Origin IGS: aaagtgcagtaatcgattgccaattacccattaaccattaatttacgtctacttgtattttataccgtatttttttatactagctctgttatgagaaagttttttaccgtaaaccgtatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatacggtttacggtaaaaaactttctcataacagagctagtataaaaaaatacggtataaaatacaagtagacgtaaattaatggttaatgggtaattggcaatcgattactgcacttt Mask Tandem Repeat Region ================================================ aaagtgcagtaatcgattgccaattacccattaaccattaatttacgtctacttgtattttataccgtatttttttatactagctctgttatgagaaagttttttaccgtaaaccgtatt Find is-nt database================================================ Query_seq: TDE1938:TDE1939|TDE1938:TDE1939:hypothetical protein:hypothetical protein:->->:1954647..1954766 120 aaagtgcagtaatcgattgccaattacccattaaccattaatttacgtctacttgtattttataccgtatttttttatactagctctgttatgagaaagttttttaccgtaaaccgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1938:TDE1939|TDE1938:TDE1939:hypothetical protein:hypothetical protein:->->:1954647..1954766 120 aaagtgcagtaatcgattgccaattacccattaaccattaatttacgtctacttgtattttataccgtatttttttatactagctctgttatgagaaagttttttaccgtaaaccgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1938:TDE1939|TDE1938:TDE1939:hypothetical protein:hypothetical protein:->->:1954647..1954766 120 aaagtgcagtaatcgattgccaattacccattaaccattaatttacgtctacttgtattttataccgtatttttttatactagctctgttatgagaaagttttttaccgtaaaccgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagtgcagtaatcgattgccaattacccattaaccattaatttacgtctacttgtattttataccgtatttttttatactagctctgttatgagaaagttttttaccgtaaaccgtatt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 16 End: 120 ............... M A N Y P L T I N L R L L V F Y T V F F Y T S S V M R K F F T V N R I aaagtgcagtaatcgattgccaattacccattaaccattaatttacgtctacttgtattttataccgtatttttttatactagctctgttatgagaaagttttttaccgtaaaccgtatt 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: 52 End: 81 ...................................................CTTGTATTTTATACCGTATTTTTTTATACT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagtgcagtaatcgattgccaattacccattaaccattaatttacgtctacttgtattttataccgtatttttttatactagctctgttatgagaaagttttttaccgtaaaccgtatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1938:TDE1939|TDE1938:TDE1939:hypothetical protein:hypothetical protein:->->:1954647..1954766 120 aaagtgcagtaatcgattgccaattacccattaaccattaatttacgtctacttgtattttataccgtatttttttatactagctctgttatgagaaagttttttaccgtaaaccgtatt Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: NC_002967_TDE1938_TDE1939|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1954647,1954766]|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 aaagtgcagtaatcgattgccaattacccattaaccattaatttacgtctacttgtattttataccgtannnnnnnatactagctctgttatgagaaagttttttaccgtaaaccgtatt aaagtgcagtaatcgattgccaattacccattaaccattaatttacgtctacttgtattttataccgtatttttttatactagctctgttatgagaaagttttttaccgtaaaccgtatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUGCAGUAAUCGAUUGCCAAUUACCCAUUAACCAUUAAUUUACGUCUACUUGUAUUUUAUACCGUAUUUUUUUAUACUAGCUCUGUUAUGAGAAAGUUUUUUACCGUAAACCGUAUU ...(.(((((.....))))))..((((...........(((..((((......))))..)))......(((((((((((.((....)).)))))))))))........))))........ (-13.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUACGGUUUACGGUAAAAAACUUUCUCAUAACAGAGCUAGUAUAAAAAAAUACGGUAUAAAAUACAAGUAGACGUAAAUUAAUGGUUAAUGGGUAAUUGGCAAUCGAUUACUGCACUUU .....((((((((.......(((..(((......)))..))).........(((.((((...))))..)))..))))))))...........((((((((.....))))))))....... (-18.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 39 5 163 124 NC_002967:TDE0571|5end_hypothetical_protein_601135..601365_POSITIVE 262 35 9 194 165 NC_002967:TDE1938|5end_hypothetical_protein_1953640..1953870_POSITIVE 260 116 71 174 134 NC_002967:TDE2009|5end_hypothetical_protein_2030382..2030612_POSITIVE 260 104 65 133 88 NC_002967:TDE1398|5end_hypothetical_protein_1437192..1437422_POSITIVE 251 90 46 121 67 NC_002967:TDE2416|5end_hypothetical_protein_2442799..2443029_NEGATIVE 238 110 63 150 104 NC_002967:TDE0540|5end_hypothetical_protein_581464..581694_POSITIVE 236 40 3 162 121 NC_002967:TDE1148|5end_hypothetical_protein_1186357..1186587_NEGATIVE 224 116 83 183 153 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 221 67 27 130 87 NC_002967:TDE0853|5end_ribosomal_protein_S9_875473..875703_POSITIVE 219 69 31 167 120 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 219 99 54 149 111 NC_002967:TDE2625|5end_ABC_transporter,_ATP-binding/permease_protein_2666664..2666894_NEGATIVE 216 85 44 171 134 NC_002967:TDE2558|5end_ABC_transporter,_ATP-binding/permease_protein_2585387..2585617_NEGATIVE 216 116 83 173 139 NC_002967:TDE2225|5end_thioesterase_family_protein_2264868..2265098_POSITIVE 216 116 83 48 14 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 216 116 83 173 139 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 216 118 81 73 18 NC_002967:TDE0058|5end_hypothetical_protein_66986..67216_POSITIVE 215 40 9 107 72 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 215 110 62 189 130 NC_002967:TDE0543|5end_hypothetical_protein_583126..583356_POSITIVE 215 109 65 69 21 NC_002967:TDE0518|5end_hypothetical_protein_565263..565493_NEGATIVE 214 36 2 172 151 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 53 12 92 42 NC_002967:TDE0574|3end_surface_protein,_putative_605862..606012_POSITIVE 260 116 71 127 87 NC_002967:TDE2008|3end_ABC_transporter,_ATP-binding/permease_protein_2030415..2030565_POSITIVE 260 104 65 121 76 NC_002967:TDE1397|3end_flagellar_synthesis_regulator_FleN,_putative_1437260..1437410_POSITIVE 251 90 46 108 54 NC_002967:TDE2417|3end_nitroimidazole_resistance_protein,_putative_2442812..2442962_NEGATIVE 238 110 63 148 102 NC_002967:TDE0539|3end_hypothetical_protein_581542..581692_POSITIVE 236 40 3 93 52 NC_002967:TDE1149|3end_hypothetical_protein_1186426..1186576_NEGATIVE 223 116 94 67 43 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE 221 67 27 104 61 NC_002967:TDE0852|3end_50S_ribosomal_protein_L13_875527..875677_POSITIVE 216 116 83 51 17 NC_002967:TDE2223|3end_hypothetical_protein_2264826..2264976_POSITIVE 215 90 42 138 90 NC_002967:TDE2206|3end_hypothetical_protein_2244921..2245071_NEGATIVE 215 118 82 136 94 NC_002967:TDE1667|3end_translation_initiation_factor_IF-2B_subunit_alpha_1719993..1720143_NEGATIVE 215 40 9 80 45 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 215 110 62 125 66 NC_002967:TDE0542|3end_acetyltransferase,_GNAT_family_583142..583292_POSITIVE 208 117 75 151 111 NC_002967:TDE0754|3end_hypothetical_protein_794507..794657_POSITIVE 199 117 82 41 3 NC_002967:TDE1718|3end_GMP_synthase_1773811..1773961_POSITIVE 197 116 72 51 3 NC_002967:TDE2102|3end_hypothetical_protein_2126616..2126766_NEGATIVE 197 105 66 66 34 NC_002967:TDE0605|3end_hypothetical_protein_642631..642781_NEGATIVE 196 56 11 91 48 NC_002967:TDE1897|3end_phosphoribosylglycinamide_formyltransferase_1917525..1917675_NEGATIVE 196 99 56 117 73 NC_002967:TDE1080|3end_dimethyladenosine_transferase_1112699..1112849_POSITIVE 196 116 84 139 97 NC_002967:TDE0635|3end_hypothetical_protein_670578..670728_POSITIVE