Origin IGS: gattatttttgtaaccaattagtgaaatatatcatacagtcaacttaaatgtttatcactgaatagattcctttgtgttttgataatattttacaaaattattgagttaacataaact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtttatgttaactcaataattttgtaaaatattatcaaaacacaaaggaatctattcagtgataaacatttaagttgactgtatgatatatttcactaattggttacaaaaataatc Mask Tandem Repeat Region ================================================ gattatttttgtaaccaattagtgaaatatatcatacagtcaacttaaatgtttatcactgaatagattcctttgtgttttgataatattttacaaaattattgagttaacataaact Find is-nt database================================================ Query_seq: TDE1559:TDE1560|TDE1559:TDE1560:hypothetical protein:YD repeat protein:->->:1611472..1611589 118 gattatttttgtaaccaattagtgaaatatatcatacagtcaacttaaatgtttatcactgaatagattcctttgtgttttgataatattttacaaaattattgagttaacataaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1559:TDE1560|TDE1559:TDE1560:hypothetical protein:YD repeat protein:->->:1611472..1611589 118 gattatttttgtaaccaattagtgaaatatatcatacagtcaacttaaatgtttatcactgaatagattcctttgtgttttgataatattttacaaaattattgagttaacataaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1559:TDE1560|TDE1559:TDE1560:hypothetical protein:YD repeat protein:->->:1611472..1611589 118 gattatttttgtaaccaattagtgaaatatatcatacagtcaacttaaatgtttatcactgaatagattcctttgtgttttgataatattttacaaaattattgagttaacataaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattatttttgtaaccaattagtgaaatatatcatacagtcaacttaaatgtttatcactgaatagattcctttgtgttttgataatattttacaaaattattgagttaacataaact Predict ORF larger than 30AA ================================================ gattatttttgtaaccaattagtgaaatatatcatacagtcaacttaaatgtttatcactgaatagattcctttgtgttttgataatattttacaaaattattgagttaacataaact 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: 82 Start: 31 End: 60 ..............................AGTGATAAACATTTAAGTTGACTGTATGAT.......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gattatttttgtaaccaattagtgaaatatatcatacagtcaacttaaatgtttatcactgaatagattcctttgtgttttgataatattttacaaaattattgagttaacataaact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1559:TDE1560|TDE1559:TDE1560:hypothetical protein:YD repeat protein:->->:1611472..1611589 118 gattatttttgtaaccaattagtgaaatatatcatacagtcaacttaaatgtttatcactgaatagattcctttgtgttttgataatattttacaaaattattgagttaacataaact Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_002967_TDE1559_TDE1560|hypothetical protein:YD repeat protein|POSITIVE:POSITIVE|[1611472,1611589]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 gattatttttgtaaccaattagtgaaatatatcatacagtcaacttaaatgtttatcactgaatagattcctttgtgttttgataatattttacaaaattattgagttaacataaact gattatttttgtaaccaattagtgaaatatatcatacagtcaacttaaatgtttatcactgaatagattcctttgtgttttgataatattttacaaaattattgagttaacataaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUAUUUUUGUAACCAAUUAGUGAAAUAUAUCAUACAGUCAACUUAAAUGUUUAUCACUGAAUAGAUUCCUUUGUGUUUUGAUAAUAUUUUACAAAAUUAUUGAGUUAACAUAAACU .....(((.((((((((((..(((((((((((((.(((..(((......((((((....)))))).......))))))..)))).)))))))))......)))).))).))).))).. (-15.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUAUGUUAACUCAAUAAUUUUGUAAAAUAUUAUCAAAACACAAAGGAAUCUAUUCAGUGAUAAACAUUUAAGUUGACUGUAUGAUAUAUUUCACUAAUUGGUUACAAAAAUAAUC .((((.(((.(((.((((..((((((((....))).)))))......(((((.((((((((....(((......))).))))...)))).)))))....)))))))))).)))).... (-13.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 230 99 58 129 84 NC_002967:TDE0464|5end_NifU_domain_protein_518175..518405_NEGATIVE 185 83 51 112 83 NC_002967:TDE2700|5end_citrate_carrier_protein,_CCS_family_2744396..2744626_POSITIVE 183 82 46 167 123 NC_002967:TDE1266|5end_phosphoribosylaminoimidazole_synthetase_1301588..1301818_NEGATIVE 182 78 33 127 89 NC_002967:TDE0999|5end_formate/nitrite_transporter_1025870..1026100_POSITIVE 179 80 39 95 48 NC_002967:TDE0768|5end_50S_ribosomal_protein_L4_806996..807226_POSITIVE 179 88 42 121 72 NC_002967:TDE0681|5end_protein_export_protein_SecD_720619..720849_NEGATIVE 175 82 55 225 198 NC_002967:TDE0355|5end_hypothetical_protein_399005..399235_POSITIVE 169 81 50 186 143 NC_002967:TDE1904|5end_hypothetical_protein_1923613..1923843_NEGATIVE 169 80 31 84 21 NC_002967:TDE1683|5end_V-type_ATP_synthase_subunit_A_1736614..1736844_NEGATIVE 168 83 52 50 17 NC_002967:TDE2441|5end_hypothetical_protein_2472496..2472726_NEGATIVE 164 76 40 103 69 NC_002967:TDE2332|5end_hypothetical_protein_2367774..2368004_NEGATIVE 164 72 34 102 66 NC_002967:TDE0296|5end_formiminotransferase,_putative_327741..327971_NEGATIVE 161 79 31 188 136 NC_002967:TDE1603|5end_ABC_transporter,_ATP-binding_protein_1654856..1655086_NEGATIVE 161 55 33 139 117 NC_002967:TDE0565|5end_hypothetical_protein_597031..597261_POSITIVE 161 78 44 110 71 NC_002967:TDE0400|5end_transcriptional_regulator,_LysR_family_451803..452033_NEGATIVE 160 84 42 79 35 NC_002967:TDE2646|5end_ABC_transporter,_ATP-binding_protein,_putative_2685348..2685578_POSITIVE 160 90 50 88 48 NC_002967:TDE0540|5end_hypothetical_protein_581464..581694_POSITIVE 159 84 59 172 142 NC_002967:TDE2269|5end_hypothetical_protein_2305920..2306150_NEGATIVE 156 88 50 171 142 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 155 66 27 214 164 NC_002967:TDE1703|5end_hypothetical_protein_1759983..1760213_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 206 71 36 132 98 NC_002967:TDE0535|3end_ABC_transporter,_ATP-binding_protein_578101..578251_POSITIVE 206 99 70 36 4 NC_002967:TDE0465|3end_PIN_domain_protein_518268..518418_NEGATIVE 202 109 67 134 75 NC_002967:TDE0270|3end_hypothetical_protein_300845..300995_NEGATIVE 185 83 51 99 70 NC_002967:TDE2699|3end_antigen,_putative_2744463..2744613_POSITIVE 183 82 46 128 84 NC_002967:TDE1267|3end_phosphoribosylamine--glycine_ligase_1301627..1301777_NEGATIVE 179 80 39 80 33 NC_002967:TDE0767|3end_ribosomal_protein_L3_807061..807211_POSITIVE 179 88 42 75 26 NC_002967:TDE0682|3end_preprotein_translocase,_YajC_subunit_720665..720815_NEGATIVE 175 77 37 49 5 NC_002967:TDE1691|3end_hypothetical_protein_1747407..1747557_NEGATIVE 175 82 55 141 114 NC_002967:TDE0354|3end_general_stress_protein_14_399001..399151_POSITIVE 169 81 50 77 34 NC_002967:TDE1905|3end_hypothetical_protein_1923722..1923872_NEGATIVE 168 83 52 75 42 NC_002967:TDE2442|3end_surface_protein,_putative_2472471..2472621_NEGATIVE 164 72 34 47 11 NC_002967:TDE0297|3end_hypothetical_protein_327796..327946_NEGATIVE 161 55 33 43 21 NC_002967:TDE0564|3end_hypothetical_protein_597015..597165_POSITIVE 161 78 44 76 37 NC_002967:TDE0401|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_451837..451987_NEGATIVE 160 84 42 95 51 NC_002967:TDE2645|3end_hypothetical_protein_2685444..2685594_POSITIVE 160 80 35 120 69 NC_002967:TDE1456|3end_GGDEF_domain_protein_1503312..1503462_NEGATIVE 160 90 50 86 46 NC_002967:TDE0539|3end_hypothetical_protein_581542..581692_POSITIVE 159 41 6 98 60 NC_002967:TDE0649|3end_hypothetical_protein_684034..684184_NEGATIVE 158 86 51 54 16 NC_002967:TDE0434|3end_rubrerythrin_489564..489714_POSITIVE 156 88 50 98 69 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE