Hotspot

trnH-GUG-psbA

LSC · 85-391 · 307 bp

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Pi 0.0524
MarkerSeek score 69.20
Primer available yes
Label trnH-GUG-psbA

Feature Metadata

label_name
trnH-GUG-psbA
feature_type
igs
region
LSC
length_bp
307
variable_sites
48
pi
0.0524
unique_haplotype_count
12
primer_available
yes
alignment_reliability
0.96
markerseek_score
69.20

Pi Curve

Alignment Viewer

                         1                                                                                                   
Salvia_aethiopis_1       CCCTCTACTAT------AAAATTCTATTAAAAATGTTTATATTTATTT--TTTTTCAATTAAAATTTTTTTAGAAATTGTAAAACAAATTTGAATCATTT
Salvia_amarissima_2      CCCTCTACTAT-------AAATTAGATTTATAATTTTTATATTTATTTACTTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTCAATCATTT
Salvia_chinensis_3       CCCTCTACTATAAAATGAAAATGATATTTATAATTTTTCTATTTATTTACTTTTTCAATTGAAATTTTTTTAGAAATTGTAAAACAAATTTCAATCATTT
Salvia_dorrii_4          CCCTCTACTAT------AAAATGAGATTTCTAATTTTTAAATTTATTTACTTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTCAATCATTT
Salvia_eremostachya_5    CCCTCTACTAT------AAAATGAGATTTCTTATTTTTAAATTTATTTACTTTTTCAATCTAAATTTTTTTAGAAATTGTAAAACAAATTTCAATCATTT
Salvia_fruticosa_6       CCCTCTACTATAACTAGAAAATTCTAGTAAAAATTTTTCTATTTATTTACTTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTGAATCATTT
Salvia_huberi_7          CCCTCTACTATAACTAGAAAATTCTAGTAAAAATTTTTCTATTTATTTACTTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTGAATCATTT
Salvia_kronenburgii_8    CCCTCTACTATAACTAGAAAATTCTAGTAAAAATTTTTCTATTTATTTACTTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTGAATCATTT
Salvia_limbata_9         CCCTCTACTAT------AAAATTCTATTAAAAATGTTTATATTTATTT--TTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTGAATCATTT
Salvia_mohavensis_10     CCCTCTACTAT------AAAATGAGATTTCTAATTTTTAAATTTATTTACTTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTCAATCATTT
Salvia_officinalis_subsp CCCTCTACTATAACTAGAAAATTCTAGTAAAAATTTTTCTATTTATTTACTTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTGAATCATTT
Salvia_pachyphylla_12    CCCTCTACTAT------AAAATGAGATTTCTAATTTTTAAATTTATTTACTTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTCAATCATTT
Salvia_pratensis_13      CCCTCTACTAT------AAAATTCTATTAAAAATTTTTATATTTATTT--TTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTGAATCATTT
Salvia_saccardiana_14    CCCTCTACTAT------AAAATTCTATTAAAAATTTTTATATTTATTT--TTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTGAATCATTT
Salvia_sonomensis_15     CCCTCTACTAT------AAAATGAGATTTCTAATTTTTAAATTTATTTACTTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTCAATCATTT
Salvia_spathacea_16      CCCTCTACTAT------AAAATGAGATTTCTAATTTTTAAATTTATTTACTTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTCAATCATTT
Salvia_verbenaca_17      CCCTCTACTAT------AAAATTCTATTAAAAATGTTTATATTTATTT--TTTTTCAATTTAATTTTTTTTCGAAATTGTAAAAGAAATTTGAATCATTT
Salvia_xanthocheila_18   CCCTCTACTAT------AAAATTCTATTAAAAATGTTTATATTTATTT--TTTTTCAATTTAAATTTTTTTAGAAATTGTAAAACAAATTTGAATCATTT
                         101                                                                                                 
Salvia_aethiopis_1       TTTG-ATCTTCTTTCTTTATTC----TCTAATGGAAATAATAATTTTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGATTCCTAATTGAAAAGA
Salvia_amarissima_2      TTTT--TTTATTTTCTTTATTC----TCGAATAGAAAGAATA---------AAGTACAATATTACTAGAAAATATGGAAAAGGACTCCTAATTGAAAAGA
Salvia_chinensis_3       TTTTTATCTTCTTTCTTTATTCTCTATCTAATGGAAAGAATCATTATAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGATCCCTAATTGAAAAGA
Salvia_dorrii_4          TTTTTATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTCTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGACTCCTAATTGAAAAGA
Salvia_eremostachya_5    TTTTTATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTCTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGACTCCTAATTGAAAAGA
Salvia_fruticosa_6       TTTT-ATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTTTAGGTAAGTCCAATACTACTAGAAAATAAAGAAAAGGATTCCTAATTGAAAAGA
Salvia_huberi_7          TTTT-ATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTTTAGGTAAGTCCAATACTACTAGAAAATAAAGAAAAGGATTCCTAATTGAAAAGA
Salvia_kronenburgii_8    TTTT-ATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTTTAGGTAAGTCCAATACTACTAGAAAATAAAGAAAAGGATTCCTAATTGAAAAGA
Salvia_limbata_9         TTTG-ATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTTTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGATTCCTAATTGAAAAGA
Salvia_mohavensis_10     TTTTTATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTCTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGACTCCTAATTGAAAAGA
Salvia_officinalis_subsp TTTT-ATCTTCTTTCTTTATTC----TCTAATGGAAAGAAAAATTTTAGGTAAGTCCAATACTACTAGAAAATAAAGAAAAGGATTCCTAATTGAAAAGA
Salvia_pachyphylla_12    TTTTTATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTCTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGACTCCTAATTGAAAAGA
Salvia_pratensis_13      TTTG-ATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTTTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGATTCCTAATTGAAAAGA
Salvia_saccardiana_14    TTTG-ATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTTTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGATTCCTAATTGAAAAGA
Salvia_sonomensis_15     TTTTTATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTCTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGACTCCTAATTGAAAAGA
Salvia_spathacea_16      TTTTTATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTCTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGACTCCTAATTGAAAAGA
Salvia_verbenaca_17      TTTG-ATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTTTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGATTCCTAATTGAAAAGA
Salvia_xanthocheila_18   TTTG-ATCTTCTTTCTTTATTC----TCTAATGGAAAGAATAATTTTAGGTAAGTCCAATACTACTAGAAAATATAGAAAAGGATTCCTAATTGAAAAGA
                         201                                                                                                 
Salvia_aethiopis_1       AAATAAAGGAGCAATAAACCCTCTTTTGGTAGAACAAG-AAAGGGTTTATTGCTCCTTATATTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_amarissima_2      AAATAAAGGAGCAATAAACCCTTTCTTGTTCTATCAAA-AGAGGGTTTATTGCTCCTTATGTTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_chinensis_3       AAATAAAGGAGCAATAAACCCTCTTTTGATAGAACAAGTAAAGGGTTTATTGCTCCTTATGTTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_dorrii_4          AAATAAAGGAGCAATCAACCCTCTTTTGATAGAACAAG-AAAGGGTTTATTGCTCCTTATGTTTA-----TCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_eremostachya_5    AAATAAAGGAGCAATAAACCCTTTCTTGTTCTATCAAA-AGAGGGTTTATTGCTCCTTATGTTTA-----TCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_fruticosa_6       AAATAAAGGAGCAATAAACCCTTTCTTGTTCTATCAAA-AGAGGGTTTATTGCTCCTTATATTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_huberi_7          AAATAAAGGAGCAATAAACCCTTTCTTGTTCTATCAAA-AGAGGGTTTATTGCTCCTTATATTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_kronenburgii_8    AAATAAAGGAGCAATAAACCCTTTCTTGTTCTATCAAA-AGAGGGTTTATTGCTCCTTATATTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_limbata_9         AAATAAAGGAGCAATAAACCCTCTTTTGGTAGAACAAG-AAAGGGTTTATTGCTCCTTATATTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_mohavensis_10     AAATAAAGGAGCAATCAACCCTCTTTTGATAGAACAAG-AAAGGGTTGATTGCTCCTTATGTTTA-----TCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_officinalis_subsp AAATAAAGGAGCAATAAACCCTTTCTTGTTCTATCAAA-AGAGGGTTTATTGCTCCTTATATTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_pachyphylla_12    AAATAAAGGAGCAATCAACCCTCTTTTGATAGAACAAG-AAAGGGTTTATTGCTCCTTATGTTTA-----TCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_pratensis_13      AAATAAAGGAGCAATAAACCCTCTTTTGGTAGAACAAG-AAAGGGTTTATTGCTCCTTATATTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_saccardiana_14    AAATAAAGGAGCAATAAACCCTCTTTTGGTAGAACAAG-AAAGGGTTTATTGCTCCTTATATTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_sonomensis_15     AAATAAAGGAGCAATCAACCCTCTTTTGATAGAACAAG-AAAGGGTTTATTGCTCCTTATGTTTA-----TCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_spathacea_16      AAATAAAGGAGCAATCAACCCTCTTTTGATAGAACAAG-AAAGGGTTTATTGCTCCTTATGTTTA-----TCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_verbenaca_17      AAATAAAGGAGCAATAAACCCTCTTTTGGTAGAACAAG-AAGGGGTTTATTGCTCCTTATATTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
Salvia_xanthocheila_18   AAATAAAGGAGCAATAAACCCTTTCTTGTTCTACCAAA-AGAGGGTTTATTGCTCCTTATATTTATCTATTCTATTTTCAAAAACTCCTACACACTAAAA
                         301    
Salvia_aethiopis_1       ACAAGTC
Salvia_amarissima_2      ACAAGTC
Salvia_chinensis_3       ACAAGTC
Salvia_dorrii_4          ACAAGTC
Salvia_eremostachya_5    ACAAGTC
Salvia_fruticosa_6       ACAAGTC
Salvia_huberi_7          ACAAGTC
Salvia_kronenburgii_8    ACAAGTC
Salvia_limbata_9         ACAAGTC
Salvia_mohavensis_10     ACAAGTC
Salvia_officinalis_subsp ACAAGTC
Salvia_pachyphylla_12    ACAAGTC
Salvia_pratensis_13      ACAAGTC
Salvia_saccardiana_14    ACAAGTC
Salvia_sonomensis_15     ACAAGTC
Salvia_spathacea_16      ACAAGTC
Salvia_verbenaca_17      ACAAGTC
Salvia_xanthocheila_18   ACAAGTC

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
trnH-GUG-psbA_p1 ATCCACTTGGCTACATCCG TATCGAAGCTCCAACAAATG 52.6 40.0 56.9 53.7 348-374 bp 1.0 52.0
trnH-GUG-psbA_p2 ATCCACTTGGCTACATCCGC TATCGAAGCTCCAACAAATG 55.0 40.0 60.2 53.7 348-374 bp 1.0 52.0
trnH-GUG-psbA_p3 CCACTTGGCTACATCCGC TATCGAAGCTCCAACAAATG 61.1 40.0 58.2 53.7 346-372 bp 1.0 52.0
trnH-GUG-psbA_p4 TCCACTTGGCTACATCCGC TATCGAAGCTCCAACAAATG 57.9 40.0 59.8 53.7 347-373 bp 1.0 52.0
trnH-GUG-psbA_p5 ATCCACTTGGCTACATCCG ATCGAAGCTCCAACAAATG 52.6 42.1 56.9 53.7 347-373 bp 1.0 52.0

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