Origin IGS: ttacattatctccttaatcgtttttaacatttcttgtttgatatcatcaggaattgtatcaatatttttaatactatcaataagcagttaaataatttacatcaataaattttctattcaagaaaattttttttcatttatttatctattctaaaatacttaatattgttttttagataatattaggtat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atacctaatattatctaaaaaacaatattaagtattttagaatagataaataaatgaaaaaaaattttcttgaatagaaaatttattgatgtaaattatttaactgcttattgatagtattaaaaatattgatacaattcctgatgatatcaaacaagaaatgttaaaaacgattaaggagataatgtaa Mask Tandem Repeat Region ================================================ ttacattatctccttaatcgtttttaacatttcttgtttgatatcatcaggaattgtatcaatatttttaatactatcaataagcagttaaataatttacatcaataaattttctattcaagaaaattttttttcatttatttatctattctaaaatacttaatattgttttttagataatattaggtat Find is-nt database================================================ Query_seq: TDE2017:TDE2018|TDE2017:TDE2018:hypothetical protein:lipoprotein, putative:<-<-:2039488..2039677 190 ttacattatctccttaatcgtttttaacatttcttgtttgatatcatcaggaattgtatcaatatttttaatactatcaataagcagttaaataatttacatcaataaattttctattcaagaaaattttttttcatttatttatctattctaaaatacttaatattgttttttagataatattaggtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2017:TDE2018|TDE2017:TDE2018:hypothetical protein:lipoprotein, putative:<-<-:2039488..2039677 190 ttacattatctccttaatcgtttttaacatttcttgtttgatatcatcaggaattgtatcaatatttttaatactatcaataagcagttaaataatttacatcaataaattttctattcaagaaaattttttttcatttatttatctattctaaaatacttaatattgttttttagataatattaggtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2017:TDE2018|TDE2017:TDE2018:hypothetical protein:lipoprotein, putative:<-<-:2039488..2039677 190 ttacattatctccttaatcgtttttaacatttcttgtttgatatcatcaggaattgtatcaatatttttaatactatcaataagcagttaaataatttacatcaataaattttctattcaagaaaattttttttcatttatttatctattctaaaatacttaatattgttttttagataatattaggtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttacattatctccttaatcgtttttaacatttcttgtttgatatcatcaggaattgtatcaatatttttaatactatcaataagcagttaaataatttacatcaataaattttctattcaagaaaattttttttcatttatttatctattctaaaatacttaatattgttttttagataatattaggtat Predict ORF larger than 30AA ================================================ ttacattatctccttaatcgtttttaacatttcttgtttgatatcatcaggaattgtatcaatatttttaatactatcaataagcagttaaataatttacatcaataaattttctattcaagaaaattttttttcatttatttatctattctaaaatacttaatattgttttttagataatattaggtat 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================================================ ttacattatctccttaatcgtttttaacatttcttgtttgatatcatcaggaattgtatcaatatttttaatactatcaataagcagttaaataatttacatcaataaattttctattcaagaaaattttttttcatttatttatctattctaaaatacttaatattgttttttagataatattaggtat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -3.8 Tail_Score: -6.0458 Start: 110 End: 126 Full_Region: ATTTACATCAATAAA TTTTCT ATTCA AGAAAA TTTTTTTTCATTTAT .............................................................................................................TTTTCTATTCAAGAAAA................................................................ Find igs database================================================ Query_seq: TDE2017:TDE2018|TDE2017:TDE2018:hypothetical protein:lipoprotein, putative:<-<-:2039488..2039677 190 ttacattatctccttaatcgtttttaacatttcttgtttgatatcatcaggaattgtatcaatatttttaatactatcaataagcagttaaataatttacatcaataaattttctattcaagaaaattttttttcatttatttatctattctaaaatacttaatattgttttttagataatattaggtat Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: NC_002967_TDE2017_TDE2018|hypothetical protein:lipoprotein, putative|NEGATIVE:NEGATIVE|[2039488,2039677]|190 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 ttacattatctccttaatcgtttttaacatttcttgtttgatatcatcaggaattgtatcaatatttttaatactatcaataagcagttaaataatttacatcaataaattttctattcaagaaaannnnnnnncatttatttatctattctaaaatacttaatattgttttttagataatattaggtat ttacattatctccttaatcgtttttaacatttcttgtttgatatcatcaggaattgtatcaatatttttaatactatcaataagcagttaaataatttacatcaataaattttctattcaagaaaattttttttcatttatttatctattctaaaatacttaatattgttttttagataatattaggtat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACAUUAUCUCCUUAAUCGUUUUUAACAUUUCUUGUUUGAUAUCAUCAGGAAUUGUAUCAAUAUUUUUAAUACUAUCAAUAAGCAGUUAAAUAAUUUACAUCAAUAAAUUUUCUAUUCAAGAAAAUUUUUUUUCAUUUAUUUAUCUAUUCUAAAAUACUUAAUAUUGUUUUUUAGAUAAUAUUAGGUAU ..........................(((.((((((..((....)).)))))).)))............................((.(((((((...........(((((((((.....)))))))))........))))))).))........(((((((((((((((.....))))))))))))))) (-29.01) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACCUAAUAUUAUCUAAAAAACAAUAUUAAGUAUUUUAGAAUAGAUAAAUAAAUGAAAAAAAAUUUUCUUGAAUAGAAAAUUUAUUGAUGUAAAUUAUUUAACUGCUUAUUGAUAGUAUUAAAAAUAUUGAUACAAUUCCUGAUGAUAUCAAACAAGAAAUGUUAAAAACGAUUAAGGAGAUAAUGUAA .......(((((((((........(((((((.(((((......))))).............(((((((((.....))))))))).)))))))......((((((..(((.((((((.(((((.....((((...))))...))))).))))))..)))....))))))...........))))))))).. (-26.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 730 60 11 151 102 NC_002967:TDE2017|5end_hypothetical_protein_2039397..2039627_NEGATIVE 214 80 33 51 17 NC_002967:TDE0846|5end_hypothetical_protein_868623..868853_POSITIVE 212 67 30 226 188 NC_002967:TDE0728|5end_FAD-binding_protein,_putative_767206..767436_POSITIVE 208 60 11 195 137 NC_002967:TDE0094|5end_hypothetical_protein_112219..112449_POSITIVE 205 50 6 142 100 NC_002967:TDE0055|5end_flagellar_biosynthesis_protein_63565..63795_POSITIVE 201 77 31 118 65 NC_002967:TDE2064|5end_ferrous_iron_transport_protein_A_2091492..2091722_NEGATIVE 197 52 11 86 43 NC_002967:TDE1643|5end_PASTA_domain_protein_1694551..1694781_NEGATIVE 195 146 121 96 71 NC_002967:TDE1135|5end_hypothetical_protein_1165542..1165772_NEGATIVE 194 60 14 221 178 NC_002967:TDE0981|5end_hypothetical_protein_1005496..1005726_POSITIVE 194 57 20 65 24 NC_002967:TDE0502|5end_ankyrin_repeat_protein_556558..556788_NEGATIVE 192 57 18 131 88 NC_002967:TDE0562|5end_hypothetical_protein_594899..595129_POSITIVE 192 41 9 127 98 NC_002967:TDE0276|5end_HD_domain_protein_308029..308259_NEGATIVE 185 55 19 84 44 NC_002967:TDE0593|5end_internalin-related_protein_633936..634166_NEGATIVE 184 52 11 162 120 NC_002967:TDE2214|5end_hypothetical_protein_2253050..2253280_POSITIVE 180 52 11 83 43 NC_002967:TDE2781|5end_ABC_transporter,_ATP-binding/permease_protein_2832468..2832698_NEGATIVE 179 49 5 130 93 NC_002967:TDE0554|5end_hypothetical_protein_590968..591198_NEGATIVE 178 49 4 136 89 NC_002967:TDE0221|5end_hypothetical_protein_254696..254926_NEGATIVE 177 49 2 132 91 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 176 50 8 122 63 NC_002967:TDE2247|5end_PemK_family_protein_2286362..2286592_POSITIVE 175 152 114 82 42 NC_002967:TDE0504|5end_hypothetical_protein_558104..558334_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 50 6 133 91 NC_002967:TDE0054|3end_flagellar_biosynthesis_protein_63636..63786_POSITIVE 201 77 31 94 41 NC_002967:TDE2065|3end_FeoA_family_protein_2091516..2091666_NEGATIVE 197 52 11 59 16 NC_002967:TDE1644|3end_methionyl-tRNA_formyltransferase_1694578..1694728_NEGATIVE 195 146 121 95 70 NC_002967:TDE1136|3end_M23/M37_peptidase_domain_protein_1165543..1165693_NEGATIVE 194 57 20 43 2 NC_002967:TDE0503|3end_hypothetical_protein_556580..556730_NEGATIVE 192 41 9 47 18 NC_002967:TDE0277|3end_hypothetical_protein_308109..308259_NEGATIVE 180 52 11 65 25 NC_002967:TDE2782|3end_ABC_transporter,_ATP-binding/permease_protein_2832486..2832636_NEGATIVE 179 49 5 115 78 NC_002967:TDE0555|3end_hypothetical_protein_590983..591133_NEGATIVE 178 55 11 151 112 NC_002967:TDE2496|3end_methyl-accepting_chemotaxis_protein_2521170..2521320_NEGATIVE 178 49 4 136 89 NC_002967:TDE0222|3end_acetyltransferase,_GNAT_family_254696..254846_NEGATIVE 177 49 2 139 98 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 176 50 8 134 75 NC_002967:TDE2246|3end_hypothetical_protein_2286454..2286604_POSITIVE 174 152 119 61 27 NC_002967:TDE1256|3end_HD_domain_protein_1289701..1289851_NEGATIVE 173 58 14 136 95 NC_002967:TDE2097|3end_hypothetical_protein_2124478..2124628_NEGATIVE 173 56 12 70 21 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 172 60 14 103 57 NC_002967:TDE1978|3end_hypothetical_protein_1991501..1991651_NEGATIVE 168 90 41 78 26 NC_002967:TDE1764|3end_hypothetical_protein_1811227..1811377_NEGATIVE 168 150 111 95 57 NC_002967:TDE1303|3end_hypothetical_protein_1339649..1339799_NEGATIVE 168 78 44 52 18 NC_002967:TDE0767|3end_ribosomal_protein_L3_807061..807211_POSITIVE 167 56 11 127 88 NC_002967:TDE1539|3end_hypothetical_protein_1584190..1584340_POSITIVE