Origin IGS: ataaaaccctcagttaatttaaaataaaaagtatcttgagatagtcttataatataaaacttgctcaagatactatggttattatatcatgtatgtttatatcctgtcaaacataaatttataaaaatttcaatttgttcacatttaaatataccggttgcattatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaataatgcaaccggtatatttaaatgtgaacaaattgaaatttttataaatttatgtttgacaggatataaacatacatgatataataaccatagtatcttgagcaagttttatattataagactatctcaagatactttttattttaaattaactgagggttttat Mask Tandem Repeat Region ================================================ ataaaaccctcagttaatttaaaataaaaagtatcttgagatagtcttataatataaaacttgctcaagatactatggttattatatcatgtatgtttatatcctgtcaaacataaatttataaaaatttcaatttgttcacatttaaatataccggttgcattatttt Find is-nt database================================================ Query_seq: TDE1870:TDE1871|TDE1870:TDE1871:CAAX amino terminal protease family protein:hypothetical protein:<-<-:1893583..1893751 169 ataaaaccctcagttaatttaaaataaaaagtatcttgagatagtcttataatataaaacttgctcaagatactatggttattatatcatgtatgtttatatcctgtcaaacataaatttataaaaatttcaatttgttcacatttaaatataccggttgcattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1870:TDE1871|TDE1870:TDE1871:CAAX amino terminal protease family protein:hypothetical protein:<-<-:1893583..1893751 169 ataaaaccctcagttaatttaaaataaaaagtatcttgagatagtcttataatataaaacttgctcaagatactatggttattatatcatgtatgtttatatcctgtcaaacataaatttataaaaatttcaatttgttcacatttaaatataccggttgcattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1870:TDE1871|TDE1870:TDE1871:CAAX amino terminal protease family protein:hypothetical protein:<-<-:1893583..1893751 169 ataaaaccctcagttaatttaaaataaaaagtatcttgagatagtcttataatataaaacttgctcaagatactatggttattatatcatgtatgtttatatcctgtcaaacataaatttataaaaatttcaatttgttcacatttaaatataccggttgcattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaaaccctcagttaatttaaaataaaaagtatcttgagatagtcttataatataaaacttgctcaagatactatggttattatatcatgtatgtttatatcctgtcaaacataaatttataaaaatttcaatttgttcacatttaaatataccggttgcattatttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 61 End: 168 ............................................................ M L K I L W L L Y H V C L Y P V K H K F I K I S I C S H L N I P V A L F . ataaaaccctcagttaatttaaaataaaaagtatcttgagatagtcttataatataaaacttgctcaagatactatggttattatatcatgtatgtttatatcctgtcaaacataaatttataaaaatttcaatttgttcacatttaaatataccggttgcattatttt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataaaaccctcagttaatttaaaataaaaagtatcttgagatagtcttataatataaaacttgctcaagatactatggttattatatcatgtatgtttatatcctgtcaaacataaatttataaaaatttcaatttgttcacatttaaatataccggttgcattatttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -13.0 Tail_Score: -5.49568 Start: 31 End: 73 Full_Region: gatataataaccata gtatcttgagcaagttttat att ataagactatctcaagatac tttttattttaaatt ..............................gtatcttgagcaagttttatattataagactatctcaagatac................................................................................................ Find igs database================================================ Query_seq: TDE1870:TDE1871|TDE1870:TDE1871:CAAX amino terminal protease family protein:hypothetical protein:<-<-:1893583..1893751 169 ataaaaccctcagttaatttaaaataaaaagtatcttgagatagtcttataatataaaacttgctcaagatactatggttattatatcatgtatgtttatatcctgtcaaacataaatttataaaaatttcaatttgttcacatttaaatataccggttgcattatttt Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: NC_002967_TDE1870_TDE1871|CAAX amino terminal protease family protein:hypothetical protein|NEGATIVE:NEGATIVE|[1893583,1893751]|169 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 ataaaaccctcagttaatttaaaataaaaagtatcttgagatagtcttataatataaaacttgctcaagatactatggttattatatcatgtatgtttatatcctgtcaaacataaatttataaaaatttcaatttgttcacatttaaatataccggttgcattatttt ataaaaccctcagttaatttaaaataaaaagtatcttgagatagtcttataatataaaacttgctcaagatactatggttattatatcatgtatgtttatatcctgtcaaacataaatttataaaaatttcaatttgttcacatttaaatataccggttgcattatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAACCCUCAGUUAAUUUAAAAUAAAAAGUAUCUUGAGAUAGUCUUAUAAUAUAAAACUUGCUCAAGAUACUAUGGUUAUUAUAUCAUGUAUGUUUAUAUCCUGUCAAACAUAAAUUUAUAAAAAUUUCAAUUUGUUCACAUUUAAAUAUACCGGUUGCAUUAUUUU ....((((..............(((((..(((((((((((..(((.((((...)))).)))..)))))))))))....))))).......(((((((((........((((...((((((....))))))...))))........))))))))).)))).......... (-29.89) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAAUGCAACCGGUAUAUUUAAAUGUGAACAAAUUGAAAUUUUUAUAAAUUUAUGUUUGACAGGAUAUAAACAUACAUGAUAUAAUAACCAUAGUAUCUUGAGCAAGUUUUAUAUUAUAAGACUAUCUCAAGAUACUUUUUAUUUUAAAUUAACUGAGGGUUUUAU ...((((.((...((((..(((((((.(((((.............(((((.((.((((((((........)))))))).))..))))).......(((((((((((..((((((((...))))))))..))))))))))).))))))))))))..))))...)).)))) (-33.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 758 110 61 201 152 NC_002967:TDE1870|5end_CAAX_amino_terminal_protease_family_protein_1893492..1893722_NEGATIVE 242 90 60 72 48 NC_002967:TDE0828|5end_glucose-inhibited_division_protein_A_850169..850399_NEGATIVE 237 108 61 140 105 NC_002967:TDE1990|5end_ATP-dependent_helicase,_DinG_family_2008496..2008726_NEGATIVE 237 136 96 81 35 NC_002967:TDE1874|5end_hypothetical_protein_1895762..1895992_NEGATIVE 211 109 65 119 66 NC_002967:TDE0077|5end_glycine_reductase_complex_proprotein_GrdE1_88732..88962_NEGATIVE 209 105 62 102 62 NC_002967:TDE2675|5end_hypothetical_protein_2713374..2713604_POSITIVE 208 107 71 163 128 NC_002967:TDE0799|5end_glycerophosphoryl_diester_phosphodiesterase,_putative_822609..822839_POSITIVE 207 49 6 157 97 NC_002967:TDE2421|5end_DNA-directed_RNA_polymerase_beta_subunit_2452762..2452992_NEGATIVE 204 38 4 73 39 NC_002967:TDE2182|5end_hypothetical_protein_2215035..2215265_NEGATIVE 199 69 24 165 126 NC_002967:TDE2530|5end_radical_SAM_domain_protein_2557362..2557592_POSITIVE 199 45 8 40 4 NC_002967:TDE0280|5end_PIN_domain_protein_310296..310526_NEGATIVE 197 70 21 181 119 NC_002967:TDE0477|5end_hypothetical_protein_534277..534507_NEGATIVE 195 109 65 59 6 NC_002967:TDE0453|5end_hypothetical_protein_510364..510594_NEGATIVE 194 110 63 209 149 NC_002967:TDE1762|5end_hydrolase,_haloacid_dehalogenase-like_family_1810904..1811134_NEGATIVE 193 81 60 69 49 NC_002967:TDE0425|5end_bacteriocin_ABC_transporter,_ATP-binding/permease,_putative_479700..479930_POSITIVE 188 113 75 175 140 NC_002967:TDE1244|5end_TPR_domain_protein_1275823..1276053_POSITIVE 185 110 74 128 94 NC_002967:TDE1960|5end_hypothetical_protein_1974298..1974528_POSITIVE 183 109 64 149 98 NC_002967:TDE2009|5end_hypothetical_protein_2030382..2030612_POSITIVE 183 97 61 73 24 NC_002967:TDE0543|5end_hypothetical_protein_583126..583356_POSITIVE 174 121 96 224 202 NC_002967:TDE1873|5end_hypothetical_protein_1895595..1895825_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 90 60 56 32 NC_002967:TDE0829|3end_putative_aminopeptidase_2_850185..850335_NEGATIVE 222 104 61 76 26 NC_002967:TDE2490|3end_primosomal_protein_N'_2512703..2512853_NEGATIVE 211 109 65 106 53 NC_002967:TDE0078|3end_glycine_reductase_complex_selenoprotein_GrdB1_88745..88895_NEGATIVE 199 45 8 43 7 NC_002967:TDE0281|3end_hypothetical_protein_310293..310443_NEGATIVE 193 109 62 57 9 NC_002967:TDE0471|3end_BNR_domain_protein_526657..526807_NEGATIVE 193 81 60 62 42 NC_002967:TDE0424|3end_bacteriocin-type_signal_domain_protein_479773..479923_POSITIVE 183 109 64 102 51 NC_002967:TDE2008|3end_ABC_transporter,_ATP-binding/permease_protein_2030415..2030565_POSITIVE 177 95 55 131 85 NC_002967:TDE0096|3end_NADH_oxidase_114137..114287_POSITIVE 174 158 129 63 32 NC_002967:TDE0383|3end_hypothetical_protein_435159..435309_POSITIVE 172 80 39 146 102 NC_002967:TDE1322|3end_hypothetical_protein_1360020..1360170_NEGATIVE 172 64 27 122 81 NC_002967:TDE0649|3end_hypothetical_protein_684034..684184_NEGATIVE 171 94 61 98 62 NC_002967:TDE1752|3end_ISTde2,_transposase_1804322..1804472_NEGATIVE 171 108 64 144 109 NC_002967:TDE1089|3end_hypothetical_protein_1119970..1120120_NEGATIVE 171 94 61 98 62 NC_002967:TDE1022|3end_ISTde2,_transposase_1053912..1054062_NEGATIVE 171 90 59 47 15 NC_002967:TDE0700|3end_hypothetical_protein_735331..735481_NEGATIVE 171 97 60 57 12 NC_002967:TDE0586|3end_hypothetical_protein_625640..625790_POSITIVE 171 158 118 86 54 NC_002967:TDE0343|3end_hydrolase,_alpha/beta_fold_family_384247..384397_NEGATIVE 171 94 61 98 62 NC_002967:TDE0140|3end_ISTde2,_transposase_163887..164037_POSITIVE 167 80 31 142 95 NC_002967:TDE0769|3end_ribosomal_protein_L23_807998..808148_POSITIVE 165 50 7 146 99 NC_002967:TDE2297|3end_TPR_domain_protein_2336339..2336489_NEGATIVE