Origin IGS: aaatttttcatatgtttttggaaataccgatctaaataaaacaaaaactgaaattgaagtagagttaaactatcctttaaattttaatatttctatatcgcattttttaaggtcttacaaggaaaattcggattcaaaatataccgagcttgaatttagggcctca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaggccctaaattcaagctcggtatattttgaatccgaattttccttgtaagaccttaaaaaatgcgatatagaaatattaaaatttaaaggatagtttaactctacttcaatttcagtttttgttttatttagatcggtatttccaaaaacatatgaaaaattt Mask Tandem Repeat Region ================================================ aaatttttcatatgtttttggaaataccgatctaaataaaacaaaaactgaaattgaagtagagttaaactatcctttaaattttaatatttctatatcgcattttttaaggtcttacaaggaaaattcggattcaaaatataccgagcttgaatttagggcctca Find is-nt database================================================ Query_seq: TDE1665:TDE1666|TDE1665:TDE1666:hypothetical protein:hypothetical protein:<-->:1719220..1719385 166 aaatttttcatatgtttttggaaataccgatctaaataaaacaaaaactgaaattgaagtagagttaaactatcctttaaattttaatatttctatatcgcattttttaaggtcttacaaggaaaattcggattcaaaatataccgagcttgaatttagggcctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1665:TDE1666|TDE1665:TDE1666:hypothetical protein:hypothetical protein:<-->:1719220..1719385 166 aaatttttcatatgtttttggaaataccgatctaaataaaacaaaaactgaaattgaagtagagttaaactatcctttaaattttaatatttctatatcgcattttttaaggtcttacaaggaaaattcggattcaaaatataccgagcttgaatttagggcctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1665:TDE1666|TDE1665:TDE1666:hypothetical protein:hypothetical protein:<-->:1719220..1719385 166 aaatttttcatatgtttttggaaataccgatctaaataaaacaaaaactgaaattgaagtagagttaaactatcctttaaattttaatatttctatatcgcattttttaaggtcttacaaggaaaattcggattcaaaatataccgagcttgaatttagggcctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatttttcatatgtttttggaaataccgatctaaataaaacaaaaactgaaattgaagtagagttaaactatcctttaaattttaatatttctatatcgcattttttaaggtcttacaaggaaaattcggattcaaaatataccgagcttgaatttagggcctca Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 53 End: 166 .................................................... M E V E L N Y P L N F N I S I S H F L R S Y K E N S D S K Y T E L E F R A S aaatttttcatatgtttttggaaataccgatctaaataaaacaaaaactgaaattgaagtagagttaaactatcctttaaattttaatatttctatatcgcattttttaaggtcttacaaggaaaattcggattcaaaatataccgagcttgaatttagggcctca 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================================================ aaatttttcatatgtttttggaaataccgatctaaataaaacaaaaactgaaattgaagtagagttaaactatcctttaaattttaatatttctatatcgcattttttaaggtcttacaaggaaaattcggattcaaaatataccgagcttgaatttagggcctca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1665:TDE1666|TDE1665:TDE1666:hypothetical protein:hypothetical protein:<-->:1719220..1719385 166 aaatttttcatatgtttttggaaataccgatctaaataaaacaaaaactgaaattgaagtagagttaaactatcctttaaattttaatatttctatatcgcattttttaaggtcttacaaggaaaattcggattcaaaatataccgagcttgaatttagggcctca Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: NC_002967_TDE1665_TDE1666|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1719220,1719385]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 aaatttttcatatgtttttggaaataccgatctaaataaaacaaaaactgaaattgaagtagagttaaactatcctttaaattttaatatttctatatcgcattttttaaggtcttacaaggaaaattcggattcaaaatataccgagcttgaatttagggcctca aaatttttcatatgtttttggaaataccgatctaaataaaacaaaaactgaaattgaagtagagttaaactatcctttaaattttaatatttctatatcgcattttttaaggtcttacaaggaaaattcggattcaaaatataccgagcttgaatttagggcctca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUUUCAUAUGUUUUUGGAAAUACCGAUCUAAAUAAAACAAAAACUGAAAUUGAAGUAGAGUUAAACUAUCCUUUAAAUUUUAAUAUUUCUAUAUCGCAUUUUUUAAGGUCUUACAAGGAAAAUUCGGAUUCAAAAUAUACCGAGCUUGAAUUUAGGGCCUCA .....(((((...(((((((.....................))))))))))))..((.(((((((((((.............))))))...))))).))..........((((((((((((.....(((((((.......)).)))))))))....)))))))).. (-23.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGGCCCUAAAUUCAAGCUCGGUAUAUUUUGAAUCCGAAUUUUCCUUGUAAGACCUUAAAAAAUGCGAUAUAGAAAUAUUAAAAUUUAAAGGAUAGUUUAACUCUACUUCAAUUUCAGUUUUUGUUUUAUUUAGAUCGGUAUUUCCAAAAACAUAUGAAAAAUUU (((((......(((((((..........)))))))..(((((.(((((.(((....)))..((((.....(((....)))....)))).))))).))))).......))))).((((((((((((...((((......))))....)))))))...)))))..... (-17.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 735 140 91 231 182 NC_002967:TDE1665|5end_hypothetical_protein_1719129..1719359_NEGATIVE 227 159 113 139 105 NC_002967:TDE1748|5end_GTP-binding_protein,_GTP1/Obg_family_1803080..1803310_NEGATIVE 217 154 111 219 172 NC_002967:TDE2716|5end_HAD-superfamily_hydrolase,_subfamily_IA_2773195..2773425_POSITIVE 217 58 11 211 159 NC_002967:TDE1927|5end_phenylalanyl-tRNA_synthetase_beta_subunit_1943984..1944214_POSITIVE 214 152 111 182 143 NC_002967:TDE0123|5end_hypothetical_protein_142223..142453_NEGATIVE 211 150 103 165 102 NC_002967:TDE2427|5end_preprotein_translocase,_SecE_subunit_2455982..2456212_NEGATIVE 208 159 113 46 8 NC_002967:TDE0638|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_673450..673680_NEGATIVE 205 154 111 214 180 NC_002967:TDE1198|5end_S-adenosyl-methyltransferase_MraW_1230392..1230622_POSITIVE 205 139 98 145 94 NC_002967:TDE0285|5end_translation_elongation_factor_G_313622..313852_POSITIVE 204 160 126 182 136 NC_002967:TDE1661|5end_hypothetical_protein_1715402..1715632_POSITIVE 201 149 102 208 158 NC_002967:TDE1711|5end_RelA/SpoT_domain_protein_1766718..1766948_NEGATIVE 201 157 120 172 141 NC_002967:TDE1241|5end_HD_domain_protein_1272269..1272499_POSITIVE 199 151 125 186 151 NC_002967:TDE1094|5end_hypothetical_protein_1128065..1128295_POSITIVE 198 150 113 47 5 NC_002967:TDE1039|5end_riboflavin_biosynthesis_protein,_putative_1067072..1067302_POSITIVE 197 149 102 133 96 NC_002967:TDE0671|5end_PIN_domain_protein_710621..710851_POSITIVE 195 154 114 94 63 NC_002967:TDE0849|5end_hypothetical_protein_871599..871829_POSITIVE 193 133 101 52 19 NC_002967:TDE1969|5end_sigma-54_dependent_transcriptional_regulator/response_regulator_1984500..1984730_NEGATIVE 192 153 111 173 129 NC_002967:TDE2727|5end_GTPase_YjeQ,_putative_2785345..2785575_NEGATIVE 192 132 96 231 196 NC_002967:TDE1844|5end_DNA_integrase_1874204..1874434_NEGATIVE 192 55 15 52 16 NC_002967:TDE0711|5end_hypothetical_protein_746181..746411_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 227 159 113 61 27 NC_002967:TDE1749|3end_50S_ribosomal_protein_L27_1803158..1803308_NEGATIVE 218 154 112 112 62 NC_002967:TDE1258|3end_grdX_protein_1291788..1291938_NEGATIVE 214 117 73 142 100 NC_002967:TDE0997|3end_glutamate_dehydrogenase_1024042..1024192_NEGATIVE 208 159 113 43 5 NC_002967:TDE0639|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_673453..673603_NEGATIVE 207 154 111 145 87 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 207 149 109 110 67 NC_002967:TDE2160|3end_hypothetical_protein_2193873..2194023_NEGATIVE 203 150 112 144 105 NC_002967:TDE1103|3end_hypothetical_protein_1136670..1136820_POSITIVE 201 149 102 60 10 NC_002967:TDE1712|3end_flagellar_filament_outer_layer_protein_1766866..1767016_NEGATIVE 198 156 125 92 59 NC_002967:TDE0818|3end_ABC_transporter,_ATP-binding/permease_protein_839926..840076_NEGATIVE 194 149 111 49 7 NC_002967:TDE1252|3end_lipoprotein,_putative_1287094..1287244_POSITIVE 194 149 127 137 110 NC_002967:TDE0941|3end_NLP/P60_family_protein_963623..963773_NEGATIVE 193 133 101 55 22 NC_002967:TDE1970|3end_sensory_box_histidine_kinase_1984497..1984647_NEGATIVE 192 55 15 52 16 NC_002967:TDE0712|3end_hypothetical_protein_746181..746331_NEGATIVE 189 130 98 115 86 NC_002967:TDE0915|3end_hypothetical_protein_933147..933297_NEGATIVE 189 58 17 59 21 NC_002967:TDE0620|3end_hypothetical_protein_653373..653523_POSITIVE 185 116 73 149 104 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 183 151 118 58 29 NC_002967:TDE2013|3end_hypothetical_protein_2034359..2034509_NEGATIVE 183 116 71 100 44 NC_002967:TDE0083|3end_GTP-binding_protein_EngA_94254..94404_NEGATIVE 181 114 71 125 79 NC_002967:TDE2213|3end_hypothetical_protein_2253137..2253287_POSITIVE 181 127 90 55 10 NC_002967:TDE0336|3end_hypothetical_protein_375193..375343_NEGATIVE