAGCCGTTTATCGA 1441–1696 0.846 85.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 GGGCCCGATCCAATAACAAT TCCCAATGAGCCGTTTATCG 1442–1697 0.846 85.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG TGAGGTTGCGAATACGAGTG 1576–1831 0.846 85.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGGCCCGATCCAATAACAAT TGAGGTTGCGAATACGAGTG 1649–1904 0.692 78.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 588–1090 1.000 89.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AGTCGCACGTTGCTTTTTAC GAGGTTCGAATCCTTCCGTC 592–1094 1.000 88.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAAGTCGCACGTTGCTTTTT GAGGTTCGAATCCTTCCGTC 594–1096 1.000 87.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTCGCACGTTGCTTTTTACC GAGGTTCGAATCCTTCCGTC 591–1093 1.000 86.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA TTCGGAGGTTCGAATCCTTC 592–1094 1.000 85.1
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG AGCAGCTTGCCAAACAAAAG 847–1010 1.000 88.0
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG CTTACAGCAGCTTGCCAAAC 852–1015 1.000 88.0
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CCTCTAGTTTGGAGCCGGTA AGCAGCTTGCCAAACAAAAG 1358–1937 1.000 87.4
trnQ-UUG-psbK_p4 trnQ-UUG-psbK CCTCTAGTTTGGAGCCGGTA CTTACAGCAGCTTGCCAAAC 1363–1942 1.000 87.4
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG TTCGATATTGGTGGGGGACT 1086–1253 0.769 78.3
trnS-GCU-trnT-CGU_p1 trnS-GCU-trnT-CGU CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 800–1027 1.000 82.1
trnS-GCU-trnT-CGU_p2 trnS-GCU-trnT-CGU AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 799–1026 1.000 82.1
trnS-GCU-trnT-CGU_p3 trnS-GCU-trnT-CGU CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 800–1027 1.000 82.0
trnS-GCU-trnT-CGU_p4 trnS-GCU-trnT-CGU AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 799–1026 1.000 82.0
trnS-GCU-trnT-CGU_p5 trnS-GCU-trnT-CGU CAATCCGACGCTTTAGTCCA AACGAATCGCACTTTTACCAC 801–1028 1.000 79.7
trnT-CGU-trnR-UCU_p1 trnT-CGU-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 425–583 1.000 75.3
trnT-CGU-trnR-UCU_p2 trnT-CGU-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 428–586 1.000 75.1
trnT-CGU-trnR-UCU_p3 trnT-CGU-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 431–589 1.000 74.7
trnT-CGU-trnR-UCU_p4 trnT-CGU-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 434–592 1.000 74.5
trnT-CGU-trnR-UCU_p5 trnT-CGU-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 429–587 1.000 72.9
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGAACAGATGGAACTCT 409–750 1.000 58.2
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGAACAGATGGAACTCTT 409–750 1.000 56.7
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAGGAACAGATGGAACTCT 410–751 1.000 56.7
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGCTATTCAGGAACAGATGGA 415–756 1.000 55.5
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TCAGGAACAGATGGAACTCT 444–785 1.000 55.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Senna alata NC_065665.1 159176 View on NCBI ↗
Senna alexandrina NC_086628.1 159573 View on NCBI ↗
Senna bicapsularis NC_047366.1 160973 View on NCBI ↗
Senna candolleana NC_083214.1 160946 View on NCBI ↗
Senna corymbosa NC_066804.1 160630 View on NCBI ↗
Senna italica NC_087782.1 158664 View on NCBI ↗
Senna marilandica NC_083215.1 159304 View on NCBI ↗
Senna multiglandulosa NC_083216.1 160642 View on NCBI ↗
Senna obtusifolia NC_047283.1 162426 View on NCBI ↗
Senna occidentalis NC_038222.1 159993 View on NCBI ↗
Senna reticulata NC_083217.1 159178 View on NCBI ↗
Senna sophera NC_083218.1 160130 View on NCBI ↗
Senna tora NC_030193.1 162426 View on NCBI ↗