Origin IGS: tatggtaatcttttcataccacgataatcataacggataaaaacaaaaaaaggtatttgaaggctaactttttttccgggaatcaaaaaaaaagcaaaaaagcaagttttttttccgctttcacatgcaatctgtaatttttttgtctatctttgcctccacgagaatcaaattaagagtaatcattacttaaagaagatagct .........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 agctatcttctttaagtaatgattactcttaatttgattctcgtggaggcaaagatagacaaaaaaattacagattgcatgtgaaagcggaaaaaaaacttgcttttttgctttttttttgattcccggaaaaaaagttagccttcaaatacctttttttgtttttatccgttatgattatcgtggtatgaaaagattaccata Mask Tandem Repeat Region ================================================ tatggtaatcttttcataccacgataatcataacggataaaaacaaaaaaaggtatttgaaggctaactttttttccgggaatcaaaaaaaaagcaaaaaagcaagttttttttccgctttcacatgcaatctgtaatttttttgtctatctttgcctccacgagaatcaaattaagagtaatcattacttaaagaagatagct Find is-nt database================================================ Query_seq: TF1959:TF1960|TF1959:TF1960:conserved hypothetical protein:TonB protein:->->:2110567..2110770 204 tatggtaatcttttcataccacgataatcataacggataaaaacaaaaaaaggtatttgaaggctaactttttttccgggaatcaaaaaaaaagcaaaaaagcaagttttttttccgctttcacatgcaatctgtaatttttttgtctatctttgcctccacgagaatcaaattaagagtaatcattacttaaagaagatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1959:TF1960|TF1959:TF1960:conserved hypothetical protein:TonB protein:->->:2110567..2110770 204 tatggtaatcttttcataccacgataatcataacggataaaaacaaaaaaaggtatttgaaggctaactttttttccgggaatcaaaaaaaaagcaaaaaagcaagttttttttccgctttcacatgcaatctgtaatttttttgtctatctttgcctccacgagaatcaaattaagagtaatcattacttaaagaagatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1959:TF1960|TF1959:TF1960:conserved hypothetical protein:TonB protein:->->:2110567..2110770 204 tatggtaatcttttcataccacgataatcataacggataaaaacaaaaaaaggtatttgaaggctaactttttttccgggaatcaaaaaaaaagcaaaaaagcaagttttttttccgctttcacatgcaatctgtaatttttttgtctatctttgcctccacgagaatcaaattaagagtaatcattacttaaagaagatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatggtaatcttttcataccacgataatcataacggataaaaacaaaaaaaggtatttgaaggctaactttttttccgggaatcaaaaaaaaagcaaaaaagcaagttttttttccgctttcacatgcaatctgtaatttttttgtctatctttgcctccacgagaatcaaattaagagtaatcattacttaaagaagatagct Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 24 End: 134 ....................... M I I T D K N K K R Y L K A N F F S G N Q K K S K K A S F F S A F T C N L ...................................................................... Protein_Len: 41 Strand: + Start: 82 End: 204 ................................................................................. M K K K A K K Q V F F P L S H A I C N F F V Y L C L H E N Q I K S N H Y L K K I A Protein_Len: 43 Strand: - Start: 3 End: 131 .. P L R K M G R Y D Y R I F V F F P I Q L S V K K G P I L F F A F F C T K K G S E C A M ......................................................................... tatggtaatcttttcataccacgataatcataacggataaaaacaaaaaaaggtatttgaaggctaactttttttccgggaatcaaaaaaaaagcaaaaaagcaagttttttttccgctttcacatgcaatctgtaatttttttgtctatctttgcctccacgagaatcaaattaagagtaatcattacttaaagaagatagct 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================================================ tatggtaatcttttcataccacgataatcataacggataaaaacaaaaaaaggtatttgaaggctaactttttttccgggaatcaaaaaaaaagcaaaaaagcaagttttttttccgctttcacatgcaatctgtaatttttttgtctatctttgcctccacgagaatcaaattaagagtaatcattacttaaagaagatagct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1959:TF1960|TF1959:TF1960:conserved hypothetical protein:TonB protein:->->:2110567..2110770 204 tatggtaatcttttcataccacgataatcataacggataaaaacaaaaaaaggtatttgaaggctaactttttttccgggaatcaaaaaaaaagcaaaaaagcaagttttttttccgctttcacatgcaatctgtaatttttttgtctatctttgcctccacgagaatcaaattaagagtaatcattacttaaagaagatagct Intra-Species Hit: Count: 1 Min: 1 Max: 204 Len: 204 Subject: tfor_TF1959_TF1960|conserved hypothetical protein:TonB protein|POSITIVE:POSITIVE|[2110567,2110770]|204 HSP 1 e-value: 2.0E-40 bit: 167.0 Len: 84 Query Start:1 Query End:84 Subject Strand: POSITIVE Subject Start: 1 Subject End: 84 tatggtaatcttttcataccacgataatcataacggataaaaacaaaaaaaggtatttgaaggctaactttttttccgggaatc........................................................................................................................ tatggtaatcttttcataccacgataatcataacggataaaaacaaaaaaaggtatttgaaggctaactttttttccgggaatc........................................................................................................................ HSP 2 e-value: 2.0E-31 bit: 137.0 Len: 90 Query Start:115 Query End:204 Subject Strand: POSITIVE Subject Start: 115 Subject End: 204 ..................................................................................................................ccgctttcacatgcaatctgtaannnnnnngtctatctttgcctccacgagaatcaaattaagagtaatcattacttaaagaagatagct ..................................................................................................................ccgctttcacatgcaatctgtaatttttttgtctatctttgcctccacgagaatcaaattaagagtaatcattacttaaagaagatagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGGUAAUCUUUUCAUACCACGAUAAUCAUAACGGAUAAAAACAAAAAAAGGUAUUUGAAGGCUAACUUUUUUUCCGGGAAUCAAAAAAAAAGCAAAAAAGCAAGUUUUUUUUCCGCUUUCACAUGCAAUCUGUAAUUUUUUUGUCUAUCUUUGCCUCCACGAGAAUCAAAUUAAGAGUAAUCAUUACUUAAAGAAGAUAGCU ((((((.(((............))).))))))..........(((((((((.((((.(((((((..............((((..((((((...((......))...))))))))))))))))).)))).........)))))))))((((((((..(((...)))...........(((((.....)))))...)))))))).. (-33.83) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUAUCUUCUUUAAGUAAUGAUUACUCUUAAUUUGAUUCUCGUGGAGGCAAAGAUAGACAAAAAAAUUACAGAUUGCAUGUGAAAGCGGAAAAAAAACUUGCUUUUUUGCUUUUUUUUUGAUUCCCGGAAAAAAAGUUAGCCUUCAAAUACCUUUUUUUGUUUUUAUCCGUUAUGAUUAUCGUGGUAUGAAAAGAUUACCAUA .((.((((.......(((((......(((...((((.(((.....))).))))...))).......))))))))).)).......((((((.(((((....(((.....((((((((((((.....)))))))))))).)))...((((........))))))))).)))))).........((((((.........)))))). (-37.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 150 105 73 33 tfor:TF1856|5end_conserved_hypothetical_protein_2009969..2010199_POSITIVE 294 160 111 116 69 tfor:TF1436|5end_phosphoglycolate_phosphatase_1521128..1521358_POSITIVE 279 120 75 120 79 tfor:TF1549|5end_conserved_hypothetical_protein_1653993..1654223_POSITIVE 278 156 116 221 182 tfor:TF1656|5end_possible_2-methylthioadenine_synthetase_1771115..1771345_POSITIVE 264 160 115 145 101 tfor:TF2504|5end_peptidyl-prolyl_cis-trans_isomerase_2680031..2680261_POSITIVE 262 169 133 145 109 tfor:TF2946|5end_conserved_hypothetical_protein;_possible_ATPase_3151750..3151980_POSITIVE 262 160 114 105 59 tfor:TF0814|5end_conserved_hypothetical_protein_872546..872776_POSITIVE 254 178 131 153 104 tfor:TF0726|5end_ABC_transporter,_permease_component_777895..778125_POSITIVE 253 136 93 61 16 tfor:TF2724|5end_anti-sigma_factor_2898193..2898423_POSITIVE 253 160 113 180 129 tfor:TF0254|5end_hypothetical_protein_285260..285490_POSITIVE 247 162 138 219 196 tfor:TF2281|5end_hypothetical_protein_2439574..2439804_POSITIVE 247 162 138 46 23 tfor:TF2282|5end_hypothetical_protein_2439401..2439631_POSITIVE 247 135 104 68 34 tfor:TF0067|5end_hypothetical_protein_73243..73473_POSITIVE 245 177 133 195 153 tfor:TF2656|5end_valyl-tRNA_synthetase_2827076..2827306_POSITIVE 245 160 115 113 58 tfor:TF1297|5end_hypothetical_protein_1379024..1379254_POSITIVE 244 160 115 210 167 tfor:TF1301|5end_hypothetical_protein_1383099..1383329_POSITIVE 244 120 75 74 24 tfor:TF1283|5end_hypothetical_protein_1367434..1367664_POSITIVE 242 164 121 64 27 tfor:TF2555|5end_50S_ribosomal_protein_L2_2736326..2736556_POSITIVE 240 151 111 219 182 tfor:TF0087|5end_ABC_transporter,_permease_component_93185..93415_POSITIVE 239 96 51 133 83 tfor:TF2696|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2870752..2870982_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 160 111 52 5 tfor:TF1435|3end_acetate_coenzyme_A_transferase_1521144..1521294_POSITIVE 286 174 131 71 26 tfor:TF2934|3end_acetyltransferase/carbonic_anhydrase_3137245..3137395_POSITIVE 278 156 116 94 55 tfor:TF1655|3end_long-chain-fatty-acid-CoA_ligase_1771068..1771218_POSITIVE 264 160 115 145 101 tfor:TF2503|3end_conserved_hypothetical_protein_2680111..2680261_POSITIVE 262 169 133 117 81 tfor:TF2945|3end_DNA-directed_RNA_polymerase_beta'_subunit_3151802..3151952_POSITIVE 262 160 114 86 40 tfor:TF0812|3end_conserved_hypothetical_protein_872607..872757_POSITIVE 254 178 131 91 42 tfor:TF0725|3end_O-acetylhomoserine_(thiol)-lyase_777913..778063_POSITIVE 247 162 138 39 16 tfor:TF2280|3end_hypothetical_protein_2439474..2439624_POSITIVE 242 164 121 54 17 tfor:TF2554|3end_50S_ribosomal_protein_L23_2736396..2736546_POSITIVE 239 160 114 135 91 tfor:TF2795|3end_hypothetical_protein_2980909..2981059_POSITIVE 238 160 111 151 94 tfor:TF0378|3end_aspartyl-tRNA_synthetase_399520..399670_POSITIVE 236 156 115 145 96 tfor:TF0001|3end_hypothetical_protein_158..308_POSITIVE 235 157 116 71 28 tfor:TF0664|3end_small_protein_B_(SMPB)_709570..709720_POSITIVE 234 157 111 96 53 tfor:TF3126|3end_glycosyltransferase,_group_2_family_3361685..3361835_POSITIVE 231 157 116 66 11 tfor:TF2226|3end_CTn_excision_protein_2395956..2396106_POSITIVE 229 180 148 89 61 tfor:TF2586|3end_conserved_hypothetical_protein_2752064..2752214_POSITIVE 228 160 116 145 103 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 226 160 116 49 8 tfor:TF0804|3end_possible_phosphatidylglycerophosphate_synthase_862899..863049_POSITIVE 224 160 111 112 48 tfor:TF2889|3end_50S_ribosomal_protein_L27_3078688..3078838_POSITIVE 224 180 133 83 39 tfor:TF0009|3end_transcriptional_regulator_4173..4323_POSITIVE