Hotspot

ccsA-ndhD

SSC · 112986-113215 · 230 bp

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Pi 0.0754
MarkerSeek score 65.70
Primer available yes
Label ccsA-ndhD

Feature Metadata

label_name
ccsA-ndhD
feature_type
igs
region
SSC
length_bp
230
variable_sites
45
pi
0.0754
unique_haplotype_count
9
primer_available
yes
alignment_reliability
0.97
markerseek_score
65.70

Pi Curve

Alignment Viewer

                         1                                                                                                   
Salvia_aethiopis_1       ATAAAAAACGCTTACTACTTACCAATAGGAATAGAAAAGTATCCAACGCATATGAATATCACTTTGTGTGAACTAGCGAGAGTCCCGCGAATCAAAGTAA
Salvia_amarissima_2      ATTCAAAAAGCTTACTACTTACGAATAGGAATAGAAAAGCATACAACACATATGAATATCACTTTGTGTGAACTAACGAGAGTCCCGTGACTTTGATTCG
Salvia_chinensis_3       ATTCAAAAAGCTTACTACTTATGAATAGGAATAGAAAAGCATACAACGCATATGAATATCATTTTGTGTGAACTAGCGAGAGCCCCGTGACTTTGATTCG
Salvia_dorrii_4          ATTCAAAAAGCTTACTACTTACGAATAGAAA----------------ACATATGAATATCACTTTGTGTGAACTAGCCAGAGCCCCGTGACTTTGATTCG
Salvia_eremostachya_5    ATTAAAAAAGCTTACTACTTACGAATAGAAA----------------ACATATGAATATCACTTTGTGTGAACTAGCCAGAGCCCCGTGACTTTGATTCG
Salvia_fruticosa_6       ATAAAAAACGCTTACTACTTACCAATAGGAATAGAAAAGTATACAACCCATATGAATATCACTTTGTGTAAACTAGCGAGAGTCCCGCGAATCAAAGTCA
Salvia_huberi_7          ATAAAAAACGCTTACTACTTACCAATAGGAATAGAAAAGTATACAACCCATATGAATATCACTTTGTGTAAACTAGCGAGAGTCCCGCGAATCAAAGTCA
Salvia_kronenburgii_8    ATAAAAAACGCTTACTACTTACCAATAGGAATAGAAAAGTATACAACCCATATGAATATCACTTTGTGTAAACTAGCGAGAGTCCCGCGAATCAAAGTCA
Salvia_limbata_9         ATAAAAAACGCTTACTACTTACCAATAGGAATAGAAAAGTATCCAACGCATATGAATATCACTTTGTGTGAACTAGCGAGAGTCCCGCGAATCAAAGTAA
Salvia_mohavensis_10     ATTCAAAAAGCTTACTACTTACGAATAGAAA----------------ACATATGAATATCACTTTGTGTGAACTAGCCAGAGCCCCGTGACTTTGATTCG
Salvia_officinalis_subsp ATAAAAAACGCTTACTACTTACCAATAGGAATAGAAAAGTATACAACCCATATGAATATCACTTTGTGTAAACTAGCGAGAGTCCCGCGAATCAAAGTCA
Salvia_pachyphylla_12    ATTCAAAAAGCTTACTACTTACGAATAGAAA----------------ACATATGAATATCACTTTGTGTGAACTAGCCAGAGCCCCGTGACTTTGATTCG
Salvia_pratensis_13      ATAAAAA--GCTTACTACTTACCAATAGGAATAGAAAAGTATCCAACGCATATGAATATCACTTTGTGTGAACTAGCGAGAGTCCCGCGAATCAAAGTAA
Salvia_saccardiana_14    ATAAAAA--GCTTACTACTTACCAATAGGAATAGAAAAGTATCCAACGCATATGAATATCACTTTGTGTGAACTAGCGAGAGTCCCGCGAATCAAAGTAA
Salvia_sonomensis_15     ATTCAAAAAGCTTACTACTTACGAATAGAAA----------------ACATATGAATATCACTTTGTGTGAACTAGCCAGAGCCCCGTGACTTTGATTCG
Salvia_spathacea_16      ATTCAAAAAGCTTACTACTTACGAATAGAAA----------------ACATATGAATATCACTTTGTGTGAACTAGCCAGAGCCCCGTGACTTTGATTCG
Salvia_verbenaca_17      ATAAAAAA-GCTTACTACTTACCAATAGGAATAGAAAAGTATCCAACGCATATGAATATCACTTTGTGTGAACTAGCGAGAGTCCCGCGAATCAAAGTCA
Salvia_xanthocheila_18   ATAAAAAACGCTTACTACTTACCAATAGGAATAGAAAAGTATCCAACGCATATGAATATCACTTTGTGTGAACTAGCGAGAGTCCCGCGAATCAAAGTAA
                         101                                                                                                 
Salvia_aethiopis_1       TGGAGCTCTCG------CTAGTTCAAATTCA-TTTTTTTTACTTAATACAAGAGAAGAAAAAGCCCTTT--TTTTTTCATTGTACAACGAACCCTTTTGT
Salvia_amarissima_2      CGAGACTCTTG------CTAGTTCAAATTCATTTTTTTTTACTTAACCCAAGAGAAGAAAAAGCCTTCTTTTTTTTTCATTGTACAACGAACCTTTTTGT
Salvia_chinensis_3       CGGCACTCTCGCCAGTTCTAGTTCAAATTTATTTTTTTTTACTTAACACAAGAGAAGAAAAAGCCTTCTTTTTTTTTCATTGTACAACGAACCTCTTTGG
Salvia_dorrii_4          CGGGATTCTCG------CTAGTTCAAATTCATTTTTTTTTACTTAACACAAG------AAAAGCCTTCT--TTTTTTCATTATACAACGAACCTTTTTGT
Salvia_eremostachya_5    CGGGACTCTCG------CTAGTTCAAATTCATTTTTTTTTACTTAACACAAGAAAAGAAAAAGCCTTCT--TTTTTTCATTATACAACGAACCTTTTTGT
Salvia_fruticosa_6       TGGAGCTCTCG------CTAGTTCTGGTTCA-TTTTTTTTACTTAACACAAGAGAAGAAAAAGCCCTCT--TTTTTTCATTGTACAACGAGCCCTTTTGT
Salvia_huberi_7          TGGAGCTCTCG------CTAGTTCTGGTTCATTTTTTTTTACTTAACACAAGAGAAGAAAAAGCCCTCT--TTTTTTCATTGTACAACGAGCCCTTTTGT
Salvia_kronenburgii_8    TGGAGCTCTCG------CTAGTTCTGGTTCATTTTTTTTTACTTAACACAAGAGAAGAAAAAGCCCTCT--TTTTTTCATTGTACAACGAGCCCTTTTGT
Salvia_limbata_9         TGGAGCTCTCG------CTAGTTCAAATTCA-TTTTTTTTACTTAATACAAGAGAAGAAAAAGCCCTTT--TTTTTTCATTGTACAACGAACCCTTTTGT
Salvia_mohavensis_10     CGGGATTCTCG------CTAGTTCAAATTCATTTTTTTTTACTTAACACAAG------AAAAGCCTTCT--TTTTTTCATTATACAACGAACCTTTTTGT
Salvia_officinalis_subsp TGGAGCTCTCG------CTAGTTCTGGTTCATTTTTTTTTACTTAACACAAGAGAAGAAAAAGCCCTCT--TTTTTTCATTGTACAACGAGCCCTTTTGT
Salvia_pachyphylla_12    CGGGATTCTCG------CTAGTTCAAATTCATTTTTTTTTACTTAACACAAG------AAAAGCCTTCT--TTTTTTCATTATACAACGAACCTTTTTGT
Salvia_pratensis_13      TGGAGCTCTCG------CTAGTTCAAATTCA-TTTTTTTTACTTAATACAAGAGAAGAAAAAGCCCTCT--TTTTCTCATTGTACAACGAACCCTTTTGT
Salvia_saccardiana_14    TGGAGCTCTCG------CTAGTTCAAATTCA-TTTTTTTTACTTAATACAAGAGAAGAAAAAGCCCTCT--TTTTCTCATTGTACAACGAACCCTTTTGT
Salvia_sonomensis_15     CGGGATTCTCG------CTAGTTCAAATTCATTTTTTTTTACTTAACACAAG------AAAAGCCTTCT--TTTTTTCATTATACAACGAACCTTTTTGT
Salvia_spathacea_16      CGGGATTCTCG------CTAGTTCAAATTCATTTTTTTTTACTTAACACAAG------AAAAGCCTTCT--TTTTTTCATTATACAACGAACCTTTTTGT
Salvia_verbenaca_17      TGGAGCTCTCG------CTAGTTCAAATTCATTTTTTTTTACTTAATACAAGAGAAGAAAAAGCCCTCT--TTTTTTCATTGTACAACGAACCCTTTTGT
Salvia_xanthocheila_18   TGGAGCTCTCG------CTAGTTCAAATTCA-TTTTTTTTACTTAATACAAGAGAAGAAAAAGCCCTTT--TTTTTTCATTGTACAACGAACCCTTTTGT
                         201                           
Salvia_aethiopis_1       AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_amarissima_2      AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_chinensis_3       AAACGATAAGATCGTTTTTTCATTTTTTTA
Salvia_dorrii_4          AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_eremostachya_5    AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_fruticosa_6       AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_huberi_7          AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_kronenburgii_8    AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_limbata_9         AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_mohavensis_10     AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_officinalis_subsp AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_pachyphylla_12    AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_pratensis_13      AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_saccardiana_14    AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_sonomensis_15     AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_spathacea_16      AAACAATAAGATCGTTTTTTCATTTTTTTA
Salvia_verbenaca_17      AAAAAATAAGATCGTTTTTTCATTTTTTTA
Salvia_xanthocheila_18   AAACAATAAGATCGTTTTTTCATTTTTTTA

Haplotype Network

Species Separation

Primer Ranking

Primer ID fwd_seq rev_seq fwd_gc rev_gc fwd_tm rev_tm amplicon_size cross_species_success_rate primer_score
ccsA-ndhD_p1 ATGGTTCATTTACATTAACATCT GGTTGAAGTTATCCTATCTAATTCT 26.1 32.0 52.1 54.2 283-312 bp 0.944444 49.8
ccsA-ndhD_p2 ATGGTTCATTTACATTAACATCT GGTTGAAGTTATCCTATCTAATTCTT 26.1 30.8 52.1 54.9 283-312 bp 0.944444 49.8
ccsA-ndhD_p3 ATGGTTCATTTACATTAACATCT GGTTGAAGTTATCCTATCTAATTC 26.1 33.3 52.1 52.8 283-312 bp 0.944444 49.8
ccsA-ndhD_p4 AGTTATGGTTCATTTACATTAACA GGTTGAAGTTATCCTATCTAATTCT 25.0 32.0 52.7 54.2 287-316 bp 0.944444 49.8
ccsA-ndhD_p5 AGTTATGGTTCATTTACATTAACATCT GGTTGAAGTTATCCTATCTAATTCT 25.9 32.0 55.7 54.2 287-316 bp 0.944444 49.8

Downloads

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