Origin IGS: aatgatgctatttctcgttgttcttattcattatgaaaaagaacaaacttaaaaaatctgattaagtttgttctttaaaacccttttgaaagacttatttcttcttgtgtcggttctttttaagtcttttcttacgcttgtgcgtcgacattttatgtctttttcttttttttccgcttggcataattcctgttgattagtgattaatcatta .........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 taatgattaatcactaatcaacaggaattatgccaagcggaaaaaaaagaaaaagacataaaatgtcgacgcacaagcgtaagaaaagacttaaaaagaaccgacacaagaagaaataagtctttcaaaagggttttaaagaacaaacttaatcagattttttaagtttgttctttttcataatgaataagaacaacgagaaatagcatcatt Mask Tandem Repeat Region ================================================ aatgatgctatttctcgttgttcttattcattatgaaaaagaacaaacttaaaaaatctgattaagtttgttctttaaaacccttttgaaagacttatttcttcttgtgtcggttctttttaagtcttttcttacgcttgtgcgtcgacattttatgtctttttcttttttttccgcttggcataattcctgttgattagtgattaatcatta Find is-nt database================================================ Query_seq: TF0578:TF0579|TF0578:TF0579:ribonuclease G:DNA-binding protein HU:->->:609651..609863 213 aatgatgctatttctcgttgttcttattcattatgaaaaagaacaaacttaaaaaatctgattaagtttgttctttaaaacccttttgaaagacttatttcttcttgtgtcggttctttttaagtcttttcttacgcttgtgcgtcgacattttatgtctttttcttttttttccgcttggcataattcctgttgattagtgattaatcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0578:TF0579|TF0578:TF0579:ribonuclease G:DNA-binding protein HU:->->:609651..609863 213 aatgatgctatttctcgttgttcttattcattatgaaaaagaacaaacttaaaaaatctgattaagtttgttctttaaaacccttttgaaagacttatttcttcttgtgtcggttctttttaagtcttttcttacgcttgtgcgtcgacattttatgtctttttcttttttttccgcttggcataattcctgttgattagtgattaatcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0578:TF0579|TF0578:TF0579:ribonuclease G:DNA-binding protein HU:->->:609651..609863 213 aatgatgctatttctcgttgttcttattcattatgaaaaagaacaaacttaaaaaatctgattaagtttgttctttaaaacccttttgaaagacttatttcttcttgtgtcggttctttttaagtcttttcttacgcttgtgcgtcgacattttatgtctttttcttttttttccgcttggcataattcctgttgattagtgattaatcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgatgctatttctcgttgttcttattcattatgaaaaagaacaaacttaaaaaatctgattaagtttgttctttaaaacccttttgaaagacttatttcttcttgtgtcggttctttttaagtcttttcttacgcttgtgcgtcgacattttatgtctttttcttttttttccgcttggcataattcctgttgattagtgattaatcatta Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 68 End: 193 ................................................................... M F F K T L L K D L F L L V S V L F K S F L T L V R R H F M S F S F F S A W H N S C .................... Protein_Len: 31 Strand: + Start: 105 End: 197 ........................................................................................................ M C R F F L S L F L R L C V D I L C L F L F F P L G I I P V D ................ Protein_Len: 30 Strand: - Start: 98 End: 187 ................................................................................................. K K K H R N K K L R K K R K H T S M K H R K R K K G S P M M .......................... Protein_Len: 51 Strand: - Start: 52 End: 204 ................................................... F I Q N L K N K L V R K F S K N R R T D T R K L D K R V S T R R C K I D K E K K E A Q C L E Q Q N T M ......... aatgatgctatttctcgttgttcttattcattatgaaaaagaacaaacttaaaaaatctgattaagtttgttctttaaaacccttttgaaagacttatttcttcttgtgtcggttctttttaagtcttttcttacgcttgtgcgtcgacattttatgtctttttcttttttttccgcttggcataattcctgttgattagtgattaatcatta 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================================================ aatgatgctatttctcgttgttcttattcattatgaaaaagaacaaacttaaaaaatctgattaagtttgttctttaaaacccttttgaaagacttatttcttcttgtgtcggttctttttaagtcttttcttacgcttgtgcgtcgacattttatgtctttttcttttttttccgcttggcataattcctgttgattagtgattaatcatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 72 HP_score: -8.0 Tail_Score: -3.57309 Start: 41 End: 73 Full_Region: ATTCATTATGAAAAA GAACAAACTTAA AAAATCTGA TTAAGTTTGTTC TTTAAAACCCTTTTG ........................................GAACAAACTTAAAAAATCTGATTAAGTTTGTTC............................................................................................................................................ TransTerm Strand: - Conf: 85 HP_score: -8.0 Tail_Score: -4.77438 Start: 41 End: 73 Full_Region: caaaagggttttaaa gaacaaacttaa tcagatttt ttaagtttgttc tttttcataatgaat ........................................gaacaaacttaatcagattttttaagtttgttc............................................................................................................................................ TransTerm Strand: + Conf: 56 HP_score: -3.9 Tail_Score: -3.91488 Start: 44 End: 70 Full_Region: CATTATGAAAAAGAA CAAACTTAA AAAATCTGA TTAAGTTTG TTCTTTAAAACCCTT ...........................................CAAACTTAAAAAATCTGATTAAGTTTG............................................................................................................................................... TransTerm Strand: + Conf: 95 HP_score: -6.3 Tail_Score: -5.94743 Start: 147 End: 159 Full_Region: TTACGCTTGTGCGTC GACAT TTT ATGTC TTTTTCTTTTTTTTC ..................................................................................................................................................GACATTTTATGTC...................................................... Find igs database================================================ Query_seq: TF0578:TF0579|TF0578:TF0579:ribonuclease G:DNA-binding protein HU:->->:609651..609863 213 aatgatgctatttctcgttgttcttattcattatgaaaaagaacaaacttaaaaaatctgattaagtttgttctttaaaacccttttgaaagacttatttcttcttgtgtcggttctttttaagtcttttcttacgcttgtgcgtcgacattttatgtctttttcttttttttccgcttggcataattcctgttgattagtgattaatcatta Intra-Species Hit: Count: 1 Min: 1 Max: 213 Len: 213 Subject: tfor_TF0578_TF0579|ribonuclease G:DNA-binding protein HU|POSITIVE:POSITIVE|[609651,609863]|213 HSP 1 e-value: 3.0E-85 bit: 315.0 Len: 159 Query Start:1 Query End:159 Subject Strand: POSITIVE Subject Start: 1 Subject End: 159 aatgatgctatttctcgttgttcttattcattatgaaaaagaacaaacttaaaaaatctgattaagtttgttctttaaaacccttttgaaagacttatttcttcttgtgtcggttctttttaagtcttttcttacgcttgtgcgtcgacattttatgtc...................................................... aatgatgctatttctcgttgttcttattcattatgaaaaagaacaaacttaaaaaatctgattaagtttgttctttaaaacccttttgaaagacttatttcttcttgtgtcggttctttttaagtcttttcttacgcttgtgcgtcgacattttatgtc...................................................... HSP 2 e-value: 3.0E-14 bit: 79.8 Len: 40 Query Start:174 Query End:213 Subject Strand: POSITIVE Subject Start: 174 Subject End: 213 .............................................................................................................................................................................ccgcttggcataattcctgttgattagtgattaatcatta .............................................................................................................................................................................ccgcttggcataattcctgttgattagtgattaatcatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUGCUAUUUCUCGUUGUUCUUAUUCAUUAUGAAAAAGAACAAACUUAAAAAAUCUGAUUAAGUUUGUUCUUUAAAACCCUUUUGAAAGACUUAUUUCUUCUUGUGUCGGUUCUUUUUAAGUCUUUUCUUACGCUUGUGCGUCGACAUUUUAUGUCUUUUUCUUUUUUUUCCGCUUGGCAUAAUUCCUGUUGAUUAGUGAUUAAUCAUUA ((((((...............................(((((((((((((((.........)))))))))))))))...........((((((((((......((......)).......))))))))))....((((.....(((((((..(((((((....................)))))))....))))))).))))....)))))). (-40.67) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAUUAAUCACUAAUCAACAGGAAUUAUGCCAAGCGGAAAAAAAAGAAAAAGACAUAAAAUGUCGACGCACAAGCGUAAGAAAAGACUUAAAAAGAACCGACACAAGAAGAAAUAAGUCUUUCAAAAGGGUUUUAAAGAACAAACUUAAUCAGAUUUUUUAAGUUUGUUCUUUUUCAUAAUGAAUAAGAACAACGAGAAAUAGCAUCAUU ...((((((.....)))))).....(((.((((...((((..............(((((...))))).((((....))))....................))).)...............(((((((....((....(((((((((((((((.........))))))))))))))).))....)))..)))).............)))).))) (-36.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 149 103 181 132 tfor:TF1610|5end_peptide_chain_release_factor_RF-2_1728635..1728865_POSITIVE 379 149 103 115 66 tfor:TF1612|5end_conserved_hypothetical_protein_1728569..1728799_POSITIVE 335 130 81 155 114 tfor:TF0266|5end_conserved_hypothetical_protein_295097..295327_POSITIVE 288 147 101 215 173 tfor:TF1416|5end_outer_membrane_protein_1497576..1497806_POSITIVE 280 210 161 181 135 tfor:TF2915|5end_hypothetical_protein_3110422..3110652_POSITIVE 280 150 101 223 181 tfor:TF0766|5end_hypothetical_protein_811934..812164_POSITIVE 280 179 131 78 21 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 280 179 131 71 14 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 279 118 72 48 9 tfor:TF2603|5end_transcriptional_regulator,_AraC_family_2776578..2776808_POSITIVE 278 147 109 166 123 tfor:TF2331|5end_conserved_hypothetical_protein_2491073..2491303_POSITIVE 276 148 101 200 157 tfor:TF2785|5end_RNA_polymerase_sigma_factor,_ECF_subfamily_(sigma-70)_2969277..2969507_POSITIVE 275 148 102 121 73 tfor:TF1270|5end_hypothetical_protein_1355273..1355503_POSITIVE 274 147 103 135 93 tfor:TF2226|5end_CTn_excision_protein_2395529..2395759_POSITIVE 273 148 101 62 7 tfor:TF2495|5end_succinate-semialdehyde_dehydrogenase_(NADP+)_2669456..2669686_POSITIVE 271 120 83 71 34 tfor:TF1540|5end_possible_ATPase_1644537..1644767_POSITIVE 270 179 138 231 196 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 269 149 105 65 13 tfor:TF0800|5end_conserved_hypothetical_protein_855864..856094_POSITIVE 267 133 95 186 148 tfor:TF2699|5end_hypothetical_protein_2872490..2872720_POSITIVE 267 133 95 171 133 tfor:TF2698|5end_hypothetical_protein_2872475..2872705_POSITIVE 267 148 103 142 98 tfor:TF1190|5end_conserved_hypothetical_protein;_possible_membrane_protein_1272980..1273210_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 149 103 86 37 tfor:TF1609|3end_hypothetical_protein_1728620..1728770_POSITIVE 335 130 81 148 107 tfor:TF0265|3end_conserved_hypothetical_protein,_Rhs_family_295170..295320_POSITIVE 292 164 123 151 109 tfor:TF3006|3end_response_regulator,_transcriptional_regulator_RprY_3227162..3227312_POSITIVE 278 147 109 122 79 tfor:TF2330|3end_conserved_hypothetical_protein_2491109..2491259_POSITIVE 276 148 101 140 97 tfor:TF2783|3end_aminotransferase,_PatB_family_2969297..2969447_POSITIVE 274 147 103 128 86 tfor:TF2225|3end_CTn_excision_protein_2395602..2395752_POSITIVE 271 147 111 81 36 tfor:TF0985|3end_fructose-bisphosphate_aldolase_1042973..1043123_POSITIVE 271 76 38 53 15 tfor:TF0578|3end_ribonuclease_G_609590..609740_POSITIVE 269 177 135 67 11 tfor:TF1295|3end_conserved_hypothetical_protein_1377256..1377406_POSITIVE 267 148 103 135 91 tfor:TF1189|3end_outer_membrane_protein,_TonB_dependent_receptor_1273053..1273203_POSITIVE 267 209 175 122 85 tfor:TF0288|3end_conserved_hypothetical_protein_318099..318249_POSITIVE 266 150 101 77 14 tfor:TF1732|3end_conserved_hypothetical_protein_1855979..1856129_POSITIVE 265 180 134 57 2 tfor:TF2694|3end_hypothetical_protein_2870863..2871013_POSITIVE 264 197 153 137 92 tfor:TF1008|3end_rod_shape-determining_protein_MreC_1064374..1064524_POSITIVE 262 177 135 65 11 tfor:TF2226|3end_CTn_excision_protein_2395956..2396106_POSITIVE 260 177 131 99 37 tfor:TF3133|3end_conserved_hypothetical_protein_3369913..3370063_POSITIVE 260 177 132 120 70 tfor:TF2343|3end_ribosome_recycling_factor_2507502..2507652_POSITIVE 259 146 107 128 95 tfor:TF2331|3end_conserved_hypothetical_protein_2491767..2491917_POSITIVE 259 148 107 150 116 tfor:TF1902|3end_two-component_system_sensor_histidine_kinase_2059055..2059205_POSITIVE 258 190 143 100 57 tfor:TF2803|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2993467..2993617_POSITIVE