Origin IGS: aaccttttgttgtttaagtctgtattaatgtttaatttgtttttacggatttcagttatccctcaaatatacgcgtttggtctgttttatacaaatattttttttgcttgatattgttaaagtgttgtatgattaagttttatatgcgtaaaaacagagagagagaaaatgttggaactattggaggaaacggtcattattttgcaggtttttggaaaacttggtcgaaggggggaaaaaagtaaaagcaacttttgtaaaaaagttgcttttactaagattttaataggtattagtttctaaggcaaaaagattgtttaggttatcacacgcaaaataacggcgaatcacactaattcacaaataaattattatattataaaacatgttttggaacttgttta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacaagttccaaaacatgttttataatataataatttatttgtgaattagtgtgattcgccgttattttgcgtgtgataacctaaacaatctttttgccttagaaactaatacctattaaaatcttagtaaaagcaacttttttacaaaagttgcttttacttttttccccccttcgaccaagttttccaaaaacctgcaaaataatgaccgtttcctccaatagttccaacattttctctctctctgtttttacgcatataaaacttaatcatacaacactttaacaatatcaagcaaaaaaaatatttgtataaaacagaccaaacgcgtatatttgagggataactgaaatccgtaaaaacaaattaaacattaatacagacttaaacaacaaaaggtt Mask Tandem Repeat Region ================================================ aaccttttgttgtttaagtctgtattaatgtttaatttgtttttacggatttcagttatccctcaaatatacgcgtttggtctgttttatacaaatattttttttgcttgatattgttaaagtgttgtatgattaagttttatatgcgtaaaaacagagagagagaaaatgttggaactattggaggaaacggtcattattttgcaggtttttggaaaacttggtcgaaggggggaaaaaagtaaaagcaacttttgtaaaaaagttgcttttactaagattttaataggtattagtttctaaggcaaaaagattgtttaggttatcacacgcaaaataacggcgaatcacactaattcacaaataaattattatattataaaacatgttttggaacttgttta Find is-nt database================================================ Query_seq: TF0319:TF0320|TF0319:TF0320:tolB protein:dihydroorotase:->->:345798..346201 404 aaccttttgttgtttaagtctgtattaatgtttaatttgtttttacggatttcagttatccctcaaatatacgcgtttggtctgttttatacaaatattttttttgcttgatattgttaaagtgttgtatgattaagttttatatgcgtaaaaacagagagagagaaaatgttggaactattggaggaaacggtcattattttgcaggtttttggaaaacttggtcgaaggggggaaaaaagtaaaagcaacttttgtaaaaaagttgcttttactaagattttaataggtattagtttctaaggcaaaaagattgtttaggttatcacacgcaaaataacggcgaatcacactaattcacaaataaattattatattataaaacatgttttggaacttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0319:TF0320|TF0319:TF0320:tolB protein:dihydroorotase:->->:345798..346201 404 aaccttttgttgtttaagtctgtattaatgtttaatttgtttttacggatttcagttatccctcaaatatacgcgtttggtctgttttatacaaatattttttttgcttgatattgttaaagtgttgtatgattaagttttatatgcgtaaaaacagagagagagaaaatgttggaactattggaggaaacggtcattattttgcaggtttttggaaaacttggtcgaaggggggaaaaaagtaaaagcaacttttgtaaaaaagttgcttttactaagattttaataggtattagtttctaaggcaaaaagattgtttaggttatcacacgcaaaataacggcgaatcacactaattcacaaataaattattatattataaaacatgttttggaacttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0319:TF0320|TF0319:TF0320:tolB protein:dihydroorotase:->->:345798..346201 404 aaccttttgttgtttaagtctgtattaatgtttaatttgtttttacggatttcagttatccctcaaatatacgcgtttggtctgttttatacaaatattttttttgcttgatattgttaaagtgttgtatgattaagttttatatgcgtaaaaacagagagagagaaaatgttggaactattggaggaaacggtcattattttgcaggtttttggaaaacttggtcgaaggggggaaaaaagtaaaagcaacttttgtaaaaaagttgcttttactaagattttaataggtattagtttctaaggcaaaaagattgtttaggttatcacacgcaaaataacggcgaatcacactaattcacaaataaattattatattataaaacatgttttggaacttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaccttttgttgtttaagtctgtattaatgtttaatttgtttttacggatttcagttatccctcaaatatacgcgtttggtctgttttatacaaatattttttttgcttgatattgttaaagtgttgtatgattaagttttatatgcgtaaaaacagagagagagaaaatgttggaactattggaggaaacggtcattattttgcaggtttttggaaaacttggtcgaaggggggaaaaaagtaaaagcaacttttgtaaaaaagttgcttttactaagattttaataggtattagtttctaaggcaaaaagattgtttaggttatcacacgcaaaataacggcgaatcacactaattcacaaataaattattatattataaaacatgttttggaacttgttta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 7 End: 108 ...... M L F K S V L M F N L F L R I S V I P Q I Y A F G L F Y T N I F F A ........................................................................................................................................................................................................................................................................................................ Protein_Len: 33 Strand: + Start: 35 End: 133 .................................. M C F Y G F Q L S L K Y T R L V C F I Q I F F L L D I V K V L Y D ............................................................................................................................................................................................................................................................................... Protein_Len: 58 Strand: + Start: 69 End: 242 .................................................................... M R V W S V L Y K Y F F C L I L L K C C M I K F Y M R K N R E R E N V G T I G G N G H Y F A G F W K T W S K G G K K .................................................................................................................................................................. Protein_Len: 53 Strand: + Start: 142 End: 300 ............................................................................................................................................. M C V K T E R E K M L E L L E E T V I I L Q V F G K L G R R G E K S K S N F C K K V A F T K I L I G I S F ........................................................................................................ Protein_Len: 58 Strand: - Start: 120 End: 293 ....................................................................................................................... L T T H N L K I H T F V S L S F I N S S N S S V T M I K C T K P F S P R L P S F L L L L K Q L F T A K V L I K I P M ............................................................................................................... aaccttttgttgtttaagtctgtattaatgtttaatttgtttttacggatttcagttatccctcaaatatacgcgtttggtctgttttatacaaatattttttttgcttgatattgttaaagtgttgtatgattaagttttatatgcgtaaaaacagagagagagaaaatgttggaactattggaggaaacggtcattattttgcaggtttttggaaaacttggtcgaaggggggaaaaaagtaaaagcaacttttgtaaaaaagttgcttttactaagattttaataggtattagtttctaaggcaaaaagattgtttaggttatcacacgcaaaataacggcgaatcacactaattcacaaataaattattatattataaaacatgttttggaacttgttta 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: 87 Start: 280 End: 309 .......................................................................................................................................................................................................................................................................................TTTGCCTTAGAAACTAATACCTATTAAAAT............................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 356 End: 385 ...................................................................................................................................................................................................................................................................................................................................................................ATTCACAAATAAATTATTATATTATAAAAC................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaccttttgttgtttaagtctgtattaatgtttaatttgtttttacggatttcagttatccctcaaatatacgcgtttggtctgttttatacaaatattttttttgcttgatattgttaaagtgttgtatgattaagttttatatgcgtaaaaacagagagagagaaaatgttggaactattggaggaaacggtcattattttgcaggtttttggaaaacttggtcgaaggggggaaaaaagtaaaagcaacttttgtaaaaaagttgcttttactaagattttaataggtattagtttctaaggcaaaaagattgtttaggttatcacacgcaaaataacggcgaatcacactaattcacaaataaattattatattataaaacatgttttggaacttgttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -17.1 Tail_Score: -5.03145 Start: 242 End: 275 Full_Region: cctattaaaatctta gtaaaagcaactttt ttac aaaagttgcttttac ttttttccccccttc .................................................................................................................................................................................................................................................gtaaaagcaacttttttacaaaagttgcttttac................................................................................................................................. Find igs database================================================ Query_seq: TF0319:TF0320|TF0319:TF0320:tolB protein:dihydroorotase:->->:345798..346201 404 aaccttttgttgtttaagtctgtattaatgtttaatttgtttttacggatttcagttatccctcaaatatacgcgtttggtctgttttatacaaatattttttttgcttgatattgttaaagtgttgtatgattaagttttatatgcgtaaaaacagagagagagaaaatgttggaactattggaggaaacggtcattattttgcaggtttttggaaaacttggtcgaaggggggaaaaaagtaaaagcaacttttgtaaaaaagttgcttttactaagattttaataggtattagtttctaaggcaaaaagattgtttaggttatcacacgcaaaataacggcgaatcacactaattcacaaataaattattatattataaaacatgttttggaacttgttta Intra-Species Hit: Count: 1 Min: 1 Max: 404 Len: 404 Subject: tfor_TF0319_TF0320|tolB protein:dihydroorotase|POSITIVE:POSITIVE|[345798, 346201]|404 HSP 1 e-value: 0.0 bit: 753.0 Len: 404 Query Start:1 Query End:404 Subject Strand: POSITIVE Subject Start: 1 Subject End: 404 aaccttttgttgtttaagtctgtattaatgtttaatttgtttttacggatttcagttatccctcaaatatacgcgtttggtctgttttatacaaatannnnnnnngcttgatattgttaaagtgttgtatgattaagttttatatgcgtaaaaacagagagagagaaaatgttggaactattggaggaaacggtcattattttgcaggtttttggaaaacttggtcgaaggggggaaaaaagtaaaagcaacttttgtaaaaaagttgcttttactaagattttaataggtattagtttctaaggcaaaaagattgtttaggttatcacacgcaaaataacggcgaatcacactaattcacaaataaattattatattataaaacatgttttggaacttgttta aaccttttgttgtttaagtctgtattaatgtttaatttgtttttacggatttcagttatccctcaaatatacgcgtttggtctgttttatacaaatattttttttgcttgatattgttaaagtgttgtatgattaagttttatatgcgtaaaaacagagagagagaaaatgttggaactattggaggaaacggtcattattttgcaggtttttggaaaacttggtcgaaggggggaaaaaagtaaaagcaacttttgtaaaaaagttgcttttactaagattttaataggtattagtttctaaggcaaaaagattgtttaggttatcacacgcaaaataacggcgaatcacactaattcacaaataaattattatattataaaacatgttttggaacttgttta HSP 2 e-value: 1.0E-6 bit: 56.0 Len: 36 Query Start:241 Query End:276 Subject Strand: NEGATIVE Subject Start: 241 Subject End: 276 ................................................................................................................................................................................................................................................agtaaaagcaacttttgtaaaaaagttgcttttact................................................................................................................................ ................................................................................................................................................................................................................................................agtaaaagcaacttttttacaaaagttgcttttact................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCUUUUGUUGUUUAAGUCUGUAUUAAUGUUUAAUUUGUUUUUACGGAUUUCAGUUAUCCCUCAAAUAUACGCGUUUGGUCUGUUUUAUACAAAUAUUUUUUUUGCUUGAUAUUGUUAAAGUGUUGUAUGAUUAAGUUUUAUAUGCGUAAAAACAGAGAGAGAGAAAAUGUUGGAACUAUUGGAGGAAACGGUCAUUAUUUUGCAGGUUUUUGGAAAACUUGGUCGAAGGGGGGAAAAAAGUAAAAGCAACUUUUGUAAAAAAGUUGCUUUUACUAAGAUUUUAAUAGGUAUUAGUUUCUAAGGCAAAAAGAUUGUUUAGGUUAUCACACGCAAAAUAACGGCGAAUCACACUAAUUCACAAAUAAAUUAUUAUAUUAUAAAACAUGUUUUGGAACUUGUUUA ...(((((.(((((((((((((((..((((.......))))..))))))))).................(((((((.(((.((...((((((((.((((((....((........)).))))))))))))))...))..))).))))))).)))))).)))))........((((((.((.((..(....).(((.(((((((((..((.....((.(((((((.(((............((((((((((((((((....)))))))))))))))).(((..(((((....)))))..)))............))).))))))).))))..))))))))).)))......)).)).))).)))..................(((((.(((....))).))))). (-84.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAAGUUCCAAAACAUGUUUUAUAAUAUAAUAAUUUAUUUGUGAAUUAGUGUGAUUCGCCGUUAUUUUGCGUGUGAUAACCUAAACAAUCUUUUUGCCUUAGAAACUAAUACCUAUUAAAAUCUUAGUAAAAGCAACUUUUUUACAAAAGUUGCUUUUACUUUUUUCCCCCCUUCGACCAAGUUUUCCAAAAACCUGCAAAAUAAUGACCGUUUCCUCCAAUAGUUCCAACAUUUUCUCUCUCUCUGUUUUUACGCAUAUAAAACUUAAUCAUACAACACUUUAACAAUAUCAAGCAAAAAAAAUAUUUGUAUAAAACAGACCAAACGCGUAUAUUUGAGGGAUAACUGAAAUCCGUAAAAACAAAUUAAACAUUAAUACAGACUUAAACAACAAAAGGUU .....(((((.......((((((..................(((.((((((.((.((..((.((((((((((((.((........((((..(((.........)))......................((((((((((((((((....))))))))))))))))....................)))).......)).))))))))))))..))..))...)).)))))))))...............(((((((((..........(((((..((((....(((..........)))...........(((((.....)))))........))))..)))))((((.......)))))))))))))....)))))).......)))))............... (-62.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 238 191 144 99 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 326 256 212 214 167 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 324 235 191 227 176 tfor:TF1297|5end_hypothetical_protein_1379024..1379254_POSITIVE 312 227 181 50 5 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 311 236 191 214 152 tfor:TF2837|5end_conserved_hypothetical_protein_3027939..3028169_POSITIVE 295 250 203 75 34 tfor:TF0574|5end_AMP_nucleosidase_604787..605017_POSITIVE 289 258 217 80 42 tfor:TF2750|5end_L-serine_dehydratase_2934432..2934662_POSITIVE 282 219 173 207 149 tfor:TF0007|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_2557..2787_POSITIVE 281 196 153 66 21 tfor:TF1982|5end_1,4-alpha-glucan_branching_enzyme_2131951..2132181_POSITIVE 281 196 153 66 21 tfor:TF1826|5end_1,4-alpha-glucan_branching_enzyme,_N-terminal_region_1974633..1974863_POSITIVE 281 249 204 130 82 tfor:TF0471|5end_conserved_hypothetical_protein_487516..487746_POSITIVE 280 208 161 74 19 tfor:TF0699|5end_pyridoxal_phosphate_biosynthetic_protein_741556..741786_POSITIVE 274 228 185 155 115 tfor:TF0204|5end_cation_efflux_system_protein_230618..230848_POSITIVE 271 249 203 219 172 tfor:TF1653|5end_hypothetical_protein_1766201..1766431_POSITIVE 271 256 212 85 35 tfor:TF1320|5end_beta-galactosidase_1398414..1398644_POSITIVE 271 249 203 219 172 tfor:TF0979|5end_hypothetical_protein_1032838..1033068_POSITIVE 270 353 315 84 42 tfor:TF2596|5end_conserved_hypothetical_protein;_possible_lipoprotein_2766667..2766897_POSITIVE 269 235 200 221 186 tfor:TF2208|5end_conserved_hypothetical_protein_2382349..2382579_POSITIVE 268 228 191 218 164 tfor:TF0013|5end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_6414..6644_POSITIVE 267 227 182 155 104 tfor:TF0236|5end_multidrug_resistance_protein_261779..262009_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 238 191 111 66 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 326 256 212 50 3 tfor:TF1239|3end_RNA_polymerase_ECF-type_sigma_factor_1324220..1324370_POSITIVE 324 235 191 105 54 tfor:TF1296|3end_possible_DNA-binding_protein,_histone-like_family_1378982..1379132_POSITIVE 295 250 203 60 19 tfor:TF0573|3end_DNA_polymerase_III,_delta_subunit_604852..605002_POSITIVE 293 236 191 125 83 tfor:TF2924|3end_DNA-binding_response_regulator/sensor_histidine_kinase_3125618..3125768_POSITIVE 289 258 217 86 48 tfor:TF2749|3end_possible_hemolysin_2934518..2934668_POSITIVE 282 219 173 150 92 tfor:TF0006|3end_3-oxyacyl_[acyl-carrier_protein]_reductase_2580..2730_POSITIVE 282 219 173 141 83 tfor:TF0004|3end_conserved_hypothetical_protein_2571..2721_POSITIVE 281 249 204 52 4 tfor:TF0470|3end_hypothetical_protein_487518..487668_POSITIVE 274 228 185 117 77 tfor:TF0203|3end_PhoH-like_protein_230660..230810_POSITIVE 273 79 36 59 9 tfor:TF3052|3end_conserved_hypothetical_protein_3278654..3278804_POSITIVE 271 256 212 51 1 tfor:TF1319|3end_outer_membrane_protein_1398460..1398610_POSITIVE 270 353 315 54 12 tfor:TF2595|3end_conserved_hypothetical_protein_2766717..2766867_POSITIVE 267 227 182 145 94 tfor:TF0235|3end_hypothetical_protein_261849..261999_POSITIVE 266 270 223 65 14 tfor:TF0626|3end_hypothetical_protein_662729..662879_POSITIVE 265 236 194 141 99 tfor:TF1537|3end_hypothetical_protein_1643336..1643486_POSITIVE 264 250 203 74 26 tfor:TF1763|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_1901481..1901631_POSITIVE 264 248 207 52 12 tfor:TF0489|3end_D-xylose-proton_symporter_513069..513219_POSITIVE 263 259 211 136 78 tfor:TF3041|3end_hypothetical_protein_3269405..3269555_POSITIVE 256 247 204 113 71 tfor:TF1209|3end_RNA_polymerase_ECF-type_sigma_factor_1295380..1295530_POSITIVE