Origin IGS: aaaagtcctccatctgttatttatacagaaaatgatatgagggaaaattccctcctcactataacataaagataaggtattgtctagttagtataagatgtgatataaatattat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataatatttatatcacatcttatactaactagacaataccttatctttatgttatagtgaggagggaattttccctcatatcattttctgtataaataacagatggaggactttt Mask Tandem Repeat Region ================================================ aaaagtcctccatctgttatttatacagaaaatgatatgagggaaaattccctcctcactataacataaagataaggtattgtctagttagtataagatgtgatataaatattat Find is-nt database================================================ Query_seq: TDE1118:TDE1119|TDE1118:TDE1119:tyrosine phenol-lyase:hypothetical protein:<-->:1151352..1151466 115 aaaagtcctccatctgttatttatacagaaaatgatatgagggaaaattccctcctcactataacataaagataaggtattgtctagttagtataagatgtgatataaatattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1118:TDE1119|TDE1118:TDE1119:tyrosine phenol-lyase:hypothetical protein:<-->:1151352..1151466 115 aaaagtcctccatctgttatttatacagaaaatgatatgagggaaaattccctcctcactataacataaagataaggtattgtctagttagtataagatgtgatataaatattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1118:TDE1119|TDE1118:TDE1119:tyrosine phenol-lyase:hypothetical protein:<-->:1151352..1151466 115 aaaagtcctccatctgttatttatacagaaaatgatatgagggaaaattccctcctcactataacataaagataaggtattgtctagttagtataagatgtgatataaatattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaagtcctccatctgttatttatacagaaaatgatatgagggaaaattccctcctcactataacataaagataaggtattgtctagttagtataagatgtgatataaatattat Predict ORF larger than 30AA ================================================ aaaagtcctccatctgttatttatacagaaaatgatatgagggaaaattccctcctcactataacataaagataaggtattgtctagttagtataagatgtgatataaatattat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 58 End: 87 .........................................................CTAGACAATACCTTATCTTTATGTTATAGT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaagtcctccatctgttatttatacagaaaatgatatgagggaaaattccctcctcactataacataaagataaggtattgtctagttagtataagatgtgatataaatattat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1118:TDE1119|TDE1118:TDE1119:tyrosine phenol-lyase:hypothetical protein:<-->:1151352..1151466 115 aaaagtcctccatctgttatttatacagaaaatgatatgagggaaaattccctcctcactataacataaagataaggtattgtctagttagtataagatgtgatataaatattat Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002967_TDE1118_TDE1119|tyrosine phenol-lyase:hypothetical protein|NEGATIVE:POSITIVE|[1151352,1151466]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 aaaagtcctccatctgttatttatacagaaaatgatatgagggaaaattccctcctcactataacataaagataaggtattgtctagttagtataagatgtgatataaatattat aaaagtcctccatctgttatttatacagaaaatgatatgagggaaaattccctcctcactataacataaagataaggtattgtctagttagtataagatgtgatataaatattat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGUCCUCCAUCUGUUAUUUAUACAGAAAAUGAUAUGAGGGAAAAUUCCCUCCUCACUAUAACAUAAAGAUAAGGUAUUGUCUAGUUAGUAUAAGAUGUGAUAUAAAUAUUAU ............(((((.......)))))..(((((((((((((....)))))).((((((((......((((((....))))))......))))....)))).....))))))) (-21.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUAUUUAUAUCACAUCUUAUACUAACUAGACAAUACCUUAUCUUUAUGUUAUAGUGAGGAGGGAAUUUUCCCUCAUAUCAUUUUCUGUAUAAAUAACAGAUGGAGGACUUUU ......................................((((((((((((..((((((((.((((((....))))))...)))....)))))...)))).)))).))))...... (-22.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 810 60 11 151 102 NC_002967:TDE1118|5end_tyrosine_phenol-lyase_1151261..1151491_NEGATIVE 269 67 37 178 141 NC_002967:TDE1497|5end_hypothetical_protein_1543208..1543438_POSITIVE 246 88 47 167 110 NC_002967:TDE1157|5end_phage_terminase,_large_subunit,_putative_1193293..1193523_NEGATIVE 245 44 1 164 119 NC_002967:TDE1884|5end_hypothetical_protein_1906857..1907087_NEGATIVE 229 85 47 134 99 NC_002967:TDE1126|5end_TPR_domain_protein_1157545..1157775_POSITIVE 226 85 52 74 41 NC_002967:TDE2509|5end_transcriptional_regulator,_AraC_family_2533188..2533418_POSITIVE 226 71 31 149 111 NC_002967:TDE2425|5end_50S_ribosomal_protein_L11_2455150..2455380_NEGATIVE 226 98 51 68 27 NC_002967:TDE0269|5end_hypothetical_protein_300687..300917_NEGATIVE 224 100 51 226 181 NC_002967:TDE1956|5end_hypothetical_protein_1971114..1971344_POSITIVE 224 72 50 159 136 NC_002967:TDE1843|5end_hypothetical_protein_1873005..1873235_NEGATIVE 216 78 33 138 86 NC_002967:TDE0132|5end_hypothetical_protein_152046..152276_POSITIVE 209 79 33 182 127 NC_002967:TDE2216|5end_galactoside_ABC_transporter,_ATP-binding_protein_2256653..2256883_NEGATIVE 205 75 52 116 94 NC_002967:TDE2479|5end_hypothetical_protein_2503290..2503520_NEGATIVE 205 58 15 228 180 NC_002967:TDE0501|5end_hypothetical_protein_555312..555542_NEGATIVE 203 84 51 124 97 NC_002967:TDE2055|5end_hemin-binding_protein_B_2083769..2083999_NEGATIVE 202 42 3 226 188 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 202 44 6 61 20 NC_002967:TDE1185|5end_lipoprotein,_putative_1212973..1213203_NEGATIVE 199 46 7 162 102 NC_002967:TDE2650|5end_transcriptional_regulator,_putative_2689031..2689261_NEGATIVE 198 42 6 102 53 NC_002967:TDE2780|5end_hypothetical_protein_2830621..2830851_NEGATIVE 196 83 49 163 121 NC_002967:TDE0697|5end_hypothetical_protein_734372..734602_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 232 89 41 105 46 NC_002967:TDE2337|3end_aminopeptidase_2374604..2374754_POSITIVE 226 71 31 57 19 NC_002967:TDE2426|3end_transcription_antitermination_protein_NusG_2455242..2455392_NEGATIVE 216 78 33 113 61 NC_002967:TDE0131|3end_hypothetical_protein_152101..152251_POSITIVE 214 44 5 58 11 NC_002967:TDE0737|3end_hypothetical_protein_775408..775558_NEGATIVE 211 89 49 140 99 NC_002967:TDE1117|3end_hypothetical_protein_1149871..1150021_POSITIVE 209 49 3 57 12 NC_002967:TDE2678|3end_alpha-amylase_family_protein_2715785..2715935_NEGATIVE 209 79 33 71 16 NC_002967:TDE2217|3end_galactose/glucose-binding_lipoprotein_2256764..2256914_NEGATIVE 207 59 25 39 4 NC_002967:TDE1669|3end_hemolysin_1723878..1724028_POSITIVE 205 75 52 40 18 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 204 58 17 46 1 NC_002967:TDE0502|3end_ankyrin_repeat_protein_555494..555644_NEGATIVE 203 84 51 34 7 NC_002967:TDE2056|3end_outer_membrane_hemin-binding_protein_A_2083859..2084009_NEGATIVE 202 44 6 49 8 NC_002967:TDE1186|3end_hypothetical_protein_1212985..1213135_NEGATIVE 198 42 6 84 35 NC_002967:TDE2781|3end_ABC_transporter,_ATP-binding/permease_protein_2830639..2830789_NEGATIVE 194 69 25 88 42 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 193 78 37 97 56 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 192 60 11 132 86 NC_002967:TDE2272|3end_hypothetical_protein_2308980..2309130_NEGATIVE 192 65 37 144 118 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 191 110 63 76 28 NC_002967:TDE0190|3end_hypothetical_protein_226479..226629_NEGATIVE 187 54 27 56 33 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 183 60 13 72 15 NC_002967:TDE1844|3end_DNA_integrase_1873197..1873347_NEGATIVE