Origin IGS: aataaatcggttgaaaccttattccctttttttcctctttgtgttagtatcgcggtcatggaaaattcacagttaaatcaaggagcccttgaaacggactccattaagaaaacgaatttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaattcgttttcttaatggagtccgtttcaagggctccttgatttaactgtgaattttccatgaccgcgatactaacacaaagaggaaaaaaagggaataaggtttcaaccgatttatt Mask Tandem Repeat Region ================================================ aataaatcggttgaaaccttattccctttttttcctctttgtgttagtatcgcggtcatggaaaattcacagttaaatcaaggagcccttgaaacggactccattaagaaaacgaatttc Find is-nt database================================================ Query_seq: TDE0848:TDE0849|TDE0848:TDE0849:hypothetical protein:hypothetical protein:->->:871619..871738 120 aataaatcggttgaaaccttattccctttttttcctctttgtgttagtatcgcggtcatggaaaattcacagttaaatcaaggagcccttgaaacggactccattaagaaaacgaatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0848:TDE0849|TDE0848:TDE0849:hypothetical protein:hypothetical protein:->->:871619..871738 120 aataaatcggttgaaaccttattccctttttttcctctttgtgttagtatcgcggtcatggaaaattcacagttaaatcaaggagcccttgaaacggactccattaagaaaacgaatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0848:TDE0849|TDE0848:TDE0849:hypothetical protein:hypothetical protein:->->:871619..871738 120 aataaatcggttgaaaccttattccctttttttcctctttgtgttagtatcgcggtcatggaaaattcacagttaaatcaaggagcccttgaaacggactccattaagaaaacgaatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataaatcggttgaaaccttattccctttttttcctctttgtgttagtatcgcggtcatggaaaattcacagttaaatcaaggagcccttgaaacggactccattaagaaaacgaatttc Predict ORF larger than 30AA ================================================ aataaatcggttgaaaccttattccctttttttcctctttgtgttagtatcgcggtcatggaaaattcacagttaaatcaaggagcccttgaaacggactccattaagaaaacgaatttc 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: 81 Start: 21 End: 50 ....................ATTCCCTTTTTTTCCTCTTTGTGTTAGTAT...................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aataaatcggttgaaaccttattccctttttttcctctttgtgttagtatcgcggtcatggaaaattcacagttaaatcaaggagcccttgaaacggactccattaagaaaacgaatttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0848:TDE0849|TDE0848:TDE0849:hypothetical protein:hypothetical protein:->->:871619..871738 120 aataaatcggttgaaaccttattccctttttttcctctttgtgttagtatcgcggtcatggaaaattcacagttaaatcaaggagcccttgaaacggactccattaagaaaacgaatttc Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: NC_002967_TDE0848_TDE0849|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[871619,871738]|120 HSP 1 e-value: 1.0E-49 bit: 196.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 aataaatcggttgaaaccttattcccnnnnnnncctctttgtgttagtatcgcggtcatggaaaattcacagttaaatcaaggagcccttgaaacggactccattaagaaaacgaatttc aataaatcggttgaaaccttattccctttttttcctctttgtgttagtatcgcggtcatggaaaattcacagttaaatcaaggagcccttgaaacggactccattaagaaaacgaatttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAUCGGUUGAAACCUUAUUCCCUUUUUUUCCUCUUUGUGUUAGUAUCGCGGUCAUGGAAAAUUCACAGUUAAAUCAAGGAGCCCUUGAAACGGACUCCAUUAAGAAAACGAAUUUC ......(((....................((((((...(((((.......)))))....))))))................((((.((.......)).))))..........)))..... (-18.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUUCGUUUUCUUAAUGGAGUCCGUUUCAAGGGCUCCUUGAUUUAACUGUGAAUUUUCCAUGACCGCGAUACUAACACAAAGAGGAAAAAAAGGGAAUAAGGUUUCAACCGAUUUAUU ((((((.(((..(((...(((((((.......)))))))................((((((........................)))))).)))..)))..))))))............ (-24.06) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 58 17 227 173 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 268 93 51 213 164 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 266 61 33 225 197 NC_002967:TDE0569|5end_hypothetical_protein_599636..599866_POSITIVE 260 62 24 226 190 NC_002967:TDE2539|5end_hypothetical_protein_2565158..2565388_NEGATIVE 258 102 80 149 128 NC_002967:TDE1108|5end_hypothetical_protein_1142859..1143089_NEGATIVE 256 57 17 215 172 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 249 100 52 73 13 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 247 94 57 142 108 NC_002967:TDE2492|5end_hypothetical_protein_2516414..2516644_NEGATIVE 244 98 59 203 165 NC_002967:TDE1403|5end_ABC_transporter,_ATP-binding_protein_1446503..1446733_NEGATIVE 242 60 18 229 172 NC_002967:TDE1646|5end_hypothetical_protein_1696180..1696410_NEGATIVE 242 60 13 102 51 NC_002967:TDE0099|5end_adenine-specific_DNA_modification_methyltransferase_115648..115878_POSITIVE 239 65 21 88 47 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 238 103 81 138 112 NC_002967:TDE0843|5end_hypothetical_protein_863850..864080_POSITIVE 237 89 49 58 23 NC_002967:TDE0139|5end_hypothetical_protein_162583..162813_NEGATIVE 237 45 6 167 125 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 236 100 58 165 115 NC_002967:TDE1930|5end_hypothetical_protein_1948556..1948786_NEGATIVE 235 60 22 208 170 NC_002967:TDE2412|5end_acetyltransferase,_GNAT_family_2440262..2440492_NEGATIVE 234 61 26 101 71 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 234 53 15 214 168 NC_002967:TDE1553|5end_hypothetical_protein_1596356..1596586_POSITIVE 233 59 11 202 161 NC_002967:TDE0343|5end_hydrolase,_alpha/beta_fold_family_385365..385595_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 60 17 61 13 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 260 96 51 77 42 NC_002967:TDE0236|3end_PIN_domain_protein_269647..269797_POSITIVE 252 120 90 30 4 NC_002967:TDE1114|3end_transcriptional_regulator,_TetR_family_1148234..1148384_NEGATIVE 243 98 52 78 32 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 240 97 52 84 41 NC_002967:TDE1533|3end_hypothetical_protein_1578657..1578807_POSITIVE 238 103 81 51 25 NC_002967:TDE0842|3end_cytoplasmic_filament_protein_A_863843..863993_POSITIVE 237 97 51 83 38 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 235 60 22 147 109 NC_002967:TDE2413|3end_hypothetical_protein_2440323..2440473_NEGATIVE 234 61 26 96 66 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 234 55 17 119 81 NC_002967:TDE0156|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_180344..180494_NEGATIVE 231 92 51 46 1 NC_002967:TDE1183|3end_ABC_transporter,_ATP-binding_protein_1211354..1211504_POSITIVE 229 51 18 129 90 NC_002967:TDE1526|3end_hypothetical_protein_1570887..1571037_POSITIVE 227 63 23 132 94 NC_002967:TDE1076|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1108056..1108206_POSITIVE 226 108 78 103 58 NC_002967:TDE2154|3end_50S_ribosomal_protein_L20_2189575..2189725_NEGATIVE 225 70 21 145 98 NC_002967:TDE0241|3end_hypothetical_protein_274701..274851_NEGATIVE 222 100 60 60 16 NC_002967:TDE1512|3end_hypothetical_protein_1560551..1560701_POSITIVE 222 62 38 48 23 NC_002967:TDE0547|3end_hypothetical_protein_585971..586121_NEGATIVE 220 60 12 130 82 NC_002967:TDE0037|3end_transcriptional_regulator,_AbrB_family_42551..42701_NEGATIVE 218 103 69 128 95 NC_002967:TDE2717|3end_phosphatidate_cytidylyltransferase,_putative_2773921..2774071_NEGATIVE 217 45 17 58 33 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE