Origin IGS: taatatcctttccttacagactttgccgcaacgatttaaatccgattatcaaagacatacggagtcaaatacgatccaataaatttatcttcgtgatttttttcattcaagtacgatgccttttaacggtaaatttaagataagagaagaatacggtctttgaataatgatacaacagtattaaaactgttaataatgcaaaaaacaactcattgttttggatacatcaaaaagatactatatgtttgcaaaacaaattttaaaaccaaaatacg .........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 cgtattttggttttaaaatttgttttgcaaacatatagtatctttttgatgtatccaaaacaatgagttgttttttgcattattaacagttttaatactgttgtatcattattcaaagaccgtattcttctcttatcttaaatttaccgttaaaaggcatcgtacttgaatgaaaaaaatcacgaagataaatttattggatcgtatttgactccgtatgtctttgataatcggatttaaatcgttgcggcaaagtctgtaaggaaaggatatta Mask Tandem Repeat Region ================================================ taatatcctttccttacagactttgccgcaacgatttaaatccgattatcaaagacatacggagtcaaatacgatccaataaatttatcttcgtgatttttttcattcaagtacgatgccttttaacggtaaatttaagataagagaagaatacggtctttgaataatgatacaacagtattaaaactgttaataatgcaaaaaacaactcattgttttggatacatcaaaaagatactatatgtttgcaaaacaaattttaaaaccaaaatacg Find is-nt database================================================ Query_seq: TF1387:TF1388|TF1387:TF1388:conserved hypothetical protein:hypothetical protein:->->:1461650..1461924 275 taatatcctttccttacagactttgccgcaacgatttaaatccgattatcaaagacatacggagtcaaatacgatccaataaatttatcttcgtgatttttttcattcaagtacgatgccttttaacggtaaatttaagataagagaagaatacggtctttgaataatgatacaacagtattaaaactgttaataatgcaaaaaacaactcattgttttggatacatcaaaaagatactatatgtttgcaaaacaaattttaaaaccaaaatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1387:TF1388|TF1387:TF1388:conserved hypothetical protein:hypothetical protein:->->:1461650..1461924 275 taatatcctttccttacagactttgccgcaacgatttaaatccgattatcaaagacatacggagtcaaatacgatccaataaatttatcttcgtgatttttttcattcaagtacgatgccttttaacggtaaatttaagataagagaagaatacggtctttgaataatgatacaacagtattaaaactgttaataatgcaaaaaacaactcattgttttggatacatcaaaaagatactatatgtttgcaaaacaaattttaaaaccaaaatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1387:TF1388|TF1387:TF1388:conserved hypothetical protein:hypothetical protein:->->:1461650..1461924 275 taatatcctttccttacagactttgccgcaacgatttaaatccgattatcaaagacatacggagtcaaatacgatccaataaatttatcttcgtgatttttttcattcaagtacgatgccttttaacggtaaatttaagataagagaagaatacggtctttgaataatgatacaacagtattaaaactgttaataatgcaaaaaacaactcattgttttggatacatcaaaaagatactatatgtttgcaaaacaaattttaaaaccaaaatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatatcctttccttacagactttgccgcaacgatttaaatccgattatcaaagacatacggagtcaaatacgatccaataaatttatcttcgtgatttttttcattcaagtacgatgccttttaacggtaaatttaagataagagaagaatacggtctttgaataatgatacaacagtattaaaactgttaataatgcaaaaaacaactcattgttttggatacatcaaaaagatactatatgtttgcaaaacaaattttaaaaccaaaatacg Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 3 End: 140 .. M S F P Y R L C R N D L N P I I K D I R S Q I R S N K F I F V I F F I Q V R C L L T V N L R ....................................................................................................................................... Protein_Len: 41 Strand: + Start: 151 End: 273 ...................................................................................................................................................... M R S L N N D T T V L K L L I M Q K T T H C F G Y I K K I L Y V C K T N F K T K I .. Protein_Len: 38 Strand: - Start: 110 End: 223 ............................................................................................................. T R H R K V T F K L Y S F F V T K S Y H Y L L I L V T L L A F F L E N N Q M .................................................... taatatcctttccttacagactttgccgcaacgatttaaatccgattatcaaagacatacggagtcaaatacgatccaataaatttatcttcgtgatttttttcattcaagtacgatgccttttaacggtaaatttaagataagagaagaatacggtctttgaataatgatacaacagtattaaaactgttaataatgcaaaaaacaactcattgttttggatacatcaaaaagatactatatgtttgcaaaacaaattttaaaaccaaaatacg 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================================================ taatatcctttccttacagactttgccgcaacgatttaaatccgattatcaaagacatacggagtcaaatacgatccaataaatttatcttcgtgatttttttcattcaagtacgatgccttttaacggtaaatttaagataagagaagaatacggtctttgaataatgatacaacagtattaaaactgttaataatgcaaaaaacaactcattgttttggatacatcaaaaagatactatatgtttgcaaaacaaattttaaaaccaaaatacg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 42 HP_score: -2.9 Tail_Score: -3.01745 Start: 173 End: 192 Full_Region: tgttttttgcattat taacagt tttaat actgttg tatcattattcaaag ............................................................................................................................................................................taacagttttaatactgttg................................................................................... TransTerm Strand: - Conf: 39 HP_score: -2.4 Tail_Score: -2.6248 Start: 179 End: 195 Full_Region: agttgttttttgcat tattaa cagtt ttaata ctgttgtatcattat ..................................................................................................................................................................................tattaacagttttaata................................................................................ Find igs database================================================ Query_seq: TF1387:TF1388|TF1387:TF1388:conserved hypothetical protein:hypothetical protein:->->:1461650..1461924 275 taatatcctttccttacagactttgccgcaacgatttaaatccgattatcaaagacatacggagtcaaatacgatccaataaatttatcttcgtgatttttttcattcaagtacgatgccttttaacggtaaatttaagataagagaagaatacggtctttgaataatgatacaacagtattaaaactgttaataatgcaaaaaacaactcattgttttggatacatcaaaaagatactatatgtttgcaaaacaaattttaaaaccaaaatacg Intra-Species Hit: Count: 1 Min: 1 Max: 275 Len: 275 Subject: tfor_TF1387_TF1388|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1461650,1461924]|275 HSP 1 e-value: 1.0E-142 bit: 504.0 Len: 275 Query Start:1 Query End:275 Subject Strand: POSITIVE Subject Start: 1 Subject End: 275 taatatcctttccttacagactttgccgcaacgatttaaatccgattatcaaagacatacggagtcaaatacgatccaataaatttatcttcgtgannnnnnncattcaagtacgatgccttttaacggtaaatttaagataagagaagaatacggtctttgaataatgatacaacagtattaaaactgttaataatgcaaaaaacaactcattgttttggatacatcaaaaagatactatatgtttgcaaaacaaattttaaaaccaaaatacg taatatcctttccttacagactttgccgcaacgatttaaatccgattatcaaagacatacggagtcaaatacgatccaataaatttatcttcgtgatttttttcattcaagtacgatgccttttaacggtaaatttaagataagagaagaatacggtctttgaataatgatacaacagtattaaaactgttaataatgcaaaaaacaactcattgttttggatacatcaaaaagatactatatgtttgcaaaacaaattttaaaaccaaaatacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUCCUUUCCUUACAGACUUUGCCGCAACGAUUUAAAUCCGAUUAUCAAAGACAUACGGAGUCAAAUACGAUCCAAUAAAUUUAUCUUCGUGAUUUUUUUCAUUCAAGUACGAUGCCUUUUAACGGUAAAUUUAAGAUAAGAGAAGAAUACGGUCUUUGAAUAAUGAUACAACAGUAUUAAAACUGUUAAUAAUGCAAAAAACAACUCAUUGUUUUGGAUACAUCAAAAAGAUACUAUAUGUUUGCAAAACAAAUUUUAAAACCAAAAUACG .....................(((((.............(((..((((((((((((.(((((((..((((............))))..)))))))(((((((((..((........((((.......)))).......))...)))))))))...))))))).))))))))..((((((......))))))......)))))..........((((((((.(.((((..............)))).).))))))))................... (-42.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUAUUUUGGUUUUAAAAUUUGUUUUGCAAACAUAUAGUAUCUUUUUGAUGUAUCCAAAACAAUGAGUUGUUUUUUGCAUUAUUAACAGUUUUAAUACUGUUGUAUCAUUAUUCAAAGACCGUAUUCUUCUCUUAUCUUAAAUUUACCGUUAAAAGGCAUCGUACUUGAAUGAAAAAAAUCACGAAGAUAAAUUUAUUGGAUCGUAUUUGACUCCGUAUGUCUUUGAUAAUCGGAUUUAAAUCGUUGCGGCAAAGUCUGUAAGGAAAGGAUAUUA .........(((((((((....))))).))))...(((((((((((((((..((((.....(((((..(((.....)))....(((((((......)))))))..)))))..((((((((............(((((((.......((.......))..((((......))))...........))))))).......((((((....))).)))....)))))))).....))))....))).((((((......)))))).)))))))))))) (-49.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 130 88 231 189 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 287 99 55 101 45 tfor:TF3026|5end_conserved_hypothetical_protein_3249137..3249367_POSITIVE 287 66 21 173 124 tfor:TF0194|5end_hypothetical_protein_215193..215423_POSITIVE 273 120 71 204 161 tfor:TF3041|5end_hypothetical_protein_3269146..3269376_POSITIVE 265 77 32 188 140 tfor:TF0884|5end_hypothetical_protein_937603..937833_POSITIVE 262 64 26 44 12 tfor:TF0486|5end_conserved_hypothetical_protein;_possible_ADP-ribose_pyrophosphatase_507813..508043_POSITIVE 258 49 8 197 151 tfor:TF1971|5end_biotin_carboxyl_carrier_protein_2117976..2118206_POSITIVE 258 67 27 107 70 tfor:TF1839|5end_conserved_hypothetical_protein_1989347..1989577_POSITIVE 257 67 22 160 115 tfor:TF2237|5end_two-component_system_response_regulator_involved_in_CTn_2412494..2412724_POSITIVE 254 158 111 83 43 tfor:TF1249|5end_phosphoglycerate_kinase_(cytosolic_phosphoglycerate_kinase)_1331017..1331247_POSITIVE 253 60 11 206 154 tfor:TF0534|5end_hypothetical_protein_559509..559739_POSITIVE 250 45 4 184 138 tfor:TF1140|5end_transcriptional_regulator,_AraC_family_1216855..1217085_POSITIVE 249 130 84 228 190 tfor:TF2482|5end_hypothetical_protein_2658503..2658733_POSITIVE 248 47 6 73 37 tfor:TF2941|5end_50S_ribosomal_protein_L1_3141828..3142058_POSITIVE 248 66 27 85 44 tfor:TF2041|5end_conserved_hypothetical_protein_2200395..2200625_POSITIVE 247 63 21 198 162 tfor:TF2161|5end_conserved_hypothetical_protein_2336972..2337202_POSITIVE 245 76 42 103 60 tfor:TF2748|5end_ATP-dependent_Clp_protease_2930459..2930689_POSITIVE 245 224 197 118 84 tfor:TF1455|5end_conserved_hypothetical_protein_1540688..1540918_POSITIVE 244 68 21 195 150 tfor:TF1507|5end_outer_membrane_receptor,_TonB-dependent_1614536..1614766_POSITIVE 243 128 84 146 102 tfor:TF2118|5end_conserved_hypothetical_protein_2289961..2290191_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 519 260 217 75 32 tfor:TF2027|3end_conserved_hypothetical_protein_2184176..2184326_POSITIVE 291 130 88 94 52 tfor:TF2013|3end_polysaccharide_deacetylase_2169341..2169491_POSITIVE 287 66 21 140 91 tfor:TF0193|3end_conserved_hypothetical_protein;_possible_internalin-like_protein_(LPXTG_motif)_215240..215390_POSITIVE 283 129 88 120 71 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 253 60 11 136 84 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 248 47 6 55 19 tfor:TF2940|3end_50S_ribosomal_protein_L11_3141890..3142040_POSITIVE 245 159 112 127 89 tfor:TF0392|3end_hypothetical_protein_412945..413095_POSITIVE 241 50 10 51 12 tfor:TF2001|3end_conserved_hypothetical_protein_2155931..2156081_POSITIVE 239 50 5 50 6 tfor:TF1638|3end_conserved_hypothetical_protein_1747732..1747882_POSITIVE 237 66 28 128 91 tfor:TF2694|3end_hypothetical_protein_2870863..2871013_POSITIVE 231 158 117 107 50 tfor:TF1436|3end_phosphoglycolate_phosphatase_1521867..1522017_POSITIVE 230 67 25 91 43 tfor:TF1743|3end_conserved_hypothetical_protein_1877909..1878059_POSITIVE 229 63 22 145 98 tfor:TF1975|3end_uridylate_kinase_2122359..2122509_POSITIVE 227 131 92 75 27 tfor:TF3138|3end_Na+-translocating_quinone_reductase,_subunit_D_3372654..3372804_POSITIVE 227 35 8 39 9 tfor:TF1430|3end_hypothetical_protein_1515153..1515303_POSITIVE 225 34 3 71 40 tfor:TF1475|3end_glucose-6-phosphate_1-dehydrogenase_1569688..1569838_POSITIVE 225 159 127 149 108 tfor:TF0083|3end_outer_membrane_efflux_protein_90643..90793_POSITIVE 224 120 73 51 1 tfor:TF2384|3end_thiol:disulfide_interchange_protein_2550756..2550906_POSITIVE 223 65 21 101 50 tfor:TF1434|3end_transketolase_1519595..1519745_POSITIVE 221 156 112 81 42 tfor:TF2873|3end_conserved_hypothetical_protein_3064966..3065116_POSITIVE