Origin IGS: acaatttacgtcgcgtaaacgcgctttatataaaaattggttccatgcgattaaattagggctgctgaaaagcagcccttttttgtaagctaaaccggatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatccggtttagcttacaaaaaagggctgcttttcagcagccctaatttaatcgcatggaaccaatttttatataaagcgcgtttacgcgacgtaaattgt Mask Tandem Repeat Region ================================================ acaatttacgtcgcgtaaacgcgctttatataaaaattggttccatgcgattaaattagggctgctgaaaagcagcccttttttgtaagctaaaccggatt Find is-nt database================================================ Query_seq: TDE0937:TDE0938|TDE0937:TDE0938:RNA polymerase sigma-70 factor family protein:hypothetical protein:-><-:960952..961052 101 acaatttacgtcgcgtaaacgcgctttatataaaaattggttccatgcgattaaattagggctgctgaaaagcagcccttttttgtaagctaaaccggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0937:TDE0938|TDE0937:TDE0938:RNA polymerase sigma-70 factor family protein:hypothetical protein:-><-:960952..961052 101 acaatttacgtcgcgtaaacgcgctttatataaaaattggttccatgcgattaaattagggctgctgaaaagcagcccttttttgtaagctaaaccggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0937:TDE0938|TDE0937:TDE0938:RNA polymerase sigma-70 factor family protein:hypothetical protein:-><-:960952..961052 101 acaatttacgtcgcgtaaacgcgctttatataaaaattggttccatgcgattaaattagggctgctgaaaagcagcccttttttgtaagctaaaccggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaatttacgtcgcgtaaacgcgctttatataaaaattggttccatgcgattaaattagggctgctgaaaagcagcccttttttgtaagctaaaccggatt Predict ORF larger than 30AA ================================================ acaatttacgtcgcgtaaacgcgctttatataaaaattggttccatgcgattaaattagggctgctgaaaagcagcccttttttgtaagctaaaccggatt 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================================================ acaatttacgtcgcgtaaacgcgctttatataaaaattggttccatgcgattaaattagggctgctgaaaagcagcccttttttgtaagctaaaccggatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.6 Tail_Score: -5.26316 Start: 59 End: 78 Full_Region: CATGCGATTAAATTA GGGCTGCT GAAA AGCAGCCC TTTTTTGTAAGCTAA ..........................................................GGGCTGCTGAAAAGCAGCCC....................... Find igs database================================================ Query_seq: TDE0937:TDE0938|TDE0937:TDE0938:RNA polymerase sigma-70 factor family protein:hypothetical protein:-><-:960952..961052 101 acaatttacgtcgcgtaaacgcgctttatataaaaattggttccatgcgattaaattagggctgctgaaaagcagcccttttttgtaagctaaaccggatt Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_002967_TDE0937_TDE0938|RNA polymerase sigma-70 factor family protein:hypothetical protein|POSITIVE:NEGATIVE|[960952,961052]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 acaatttacgtcgcgtaaacgcgctttatataaaaattggttccatgcgattaaattagggctgctgaaaagcagcccttttttgtaagctaaaccggatt acaatttacgtcgcgtaaacgcgctttatataaaaattggttccatgcgattaaattagggctgctgaaaagcagcccttttttgtaagctaaaccggatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAUUUACGUCGCGUAAACGCGCUUUAUAUAAAAAUUGGUUCCAUGCGAUUAAAUUAGGGCUGCUGAAAAGCAGCCCUUUUUUGUAAGCUAAACCGGAUU .........(.((((....)))))............((((((....((...((((..(((((((((....)))))))))..))))...))..))))))... (-35.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCCGGUUUAGCUUACAAAAAAGGGCUGCUUUUCAGCAGCCCUAAUUUAAUCGCAUGGAACCAAUUUUUAUAUAAAGCGCGUUUACGCGACGUAAAUUGU .....(((((.((.........(((((((((....))))))))).........))...)))))..............(((((....)))).)......... (-29.27) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 77 37 155 121 NC_002967:TDE1340|5end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1376317..1376547_POSITIVE 301 99 59 155 119 NC_002967:TDE1910|5end_1-deoxy-D-xylulose-5-phosphate_synthase_1928837..1929067_NEGATIVE 297 76 31 119 73 NC_002967:TDE2137|5end_hypothetical_protein_2166125..2166355_POSITIVE 290 91 56 192 153 NC_002967:TDE0515|5end_hypothetical_protein_563783..564013_NEGATIVE 285 98 57 161 117 NC_002967:TDE2383|5end_cobalamin_5'-phosphate_synthase_2412826..2413056_POSITIVE 283 91 58 154 124 NC_002967:TDE1258|5end_grdX_protein_1292183..1292413_NEGATIVE 278 79 41 216 178 NC_002967:TDE2142|5end_methyl-accepting_chemotaxis_protein_2175769..2175999_POSITIVE 269 98 60 177 128 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 264 98 60 224 181 NC_002967:TDE2475|5end_MATE_efflux_family_protein_2498521..2498751_NEGATIVE 264 77 40 47 15 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 260 88 46 70 30 NC_002967:TDE0861|5end_tyrosyl-tRNA_synthetase_883098..883328_NEGATIVE 259 100 65 64 35 NC_002967:TDE1866|5end_hypothetical_protein_1892354..1892584_NEGATIVE 259 100 65 224 195 NC_002967:TDE1865|5end_peptidase,_M16_family_1892194..1892424_NEGATIVE 259 78 40 206 170 NC_002967:TDE1353|5end_rod_shape-determining_protein_RodA_1393550..1393780_POSITIVE 256 90 45 181 116 NC_002967:TDE2069|5end_endoribonuclease_L-PSP,_putative_2096632..2096862_POSITIVE 256 100 58 216 173 NC_002967:TDE0873|5end_hypothetical_protein_896143..896373_POSITIVE 255 85 41 74 33 NC_002967:TDE1657|5end_transcription_antitermination_protein_NusB_1707640..1707870_NEGATIVE 254 91 54 75 33 NC_002967:TDE1146|5end_hypothetical_protein_1185414..1185644_NEGATIVE 251 98 60 61 5 NC_002967:TDE2746|5end_type_I_restriction-modification_system,_M_subunit_2802135..2802365_NEGATIVE 250 89 43 121 61 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 93 58 54 12 NC_002967:TDE0937|3end_RNA_polymerase_sigma-70_factor_family_protein_960891..961041_POSITIVE 301 99 59 49 13 NC_002967:TDE1911|3end_hypothetical_protein_1928943..1929093_NEGATIVE 283 91 58 91 61 NC_002967:TDE1259|3end_amino_acid_carrier_family_protein_1292246..1292396_NEGATIVE 277 98 56 148 91 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 270 75 39 52 16 NC_002967:TDE0991|3end_ribosomal_protein_L28_1017874..1018024_NEGATIVE 269 100 59 75 33 NC_002967:TDE0826|3end_hypothetical_protein_847860..848010_POSITIVE 259 100 65 67 38 NC_002967:TDE1867|3end_hypothetical_protein_1892351..1892501_NEGATIVE 258 86 49 141 106 NC_002967:TDE0636|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_670532..670682_NEGATIVE 255 85 41 59 18 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 252 90 46 147 98 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 251 98 60 58 2 NC_002967:TDE2747|3end_type_I_restriction-modification_system,_R_subunit_2802138..2802288_NEGATIVE 250 100 58 110 66 NC_002967:TDE2777|3end_hypothetical_protein_2829351..2829501_POSITIVE 248 91 56 65 18 NC_002967:TDE2068|3end_antigen,_putative_2096595..2096745_POSITIVE 248 65 22 81 38 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 248 79 34 92 61 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 247 84 43 68 15 NC_002967:TDE0397|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_447834..447984_POSITIVE 246 90 44 83 44 NC_002967:TDE2219|3end_hypothetical_protein_2258961..2259111_NEGATIVE 244 79 38 105 57 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 244 77 39 74 36 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 244 67 36 80 47 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE