Origin IGS: ccttaaactttttttgagttgcaaaggaatataaaaacgtctgttacgacaatcactacatgtagtgattttttactttttgtccggtcgtattttttttatacagttgtctgtttgcatgttaaggatttgatgagagaacacgaaaaacctcatgctatccttacatgcttctctttatttttcagtcgggtaattaatttgggtaagttgatttttttcagcctcaaaaaaacagttcatattttgtcgcattcctcatctcgattctttccgacattctttgtcttatcctcggcaacaaagatgttttatca .........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 tgataaaacatctttgttgccgaggataagacaaagaatgtcggaaagaatcgagatgaggaatgcgacaaaatatgaactgtttttttgaggctgaaaaaaatcaacttacccaaattaattacccgactgaaaaataaagagaagcatgtaaggatagcatgaggtttttcgtgttctctcatcaaatccttaacatgcaaacagacaactgtataaaaaaaatacgaccggacaaaaagtaaaaaatcactacatgtagtgattgtcgtaacagacgtttttatattcctttgcaactcaaaaaaagtttaagg Mask Tandem Repeat Region ================================================ ccttaaactttttttgagttgcaaaggaatataaaaacgtctgttacgacaatcactacatgtagtgattttttactttttgtccggtcgtattttttttatacagttgtctgtttgcatgttaaggatttgatgagagaacacgaaaaacctcatgctatccttacatgcttctctttatttttcagtcgggtaattaatttgggtaagttgatttttttcagcctcaaaaaaacagttcatattttgtcgcattcctcatctcgattctttccgacattctttgtcttatcctcggcaacaaagatgttttatca Find is-nt database================================================ Query_seq: TF0318:TF0319|TF0318:TF0319:outer membrane protein, TonB dependent receptor:tolB protein:->->:344362..344678 317 ccttaaactttttttgagttgcaaaggaatataaaaacgtctgttacgacaatcactacatgtagtgattttttactttttgtccggtcgtattttttttatacagttgtctgtttgcatgttaaggatttgatgagagaacacgaaaaacctcatgctatccttacatgcttctctttatttttcagtcgggtaattaatttgggtaagttgatttttttcagcctcaaaaaaacagttcatattttgtcgcattcctcatctcgattctttccgacattctttgtcttatcctcggcaacaaagatgttttatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0318:TF0319|TF0318:TF0319:outer membrane protein, TonB dependent receptor:tolB protein:->->:344362..344678 317 ccttaaactttttttgagttgcaaaggaatataaaaacgtctgttacgacaatcactacatgtagtgattttttactttttgtccggtcgtattttttttatacagttgtctgtttgcatgttaaggatttgatgagagaacacgaaaaacctcatgctatccttacatgcttctctttatttttcagtcgggtaattaatttgggtaagttgatttttttcagcctcaaaaaaacagttcatattttgtcgcattcctcatctcgattctttccgacattctttgtcttatcctcggcaacaaagatgttttatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0318:TF0319|TF0318:TF0319:outer membrane protein, TonB dependent receptor:tolB protein:->->:344362..344678 317 ccttaaactttttttgagttgcaaaggaatataaaaacgtctgttacgacaatcactacatgtagtgattttttactttttgtccggtcgtattttttttatacagttgtctgtttgcatgttaaggatttgatgagagaacacgaaaaacctcatgctatccttacatgcttctctttatttttcagtcgggtaattaatttgggtaagttgatttttttcagcctcaaaaaaacagttcatattttgtcgcattcctcatctcgattctttccgacattctttgtcttatcctcggcaacaaagatgttttatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccttaaactttttttgagttgcaaaggaatataaaaacgtctgttacgacaatcactacatgtagtgattttttactttttgtccggtcgtattttttttatacagttgtctgtttgcatgttaaggatttgatgagagaacacgaaaaacctcatgctatccttacatgcttctctttatttttcagtcgggtaattaatttgggtaagttgatttttttcagcctcaaaaaaacagttcatattttgtcgcattcctcatctcgattctttccgacattctttgtcttatcctcggcaacaaagatgttttatca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 41 End: 130 ........................................ M L R Q S L H V V I F Y F L S G R I F F I Q L S V C M L R I ........................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 19 End: 315 .................. M Q R N I K T S V T T I T T C S D F L L F V R S Y F F Y T V V C L H V K D L M R E H E K P H A I L T C F S L F F S R V I .. ccttaaactttttttgagttgcaaaggaatataaaaacgtctgttacgacaatcactacatgtagtgattttttactttttgtccggtcgtattttttttatacagttgtctgtttgcatgttaaggatttgatgagagaacacgaaaaacctcatgctatccttacatgcttctctttatttttcagtcgggtaattaatttgggtaagttgatttttttcagcctcaaaaaaacagttcatattttgtcgcattcctcatctcgattctttccgacattctttgtcttatcctcggcaacaaagatgttttatca 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================================================ ccttaaactttttttgagttgcaaaggaatataaaaacgtctgttacgacaatcactacatgtagtgattttttactttttgtccggtcgtattttttttatacagttgtctgtttgcatgttaaggatttgatgagagaacacgaaaaacctcatgctatccttacatgcttctctttatttttcagtcgggtaattaatttgggtaagttgatttttttcagcctcaaaaaaacagttcatattttgtcgcattcctcatctcgattctttccgacattctttgtcttatcctcggcaacaaagatgttttatca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -6.2 Tail_Score: -5.56112 Start: 53 End: 68 Full_Region: CGTCTGTTACGACAA TCACTA CATG TAGTGA TTTTTTACTTTTTGT ....................................................TCACTACATGTAGTGA......................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 50 HP_score: -3.4 Tail_Score: -3.40403 Start: 276 End: 288 Full_Region: ATCTCGATTCTTTCC GACA TTCTT TGTC TTATCCTCGGCAACA ...................................................................................................................................................................................................................................................................................GACATTCTTTGTC............................. Find igs database================================================ Query_seq: TF0318:TF0319|TF0318:TF0319:outer membrane protein, TonB dependent receptor:tolB protein:->->:344362..344678 317 ccttaaactttttttgagttgcaaaggaatataaaaacgtctgttacgacaatcactacatgtagtgattttttactttttgtccggtcgtattttttttatacagttgtctgtttgcatgttaaggatttgatgagagaacacgaaaaacctcatgctatccttacatgcttctctttatttttcagtcgggtaattaatttgggtaagttgatttttttcagcctcaaaaaaacagttcatattttgtcgcattcctcatctcgattctttccgacattctttgtcttatcctcggcaacaaagatgttttatca Intra-Species Hit: Count: 1 Min: 16 Max: 317 Len: 302 Subject: tfor_TF0318_TF0319|outer membrane protein, TonB dependent receptor:tolB protein|POSITIVE:POSITIVE|[344362,344678]|317 HSP 1 e-value: 1.0E-131 bit: 468.0 Len: 302 Query Start:16 Query End:317 Subject Strand: POSITIVE Subject Start: 16 Subject End: 317 ...............gagttgcaaaggaatataaaaacgtctgttacgacaatcactacatgtagtgattttttactttttgtccggtcgtannnnnnnnatacagttgtctgtttgcatgttaaggatttgatgagagaacacgaaaaacctcatgctatccttacatgcttctctttatttttcagtcgggtaattaatttgggtaagttgannnnnnncagcctcnnnnnnncagttcatattttgtcgcattcctcatctcgattctttccgacattctttgtcttatcctcggcaacaaagatgttttatca ...............gagttgcaaaggaatataaaaacgtctgttacgacaatcactacatgtagtgattttttactttttgtccggtcgtattttttttatacagttgtctgtttgcatgttaaggatttgatgagagaacacgaaaaacctcatgctatccttacatgcttctctttatttttcagtcgggtaattaatttgggtaagttgatttttttcagcctcaaaaaaacagttcatattttgtcgcattcctcatctcgattctttccgacattctttgtcttatcctcggcaacaaagatgttttatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUUGCAAAGGAAUAUAAAAACGUCUGUUACGACAAUCACUACAUGUAGUGAUUUUUUACUUUUUGUCCGGUCGUAUUUUUUUUAUACAGUUGUCUGUUUGCAUGUUAAGGAUUUGAUGAGAGAACACGAAAAACCUCAUGCUAUCCUUACAUGCUUCUCUUUAUUUUUCAGUCGGGUAAUUAAUUUGGGUAAGUUGAUUUUUUUCAGCCUCAAAAAAACAGUUCAUAUUUUGUCGCAUUCCUCAUCUCGAUUCUUUCCGACAUUCUUUGUCUUAUCCUCGGCAACAAAGAUGUUUUAUCA ..................(((((((((..((((((.(((((((....))))))).....((.....))...)))))).............((((((.....((((((.((((((...(((((..............)))))...))))))))))))...............(((((((.......((((((...(((((......)))))))))))...((((........))))............)))))))......((((.....))))........))))))..))))))))).... (-66.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAAAACAUCUUUGUUGCCGAGGAUAAGACAAAGAAUGUCGGAAAGAAUCGAGAUGAGGAAUGCGACAAAAUAUGAACUGUUUUUUUGAGGCUGAAAAAAAUCAACUUACCCAAAUUAAUUACCCGACUGAAAAAUAAAGAGAAGCAUGUAAGGAUAGCAUGAGGUUUUUCGUGUUCUCUCAUCAAAUCCUUAACAUGCAAACAGACAACUGUAUAAAAAAAAUACGACCGGACAAAAAGUAAAAAAUCACUACAUGUAGUGAUUGUCGUAACAGACGUUUUUAUAUUCCUUUGCAACUC ...............(((((.(((((.......(((((((((.((.....))...........((((((.........(((.......((((..(((......))).))))..............(((..................((((((((((((((((((((....))))))))..........)))))).))))))..((((....))))................)))......)))....((((((((....))))))))))))))...)))))))))....))))).))))).. (-65.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 132 96 198 165 tfor:TF0271|5end_oxidase/dehydrogenase_298262..298492_POSITIVE 319 83 41 125 87 tfor:TF1490|5end_hypothetical_protein_1590238..1590468_POSITIVE 311 199 152 153 89 tfor:TF1664|5end_conserved_hypothetical_protein_1778761..1778991_POSITIVE 306 159 114 216 157 tfor:TF1041|5end_dihydroorotate_dehydrogenase,_catalytic_subunit_1102029..1102259_POSITIVE 298 280 231 143 98 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 290 213 173 197 152 tfor:TF0685|5end_hypothetical_protein_730852..731082_POSITIVE 287 286 244 210 159 tfor:TF1914|5end_conserved_hypothetical_protein_2066599..2066829_POSITIVE 286 156 111 229 179 tfor:TF1737|5end_outer_membrane_protein,_TonB_dependent_receptor_1861834..1862064_POSITIVE 286 156 111 78 28 tfor:TF1736|5end_hypothetical_protein_1861683..1861913_POSITIVE 283 214 171 231 182 tfor:TF1539|5end_conserved_hypothetical_protein_1644067..1644297_POSITIVE 283 284 241 86 36 tfor:TF0994|5end_maltose_O-acetyltransferase_1049127..1049357_POSITIVE 281 139 92 105 66 tfor:TF0471|5end_conserved_hypothetical_protein_487516..487746_POSITIVE 280 279 231 177 129 tfor:TF2904|5end_ATP-dependent__helicase,_possible_UvrD/REP_helicase_domain_protein_3098903..3099133_POSITIVE 279 176 138 113 78 tfor:TF2419|5end_conserved_hypothetical_protein;_possible_DNA_uptake-related_protein_2598358..2598588_POSITIVE 279 180 140 213 160 tfor:TF1468|5end_beta-galactosidase_1557785..1558015_POSITIVE 276 107 61 187 140 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 275 107 62 93 53 tfor:TF1002|5end_replicative_DNA_helicase_1056620..1056850_POSITIVE 275 191 154 202 168 tfor:TF0463|5end_precorrin-6Y_C5,15-methyltransferase_479015..479245_POSITIVE 275 285 243 216 173 tfor:TF0310|5end_conserved_hypothetical_protein_334685..334915_POSITIVE 274 294 253 73 35 tfor:TF2722|5end_conserved_hypothetical_protein_2896792..2897022_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 83 41 125 87 tfor:TF1489|3end_argininosuccinate_lyase_1590318..1590468_POSITIVE 311 199 152 67 3 tfor:TF1663|3end_ABC_transporter,_permease_component_1778755..1778905_POSITIVE 286 286 249 96 51 tfor:TF1730|3end_diaminopimelate_decarboxylase_1855907..1856057_POSITIVE 283 148 105 86 37 tfor:TF0684|3end_conserved_hypothetical_protein_730564..730714_POSITIVE 279 176 138 59 24 tfor:TF2418|3end_GTP-binding_protein_2598384..2598534_POSITIVE 273 106 66 151 107 tfor:TF0411|3end_methyltransferase_429755..429905_POSITIVE 271 285 242 85 46 tfor:TF2311|3end_conserved_hypothetical_protein_2471612..2471762_POSITIVE 269 161 122 108 69 tfor:TF2158|3end_conserved_hypothetical_protein_2334584..2334734_POSITIVE 267 179 137 122 76 tfor:TF2607|3end_conserved_hypothetical_protein_2784645..2784795_POSITIVE 266 149 101 125 78 tfor:TF2597|3end_outer_membrane_receptor_protein;_possible_TonB_dependent_receptor_2770851..2771001_POSITIVE 262 76 32 107 61 tfor:TF2832|3end_possible_proton/sodium:glutamate_symporter_protein_3023939..3024089_POSITIVE 262 113 72 70 33 tfor:TF2146|3end_secreted_sulfatase_ydeN_precursor_2321858..2322008_POSITIVE 260 190 142 141 87 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 260 278 234 74 33 tfor:TF2768|3end_ferredoxin_oxidoreductase,_beta_subunit_2955169..2955319_POSITIVE 258 180 134 110 59 tfor:TF2604|3end_possible_membrane_transport_protein_2779832..2779982_POSITIVE 257 274 236 67 25 tfor:TF2803|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2993467..2993617_POSITIVE 255 191 152 54 16 tfor:TF2430|3end_hypothetical_protein_2613204..2613354_POSITIVE 251 158 111 88 43 tfor:TF2901|3end_conserved_hypothetical_protein_3097890..3098040_POSITIVE 251 108 61 109 70 tfor:TF1785|3end_histidine_ammonia-lyase_1926070..1926220_POSITIVE 251 101 68 47 15 tfor:TF0095|3end_methyltransferase_106845..106995_POSITIVE