Origin IGS: gcagaaaagaaatgacattgggtaaatggttgtgaggtaatatatatgtaaagtagtagagaaagaacaaaaatcattcaaggcaaattctacatagtgtattatgacgaagaaaaatagtattttgtatatacataatagttagactgtatttttctgcaaaattgatattttgcaaaacaaagccgtgtttttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaaaacacggctttgttttgcaaaatatcaattttgcagaaaaatacagtctaactattatgtatatacaaaatactatttttcttcgtcataatacactatgtagaatttgccttgaatgatttttgttctttctctactactttacatatatattacctcacaaccatttacccaatgtcatttcttttctgc Mask Tandem Repeat Region ================================================ gcagaaaagaaatgacattgggtaaatggttgtgaggtaatatatatgtaaagtagtagagaaagaacaaaaatcattcaaggcaaattctacatagtgtattatgacgaagaaaaatagtattttgtatatacataatagttagactgtatttttctgcaaaattgatattttgcaaaacaaagccgtgtttttat Find is-nt database================================================ Query_seq: TDE0912:TDE0913|TDE0912:TDE0913:hypothetical protein:hypothetical protein:-><-:931589..931785 197 gcagaaaagaaatgacattgggtaaatggttgtgaggtaatatatatgtaaagtagtagagaaagaacaaaaatcattcaaggcaaattctacatagtgtattatgacgaagaaaaatagtattttgtatatacataatagttagactgtatttttctgcaaaattgatattttgcaaaacaaagccgtgtttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0912:TDE0913|TDE0912:TDE0913:hypothetical protein:hypothetical protein:-><-:931589..931785 197 gcagaaaagaaatgacattgggtaaatggttgtgaggtaatatatatgtaaagtagtagagaaagaacaaaaatcattcaaggcaaattctacatagtgtattatgacgaagaaaaatagtattttgtatatacataatagttagactgtatttttctgcaaaattgatattttgcaaaacaaagccgtgtttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0912:TDE0913|TDE0912:TDE0913:hypothetical protein:hypothetical protein:-><-:931589..931785 197 gcagaaaagaaatgacattgggtaaatggttgtgaggtaatatatatgtaaagtagtagagaaagaacaaaaatcattcaaggcaaattctacatagtgtattatgacgaagaaaaatagtattttgtatatacataatagttagactgtatttttctgcaaaattgatattttgcaaaacaaagccgtgtttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcagaaaagaaatgacattgggtaaatggttgtgaggtaatatatatgtaaagtagtagagaaagaacaaaaatcattcaaggcaaattctacatagtgtattatgacgaagaaaaatagtattttgtatatacataatagttagactgtatttttctgcaaaattgatattttgcaaaacaaagccgtgtttttat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 105 End: 197 ........................................................................................................ S S S F Y Y K T Y V Y Y N S Q I K R C F Q Y K A F C L R T K M Protein_Len: 34 Strand: - Start: 77 End: 178 ............................................................................ E L C I R C L T N H R L F I T N Q I Y M I T L S Y K E A F N I N Q M ................... Protein_Len: 44 Strand: - Start: 1 End: 132 C F L F S M P Y I T T L Y Y I H L T T S F S C F D N L A F E V Y H I I V F F F L I K Y M ................................................................. gcagaaaagaaatgacattgggtaaatggttgtgaggtaatatatatgtaaagtagtagagaaagaacaaaaatcattcaaggcaaattctacatagtgtattatgacgaagaaaaatagtattttgtatatacataatagttagactgtatttttctgcaaaattgatattttgcaaaacaaagccgtgtttttat 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================================================ gcagaaaagaaatgacattgggtaaatggttgtgaggtaatatatatgtaaagtagtagagaaagaacaaaaatcattcaaggcaaattctacatagtgtattatgacgaagaaaaatagtattttgtatatacataatagttagactgtatttttctgcaaaattgatattttgcaaaacaaagccgtgtttttat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0912:TDE0913|TDE0912:TDE0913:hypothetical protein:hypothetical protein:-><-:931589..931785 197 gcagaaaagaaatgacattgggtaaatggttgtgaggtaatatatatgtaaagtagtagagaaagaacaaaaatcattcaaggcaaattctacatagtgtattatgacgaagaaaaatagtattttgtatatacataatagttagactgtatttttctgcaaaattgatattttgcaaaacaaagccgtgtttttat Intra-Species Hit: Count: 1 Min: 1 Max: 197 Len: 197 Subject: NC_002967_TDE0912_TDE0913|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[931589,931785]|197 HSP 1 e-value: 1.0E-108 bit: 391.0 Len: 197 Query Start:1 Query End:197 Subject Strand: POSITIVE Subject Start: 1 Subject End: 197 gcagaaaagaaatgacattgggtaaatggttgtgaggtaatatatatgtaaagtagtagagaaagaacaaaaatcattcaaggcaaattctacatagtgtattatgacgaagaaaaatagtattttgtatatacataatagttagactgtatttttctgcaaaattgatattttgcaaaacaaagccgtgtttttat gcagaaaagaaatgacattgggtaaatggttgtgaggtaatatatatgtaaagtagtagagaaagaacaaaaatcattcaaggcaaattctacatagtgtattatgacgaagaaaaatagtattttgtatatacataatagttagactgtatttttctgcaaaattgatattttgcaaaacaaagccgtgtttttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGAAAAGAAAUGACAUUGGGUAAAUGGUUGUGAGGUAAUAUAUAUGUAAAGUAGUAGAGAAAGAACAAAAAUCAUUCAAGGCAAAUUCUACAUAGUGUAUUAUGACGAAGAAAAAUAGUAUUUUGUAUAUACAUAAUAGUUAGACUGUAUUUUUCUGCAAAAUUGAUAUUUUGCAAAACAAAGCCGUGUUUUUAU ..................((((...((((((.((..((((((((((((((.(((.((...(((.((.......)).)))...))..))).))))).))))))))).....((((((((.((((.......))))...((((.....))))))))))))(((((((....)))))))....)).))))))...)))). (-30.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAACACGGCUUUGUUUUGCAAAAUAUCAAUUUUGCAGAAAAAUACAGUCUAACUAUUAUGUAUAUACAAAAUACUAUUUUUCUUCGUCAUAAUACACUAUGUAGAAUUUGCCUUGAAUGAUUUUUGUUCUUUCUCUACUACUUUACAUAUAUAUUACCUCACAACCAUUUACCCAAUGUCAUUUCUUUUCUGC ..........(((.((((((((((((((....)))))))))))..............(((((((.......((((......))))......)))))))...((((((((.........(((.((.......)).)))........))))))))........................))).)))............. (-21.95) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 67 21 224 180 NC_002967:TDE2628|5end_hypothetical_protein_2669068..2669298_POSITIVE 250 127 81 63 10 NC_002967:TDE2177|5end_hypothetical_protein_2206524..2206754_NEGATIVE 244 96 51 194 143 NC_002967:TDE1840|5end_hypothetical_protein_1871581..1871811_NEGATIVE 244 96 51 194 143 NC_002967:TDE1800|5end_hypothetical_protein_1837684..1837914_NEGATIVE 239 190 154 165 133 NC_002967:TDE0546|5end_hypothetical_protein_584909..585139_POSITIVE 233 189 141 174 133 NC_002967:TDE1401|5end_DedA_family_protein_1442365..1442595_POSITIVE 228 162 124 50 12 NC_002967:TDE0414|5end_hypothetical_protein_467260..467490_POSITIVE 225 180 133 171 130 NC_002967:TDE0413|5end_lipoprotein,_putative_466338..466568_POSITIVE 225 190 141 189 145 NC_002967:TDE0026|5end_TraB_family_protein_33016..33246_NEGATIVE 222 129 81 196 151 NC_002967:TDE2498|5end_metallo-beta-lactamase_family_protein_2522961..2523191_NEGATIVE 221 180 142 172 132 NC_002967:TDE0950|5end_hypothetical_protein_974312..974542_NEGATIVE 220 180 133 171 130 NC_002967:TDE0421|5end_lipoprotein,_putative_473416..473646_POSITIVE 213 187 142 150 94 NC_002967:TDE0885|5end_50S_ribosomal_protein_L19_902945..903175_POSITIVE 212 110 64 72 15 NC_002967:TDE1543|5end_conserved_hypothetical_protein_TIGR00247_1586068..1586298_POSITIVE 205 190 157 30 1 NC_002967:TDE0545|5end_hypothetical_protein_584774..585004_POSITIVE 204 180 144 61 28 NC_002967:TDE1902|5end_hypothetical_protein_1922475..1922705_NEGATIVE 203 87 50 49 15 NC_002967:TDE2227|5end_hypothetical_protein_2266395..2266625_POSITIVE 202 188 143 144 91 NC_002967:TDE2269|5end_hypothetical_protein_2305920..2306150_NEGATIVE 196 41 1 180 140 NC_002967:TDE2132|5end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2163541..2163771_NEGATIVE 196 41 2 65 38 NC_002967:TDE1275|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1310523..1310753_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 190 154 146 114 NC_002967:TDE0545|3end_hypothetical_protein_584970..585120_POSITIVE 239 190 154 42 10 NC_002967:TDE0544|3end_hypothetical_protein_584866..585016_POSITIVE 228 162 124 78 40 NC_002967:TDE0413|3end_lipoprotein,_putative_467368..467518_POSITIVE 214 176 133 80 42 NC_002967:TDE0156|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_180344..180494_NEGATIVE 200 110 80 52 23 NC_002967:TDE2419|3end_hypothetical_protein_2444023..2444173_NEGATIVE 199 110 80 52 21 NC_002967:TDE1542|3end_hypothetical_protein_1586128..1586278_POSITIVE 196 41 2 61 34 NC_002967:TDE1276|3end_hypothetical_protein_1310527..1310677_NEGATIVE 192 84 50 62 26 NC_002967:TDE0793|3end_hypothetical_protein_819205..819355_POSITIVE 191 114 73 145 95 NC_002967:TDE0064|3end_diphosphate--fructose-6-phosphate_1-phosphotransferase_71335..71485_NEGATIVE 189 177 133 69 28 NC_002967:TDE2545|3end_hypothetical_protein_2571170..2571320_NEGATIVE 189 190 144 137 97 NC_002967:TDE0244|3end_ABC_transporter,_ATP-binding/permease_protein_277489..277639_NEGATIVE 188 189 141 71 22 NC_002967:TDE1799|3end_hypothetical_protein_1836689..1836839_NEGATIVE 187 178 142 148 101 NC_002967:TDE0884|3end_tRNA_(guanine-N(1)-)-methyltransferase_903032..903182_POSITIVE 187 190 146 80 34 NC_002967:TDE0779|3end_ribosomal_protein_L5_812432..812582_POSITIVE 186 37 1 150 119 NC_002967:TDE0453|3end_hypothetical_protein_510143..510293_NEGATIVE 185 81 48 40 11 NC_002967:TDE2703|3end_hypothetical_protein_2747605..2747755_NEGATIVE 184 50 2 82 16 NC_002967:TDE1620|3end_hypothetical_protein_1666959..1667109_NEGATIVE 183 39 1 80 41 NC_002967:TDE1387|3end_RNA_pseudouridylate_synthase_family_protein_1426815..1426965_NEGATIVE 180 60 12 68 16 NC_002967:TDE2597|3end_ribulose-phosphate_3-epimerase_2632036..2632186_NEGATIVE 180 186 151 114 72 NC_002967:TDE1515|3end_permease_domain_protein_1563179..1563329_POSITIVE