Origin IGS: agtatctcataattttaacttatggtcaagataaaaaaaagagctattgaacatttaattatataagagtatactattgctaacaaaatcttgtttacggaggaatatgataaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttatcatattcctccgtaaacaagattttgttagcaatagtatactcttatataattaaatgttcaatagctcttttttttatcttgaccataagttaaaattatgagatact Mask Tandem Repeat Region ================================================ agtatctcataattttaacttatggtcaagataaaaaaaagagctattgaacatttaattatataagagtatactattgctaacaaaatcttgtttacggaggaatatgataaaa Find is-nt database================================================ Query_seq: TDE2462:TDE2463|TDE2462:TDE2463:hypothetical protein:hypothetical protein:<-->:2488515..2488629 115 agtatctcataattttaacttatggtcaagataaaaaaaagagctattgaacatttaattatataagagtatactattgctaacaaaatcttgtttacggaggaatatgataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2462:TDE2463|TDE2462:TDE2463:hypothetical protein:hypothetical protein:<-->:2488515..2488629 115 agtatctcataattttaacttatggtcaagataaaaaaaagagctattgaacatttaattatataagagtatactattgctaacaaaatcttgtttacggaggaatatgataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2462:TDE2463|TDE2462:TDE2463:hypothetical protein:hypothetical protein:<-->:2488515..2488629 115 agtatctcataattttaacttatggtcaagataaaaaaaagagctattgaacatttaattatataagagtatactattgctaacaaaatcttgtttacggaggaatatgataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtatctcataattttaacttatggtcaagataaaaaaaagagctattgaacatttaattatataagagtatactattgctaacaaaatcttgtttacggaggaatatgataaaa Predict ORF larger than 30AA ================================================ agtatctcataattttaacttatggtcaagataaaaaaaagagctattgaacatttaattatataagagtatactattgctaacaaaatcttgtttacggaggaatatgataaaa 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: 58 End: 87 .........................................................TTTGTTAGCAATAGTATACTCTTATATAAT............................ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 46 End: 75 .............................................ATTGAACATTTAATTATATAAGAGTATACT........................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 1 End: 30 CTTGACCATAAGTTAAAATTATGAGATACT..................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtatctcataattttaacttatggtcaagataaaaaaaagagctattgaacatttaattatataagagtatactattgctaacaaaatcttgtttacggaggaatatgataaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2462:TDE2463|TDE2462:TDE2463:hypothetical protein:hypothetical protein:<-->:2488515..2488629 115 agtatctcataattttaacttatggtcaagataaaaaaaagagctattgaacatttaattatataagagtatactattgctaacaaaatcttgtttacggaggaatatgataaaa Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002967_TDE2462_TDE2463|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2488515,2488629]|115 HSP 1 e-value: 6.0E-45 bit: 180.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 agtatctcataattttaacttatggtcaagatnnnnnnnngagctattgaacatttaattatataagagtatactattgctaacaaaatcttgtttacggaggaatatgataaaa agtatctcataattttaacttatggtcaagataaaaaaaagagctattgaacatttaattatataagagtatactattgctaacaaaatcttgtttacggaggaatatgataaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUCUCAUAAUUUUAACUUAUGGUCAAGAUAAAAAAAAGAGCUAUUGAACAUUUAAUUAUAUAAGAGUAUACUAUUGCUAACAAAAUCUUGUUUACGGAGGAAUAUGAUAAAA ((((((((((((((.......(((.((((.................)))).)))..))))))....))).)))))............(((.(((((......))))).))).... (-10.53) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUCAUAUUCCUCCGUAAACAAGAUUUUGUUAGCAAUAGUAUACUCUUAUAUAAUUAAAUGUUCAAUAGCUCUUUUUUUUAUCUUGACCAUAAGUUAAAAUUAUGAGAUACU ...((((...............((((((......(((.((.(...((..(((......)))..)).).)).))).........))))))..(((((.......))))).)))).. (-10.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 753 110 61 201 152 NC_002967:TDE2462|5end_hypothetical_protein_2488424..2488654_NEGATIVE 224 102 68 214 181 NC_002967:TDE0361|5end_transporter,_putative_405989..406219_POSITIVE 209 103 66 146 118 NC_002967:TDE2743|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2797670..2797900_POSITIVE 206 49 4 174 119 NC_002967:TDE0189|5end_hypothetical_protein_226460..226690_NEGATIVE 195 80 31 58 5 NC_002967:TDE0128|5end_HAMP_domain/GGDEF_domain/EAL_domain_protein_146240..146470_POSITIVE 180 103 63 103 71 NC_002967:TDE0089|5end_transglutaminase-like_domain_protein_108554..108784_NEGATIVE 176 110 69 229 187 NC_002967:TDE2642|5end_hypothetical_protein_2682254..2682484_NEGATIVE 174 44 1 57 23 NC_002967:TDE1045|5end_hypothetical_protein_1073240..1073470_POSITIVE 174 101 67 61 26 NC_002967:TDE0548|5end_hypothetical_protein_586995..587225_NEGATIVE 174 101 67 174 139 NC_002967:TDE0547|5end_hypothetical_protein_586882..587112_NEGATIVE 174 108 64 194 140 NC_002967:TDE0477|5end_hypothetical_protein_534277..534507_NEGATIVE 169 71 42 203 175 NC_002967:TDE1224|5end_zinc_ABC_transporter,_permease_protein_1258754..1258984_NEGATIVE 167 110 65 87 34 NC_002967:TDE0297|5end_hypothetical_protein_327978..328208_NEGATIVE 163 78 43 188 154 NC_002967:TDE1842|5end_hypothetical_protein_1872005..1872235_NEGATIVE 163 78 43 188 154 NC_002967:TDE1802|5end_hypothetical_protein_1838108..1838338_NEGATIVE 161 109 69 66 29 NC_002967:TDE2631|5end_peptide_ABC_transporter,_permease_protein,_putative_2671829..2672059_POSITIVE 160 52 17 231 204 NC_002967:TDE1037|5end_hypothetical_protein_1064470..1064700_POSITIVE 159 110 69 229 193 NC_002967:TDE2484|5end_hypothetical_protein_2507720..2507950_NEGATIVE 158 44 3 146 108 NC_002967:TDE1059|5end_hypothetical_protein_1086605..1086835_NEGATIVE 157 105 62 133 93 NC_002967:TDE0710|5end_hypothetical_protein_745432..745662_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 180 103 63 113 81 NC_002967:TDE0090|3end_hypothetical_protein_108544..108694_NEGATIVE 179 102 61 56 6 NC_002967:TDE2594|3end_hypothetical_protein_2628930..2629080_NEGATIVE 174 101 67 59 24 NC_002967:TDE0549|3end_TfoX_N-terminal_domain_family_protein_586997..587147_NEGATIVE 166 109 65 45 12 NC_002967:TDE0967|3end_hypothetical_protein_992529..992679_POSITIVE 165 103 66 70 23 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 162 110 65 115 73 NC_002967:TDE2230|3end_hypothetical_protein_2269453..2269603_POSITIVE 161 109 69 69 32 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 161 110 79 50 19 NC_002967:TDE2254|3end_hypothetical_protein_2291445..2291595_NEGATIVE 159 110 69 46 10 NC_002967:TDE2485|3end_hypothetical_protein_2507903..2508053_NEGATIVE 157 80 43 108 66 NC_002967:TDE0180|3end_hypothetical_protein_212854..213004_NEGATIVE 156 102 86 49 34 NC_002967:TDE0299|3end_mutator_mutT_protein_330579..330729_POSITIVE 154 100 67 128 98 NC_002967:TDE0070|3end_RNA_polymerase_sigma-70_factor,_region_2_family_78620..78770_POSITIVE 151 101 69 51 13 NC_002967:TDE0820|3end_transcriptional_regulator,_TetR_family_843714..843864_NEGATIVE 149 99 51 148 105 NC_002967:TDE2098|3end_hypothetical_protein_2124951..2125101_NEGATIVE 148 106 74 120 88 NC_002967:TDE1149|3end_hypothetical_protein_1186426..1186576_NEGATIVE 148 48 6 82 53 NC_002967:TDE0345|3end_methyl-accepting_chemotaxis_protein_DmcB_385744..385894_NEGATIVE 147 109 76 127 95 NC_002967:TDE0464|3end_NifU_domain_protein_517948..518098_NEGATIVE 147 103 66 66 29 NC_002967:TDE0405|3end_major_outer_sheath_protein_457181..457331_POSITIVE 146 104 69 151 117 NC_002967:TDE1198|3end_S-adenosyl-methyltransferase_MraW_1231419..1231569_POSITIVE 146 44 1 145 102 NC_002967:TDE0182|3end_ABC_transporter,_ATP-binding_protein_215134..215284_NEGATIVE