Origin IGS: ttttacctacaagagcattatagcacgtattaacacgtgttgtcaatcgttttttgtagagtttatcttgttggcgaaagtgcaaaaaatatgcaggtattaaacaaagtagattgacaaagaaataagcatcatatatgataccataca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtatggtatcatatatgatgcttatttctttgtcaatctactttgtttaatacctgcatattttttgcactttcgccaacaagataaactctacaaaaaacgattgacaacacgtgttaatacgtgctataatgctcttgtaggtaaaa Mask Tandem Repeat Region ================================================ ttttacctacaagagcattatagcacgtattaacacgtgttgtcaatcgttttttgtagagtttatcttgttggcgaaagtgcaaaaaatatgcaggtattaaacaaagtagattgacaaagaaataagcatcatatatgataccataca Find is-nt database================================================ Query_seq: TDE1959:TDE1960|TDE1959:TDE1960:hypothetical protein:hypothetical protein:<-->:1974288..1974437 150 ttttacctacaagagcattatagcacgtattaacacgtgttgtcaatcgttttttgtagagtttatcttgttggcgaaagtgcaaaaaatatgcaggtattaaacaaagtagattgacaaagaaataagcatcatatatgataccataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1959:TDE1960|TDE1959:TDE1960:hypothetical protein:hypothetical protein:<-->:1974288..1974437 150 ttttacctacaagagcattatagcacgtattaacacgtgttgtcaatcgttttttgtagagtttatcttgttggcgaaagtgcaaaaaatatgcaggtattaaacaaagtagattgacaaagaaataagcatcatatatgataccataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1959:TDE1960|TDE1959:TDE1960:hypothetical protein:hypothetical protein:<-->:1974288..1974437 150 ttttacctacaagagcattatagcacgtattaacacgtgttgtcaatcgttttttgtagagtttatcttgttggcgaaagtgcaaaaaatatgcaggtattaaacaaagtagattgacaaagaaataagcatcatatatgataccataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttacctacaagagcattatagcacgtattaacacgtgttgtcaatcgttttttgtagagtttatcttgttggcgaaagtgcaaaaaatatgcaggtattaaacaaagtagattgacaaagaaataagcatcatatatgataccataca Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: - Start: 2 End: 142 . K G V L A N Y C T N V R T T L R K K Y L K D Q Q R F H L F Y A P I L C L L N V F F Y A D Y I M ........ ttttacctacaagagcattatagcacgtattaacacgtgttgtcaatcgttttttgtagagtttatcttgttggcgaaagtgcaaaaaatatgcaggtattaaacaaagtagattgacaaagaaataagcatcatatatgataccataca 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: 88 Start: 113 End: 142 ................................................................................................................ATTGACAAAGAAATAAGCATCATATATGAT........ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttacctacaagagcattatagcacgtattaacacgtgttgtcaatcgttttttgtagagtttatcttgttggcgaaagtgcaaaaaatatgcaggtattaaacaaagtagattgacaaagaaataagcatcatatatgataccataca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1959:TDE1960|TDE1959:TDE1960:hypothetical protein:hypothetical protein:<-->:1974288..1974437 150 ttttacctacaagagcattatagcacgtattaacacgtgttgtcaatcgttttttgtagagtttatcttgttggcgaaagtgcaaaaaatatgcaggtattaaacaaagtagattgacaaagaaataagcatcatatatgataccataca Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: NC_002967_TDE1959_TDE1960|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1974288,1974437]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 ttttacctacaagagcattatagcacgtattaacacgtgttgtcaatcgttttttgtagagtttatcttgttggcgaaagtgcaaaaaatatgcaggtattaaacaaagtagattgacaaagaaataagcatcatatatgataccataca ttttacctacaagagcattatagcacgtattaacacgtgttgtcaatcgttttttgtagagtttatcttgttggcgaaagtgcaaaaaatatgcaggtattaaacaaagtagattgacaaagaaataagcatcatatatgataccataca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUACCUACAAGAGCAUUAUAGCACGUAUUAACACGUGUUGUCAAUCGUUUUUUGUAGAGUUUAUCUUGUUGGCGAAAGUGCAAAAAAUAUGCAGGUAUUAAACAAAGUAGAUUGACAAAGAAAUAAGCAUCAUAUAUGAUACCAUACA ............((((...(((((((((......)))))))))......((((((((..((((((..(((((.((....))(((.......)))........)))))..)))))).))))))))....)).))...((((....)))).. (-30.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAUGGUAUCAUAUAUGAUGCUUAUUUCUUUGUCAAUCUACUUUGUUUAAUACCUGCAUAUUUUUUGCACUUUCGCCAACAAGAUAAACUCUACAAAAAACGAUUGACAACACGUGUUAAUACGUGCUAUAAUGCUCUUGUAGGUAAAA .....(((((((....))))))).......(((((((((...(((((........((((.......))))...((........))........)))))....)))))))))((((((....))))))((((((.....))))))...... (-26.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 833 50 1 141 92 NC_002967:TDE1959|5end_hypothetical_protein_1974197..1974427_NEGATIVE 282 32 5 123 96 NC_002967:TDE1285|5end_flagellar_motor_switch_protein_FliG_,_putative_1320924..1321154_POSITIVE 274 48 6 69 32 NC_002967:TDE2756|5end_bacterial_extracellular_solute-binding_protein,_family_5_2813517..2813747_NEGATIVE 256 76 35 46 8 NC_002967:TDE1710|5end_ribosomal_protein_S20_1765485..1765715_NEGATIVE 253 74 45 178 147 NC_002967:TDE2469|5end_hexokinase_family_protein_2492549..2492779_NEGATIVE 253 98 54 97 52 NC_002967:TDE1401|5end_DedA_family_protein_1442365..1442595_POSITIVE 245 78 40 67 34 NC_002967:TDE0820|5end_transcriptional_regulator,_TetR_family_844373..844603_NEGATIVE 245 76 35 160 117 NC_002967:TDE0059|5end_hypothetical_protein_67294..67524_POSITIVE 236 75 36 86 44 NC_002967:TDE1604|5end_ABC_transporter,_permease_protein,_putative_1655533..1655763_NEGATIVE 235 100 52 54 3 NC_002967:TDE2098|5end_hypothetical_protein_2125085..2125315_NEGATIVE 234 41 6 135 101 NC_002967:TDE1505|5end_hypothetical_protein_1553614..1553844_POSITIVE 228 75 43 186 151 NC_002967:TDE1882|5end_glycosyl_hydrolase,_family_1_1903544..1903774_POSITIVE 226 78 36 230 173 NC_002967:TDE0888|5end_hypothetical_protein_904975..905205_NEGATIVE 225 60 12 101 48 NC_002967:TDE2478|5end_excinuclease_ABC,_C_subunit_2500873..2501103_POSITIVE 223 84 43 221 188 NC_002967:TDE0636|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_671500..671730_NEGATIVE 217 83 41 78 38 NC_002967:TDE0943|5end_hypothetical_protein_965983..966213_POSITIVE 215 99 51 208 167 NC_002967:TDE0871|5end_hypothetical_protein_894797..895027_NEGATIVE 214 113 78 68 32 NC_002967:TDE2287|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2325058..2325288_NEGATIVE 212 113 71 74 33 NC_002967:TDE2096|5end_hypothetical_protein_2123200..2123430_POSITIVE 210 41 6 228 180 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 48 10 141 102 NC_002967:TDE0097|3end_hypothetical_protein_114801..114951_POSITIVE 282 32 5 42 15 NC_002967:TDE1284|3end_methyl-accepting_chemotaxis_protein,_putative_1320923..1321073_POSITIVE 260 105 68 45 8 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 253 74 45 128 97 NC_002967:TDE2470|3end_S-adenosylmethionine_synthetase_2492599..2492749_NEGATIVE 253 98 54 86 41 NC_002967:TDE1400|3end_NAD(+)_synthetase_1442434..1442584_POSITIVE 242 99 53 109 59 NC_002967:TDE1902|3end_hypothetical_protein_1922377..1922527_NEGATIVE 236 75 36 86 44 NC_002967:TDE1605|3end_hypothetical_protein_1655533..1655683_NEGATIVE 234 41 6 74 40 NC_002967:TDE1504|3end_ribosomal_protein_L31_1553633..1553783_POSITIVE 225 60 12 97 44 NC_002967:TDE2477|3end_selenocysteine_synthase_2500949..2501099_POSITIVE 224 99 59 48 4 NC_002967:TDE2393|3end_hypothetical_protein_2422588..2422738_POSITIVE 215 78 39 147 90 NC_002967:TDE2011|3end_hypothetical_protein_2033482..2033632_POSITIVE 214 75 37 137 85 NC_002967:TDE0059|3end_hypothetical_protein_67481..67631_POSITIVE 214 75 37 54 2 NC_002967:TDE0058|3end_hypothetical_protein_67398..67548_POSITIVE 213 83 43 134 91 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 212 113 71 77 36 NC_002967:TDE2095|3end_hypothetical_protein_2123283..2123433_POSITIVE 211 82 45 76 37 NC_002967:TDE0266|3end_hypothetical_protein_297767..297917_NEGATIVE 207 60 15 46 3 NC_002967:TDE2405|3end_hypothetical_protein_2430716..2430866_NEGATIVE 205 110 66 62 15 NC_002967:TDE0538|3end_hypothetical_protein_581129..581279_POSITIVE 203 98 63 144 102 NC_002967:TDE2646|3end_ABC_transporter,_ATP-binding_protein,_putative_2686030..2686180_POSITIVE 203 60 26 55 12 NC_002967:TDE0902|3end_hypothetical_protein_919380..919530_NEGATIVE