| 1 | /*ARBDB ASCII*/ |
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| 2 | genom_db %i 0 |
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| 3 | presets %% (% |
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| 4 | alignment :6000 %% (% |
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| 5 | alignment_name :7600 "ali_mini" |
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| 6 | alignment_len :7000 %i 187 |
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| 7 | aligned :7000 %i 1 |
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| 8 | alignment_write_security :7600 %i 0 |
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| 9 | alignment_type :7000 "rna" |
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| 10 | auto_format %i 0 |
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| 11 | alignment_rem "<NONE>" |
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| 12 | %) /*alignment*/ |
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| 13 | |
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| 14 | key_data %% (% |
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| 15 | key %% (% |
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| 16 | key_name "name" |
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| 17 | key_type %i 12 |
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| 18 | key_hidden %i 0 |
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| 19 | %) /*key*/ |
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| 20 | |
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| 21 | key %% (% |
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| 22 | key_name "acc" |
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| 23 | key_type %i 12 |
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| 24 | key_hidden %i 0 |
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| 25 | %) /*key*/ |
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| 26 | |
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| 27 | key %% (% |
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| 28 | key_name "ali_mini" |
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| 29 | key_type %i 15 |
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| 30 | key_hidden %i 0 |
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| 31 | %) /*key*/ |
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| 32 | |
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| 33 | key %% (% |
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| 34 | key_name "ali_mini/data" |
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| 35 | key_type %i 12 |
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| 36 | key_hidden %i 0 |
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| 37 | %) /*key*/ |
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| 38 | |
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| 39 | %) /*key_data*/ |
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| 40 | |
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| 41 | use "ali_mini" |
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| 42 | %) /*presets*/ |
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| 43 | |
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| 44 | species_data %% (% |
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| 45 | species %% (% |
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| 46 | name :7600 "BcSSSS00" |
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| 47 | ali_mini %% (% |
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| 48 | data :7000 "UUUAUCGGAGAGUUUGAUCAAGUCGAGCGG--ACAGA----U--GGGAGCUUGCUCCC-------UGAU--GUUAGCGGC-GGACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGU-GAUGAUUGGGGUGAAGUCGUAACAA-GGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU" |
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| 49 | %) /*ali_mini*/ |
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| 50 | |
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| 51 | acc "ARB_2CA9F764" |
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| 52 | %) /*species*/ |
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| 53 | |
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| 54 | species %% (% |
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| 55 | name :7600 "Bl0LLL00" |
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| 56 | ali_mini %% (% |
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| 57 | data :7000 "........AGAGUUUGAUCAAGUCGAGCGG--ACCGA----C--GGGAGCUUGCUCCC-------UUAG--GUCAGCGGC-GGACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGCU-GAUGAUUGGGGUGAAGUCGUAACAA-GGUAGCCGUAUCGGAAGGUGCGGCUGGAUC..........." |
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| 58 | %) /*ali_mini*/ |
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| 59 | |
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| 60 | start %i 10 |
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| 61 | stop %i 20 |
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| 62 | acc "ARB_6B04C30A" |
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| 63 | %) /*species*/ |
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| 64 | |
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| 65 | species %% (% |
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| 66 | name :7600 "ClnCorin" |
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| 67 | ali_mini %% (% |
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| 68 | data :7000 ".........GAGUUUGAUCAAGUCGAG-------CGA----U--GAAGUUCCUUCGGGA------AUGG--AUUAGCGGC-GGACGGGCCUUUCGAAAGGAAGAUUAAUACCGCAUAAG-ACAGCGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGAGAACCUU--GCCUGGCUGGAUCAUC.." |
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| 69 | %) /*ali_mini*/ |
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| 70 | |
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| 71 | acc "ARB_CEB24FD3" |
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| 72 | %) /*species*/ |
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| 73 | |
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| 74 | species %% (% |
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| 75 | name :7600 "CltBotul" |
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| 76 | ali_mini %% (% |
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| 77 | data :7000 "................AUCAAGUCGAG-------CGA----U--GAAGCUUCUUCGGAA------GUGG--AUUAGCGGC-GGACGGGCCUUUCGAAAGGAAGAUUAAUACCUCAUAAG-ACAGCGAUUGGGGUGAAGUCGUAACAG---------------G--U------------------U.." |
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| 78 | %) /*ali_mini*/ |
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| 79 | |
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| 80 | acc "ARB_4FCDD74F" |
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| 81 | %) /*species*/ |
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| 82 | |
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| 83 | species %% (% |
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| 84 | name :7600 "CPPParap" |
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| 85 | ali_mini %% (% |
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| 86 | data :7000 "NNNNNNGA-GAGUUUGAUCAAGUCGAG-------CGA----U--GAAGUUCCUUCGGGA------ACGG--AUUAGCGGC-GGACGGGCCUUCCGAAAGGAAGAUUAAUACCGCAUAAGAUCAGCGAUUGGGGU-AAGUCGUAACAAGGUAGCCGUAGGAGAACCUGCGGNUGGAUCACCUCCUU.." |
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| 87 | %) /*ali_mini*/ |
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| 88 | |
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| 89 | acc "ARB_CF69AC5C" |
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| 90 | %) /*species*/ |
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| 91 | |
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| 92 | species %% (% |
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| 93 | name :7600 "ClfPerfr" |
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| 94 | ali_mini %% (% |
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| 95 | data :7000 "-AAAUUGA-GAGUUUGAUCAAGUCGAG-------CGA----U--GAAGUUUCCUUCGGGAA----ACGG--AUUAGCGGCGGGACGGGCCUUCAGAACCUGCGGCUGGAUCAUCAUAAUGCAGCGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGCGAAAGGAAGAUUAAUACCCCUCCUUUCU" |
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| 96 | %) /*ali_mini*/ |
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| 97 | |
|---|
| 98 | acc "ARB_5BEE4C92" |
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| 99 | %) /*species*/ |
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| 100 | |
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| 101 | species %% (% |
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| 102 | name :7600 "DlcTolu2" |
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| 103 | ali_mini %% (% |
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| 104 | data :7000 "........AGAGUUUGAUCAAGUCGAACGA--G-AA-----AGGGAUUGCUUGCAAUCCU------GAG--UAGAGUGGC-GCACGGACUGCCCGAAAGGACAGCUAAUACCGGAUGAA-GAUAAUUGGGGUGAAGUCGUAACAA-GGUAGCCGUUGAGGAAUCAGCGGCUGGAUCACCUCCUUNNN" |
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| 105 | %) /*ali_mini*/ |
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| 106 | |
|---|
| 107 | acc "ARB_815E94DB" |
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| 108 | %) /*species*/ |
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| 109 | |
|---|
| 110 | species %% (% |
|---|
| 111 | name :7600 "PbcAcet2" |
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| 112 | ali_mini %% (% |
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| 113 | data :7000 "........AGAGUUUGAUCAAGUCGAACGU--G-AA-----A--GGGACUUCGGUCCU--------GAG--UAAAGUGGC-GCACGGACACUUCGAAAGGGGUGCUAAUACCGGAUAAG-GGUAACUGGGGUGAAGUCGUAACAA-GGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUUNN" |
|---|
| 114 | %) /*ali_mini*/ |
|---|
| 115 | |
|---|
| 116 | acc "ARB_CC2D184F" |
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| 117 | %) /*species*/ |
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| 118 | |
|---|
| 119 | species %% (% |
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| 120 | name :7600 "PbrPropi" |
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| 121 | ali_mini %% (% |
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| 122 | data :7000 "........AGAGUUUGAUCAAGUCGAACGG--G-AUU----A--AGGGGCUUGCUCCU--------UAA--UCUAGUGGC-GCACGGACACUUCGAAAGAGGUGCUAAUACCUGAUAAG-GGUGACUGGGGUGAAGUCGUAACAA-GGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUUNN" |
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| 123 | %) /*ali_mini*/ |
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| 124 | |
|---|
| 125 | acc "ARB_2B59EE6C" |
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| 126 | %) /*species*/ |
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| 127 | |
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| 128 | species %% (% |
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| 129 | name :7600 "Stsssola" |
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| 130 | ali_mini %% (% |
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| 131 | data :7000 "AAACUGG-AGAGUUUGAUCAAGUCGAACGU--G-AA-----A-----GUCUUCGGGAU--------GAG--UAAAGUGGC-GCACGGACGGCUGGAAACGGUCGCUAAUACCGGAUAAC-AAUGAUUGGGGUGAAGUCGUAACAA-GGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUU.." |
|---|
| 132 | %) /*ali_mini*/ |
|---|
| 133 | |
|---|
| 134 | acc "ARB_219182CE" |
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| 135 | %) /*species*/ |
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| 136 | |
|---|
| 137 | species %% (% |
|---|
| 138 | name :7600 "DsssDesu" |
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| 139 | ali_mini %% (% |
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| 140 | data :7000 "-AACUGG-AGAGUUUGAUCAAGUCGUACGA--G-AA-----AGGGG----CUUCGGCCCU------GAG--UAGAGUGGC-GCACGGACUCUGCGAAAGUGGAGCUAAUACCGGAUACA-G--------------A--------------------------------------------------G" |
|---|
| 141 | %) /*ali_mini*/ |
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| 142 | |
|---|
| 143 | acc "ARB_2F95EE99" |
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| 144 | %) /*species*/ |
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| 145 | |
|---|
| 146 | species %% (% |
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| 147 | name :7600 "LgtLytic" |
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| 148 | ali_mini %% (% |
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| 149 | data :7000 "........AGAGUUUGAUCAAGUCGAACGGCAG-CACAGUCU--AGCUUGCUAGACGG--------GUG--GCGAGNGGC-GAACGGACUUGGGGAAACUCAAGCUAAUACCGCAUAAU-CAUGACUGGGGUGAAGUCGUAACAA-GGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUN..." |
|---|
| 150 | %) /*ali_mini*/ |
|---|
| 151 | |
|---|
| 152 | acc "ARB_470564F9" |
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| 153 | %) /*species*/ |
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| 154 | |
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| 155 | species %% (% |
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| 156 | name :7600 "DcdNodos" |
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| 157 | ali_mini %% (% |
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| 158 | data :7000 "......AACUGAAGAGUUUGAUCAAGUCGAACGGGGUUAUGU----AGCUUGCUAUGUAA-----------CCUAGUGGC-GGACGGACGUAUGGAAACGUACGCUAAUACCGCAUAAG-GAUGACUGGGGUGAAGUCGUAACAA-GGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUU." /* unformatted sequence (shorter than ali) */ |
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| 159 | %) /*ali_mini*/ |
|---|
| 160 | |
|---|
| 161 | acc "ARB_30B40050" |
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| 162 | %) /*species*/ |
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| 163 | |
|---|
| 164 | species %% (% |
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| 165 | name :7600 "FrhhPhil" |
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| 166 | ali_mini %% (% |
|---|
| 167 | data :7000 "UUG-----AAGAGUUGAUCAAGUCGAACGG--U-AA-----C--AGGUCUUCGGAUGC--------UGA--CGA-GUGGC-GGACGGCCAGUUGGAAACGACUGUUAAUACCGCAUAAU-CAUGACUGGGGUGAAGUCGUAACAAUGGUAGCCGUA-GGGAACCUGCGGCUGGAUCACCUCCUU..." |
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| 168 | %) /*ali_mini*/ |
|---|
| 169 | |
|---|
| 170 | acc "ARB_948948A3" |
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| 171 | %) /*species*/ |
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| 172 | |
|---|
| 173 | species %% (% |
|---|
| 174 | name :7600 "PsAAAA00" |
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| 175 | ali_mini %% (% |
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| 176 | data :7000 "N-----UACUGAAGAGUUUGAUCAAGUCGAGCGGAUG---AAGGG-AGCUUGCUCCUGGAUUC--------A---GCGGC-GGACGGACGUCCGGAAACGGGCGCUAAUACCGCAUACG-CAU------G--G------UAACAA-GG------------AA----C---C------------UG.." |
|---|
| 177 | %) /*ali_mini*/ |
|---|
| 178 | |
|---|
| 179 | acc "ARB_AEBB7869" |
|---|
| 180 | %) /*species*/ |
|---|
| 181 | |
|---|
| 182 | species %% (% |
|---|
| 183 | name :7600 "PslFlave" |
|---|
| 184 | ali_mini %% (% |
|---|
| 185 | data :7000 "........AGAGUUUGAUCAAGUCGAGCGGU...AGGGG-----AGCUUGCUCCCUGA--------UUC-----AGCGGC-GGACGGACGUUUCGAAAGGAACGCUAAUACCGCAUACG-CAUGACUGGGGUGAAGUCGUAACAA-GGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCU...." |
|---|
| 186 | %) /*ali_mini*/ |
|---|
| 187 | |
|---|
| 188 | acc "ARB_1763CF6" |
|---|
| 189 | %) /*species*/ |
|---|
| 190 | |
|---|
| 191 | species %% (% |
|---|
| 192 | name :7600 "HllHalod" |
|---|
| 193 | ali_mini %% (% |
|---|
| 194 | data :7000 "........AGAGUUUGAUCAAGUCGAGCGG--A-AACGAUGG--AAGCUUGCUUCCAG--------GCG--UCGAGCGGC-GGACGGACCUGGGGAAACUCAGGCUAAUACCGCAUACG-CAUGACUGGGGUGAAGUCGUAACAA-GGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUU..." |
|---|
| 195 | %) /*ali_mini*/ |
|---|
| 196 | |
|---|
| 197 | acc "ARB_2180C521" |
|---|
| 198 | %) /*species*/ |
|---|
| 199 | |
|---|
| 200 | species %% (% |
|---|
| 201 | name :7600 "VbrFurni" |
|---|
| 202 | ali_mini %% (% |
|---|
| 203 | data :7000 "........AGAGUUUGAUCAAGUCGAGCGG--C-AGCGACA-ACAUUGAACCUUCGGGGGAUUUGUUGGGCGGCGAGCGGCGGACGGACCAUUGGAAACGAUGGCUAAUACCGCAUGAU-CAUGACUGGGGUGAAGUCGUAACAA-GGUAGCGCUAGGGGAACCUGGCGCUGGAUCACCUCCUUU.." |
|---|
| 204 | %) /*ali_mini*/ |
|---|
| 205 | |
|---|
| 206 | start %i 20 |
|---|
| 207 | stop %i 170 |
|---|
| 208 | acc "ARB_4C6C9E8C" |
|---|
| 209 | %) /*species*/ |
|---|
| 210 | |
|---|
| 211 | species %% (% |
|---|
| 212 | name :7600 "VblVulni" |
|---|
| 213 | ali_mini %% (% |
|---|
| 214 | data :7000 "........AGAGUUUGAUCAAGUCGAGCGG--C-AGC-----ACAGAGAAACUUG------UUUCUCGGGUGGCGAGCGGCGGACGGACCAUUGGAAACGAUGGCUAAUACCGCAUGAU-CAUGACUGGGGUGAAGUCGUAACAA-GGUAGCGCUAGGGGAACCUGGCGCUGGAUCACCUCCUUU.." |
|---|
| 215 | %) /*ali_mini*/ |
|---|
| 216 | |
|---|
| 217 | acc "ARB_4E1D58F9" |
|---|
| 218 | %) /*species*/ |
|---|
| 219 | |
|---|
| 220 | species %% (% |
|---|
| 221 | name :7600 "VbhChole" |
|---|
| 222 | ali_mini %% (% |
|---|
| 223 | data :7000 "........AGAGUUUGAUCAAGUCGAGCGG--C-AGC-----ACAGAGGAACUUG------UUCCUUGGGUGGCGAGCGGCGGACGGACCAUUGGAAACGAUGGCUAAUACCGCAUAAC-CAUGACUGGGGUGAAGUCGUAACAA-GGUAGCGCUAGGGGAACCUGGCGCUGGAUCACCUCCUUU.." |
|---|
| 224 | %) /*ali_mini*/ |
|---|
| 225 | |
|---|
| 226 | acc "ARB_FD102EA4" |
|---|
| 227 | %) /*species*/ |
|---|
| 228 | |
|---|
| 229 | species %% (% |
|---|
| 230 | name :7600 "AclPleur" |
|---|
| 231 | ali_mini %% (% |
|---|
| 232 | data :7000 "UG----AAUUGAAGAGUUUGAUCAAGUCGAACGGUAACGGGAAGGGAGCUUGCUUUCUUUGCCG-------ACGAGUGGC-GGACGGACUACGGGAAACUGUAGCUAAUACCGCGUAAU-CAUGACUGGGGUGAAGUCGUAGCAA-GGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA.." |
|---|
| 233 | %) /*ali_mini*/ |
|---|
| 234 | |
|---|
| 235 | acc "ARB_9E1D1B16" |
|---|
| 236 | %) /*species*/ |
|---|
| 237 | |
|---|
| 238 | species %% (% |
|---|
| 239 | name :7600 "PtVVVulg" |
|---|
| 240 | ali_mini %% (% |
|---|
| 241 | data :7000 "U-----AAUUGAAGAGUUUGAUCAAGUCGAGCGGU...AGGAGAA-AGCUUGCUUUCUUGCUG--------ACGAGCGGC-GGACGGACUACUGGAAACGGUGGCUAAUACCGCAUGAC-CAUGACUGGGGUGAAGUCGUAACAA-GGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA.." |
|---|
| 242 | %) /*ali_mini*/ |
|---|
| 243 | |
|---|
| 244 | acc "ARB_ED8B86F" |
|---|
| 245 | %) /*species*/ |
|---|
| 246 | |
|---|
| 247 | %) /*species_data*/ |
|---|
| 248 | |
|---|
| 249 | extended_data :7000 %% (% |
|---|
| 250 | extended %% (% |
|---|
| 251 | name :7000 "ECOLI" |
|---|
| 252 | errors %i 0 |
|---|
| 253 | acc "J01695" |
|---|
| 254 | full_name "Escherichia coli" |
|---|
| 255 | ali_mini %% (% |
|---|
| 256 | data :7000 ".AAAUUGAAGAGUUUGAUCAUG----UCGAGCGGGCGGAACACAUGCAAAGCUUGCUUCUUUGCG------ACGAGUGGC-GGACGGGUGAGGGGAAACGGUAGCUAAUACCGCAUAAC-GAUGACUAAAGUUAAUACCUAUUGA-CGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAG.." |
|---|
| 257 | %) /*ali_mini*/ |
|---|
| 258 | |
|---|
| 259 | %) /*extended*/ |
|---|
| 260 | |
|---|
| 261 | %) /*extended_data*/ |
|---|
| 262 | |
|---|
| 263 | tree_data :7000 %% (% |
|---|
| 264 | tree_ph_24306 %% (% |
|---|
| 265 | tree "N0.03618,0.03618;N0.04082,0.06452;N0.0404,0.28364;N0.0473,0.2638;N0.06826,0.13072;N0.09494,0.11285;LHllHalod\ALLgtLytic\ALPslFlave\AN0.04416,0.07602;N0.02484,0.01242;LVbhChole\ALVblVulni\ALVbrFurni\AN0.13971,0.16265;N0.02,0.35135;N0.07947,0.09524;LClnCorin\ALCPPParap\ALCltBotul\ALClfPerfr\AN0.28846,0.2;N0.06844,0.10559;N0.06211,0.58369;N0.09357,0.06548;LAclPleur\ALPtVVVulg\ALPsAAAA00\ALDcdNodos\ALFrhhPhil\AN0.19802,0.06369;N0.04192,0.02516;LBcSSSS00\ALBl0LLL00\AN0.04516,0.04487;N0.03974,0.04516;N0.09717,0.10759;N0.10726,0.77778;LDlcTolu2\ALDsssDesu\ALStsssola\ALPbcAcet2\ALPbrPropi\A" |
|---|
| 266 | nnodes %i 21 |
|---|
| 267 | remark "PRG=neighbor CORR=F84 FILTER=none PKG=phylip\n\nSun Aug 22 21:38:37 2010: Loaded from outtree\n\nTree loaded from 'outtree' on Sun Aug 22 21:38:37 2010\nSun Aug 22 22:01:06 2010: tree_ph_24306 saved to /home/ralf/data/db/ph_24306.tree\nSun Aug 22 22:02:33 2010: Loaded from /home/ralf/data/db/ph_24306.tree\n" |
|---|
| 268 | security %i 0 |
|---|
| 269 | ruler %% (% |
|---|
| 270 | size %f 0.1 |
|---|
| 271 | LIST %% (% |
|---|
| 272 | ruler_y %f 0 |
|---|
| 273 | ruler_x %f 0 |
|---|
| 274 | text_x %f 0 |
|---|
| 275 | text_y %f 0 |
|---|
| 276 | %) /*LIST*/ |
|---|
| 277 | |
|---|
| 278 | ruler_width %i 0 |
|---|
| 279 | %) /*ruler*/ |
|---|
| 280 | |
|---|
| 281 | %) /*tree_ph_24306*/ |
|---|
| 282 | |
|---|
| 283 | %) /*tree_data*/ |
|---|
| 284 | |
|---|
| 285 | focus %% (% |
|---|
| 286 | tree_name "tree_ph_24306" |
|---|
| 287 | %) /*focus*/ |
|---|
| 288 | |
|---|
| 289 | description "db for unit-test pt-server" |
|---|
| 290 | checks %% (% |
|---|
| 291 | check "fix gene_data" |
|---|
| 292 | check "fix_dict_compress" |
|---|
| 293 | check "del_mark_move_REF" |
|---|
| 294 | check "duplicated_item_colors" |
|---|
| 295 | %) /*checks*/ |
|---|
| 296 | |
|---|
