Markers + reference

Streptocarpus

6 species · Gesneriaceae · Lamiales

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Species 6
Genome length 153–153 kb
Candidate markers 269
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 346 0.0019 1.00 34.5 yes View details
rps16 LSC 1877 0.0032 1.00 52.5 yes View details
atpA LSC 1524 0.0000 1.00 25.6 yes View details
trnC-GCA-petN LSC 830 0.0040 0.98 60.0 yes View details
trnS-UGA-psbZ LSC 321 0.0027 1.00 41.3 yes View details
psaA-ycf3 LSC 832 0.0041 1.00 44.8 yes View details
ycf4-cemA LSC 497 0.0034 1.00 31.1 yes View details
ycf1 IRb 864 0.0004 1.00 43.4 no View details
rpl32-trnL-UAG SSC 878 0.0035 1.00 51.1 yes View details
ccsA-ndhD SSC 255 0.0209 1.00 58.4 yes View details
ndhD SSC 1530 0.0020 1.00 37.6 yes View details
ycf1 SSC 5496 0.0024 1.00 46.3 yes View details
atpA-atpF LSC 69 0.0435 1.00 78.6 yes View details
trnK-UUU-rps16 LSC 805 0.0022 1.00 64.7 yes View details
ndhA SSC 2201 0.0020 1.00 61.0 yes View details
trnT-GGU-psbD LSC 1179 0.0020 1.00 60.4 yes View details
psbK-psbI LSC 474 0.0044 1.00 56.2 yes View details
rpl20-rps12 LSC 811 0.0016 1.00 55.2 yes View details
rpoC2 LSC 4146 0.0013 1.00 55.0 yes View details
psbH-petB LSC 836 0.0016 1.00 54.0 yes View details
trnS-CGA-trnR-UCU LSC 56 0.0238 1.00 53.7 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 461–498 1.000 77.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 475–512 1.000 76.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 474–511 1.000 76.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 476–513 1.000 76.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 462–499 1.000 76.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 GTCGGGGTCTTCCAAACTTT GGTGCTCAACCTACAGGAAC 975–1006 1.000 81.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 893–924 1.000 80.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 892–923 1.000 80.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GGTGCTCAACCTACAGGAAC 907–938 1.000 79.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 902–933 1.000 79.2
rps16_p1 rps16 TATGAATCGAGCAGGAAGGG ACTCAAGCCTATCCCTATGT 2078–2096 1.000 47.1
rps16_p2 rps16 TATGAATCGAGCAGGAAGGG ACTCAAGCCTATCCCTATGTT 2078–2096 1.000 45.9
rps16_p3 rps16 ATGAATCGAGCAGGAAGGGG ACTCAAGCCTATCCCTATGT 2077–2095 1.000 44.6
rps16_p4 rps16 ATGAATCGAGCAGGAAGGGG ACTCAAGCCTATCCCTATGTT 2077–2095 1.000 43.3
rps16_p5 rps16 ATATGAATCGAGCAGGAAGGG ACTCAAGCCTATCCCTATGT 2079–2097 1.000 43.3
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT TCTTCACGTCCAGGATTACG 591–634 1.000 76.9
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 586–629 1.000 76.9
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT TCTTAGTCTTCACGTCCAGGA 597–640 1.000 75.1
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTAGTCTTCACGTCCAGGA 592–635 1.000 75.1
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 583–626 1.000 74.9
trnS-CGA-trnR-UCU_p1 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 137–269 1.000 65.5
trnS-CGA-trnR-UCU_p2 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 140–272 1.000 65.3
trnS-CGA-trnR-UCU_p3 trnS-CGA-trnR-UCU CAAAATGCTGAACCGACGTC AGAAGACCTCTGTCCTATCCA 170–302 1.000 65.1
trnS-CGA-trnR-UCU_p4 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 143–275 1.000 64.8
trnS-CGA-trnR-UCU_p5 trnS-CGA-trnR-UCU CAAAATGCTGAACCGACGTC AGGTTTAGAAGACCTCTGTCCT 176–308 1.000 64.4
atpA_p1 atpA AGCCTTCCAAGCTAACGATG GTAATTGAGCGTGAGAGCCA 2353–2483 1.000 80.3
atpA_p2 atpA CAAAATGCTGAACCGACGTC GTAATTGAGCGTGAGAGCCA 2386–2516 1.000 80.1
atpA_p3 atpA CGCTACCCGCTTATTTCCTT GTAATTGAGCGTGAGAGCCA 2320–2450 1.000 80.1
atpA_p4 atpA AGCCTTCCAAGCTAACGATG GGAAGCCGATGAGTTTAGGG 2129–2259 1.000 80.1
atpA_p5 atpA CCTAGCCTTCCAAGCTAACG GTAATTGAGCGTGAGAGCCA 2356–2486 1.000 80.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Streptocarpus ionanthus subsp. grandifolius MN935471.1 153208 View on NCBI ↗
Streptocarpus ionanthus subsp. grotei MN935469.1 153215 View on NCBI ↗
Streptocarpus ionanthus subsp. orbicularis MN935470.1 153377 View on NCBI ↗
Streptocarpus ionanthus subsp. rupicola MN935473.1 153290 View on NCBI ↗
Streptocarpus ionanthus subsp. velutinus MN935472.1 153307 View on NCBI ↗
Streptocarpus teitensis NC_037184.1 153207 View on NCBI ↗