Origin IGS: tgagtgaataagatgatgcccgcaaaataatttatttcaattgcttattccttttgcgacaaaaacagatatttttttgataagtgaaaaaatattttcatctttgcagaaaataaagaataagtaaaaattgcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggcaatttttacttattctttattttctgcaaagatgaaaatattttttcacttatcaaaaaaatatctgtttttgtcgcaaaaggaataagcaattgaaataaattattttgcgggcatcatcttattcactca Mask Tandem Repeat Region ================================================ tgagtgaataagatgatgcccgcaaaataatttatttcaattgcttattccttttgcgacaaaaacagatatttttttgataagtgaaaaaatattttcatctttgcagaaaataaagaataagtaaaaattgcc Find is-nt database================================================ Query_seq: TF0152:TF0153|TF0152:TF0153:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:162743..162877 135 tgagtgaataagatgatgcccgcaaaataatttatttcaattgcttattccttttgcgacaaaaacagatatttttttgataagtgaaaaaatattttcatctttgcagaaaataaagaataagtaaaaattgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0152:TF0153|TF0152:TF0153:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:162743..162877 135 tgagtgaataagatgatgcccgcaaaataatttatttcaattgcttattccttttgcgacaaaaacagatatttttttgataagtgaaaaaatattttcatctttgcagaaaataaagaataagtaaaaattgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0152:TF0153|TF0152:TF0153:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:162743..162877 135 tgagtgaataagatgatgcccgcaaaataatttatttcaattgcttattccttttgcgacaaaaacagatatttttttgataagtgaaaaaatattttcatctttgcagaaaataaagaataagtaaaaattgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagtgaataagatgatgcccgcaaaataatttatttcaattgcttattccttttgcgacaaaaacagatatttttttgataagtgaaaaaatattttcatctttgcagaaaataaagaataagtaaaaattgcc Predict ORF larger than 30AA ================================================ tgagtgaataagatgatgcccgcaaaataatttatttcaattgcttattccttttgcgacaaaaacagatatttttttgataagtgaaaaaatattttcatctttgcagaaaataaagaataagtaaaaattgcc 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================================================ tgagtgaataagatgatgcccgcaaaataatttatttcaattgcttattccttttgcgacaaaaacagatatttttttgataagtgaaaaaatattttcatctttgcagaaaataaagaataagtaaaaattgcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0152:TF0153|TF0152:TF0153:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:162743..162877 135 tgagtgaataagatgatgcccgcaaaataatttatttcaattgcttattccttttgcgacaaaaacagatatttttttgataagtgaaaaaatattttcatctttgcagaaaataaagaataagtaaaaattgcc Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: tfor_TF0152_TF0153|RNA polymerase ECF-type sigma factor:conserved hypothetical protein|POSITIVE:POSITIVE|[162743,162877]|135 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 tgagtgaataagatgatgcccgcaaaataatttatttcaattgcttattccttttgcgacaaaaacagatannnnnnngataagtgaaaaaatattttcatctttgcagaaaataaagaataagtaaaaattgcc tgagtgaataagatgatgcccgcaaaataatttatttcaattgcttattccttttgcgacaaaaacagatatttttttgataagtgaaaaaatattttcatctttgcagaaaataaagaataagtaaaaattgcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGUGAAUAAGAUGAUGCCCGCAAAAUAAUUUAUUUCAAUUGCUUAUUCCUUUUGCGACAAAAACAGAUAUUUUUUUGAUAAGUGAAAAAAUAUUUUCAUCUUUGCAGAAAAUAAAGAAUAAGUAAAAAUUGCC .((((((((...((..((....))..)).))))))))...((((((((((.((((((((.......((((((((((((.......))))))))))))......))))))))......))))))))))........ (-23.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCAAUUUUUACUUAUUCUUUAUUUUCUGCAAAGAUGAAAAUAUUUUUUCACUUAUCAAAAAAAUAUCUGUUUUUGUCGCAAAAGGAAUAAGCAAUUGAAAUAAAUUAUUUUGCGGGCAUCAUCUUAUUCACUCA .((((......((((((((((......(((.(((.((((((....)))))))))..((((((........))))))..))).)))))))))).((((......))))...))))..................... (-18.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 44 11 168 137 tfor:TF2037|5end_conserved_hypothetical_protein;_possible_anaerobic_ribonucleoside-triphosphate_reductase_2196754..2196984_POSITIVE 244 45 4 124 79 tfor:TF1908|5end_possible_phosphoglycerate_mutase_2062695..2062925_POSITIVE 241 58 12 182 145 tfor:TF0250|5end_glycosyltransferase_Family_2_protein_279176..279406_POSITIVE 239 60 11 130 69 tfor:TF0435|5end_DNA_mismatch_repair_protein_457182..457412_POSITIVE 236 50 2 150 105 tfor:TF0812|5end_conserved_hypothetical_protein_872087..872317_POSITIVE 233 60 16 125 78 tfor:TF1891|5end_hypothetical_protein_2043389..2043619_POSITIVE 233 72 41 209 174 tfor:TF1393|5end_conserved_hypothetical_protein_1465734..1465964_POSITIVE 228 57 13 159 117 tfor:TF1116|5end_conserved_hypothetical_protein_1186491..1186721_POSITIVE 225 67 22 223 177 tfor:TF2143|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2319331..2319561_POSITIVE 222 119 76 125 84 tfor:TF2676|5end_conserved_hypothetical_protein_2849645..2849875_POSITIVE 219 35 1 116 76 tfor:TF0244|5end_DNA_recombination_protein_274683..274913_POSITIVE 219 97 56 152 112 tfor:TF0228|5end_probable_integral_outer_membrane_protein_253851..254081_POSITIVE 216 74 41 85 51 tfor:TF0758|5end_peptidyl-tRNA_hydrolase_805307..805537_POSITIVE 214 83 43 108 67 tfor:TF2216|5end_fumarate_hydratase,_class_I_2388227..2388457_POSITIVE 208 33 4 229 197 tfor:TF0038|5end_conserved_hypothetical_protein_39907..40137_POSITIVE 205 58 12 56 8 tfor:TF0028|5end_hypothetical_protein_24249..24479_POSITIVE 204 27 6 73 52 tfor:TF1982|5end_1,4-alpha-glucan_branching_enzyme_2131951..2132181_POSITIVE 204 27 6 73 52 tfor:TF1826|5end_1,4-alpha-glucan_branching_enzyme,_N-terminal_region_1974633..1974863_POSITIVE 200 58 13 71 24 tfor:TF3099|5end_conserved_hypothetical_protein_3330461..3330691_POSITIVE 200 60 11 168 119 tfor:TF2434|5end_conserved_hypothetical_protein_2613969..2614199_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 45 4 66 21 tfor:TF1907|3end_ADP-heptose:LPS_heptosyltransferase_II_2062717..2062867_POSITIVE 228 57 13 132 90 tfor:TF1115|3end_lantibiotic_biosynthesis_protein_1186544..1186694_POSITIVE 224 24 2 143 119 tfor:TF0813|3end_glycosyl_hydrolase,_secreted_872181..872331_POSITIVE 219 35 1 111 71 tfor:TF0243|3end_conserved_hypothetical_protein_274758..274908_POSITIVE 219 97 56 68 28 tfor:TF0226|3end_hypothetical_protein_253847..253997_POSITIVE 214 83 43 50 9 tfor:TF2215|3end_conserved_hypothetical_protein_2388249..2388399_POSITIVE 213 58 16 51 4 tfor:TF0947|3end_extracellular_protease_993550..993700_POSITIVE 209 57 14 61 17 tfor:TF0010|3end_conserved_hypothetical_protein_4790..4940_POSITIVE 202 56 18 148 107 tfor:TF2452|3end_outer_membrane_protein,_OmpH_family_2630415..2630565_POSITIVE 200 58 13 65 18 tfor:TF3098|3end_conserved_hypothetical_protein_3330535..3330685_POSITIVE 199 59 14 64 12 tfor:TF2959|3end_type_I_restriction_enzyme_methyltransferase,_M_protein_3170786..3170936_POSITIVE 199 60 17 141 94 tfor:TF2936|3end_conserved_hypothetical_protein;_possible_ribosomal_subunit_interface_protein_3138898..3139048_POSITIVE 193 98 54 88 48 tfor:TF0710|3end_two_component_system_histidine_kinase_761385..761535_POSITIVE 193 123 84 91 44 tfor:TF0325|3end_LysM_domain_protein_353784..353934_POSITIVE 192 87 42 73 31 tfor:TF2111|3end_RNA_polymerase_sigma-54_factor_2282115..2282265_POSITIVE 192 53 13 131 91 tfor:TF1589|3end_surface_antigen_BspA_1705746..1705896_POSITIVE 192 108 68 45 1 tfor:TF0706|3end_possible_outer_membrane_transport_protein_750619..750769_POSITIVE 191 44 1 94 50 tfor:TF1641|3end_hypothetical_protein_1749186..1749336_POSITIVE 190 57 11 46 1 tfor:TF1930|3end_two-component_response_regulator_2078203..2078353_POSITIVE 189 117 71 128 80 tfor:TF2312|3end_conserved_hypothetical_protein;_possible_glycosyl_transferase_2472522..2472672_POSITIVE