Hotspot

petA-psbJ

LSC · 62246-63303 · 1058 bp

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Pi 0.0333
MarkerSeek score 67.40
Primer available yes
Label petA-psbJ

Feature Metadata

label_name
petA-psbJ
feature_type
igs
region
LSC
length_bp
1058
variable_sites
110
pi
0.0333
unique_haplotype_count
14
primer_available
yes
alignment_reliability
0.96
markerseek_score
67.40

Pi Curve

Alignment Viewer

                         1                                                                                                   
Salvia_aethiopis_1       ACTCGCGGATTTATCGACATCAGGTTTGTAAAAAGAA-AAAATTTTGGTTGTCAATTCTTTATGATC---AAAAAATCAATTCGGAAAAACCTTTTATTT
Salvia_amarissima_2      ACTCGCGGATTTATCGACATCGGGTTCGTAAAAAGAACAAAATTTTTGTTGTCAATTTTATATGATC-AAAAAAAATAAATTCTGAAAAACCTTTTATTT
Salvia_chinensis_3       ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAGAACAAAATTGGGGTTGTCAATTCTATATGATCAAAAAAAAATAAATTCTGAAAAACCTTTTATTT
Salvia_dorrii_4          ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAGAACAAAATTTTTGTTGTCAATTTTATATGATC-AAAAAAAAGAAATTCTGAAAAACTTTTTATTT
Salvia_eremostachya_5    ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAGAACAAAATTTTTGTTGTCAATTTTATATGATC-AAAAAAAAGAAATTCTGAAAAACCTTTTATTT
Salvia_fruticosa_6       ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAG-A-AAAATTTTTGTTGTCAATTCTATATGATC--AAAAAAATCCATTCTGAAAAACCTTTTATTT
Salvia_huberi_7          ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAG-A-AAAATTTTTGTTGTCAATTCTATATGATC--AAAAAAATCCATTCTGAAAAACCTTTTATTT
Salvia_kronenburgii_8    ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAG-A-AAAATTTTTGTTGTCAATTCTATATGATC--AAAAAAATCCATTCTGAAAAACCTTTTATTT
Salvia_limbata_9         ACTCGCGGATTTATCGACATCAGGTTTGTAAAAAGAA-AAAATTTTGGTTGTCAATTCTTTATGATC---AAAAAATCAATTCGGAAAAACCTTTTATTT
Salvia_mohavensis_10     ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAGAACAAAATTTTTGTTGTCAATTTTATATGATC-AAAAAAAAGAAATTCTGAAAAACCTTTTATTT
Salvia_officinalis_subsp ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAG-A-AAAATTTTTGTTGTCAATTCTATATGATC--AAAAAAATCCATTCTGAAAAACCTTTTATTT
Salvia_pachyphylla_12    ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAGAACAAAATTTTTGTTGTCAATTTTATATGATC-AAAAAAAAGAAATTCTGAAAAACCTTTTATTT
Salvia_pratensis_13      ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAGAA-AAAATTTTGGTTGTCAATTCTTTATGATC---AAAAAATCAATTCTGAAAAACCTTTTATTT
Salvia_saccardiana_14    ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAGAA-AAAATTTTGGTTGTCAATTCTTTATGATC---AAAAAATCAATTCTGAAAAACCTTTTATTT
Salvia_sonomensis_15     ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAGAACAAAATTTTTGTTGTCAATTTTATATGATC-AAAAAAAAGAAATTCTGAAAAACCTTTTATTT
Salvia_spathacea_16      ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAGAACAAAATTTTTGTTGTCAATTTTATATGATC-AAAAAAAAGAAATTCTGAAAAACTTTTTATTT
Salvia_verbenaca_17      ACTCGCGGATTTATCGACATCAGGTTCGTAAAAAGAA-AAAATTTTGGTTGTCAATTCTTTATGATC---AAAAAATCAATTCTGAAAAACCTTTTATTT
Salvia_xanthocheila_18   ACTCGCGGATTTATCGACATCAGGTTTGTAAAAAGAA-AAAATTTTGGTTGTCAATTCTTTATGATC---AAAAAATCAATTCGGAAAAACCTTTTATTT
                         101                                                                                                 
Salvia_aethiopis_1       ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGT-----------------CATAATAGGTAGATTTTTGTTTGAAGAAG--
Salvia_amarissima_2      ATTTGCTCTTTTTCTACCAACTTCGGGGACTCCCTTGTAGCGCAATCTTAGTCATAACGCACGCTTAGTCATAATAGGTAGATTTTTGTTTGAAGAAGAC
Salvia_chinensis_3       ACTTGCTCTTTTTCTACAAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGTCATAACGCATTCTTAGTCATAATAGGTAGGTTTTTGTTTGAAGAAGAC
Salvia_dorrii_4          ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGTCACAACGCACGCTTAGTCATAATAGGTAGATTTTTGTTTGAAGAAGAC
Salvia_eremostachya_5    ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGTCACAACGCACGCTTAGTCATAATAGGTAGATTTTTGTTTTAAGAAGAC
Salvia_fruticosa_6       ACTTGCTCTTTTTCGACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTATT-----------------CATAATAGGTAGATTTTTGTTTGAAGAAGAC
Salvia_huberi_7          ACTTGCTCTTTTTCGACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTATT-----------------CATAATAGGTAGATTTTTGTTTGAAGAAGAC
Salvia_kronenburgii_8    ACTTGCTCTTTTTCGACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTATT-----------------CATAATAGGTAGATTTTTGTTTGAAGAAGAC
Salvia_limbata_9         ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGT-----------------CATAATAGGTAGATTTTTGTTTGAAGAAG--
Salvia_mohavensis_10     ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGTCACAACGCACGCTTAGTCATAATAGGTAGATTTTTGTTTGAAGAAGAC
Salvia_officinalis_subsp ACTTGCTCTTTTTCGACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTA---------------------------GTAGATTTTTGTTTGAAGAAGAC
Salvia_pachyphylla_12    ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGTCACAACGCACGCTTAGTCATAATAGGTAGATTTTTGTTTGAAGAAGAC
Salvia_pratensis_13      ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGTCA------------TAACATAATAGGTAGATTTTTGTTTGAAGAAG--
Salvia_saccardiana_14    ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGTCA------------TAACATAATAGGTAGATTTTTGTTTGAAGAAG--
Salvia_sonomensis_15     ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGTCACAACGCACGCTTAGTCATAATAGGTAGATTTTTGTTTGAAGAAGAC
Salvia_spathacea_16      ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGTCACAACGCACGCTTAGTCATAATAGGTAGATTTTTGTTTGAAGAAGAC
Salvia_verbenaca_17      ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGT-----------------CATAATAGGTAGATTTTTGTTTGAAGAAG--
Salvia_xanthocheila_18   ACTTGCTCTTTTTCTACGAACTTCGGGGACTCCCTTGTAGCGCACTCTTAGT-----------------CATAATAGGTAGATTTTTGTTTGAAGAAG--
                         201                                                                                                 
Salvia_aethiopis_1       -------------TTTATGGCTTTACCGCCTTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATGGGG
Salvia_amarissima_2      TATTTTATTTGACTTTATGGCTTTACCACCCTTTTCTTTGTTCAAATTGAATTGACAGGGCTGTGTTACTATTGCCATATTTCAATGCCATAAAATTGGG
Salvia_chinensis_3       TATTTTATTTGACTTTAGGGCTTTACCACCCTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATTGGC
Salvia_dorrii_4          TATTTTTTTTTACTTTATGGCTTTACCACCCTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATTGGG
Salvia_eremostachya_5    TATTTTTTTTTACTTTATGGCTTTACCACCCTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAACTGGG
Salvia_fruticosa_6       TA-----TTTTACTTTATGGCTTTACCACCTTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATGGGG
Salvia_huberi_7          TA-----TTTTACTTTATGGCTTTACCACCTTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATGGGG
Salvia_kronenburgii_8    TA-----TTTTACTTTATGGCTTTACCACCTTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATGGGG
Salvia_limbata_9         -------------TTTATGGCTTTACCGCCTTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATGGGG
Salvia_mohavensis_10     TATTTTTTTTTACTTTATGGCTTTACCACCCTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATTGGG
Salvia_officinalis_subsp TA-----TTTTACTTTATGGCTTTACCACCTTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATGGGG
Salvia_pachyphylla_12    TATTTTTTTTTACTTTATGGCTTTACCACCCTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATTGGG
Salvia_pratensis_13      -------------TTTATGGCTTTACCGCCTTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATGGGG
Salvia_saccardiana_14    -------------TTTATGGCTTTACCGCCTTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATGGGG
Salvia_sonomensis_15     TCTTTTTTTTTACTTTATGGCTTTACCACCCTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATTGGG
Salvia_spathacea_16      TATTTTTTTTTACTTTATGGCTTTACCACCCTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATTGGG
Salvia_verbenaca_17      -------------TTTATGGCTTTACCGCCTTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATGGGG
Salvia_xanthocheila_18   -------------TTTATGGCTTTACCGCCTTTTTCTTTGTTCAAATTGAATTGACAGGACTGTGTTACTATTGCCAGATTTCAATGCCATAAAATGGGG
                         301                                                                                                 
Salvia_aethiopis_1       ATAGAGATTAGCATAAAAAAGCGGGTAATCGAAC--------GAACTAGAAGTGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTTTTCCTA
Salvia_amarissima_2      ATAGAGATTAGCATAAATAAGCGGGGAATCGGAT--------GAACCAGAAGCGTGGGGAACAAAAAATTATAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_chinensis_3       ATAGAGATTAGCATAAATAAGCGGGTAATCGAACGAACTAGCGAACTAGAAGTGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_dorrii_4          ATAGAGATTAGCATAAATAAGCGGGTAATCGAAC--------CAACCAGAAGCGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_eremostachya_5    ATAGAGATTAGCATAAATAAGCGGGTAATCGAAC--------GAACCAGAAGCGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_fruticosa_6       ATAGAGATTAGCCTAAATAAGCGGGTAATCAAAC--------GAACTAGAAGTGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_huberi_7          ATAGAGATTAGCCTAAATAAGCGGGTAATCAAAC--------GAACTAGAAGTGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_kronenburgii_8    ATAGAGATTAGCCTAAATAAGCGGGTAATCAAAC--------GAACTAGAAGTGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_limbata_9         ATAGAGATTAGCATAAAAAAGCGGGTAATCGAAC--------GAACTAGAAGTGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTTTTCCTA
Salvia_mohavensis_10     ATAGAGATTAGCATAAATAAGCGGGTAATCGAAC--------GAACCAGAAGCGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_officinalis_subsp ATAGAGATTAGCCTAAATAAGCGGGTAATCAAAC--------GAACTAGAAGTGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_pachyphylla_12    ATAGAGATTAGCATAAATAAGCGGGTAATCGAAC--------GAACCAGAAGCGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_pratensis_13      ATAGAGATTAGCATAAATAAGCGGGTAATCGAAC--------GAACTAGAAGTGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTTTTCCTA
Salvia_saccardiana_14    ATAGAGATTAGCATAAATAAGCGGGTAATCGAAC--------GAACTAGAAGTGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTTTTCCTA
Salvia_sonomensis_15     ATAGAGATTAGCATAAATAAGCGGGTAATCGAAC--------GAACCAGAAGCGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_spathacea_16      ATAGAGATTAGCATAAATAAGCGGGTAATCGAAC--------CAACCAGAAGCGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTCTTCCTA
Salvia_verbenaca_17      ATAGAGATTAGCATAAATAAGCGGGTAATCGAAC--------GAACTAGAAGTGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTTTTCCTA
Salvia_xanthocheila_18   ATAGAGATTAGCATAAAAAAGCGGGTAATCGAAC--------GAACTAGAAGTGTGGGGAACAAAAAATTCTAGGAGGCATTATTTGTTTTGTTTTCCTA
                         401                                                                                                 
Salvia_aethiopis_1       GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCTTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTTTTTTCGGTTTTCCAGA
Salvia_amarissima_2      GTCTTCGACACAAGAAAAGGAATTTTCCAAA-CCCCCTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGTTTTTCCAGA
Salvia_chinensis_3       GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCCTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGGTTTTACAGA
Salvia_dorrii_4          GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCCTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGGTTTTCCAGA
Salvia_eremostachya_5    GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCCTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGGTTTTCCAGA
Salvia_fruticosa_6       GTCTTCGACACAAGAAAAGGCATTTTCTAAACCCCCTTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGGTTTTCCAGA
Salvia_huberi_7          GTCTTCGACACAAGAAAAGGCATTTTCTAAACCCCCTTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGGTTTTCCAGA
Salvia_kronenburgii_8    GTCTTCGACACAAGAAAAGGCATTTTCTAAACCCCCTTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGGTTTTCCAGA
Salvia_limbata_9         GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCTTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTTTTTTCGGTTTTCCAGA
Salvia_mohavensis_10     GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCCTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGGTTTTCCAGA
Salvia_officinalis_subsp GTCTTCGACACAAGAAAAGGCATTTTCTAAACCCCCTTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGGTTTTCCAGA
Salvia_pachyphylla_12    GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCCTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGGTTTTCCAGA
Salvia_pratensis_13      GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCTTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTTTTTTCGGTTTTCCAGA
Salvia_saccardiana_14    GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCTTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTTTTTTCGGTTTTCCAGA
Salvia_sonomensis_15     GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCCTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGGTTTTCCAGA
Salvia_spathacea_16      GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCCTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTGTTTTCGGTTTTCCAGA
Salvia_verbenaca_17      GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCTTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTTTTTTCGGTTTTCCAGA
Salvia_xanthocheila_18   GTCTTCGACACAAGAAAAGGAATTTTCTAAACCCCCTTTCTTGTGTCGAAAGAGTAATCTGTTTGTCAAAAACTCCTAGTCTTTTTTTCGGTTTTCCAGA
                         501                                                                                                 
Salvia_aethiopis_1       TGTAGTGGAACTTTACTTTTTTTTTCGATTTATTACGTACAATAAAATATAT---------AAAAAAAGTAGTGGACAAAAAAATAAAACTTAGGCAATG
Salvia_amarissima_2      TGTATCGTAACTTTACTTTTTTTTTCGATTTATTACGTATAAT------------------AAATAAAGTAGTGGACAAA--------------------
Salvia_chinensis_3       TGTATCGGAACTTTACTTTTTTTTTCGATTTATTACGTACAATAAAATATATATTATATTTATAGAAAGTAGTGGACAAAAAAATAAAACTTAGTCAATG
Salvia_dorrii_4          TGTATCGGAACTTTAC-TTTTTTTTCGATTTATTACGTATAATAAAATATATA--------AAATAAAGTAGTGGACAAAAAAAGAAAACTTAGTCAATG
Salvia_eremostachya_5    TGTATCGGAACTTTACTTTTTTTTTCGATTTATTACGTATAATAAAATATATA--------AAATAAAGTAGTGGACAAAAAAAGAAAACTTAGTCAATG
Salvia_fruticosa_6       TGTAGCGGAACTTTACTTTTTTTTTCGATTTATTACGTACAATAAAATATATA--------AAAAAAAGTAGTGGACAAAAAAATAAAACTTAGGCAATG
Salvia_huberi_7          TGTAGCGGAACTTTACTTTTTTTTTCGATTTATTACGTACAATAAAATATATA--------AAAAAAAGTAGTGGACAAAAAAATAAAACTTAGGCAATG
Salvia_kronenburgii_8    TGTAGCGGAACTTTACTTTTTTTTTCGATTTATTACGTACAATAAAATATATA--------AAAAAAAGTAGTGGACAAAAAAATAAAACTTAGGCAATG
Salvia_limbata_9         TGTAGCGGAACTTTACTTTTTTTTTCGATTTATTACGTACAATAAAATATAT---------AAAAAAAGTAGTGGACAAAAAAATAAAACTTAGGCAATG
Salvia_mohavensis_10     TGTATCGGAACTTTAC-TTTTTTTTCGATTTATTACGTATAATAAAATATATA--------AAATAAAGTAGTGGACAAAAAAAGAAAACTTAGTCAATG
Salvia_officinalis_subsp TGTAGCGGAACTTTACTTTTTTTTTCGATTTATTACGTACAATAAAATATATA--------AAAAAAAGTAGTGGACAAAAAAATAAAACTTAGGCAATG
Salvia_pachyphylla_12    TGTATCGGAACTTTAC-TTTTTTTTCGATTTATTACGTATAATAAAATATATA--------AAATAAAGTAGTGGACAAAAAAAGAAAACTTAGTCAATG
Salvia_pratensis_13      TGTAGCGGAACTTTACTTTTTTTTTCGATTTATTACGTACAATAAAATATAT---------AAAAAAAGTAGTGGACAAAAAAATAAAACTTAGGCAATG
Salvia_saccardiana_14    TGTAGCGGAACTTTACTTTTTTTTTCGATTTATTACGTACAATAAAATATAT---------AAAAAAAGTAGTGGACAAAAAAATAAAACTTAGGCAATG
Salvia_sonomensis_15     TGTATCGGAACTTTAC-TTTTTTTTCGATTTATTACGTATAATAAAATATATA--------AAATAAAGTAGTGGACAAAAAAAGAAAACTTAGTCAATG
Salvia_spathacea_16      TGTATCGGAACTTTAC-TTTTTTTTCGATTTATTACGTATAATAAAATATATA--------AAATAAAGTAGTGGACAAAAAAAGAAAACTTAGTCAATG
Salvia_verbenaca_17      TGTAGCGGAACTTTAC-TTTTTTTTCGATTTATTACGTACAATAAAATATAT---------AAAAAAAGTAGTGGACAAAAAAATAAAACTTAGGCAATG
Salvia_xanthocheila_18   TGTAGCGGAACTTTACTTTTTTTTTCGATTTATTACGTACAATAAAATATAT---------AAAAAAAGTAGTGGACAAAAAAATAAAACTTAGGCAATG
                         601                                                                                                 
Salvia_aethiopis_1       AACTTTCCATTGA-----TCAAATAT-AAAAAATATAGGGATAAATGGGGTAAGAAAGAGTATAGAAGGTATTTGTGCGAGATCTAATCTACAGAAATCT
Salvia_amarissima_2      ------CCATTGAGATACTCAAATCT-AAAAAATATAGGGATAAGTAGGGTAAGAAAGAGTATCGAAAGTATTTGTGCGAGATCTAATCTACAGAAATAG
Salvia_chinensis_3       AACTTTCCATTGAGATACTCAAATCTCAAAAAATATAGGAATAAATAGGGTAAGAAAGAGTCTAGAAAGTATTTGTGCGAGATCTAATCTACAGAAATAG
Salvia_dorrii_4          AACTTTCCTTTGAGATACTCAAATCT-AAAAAATATAGGGATAAATAGGGTAAGAAAGAGTATCGAAAGTATTTGTGCGAGATCTAATCTACAGAAATAT
Salvia_eremostachya_5    AACTTTCTTTTGAGATACTCAAATCT-AAAAAATATAGGGATAAATAGGGTAAGAAAGAGTATCGAAAGTATTTGTGCGAGATCTAATCTACAGAAATAG
Salvia_fruticosa_6       AACTTTCCATTGAGATACTCAAATAT-AAAAAATATAGGGATAAATGGGGTAAGAAAGAGTATAGAAGGTATTTGTACGAGAACTAATCTGCAG------
Salvia_huberi_7          AACTTTCCATTGAGATACTCAAATAT-AAAAAATATAGGGATAAATGGGGTAAGAAAGAGTATAGAAGGTATTTGTACGAGAACTAATCTGCAG------
Salvia_kronenburgii_8    AACTTTCCATTGAGATACTCAAATAT-AAAAAATATAGGGATAAATGGGGTAAGAAAGAGTATAGAAGGTATTTGTACGAGAACTAATCTGCAG------
Salvia_limbata_9         AACTTTCCATTGA-----TCAAATAT-AAAAAATATAGGGATAAATGGGGTAAGAAAGAGTATAGAAGGTATTTGTGCGAGATCTAATCTACAGAAATCT
Salvia_mohavensis_10     AACTTTCCTTTGAGATACTCAAATCT-AAAAAATATAGGGATAAATAGGGTAAGAAAGAGTATCGAAAGTATTTGTGCGAGATCTAATCTACAGAAATAT
Salvia_officinalis_subsp AACTTTCCATTGAGATACTCAAATAT-AAAAAATATAGGGATAAATGGGGTAAGAAAGAGTATAGAAGGTATTTGTACGAGAACTAATCTGCAG------
Salvia_pachyphylla_12    AACTTTCCTTTGAGATACTCAAATCT-AAAAAATATAGGGATAAATAGGGTAAGAAAGAGTATCGAAAGTATTTGTGCGAGATCTAATCTACAGAAATAT
Salvia_pratensis_13      AACTTTCCATTGAGATACTCAAATAT-AAAAAATATAGGGATAAATGGGGTAAGAAAGAGTATAGAAGGTATTTGTGCGAGATCTAATCTACAGAAATCT
Salvia_saccardiana_14    AACTTTCCATTGAGATACTCAAATAT-AAAAAATATAGGGATAAATGGGGTAAGAAAGAGTATAGAAGGTATTTGTGCGAGATCTAATCTACAGAAATCT
Salvia_sonomensis_15     AACTTTCCTTTGAGATACTCAAATCT-AAAAAATATAGGGATAAATAGGGTAAGAAAGAGTATCGAAAGTATTTGTGCGAGATCTAATCTACAGAAATAT
Salvia_spathacea_16      AACTTTCCTTTGAGATACTCAAATCT-AAAAAATATAGGGATAAATAGGGTAAGAAAGAGTATCGAAAGTATTTGTGCGAGATCTAATCTACAGAAATAT
Salvia_verbenaca_17      AACTTTCCATTGAGATACTCAAATAT-AAAAAATATAGGGATAAATGGGGTAAGAAAGAGTATAGAAGGTATTTGTGCGAGATCTAATCTACAGAAATAG
Salvia_xanthocheila_18   AACTTTCCATTGA-----TCAAATAT-AAAAAATATAGGGATAAATGGGGTAAGAAAGAGTATAGAAGGTATTTGTGCGAGATCTAATCTACAGAAATCT
                         701                                                                                                 
Salvia_aethiopis_1       AATCTGCAGAAATATAAAATATAGAATATTTAT-------ATAAAATAGGATTCTAATCCAGGAAATTGAGTGATTCCCCCTTTGTTCTAACTTGTAAAG
Salvia_amarissima_2      AATCTGCAGAAATAAAAAATATAGAATAATTCT---ATATATAAAATAGAATTAGAATCCAGGAAATTGAGTGATTCCCCCTTTGTTCTAACTTTGAAAG
Salvia_chinensis_3       AATCTGAAGAAACCGAAAATATAGAATAATTATATAATATATAAAATAGAATTATAATCCAGGAAATTGAGTGATTCCCTCTTTGTTCTAACTTGGAAAG
Salvia_dorrii_4          AATCTGCAGAAATAAAAAATATAGAATAATTCT---ATATATAAAATAGAATTAGAATCCGGGAAATTGAGTGATTCCCTCTTTGTTCTAACTTGGAAAG
Salvia_eremostachya_5    AATCTGCAGAAATCAAAAATATAGAATAATTCT---ATATATAAAATAGAATTAGAATCCGGGAAATTGAGTGATTCCCTCTTTGTTCTAACTTGGAAAG
Salvia_fruticosa_6       ----------------AAATATAGAATATTTAT-------ATAAAATAGGATTATAATCCAGGAAATTGAGTGATTCCCCCTTTGTTCTAACTTGCAAAG
Salvia_huberi_7          ----------------AAATATAGAATATTTCT-------ATAAAATAGGATTATAATCCAGGAAATTGAGTGATTCCCCCTTTGTTCTAACTTGCAAAG
Salvia_kronenburgii_8    ----------------AAATATAGAATATTTAT-------ATAAAATAGGATTATAATCCAGGAAATTGAGTGATTCCCCCTTTGTTCTAACTTGCAAAG
Salvia_limbata_9         AATCTGCAGAAATATAAAATATAGAATATTTAT-------ATAAAATAGGATTCTAATCCAGGAAATTGAGTGATTCCCCCTTTGTTCTAACTTGTAAAG
Salvia_mohavensis_10     AATCTGCAGAAATAAAAAATATAGAATAATTCT---ATATATAAAATAGAATTAGAATCCGGGAAATTGAGTGATTCCCTCTTTGTTCTAACTTGGAAAG
Salvia_officinalis_subsp ----------------AAATATAGAATATTTAT-------ATAAAATAGGATTATAATCCAGGAAATTGAGTGATTCCCCCTTTGTTCTAACTTGCAAAG
Salvia_pachyphylla_12    AATCTGCAGAAATAAAAAATATAGAATAATTCT---ATATATAAAATAGAATTAGAATCCGGGAAATTGAGTGATTCCCTCTTTGTTCTAACTTGGAAAG
Salvia_pratensis_13      AATCTGCAGAAATATAAAATATAGAATATTTAT-------ATAAAATAGGATTCTAATCCAGGAAATTGAGTGATTCCCCCTTTGTTCTAACTTGTAAAG
Salvia_saccardiana_14    AATCTGCAGAAATATAAAATATAGAATATTTAT-------ATAAAATAGGATTCTAATCCAGGAAATTGAGTGATTCCCCCTTTGTTCTAACTTGTAAAG
Salvia_sonomensis_15     AATCTGCAGAAATAAAAAATATAGAATAATTCT---ATATATAAAATAGAATTAGAATCCGGGAAATTGAGTGATTCCCTCTTTGTTCTAACTTGGAAAG
Salvia_spathacea_16      AATCTGCAGAAATAAAAAATATAGAATAATTCT---ATATATAAAATAGAATTAGAATCCGGGAAATTGAGTGATTCCCTCTTTGTTCTAACTTGGAAAG
Salvia_verbenaca_17      AATCTGCAGAAATATAAAATATAGAATATTTAT-------ATAAAATAGGATTCTAATCCAGGAAATTGAGTGATTTCCCCTTTGTTCTAACTTGTAAAG
Salvia_xanthocheila_18   AATCTGCAGAAATATAAAATATAGAATATTTAT-------ATAAAATAGGATTCTAATCCGGGAAATTGAGTGATTCCCCCTTTGTTCTAACTTGTAAAG
                         801                                                                                                 
Salvia_aethiopis_1       TACCCATAGATACT------ATCAAGGAAGAGGTGTTTTGAATCAACCAATGCAGTTCATTTTTCAAAAACATCATC-AAAAAAATAGAATGGAGTTTTT
Salvia_amarissima_2      TACCCATAGATACTATCAAGATCAAAGAAGAGGTGTTCTGAATCAACCAATGAAGTTCATTTTTCAAAAGCATCATCAGAAAAAATAGAATGGAGTTTTT
Salvia_chinensis_3       TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTCTGAATCAACCAATGAAGTGCATTTTTCAAAAGCATCATCAGAAAAAATAGAATGGAGTTTTT
Salvia_dorrii_4          TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTCTGAATCAACCAATGAAGTTCATTTTTGAAAAGCATCATCAGAAAAAATAGAATGGAGTTTTT
Salvia_eremostachya_5    TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTCTGAATCAACCAATGAAGTTCATTTTTGAAAAGCATCATCAGAAAAAATAGAATGGAGTTTTT
Salvia_fruticosa_6       TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTCTGAATCAACCAATGCAGTTCATTTTTCAAAAGCATCATCAAAAAAAATAGAATGGAGTTTTT
Salvia_huberi_7          TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTCTGAATCAACCAATGCAGTTCATTTTTCAAAAGCATCATCAAAAAAAATAGAATGGAGTTTTT
Salvia_kronenburgii_8    TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTCTGAATCAACCAATGCAGTTCATTTTTCAAAAGCATCATCAAAAAAAATAGAATGGAGTTTTT
Salvia_limbata_9         TACCCATAGATACT------ATCAAGGAAGAGGTGTTTTGAATCAACCAATGCAGTTCATTTTTCAAAAACATCATC-AAAAAAATAGAATGGAGTTTTT
Salvia_mohavensis_10     TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTCTGAATCAACCAATGAAGTTCATTTTTGAAAAGCATCATCAGAAAAAATAGAATGGAGTTTTT
Salvia_officinalis_subsp TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTCTGAATCAACCAATGCAGTTCATTTTTCAAAAGCATCATCAAAAAAAATAGAATGGCGTTTTT
Salvia_pachyphylla_12    TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTCTGAATCAACCAATGAAGTTCATTTTTGAAAAGCATCATCAGAAAAAATAGAATGGAGTTTTT
Salvia_pratensis_13      TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTTTGAATCAACCAATGCAGTTCATTTTTCAAAAACATCATC-AAAAAAATAGAATGGAGTTTTT
Salvia_saccardiana_14    TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTTTGAATCAACCAATGCAGTTCATTTTTCAAAAACATCATC-AAAAAAATAGAATGGAGTTTTT
Salvia_sonomensis_15     TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTCTGAATCAACCAATGAAGTTCATTTTTGAAAAGCATCATCAGAAAAAATAGAATGGAGTTTTT
Salvia_spathacea_16      TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTCTGAATCAACCAATGAAGTTCATTTTTGAAAAGCATCATCAGAAAAAATAGAATGGAGTTTTT
Salvia_verbenaca_17      TACCCATAGATACTATCAAGATCAAGGAAGAGGTGTTTTGAATCAACCAATGCAGTTCATTTTTCAAAAACATCATC-AAAAAAATAGAATGGAGTTTTT
Salvia_xanthocheila_18   TACCCATAGATACT------ATCAAGGAAGAGGTGTTTTGAATCAACCAATGCAGTTCATTTTTCAAAAACATCATC-AAAAAAATAGAATGGAGTTTTT
                         901                                                                                                 
Salvia_aethiopis_1       TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGAAAAAAAAAACTCTGATTCTTAAGAACCCAACGGGTTCCTTCCCCTCGAATCAGACAAACTAA
Salvia_amarissima_2      TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGACAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCTTTCCCCTCGAATCAGACAAACTAA
Salvia_chinensis_3       TGAACCAGCAGAAAAAGAAATCCACTTTGCCATTTAGACAAAAAAGACTCTGATTCTTAAGAACCCAACGGGCCCTTTCCCCTCGAATCAGACAAACTAA
Salvia_dorrii_4          TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGACAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCTTTCCCCTCGAATCAGACAAACTAA
Salvia_eremostachya_5    TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGACAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCTTTCCCCTCGAATCAGACAAACTAA
Salvia_fruticosa_6       TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGACAAAAAAAACTCCGATTCTTAAGAACCCAACGGGCCCCTTCCCCTCGAATCAGACAAACTAA
Salvia_huberi_7          TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGACAAAAAAAACTCCGATTCTTAAGAACCCAACGGGCCCCTTCCCCTCGAATCAGACAAACTAA
Salvia_kronenburgii_8    TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGACAAAAAAAACTCCGATTCTTAAGAACCCAACGGGCCCCTTCCCCTCGAATCAGACAAACTAA
Salvia_limbata_9         TGAACCAGCAGAAAAATAAATCCACTTTGTCATTTAGAAAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCCTTCCCCTCGAATCAGACAAACTAA
Salvia_mohavensis_10     TGAACCAGCAGAAAAAGAAATCCACT------TTTAGACAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCTTTCCCCTCGAATCAGACAAACTAA
Salvia_officinalis_subsp TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGACAAAAAAAACTCCGATTCTTAAGAACCCAACGGGCCCCTTCCCCTCGAATCAGACAAACTAA
Salvia_pachyphylla_12    TGAACCAGCAGAAAAAGAAATCCACT------TTTAGACAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCTTTCCCCTCGAATCAGACAAACTAA
Salvia_pratensis_13      TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGAAAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCCTTCCCCTCGAATCAGACAAACTAA
Salvia_saccardiana_14    TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGAAAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCCTTCCCCTCGAATCAGACAAACTAA
Salvia_sonomensis_15     TGAACCAGCAGAAAAAGAAATCCACT------TTTAGACAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCTTTCCCCTCGAATCAGACAAACTAA
Salvia_spathacea_16      TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGACAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCTTTCCCCTCGAATCAGACAAACTAA
Salvia_verbenaca_17      TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGAAAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCCTTCCCCTCGAAGCAGACAAACTAA
Salvia_xanthocheila_18   TGAACCAGCAGAAAAAGAAATCCACTTTGTCATTTAGAAAAAAAAAACTCTGATTCTTAAGAACCCAACGGGCCCCTTCCCCTCGAATCAGACAAACTAA
                         1001                                                      
Salvia_aethiopis_1       AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATTCGATTA
Salvia_amarissima_2      AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCTATTA
Salvia_chinensis_3       AGAAGGGAATCCCGTTGAGTTCTTACGCTTTCATGTCACAACTCCATTCATCCGATTA
Salvia_dorrii_4          AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCCATTA
Salvia_eremostachya_5    AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCCATTA
Salvia_fruticosa_6       AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCGATTA
Salvia_huberi_7          AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCGATTA
Salvia_kronenburgii_8    AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCGATTA
Salvia_limbata_9         AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCGATTA
Salvia_mohavensis_10     AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCCATTA
Salvia_officinalis_subsp AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCGATTA
Salvia_pachyphylla_12    AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCCATTA
Salvia_pratensis_13      AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCTATTCATCCGATTA
Salvia_saccardiana_14    AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCTATTCATCCGATTA
Salvia_sonomensis_15     AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCCATTA
Salvia_spathacea_16      AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCCATTA
Salvia_verbenaca_17      AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCGATTA
Salvia_xanthocheila_18   AGAAGGGAATCCCGTTGAGTTCCTACGCTTTCATGTCACAACTCCATTCATCCGATTA

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
petA-psbJ_p1 ATCCATTACGTGTCCAAGGC GTCTCTAGCACGACCACTTG 50.0 55.0 58.0 58.0 1267-1346 bp 1.0 90.7
petA-psbJ_p2 TTTATCCCGACGGAAGCAAG GTCTCTAGCACGACCACTTG 50.0 55.0 58.0 58.0 1531-1610 bp 1.0 90.2
petA-psbJ_p3 TCCGATCGTATTTCTCCCGA GTCTCTAGCACGACCACTTG 50.0 55.0 58.0 58.0 1751-1830 bp 1.0 89.5
petA-psbJ_p4 TTTATCCCGACGGAAGCAAG GAGCCGACAAGGAATTCCAT 50.0 50.0 58.0 58.0 1967-2046 bp 1.0 89.0
petA-psbJ_p5 TTTATCCCGACGGAAGCAAG TCCCTATTCATTGCGGGTTG 50.0 50.0 58.0 57.9 2056-2135 bp 1.0 88.8

Downloads

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