Origin IGS: acacgatagaagtaatacgctcgataatcacttttttacattcacattcattttcaattattttgttattagtgatttagcttcttttatgttagccagactattaatcagcttttttgaccgacaaaatattagccgaaaaacaaatcgttcttcggccatatctggaaatctttggtttatcctactta .........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 taagtaggataaaccaaagatttccagatatggccgaagaacgatttgtttttcggctaatattttgtcggtcaaaaaagctgattaatagtctggctaacataaaagaagctaaatcactaataacaaaataattgaaaatgaatgtgaatgtaaaaaagtgattatcgagcgtattacttctatcgtgt Mask Tandem Repeat Region ================================================ acacgatagaagtaatacgctcgataatcacttttttacattcacattcattttcaattattttgttattagtgatttagcttcttttatgttagccagactattaatcagcttttttgaccgacaaaatattagccgaaaaacaaatcgttcttcggccatatctggaaatctttggtttatcctactta Find is-nt database================================================ Query_seq: TF2032:TF2033|TF2032:TF2033:outer membrane protein, TonB dependent receptor:conserved hypothetical protein:->->:2191478..2191668 191 acacgatagaagtaatacgctcgataatcacttttttacattcacattcattttcaattattttgttattagtgatttagcttcttttatgttagccagactattaatcagcttttttgaccgacaaaatattagccgaaaaacaaatcgttcttcggccatatctggaaatctttggtttatcctactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2032:TF2033|TF2032:TF2033:outer membrane protein, TonB dependent receptor:conserved hypothetical protein:->->:2191478..2191668 191 acacgatagaagtaatacgctcgataatcacttttttacattcacattcattttcaattattttgttattagtgatttagcttcttttatgttagccagactattaatcagcttttttgaccgacaaaatattagccgaaaaacaaatcgttcttcggccatatctggaaatctttggtttatcctactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2032:TF2033|TF2032:TF2033:outer membrane protein, TonB dependent receptor:conserved hypothetical protein:->->:2191478..2191668 191 acacgatagaagtaatacgctcgataatcacttttttacattcacattcattttcaattattttgttattagtgatttagcttcttttatgttagccagactattaatcagcttttttgaccgacaaaatattagccgaaaaacaaatcgttcttcggccatatctggaaatctttggtttatcctactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acacgatagaagtaatacgctcgataatcacttttttacattcacattcattttcaattattttgttattagtgatttagcttcttttatgttagccagactattaatcagcttttttgaccgacaaaatattagccgaaaaacaaatcgttcttcggccatatctggaaatctttggtttatcctactta Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 50 End: 190 ................................................. M F N Y F V I S D L A S F M L A R L L I S F F D R Q N I S R K T N R S S A I S G N L W F I L L . Protein_Len: 41 Strand: - Start: 61 End: 183 ............................................................ K T I L S K A E K I N A L S N I L K K S R C F I L R F V F R E E A M D P F R Q N M ........ acacgatagaagtaatacgctcgataatcacttttttacattcacattcattttcaattattttgttattagtgatttagcttcttttatgttagccagactattaatcagcttttttgaccgacaaaatattagccgaaaaacaaatcgttcttcggccatatctggaaatctttggtttatcctactta 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================================================ acacgatagaagtaatacgctcgataatcacttttttacattcacattcattttcaattattttgttattagtgatttagcttcttttatgttagccagactattaatcagcttttttgaccgacaaaatattagccgaaaaacaaatcgttcttcggccatatctggaaatctttggtttatcctactta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 76 HP_score: -6.9 Tail_Score: -4.42386 Start: 130 End: 163 Full_Region: ccaaagatttccaga tatggccgaagaacg att tgtttttcggctaata ttttgtcggtcaaaa .................................................................................................................................tatggccgaagaacgatttgtttttcggctaata............................ TransTerm Strand: - Conf: 74 HP_score: -7.6 Tail_Score: -3.82117 Start: 132 End: 162 Full_Region: caaagatttccagat atggccgaagaacg att tgtttttcggctaa tattttgtcggtcaa ...................................................................................................................................atggccgaagaacgatttgtttttcggctaa............................. Find igs database================================================ Query_seq: TF2032:TF2033|TF2032:TF2033:outer membrane protein, TonB dependent receptor:conserved hypothetical protein:->->:2191478..2191668 191 acacgatagaagtaatacgctcgataatcacttttttacattcacattcattttcaattattttgttattagtgatttagcttcttttatgttagccagactattaatcagcttttttgaccgacaaaatattagccgaaaaacaaatcgttcttcggccatatctggaaatctttggtttatcctactta Intra-Species Hit: Count: 1 Min: 1 Max: 191 Len: 191 Subject: tfor_TF2032_TF2033|outer membrane protein, TonB dependent receptor:conserved hypothetical protein|POSITIVE:POSITIVE|[2191478,2191668]|191 HSP 1 e-value: 1.0E-104 bit: 379.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 acacgatagaagtaatacgctcgataatcacttttttacattcacattcattttcaattattttgttattagtgatttagcttcttttatgttagccagactattaatcagcttttttgaccgacaaaatattagccgaaaaacaaatcgttcttcggccatatctggaaatctttggtttatcctactta acacgatagaagtaatacgctcgataatcacttttttacattcacattcattttcaattattttgttattagtgatttagcttcttttatgttagccagactattaatcagcttttttgaccgacaaaatattagccgaaaaacaaatcgttcttcggccatatctggaaatctttggtttatcctactta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACGAUAGAAGUAAUACGCUCGAUAAUCACUUUUUUACAUUCACAUUCAUUUUCAAUUAUUUUGUUAUUAGUGAUUUAGCUUCUUUUAUGUUAGCCAGACUAUUAAUCAGCUUUUUUGACCGACAAAAUAUUAGCCGAAAAACAAAUCGUUCUUCGGCCAUAUCUGGAAAUCUUUGGUUUAUCCUACUUA (((..(.((((((....(....)..(((((((.....(((.......................)))....)))))))..)))))).)..)))...(((((..............(((((.....))))).....((((((.(((.....))).))))))....)))))........((.....))...... (-30.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUAGGAUAAACCAAAGAUUUCCAGAUAUGGCCGAAGAACGAUUUGUUUUUCGGCUAAUAUUUUGUCGGUCAAAAAAGCUGAUUAAUAGUCUGGCUAACAUAAAAGAAGCUAAAUCACUAAUAACAAAAUAAUUGAAAAUGAAUGUGAAUGUAAAAAAGUGAUUAUCGAGCGUAUUACUUCUAUCGUGU ...((((((..............((((((.((((((((((((.....)))))))))))).((((..((((((.......)))))).))))))))))..............(((.(((((((....(((..(((.((......)).)))...))).....)))))))....))).......))))))..... (-40.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 179 133 75 34 tfor:TF2343|5end_ribosome_recycling_factor_2506862..2507092_POSITIVE 302 185 147 213 166 tfor:TF2615|5end_conserved_hypothetical_protein_2790569..2790799_POSITIVE 285 178 136 55 18 tfor:TF0191|5end_conserved_hypothetical_protein,_possible_Iojap-related_protein_206053..206283_POSITIVE 284 158 111 171 102 tfor:TF3078|5end_ribonucleoside_diphosphate_reductase,_alpha_subunit_3306609..3306839_POSITIVE 281 151 115 70 27 tfor:TF0493|5end_outer_membrane_protein_517537..517767_POSITIVE 278 177 135 42 2 tfor:TF1621|5end_DNA_replication_and_repair_protein_RecF_1735293..1735523_POSITIVE 278 157 111 71 24 tfor:TF0012|5end_conserved_hypothetical_protein_5512..5742_POSITIVE 272 161 135 57 29 tfor:TF2853|5end_2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_3040172..3040402_POSITIVE 268 177 136 45 1 tfor:TF2681|5end_conserved_hypothetical_protein_2855796..2856026_POSITIVE 266 170 122 128 69 tfor:TF1740|5end_hypothetical_protein_1868645..1868875_POSITIVE 261 178 146 168 125 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 260 187 146 90 47 tfor:TF1325|5end_L-fucose_isomerase_1404000..1404230_POSITIVE 260 181 147 227 184 tfor:TF0494|5end_conserved_hypothetical_protein_519174..519404_POSITIVE 259 168 121 109 62 tfor:TF2204|5end_conserved_hypothetical_protein_2378866..2379096_POSITIVE 257 159 112 65 25 tfor:TF2134|5end_conserved_hypothetical_protein_2308689..2308919_POSITIVE 253 180 131 103 48 tfor:TF0809|5end_cation_efflux_protein_865358..865588_POSITIVE 253 159 111 115 72 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 249 185 156 154 120 tfor:TF3122|5end_ABC_transporter,_ATP-binding_protein_3356047..3356277_POSITIVE 248 180 134 151 103 tfor:TF1507|5end_outer_membrane_receptor,_TonB-dependent_1614536..1614766_POSITIVE 247 159 111 202 155 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 281 151 115 54 11 tfor:TF0492|3end_outer_membrane_protein,_TonB_dependent_receptor_517601..517751_POSITIVE 280 180 147 148 115 tfor:TF1213|3end_D-3-phosphoglycerate_dehydrogenase_1301196..1301346_POSITIVE 260 187 146 110 67 tfor:TF1326|3end_hypothetical_protein_1404100..1404250_POSITIVE 257 159 112 65 25 tfor:TF2132|3end_TIM-barrel_protein,_NifR3_family_2308769..2308919_POSITIVE 253 180 131 86 31 tfor:TF0808|3end_cation_efflux_system_protein_865421..865571_POSITIVE 253 159 111 82 39 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 251 172 134 120 81 tfor:TF0001|3end_hypothetical_protein_158..308_POSITIVE 249 185 156 151 117 tfor:TF3121|3end_nicotinate_phosphoribosyltransferase_3356124..3356274_POSITIVE 246 185 146 50 17 tfor:TF0308|3end_hypothetical_protein_334082..334232_POSITIVE 246 159 114 80 35 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 244 178 133 149 96 tfor:TF2600|3end_ribose-phosphate_pyrophosphokinase_2774709..2774859_POSITIVE 237 178 138 136 93 tfor:TF2467|3end_3-dehydroquinate_dehydratase_II_2646323..2646473_POSITIVE 236 161 134 26 2 tfor:TF2852|3end_conserved_hypothetical_protein_3040221..3040371_POSITIVE 235 181 142 40 1 tfor:TF2800|3end_anti-sigma_factor_2986346..2986496_POSITIVE 235 126 89 151 116 tfor:TF0351|3end_hypothetical_protein_371226..371376_POSITIVE 234 160 111 147 97 tfor:TF2817|3end_hypothetical_protein_3007626..3007776_POSITIVE 234 160 111 62 12 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 232 180 136 49 7 tfor:TF0524|3end_possible_cation_efflux_pump_(multidrug_resistance_protein)_549332..549482_POSITIVE 231 170 121 142 96 tfor:TF3003|3end_hypothetical_protein_3220629..3220779_POSITIVE 231 159 121 109 70 tfor:TF2611|3end_conserved_hypothetical_protein_2788069..2788219_POSITIVE