Origin IGS: aggcacttcctccttttatagaataatattctatagacattatagaacattgttctacaaaatgcaaggggttttattgcctcacgttaaatctaacctaaaaaaattgtctggacttaccggaataagcct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggcttattccggtaagtccagacaatttttttaggttagatttaacgtgaggcaataaaaccccttgcattttgtagaacaatgttctataatgtctatagaatattattctataaaaggaggaagtgcct Mask Tandem Repeat Region ================================================ aggcacttcctccttttatagaataatattctatagacattatagaacattgttctacaaaatgcaaggggttttattgcctcacgttaaatctaacctaaaaaaattgtctggacttaccggaataagcct Find is-nt database================================================ Query_seq: TDE1114:TDE1115|TDE1114:TDE1115:transcriptional regulator, TetR family:DNA-binding protein, putative:<-<-:1148996..1149127 132 aggcacttcctccttttatagaataatattctatagacattatagaacattgttctacaaaatgcaaggggttttattgcctcacgttaaatctaacctaaaaaaattgtctggacttaccggaataagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1114:TDE1115|TDE1114:TDE1115:transcriptional regulator, TetR family:DNA-binding protein, putative:<-<-:1148996..1149127 132 aggcacttcctccttttatagaataatattctatagacattatagaacattgttctacaaaatgcaaggggttttattgcctcacgttaaatctaacctaaaaaaattgtctggacttaccggaataagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1114:TDE1115|TDE1114:TDE1115:transcriptional regulator, TetR family:DNA-binding protein, putative:<-<-:1148996..1149127 132 aggcacttcctccttttatagaataatattctatagacattatagaacattgttctacaaaatgcaaggggttttattgcctcacgttaaatctaacctaaaaaaattgtctggacttaccggaataagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggcacttcctccttttatagaataatattctatagacattatagaacattgttctacaaaatgcaaggggttttattgcctcacgttaaatctaacctaaaaaaattgtctggacttaccggaataagcct Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 23 End: 130 ...................... M I F Y R H Y R T L F Y K M Q G V L L P H V K S N L K K L S G L T G I S .. aggcacttcctccttttatagaataatattctatagacattatagaacattgttctacaaaatgcaaggggttttattgcctcacgttaaatctaacctaaaaaaattgtctggacttaccggaataagcct 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: 84 Start: 39 End: 68 ......................................CTTGCATTTTGTAGAACAATGTTCTATAAT................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggcacttcctccttttatagaataatattctatagacattatagaacattgttctacaaaatgcaaggggttttattgcctcacgttaaatctaacctaaaaaaattgtctggacttaccggaataagcct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 57 HP_score: -4.3 Tail_Score: -3.88232 Start: 27 End: 49 Full_Region: cattttgtagaacaa tgttctata atgtc tatagaata ttattctataaaagg ..........................tgttctataatgtctatagaata................................................................................... TransTerm Strand: - Conf: 55 HP_score: -4.7 Tail_Score: -3.52874 Start: 29 End: 47 Full_Region: ttttgtagaacaatg ttctata atgtc tatagaa tattattctataaaa ............................ttctataatgtctatagaa..................................................................................... Find igs database================================================ Query_seq: TDE1114:TDE1115|TDE1114:TDE1115:transcriptional regulator, TetR family:DNA-binding protein, putative:<-<-:1148996..1149127 132 aggcacttcctccttttatagaataatattctatagacattatagaacattgttctacaaaatgcaaggggttttattgcctcacgttaaatctaacctaaaaaaattgtctggacttaccggaataagcct Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: NC_002967_TDE1114_TDE1115|transcriptional regulator, TetR family:DNA-binding protein, putative|NEGATIVE:NEGATIVE|[1148996,1149127]|132 HSP 1 e-value: 9.0E-57 bit: 220.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 aggcacttcctccttttatagaataatattctatagacattatagaacattgttctacaaaatgcaaggggttttattgcctcacgttaaatctaacctnnnnnnnttgtctggacttaccggaataagcct aggcacttcctccttttatagaataatattctatagacattatagaacattgttctacaaaatgcaaggggttttattgcctcacgttaaatctaacctaaaaaaattgtctggacttaccggaataagcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCACUUCCUCCUUUUAUAGAAUAAUAUUCUAUAGACAUUAUAGAACAUUGUUCUACAAAAUGCAAGGGGUUUUAUUGCCUCACGUUAAAUCUAACCUAAAAAAAUUGUCUGGACUUACCGGAAUAAGCCU ((((.........((((.(((((((((.((((((((...)))))))).))))))))).)))).....(((((......)))))..........................(((((.....)))))....)))) (-31.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCUUAUUCCGGUAAGUCCAGACAAUUUUUUUAGGUUAGAUUUAACGUGAGGCAAUAAAACCCCUUGCAUUUUGUAGAACAAUGUUCUAUAAUGUCUAUAGAAUAUUAUUCUAUAAAAGGAGGAAGUGCCU ((((...((((..((((((..(((...........))).))))))..(..(((..........)))..).((((((((((.(((((((((((.....))))))))))).))))))))))...))))..)))) (-37.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 827 100 51 191 142 NC_002967:TDE1114|5end_transcriptional_regulator,_TetR_family_1148905..1149135_NEGATIVE 346 106 63 201 157 NC_002967:TDE2323|5end_mechanosensitive_ion_channel_family_protein_2359084..2359314_NEGATIVE 254 98 62 190 153 NC_002967:TDE1651|5end_BioY_family_protein_1698732..1698962_NEGATIVE 247 94 51 179 136 NC_002967:TDE2304|5end_hypothetical_protein_2343440..2343670_POSITIVE 243 49 2 171 119 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 243 91 62 170 141 NC_002967:TDE0968|5end_translation_elongation_factor_P_993126..993356_NEGATIVE 241 86 47 206 163 NC_002967:TDE1937|5end_hypothetical_protein_1953264..1953494_POSITIVE 238 110 63 188 144 NC_002967:TDE1965|5end_sodium/hydrogen_exchanger_family_protein_1980151..1980381_NEGATIVE 238 84 63 74 50 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 234 130 107 216 192 NC_002967:TDE2466|5end_hypothetical_protein_2489860..2490090_NEGATIVE 233 91 60 108 74 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 220 84 48 195 167 NC_002967:TDE1214|5end_flagellar_basal_body_protein_1246307..1246537_POSITIVE 219 99 53 146 98 NC_002967:TDE1791|5end_hypothetical_protein_1828775..1829005_NEGATIVE 219 103 63 40 8 NC_002967:TDE1731|5end_hypothetical_protein_1786935..1787165_NEGATIVE 218 90 45 72 24 NC_002967:TDE1175|5end_chaperonin_GroEL_1205151..1205381_NEGATIVE 214 66 24 229 185 NC_002967:TDE1816|5end_hypothetical_protein_1851673..1851903_NEGATIVE 214 110 64 173 124 NC_002967:TDE0474|5end_hypothetical_protein_530740..530970_POSITIVE 210 86 48 171 119 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 206 87 61 70 47 NC_002967:TDE2603|5end_DNA_mismatch_repair_protein_2641476..2641706_POSITIVE 206 124 85 231 183 NC_002967:TDE1140|5end_hypothetical_protein_1169845..1170075_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 102 66 55 18 NC_002967:TDE2588|3end_integrase_domain_protein_2624778..2624928_POSITIVE 254 98 62 65 28 NC_002967:TDE1652|3end_ABC_transporter,_ATP-binding/permease_protein_1698857..1699007_NEGATIVE 247 110 66 53 4 NC_002967:TDE1088|3end_hypothetical_protein_1119275..1119425_NEGATIVE 243 49 2 58 6 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 242 69 24 141 92 NC_002967:TDE1817|3end_hypothetical_protein_1851766..1851916_NEGATIVE 240 96 62 61 17 NC_002967:TDE2140|3end_protease_II_2173083..2173233_NEGATIVE 238 84 63 74 50 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 233 91 60 111 77 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 218 83 43 134 92 NC_002967:TDE0680|3end_protein-export_membrane_protein_SecF_717613..717763_NEGATIVE 212 80 35 120 79 NC_002967:TDE2659|3end_GAF_domain/HD_domain_protein_2697183..2697333_POSITIVE 206 87 61 77 54 NC_002967:TDE2602|3end_outer_membrane_protein,_putative_2641563..2641713_POSITIVE 204 98 52 69 12 NC_002967:TDE1919|3end_hypothetical_protein_1938319..1938469_NEGATIVE 203 70 30 128 79 NC_002967:TDE0450|3end_hypothetical_protein_507096..507246_NEGATIVE 200 128 85 125 73 NC_002967:TDE0322|3end_regulatory_protein,_P-II_family_355106..355256_NEGATIVE 197 100 51 61 8 NC_002967:TDE2685|3end_flagellar_synthesis_regulator_FleN_2724896..2725046_NEGATIVE 195 88 63 49 24 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 194 86 52 76 38 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 194 49 10 126 85 NC_002967:TDE1799|3end_hypothetical_protein_1836689..1836839_NEGATIVE 193 88 43 70 25 NC_002967:TDE2039|3end_lipoprotein_releasing_system,_permease_protein,_putative_2068198..2068348_NEGATIVE 192 82 45 61 14 NC_002967:TDE0884|3end_tRNA_(guanine-N(1)-)-methyltransferase_903032..903182_POSITIVE