Origin IGS: tttttttgttgttataaagaattaatatagaaaaagtattgttcgcaggtatgatcgtcacagattatggggtgacggagacaggaaaatattatatagaggctctttcgtttctgttatactcaatggggaaagaacattccaatgatatagattcatttttgctataatattgaattacggcgcaaaaataaatgatttttttaaaacaacaattctttgataaaaaaacacaaagagaaaaacgaatgatgcgttt .........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 aaacgcatcattcgtttttctctttgtgtttttttatcaaagaattgttgttttaaaaaaatcatttatttttgcgccgtaattcaatattatagcaaaaatgaatctatatcattggaatgttctttccccattgagtataacagaaacgaaagagcctctatataatattttcctgtctccgtcaccccataatctgtgacgatcatacctgcgaacaatactttttctatattaattctttataacaacaaaaaaa Mask Tandem Repeat Region ================================================ tttttttgttgttataaagaattaatatagaaaaagtattgttcgcaggtatgatcgtcacagattatggggtgacggagacaggaaaatattatatagaggctctttcgtttctgttatactcaatggggaaagaacattccaatgatatagattcatttttgctataatattgaattacggcgcaaaaataaatgatttttttaaaacaacaattctttgataaaaaaacacaaagagaaaaacgaatgatgcgttt Find is-nt database================================================ Query_seq: TF3163:TF3164|TF3163:TF3164:conserved hypothetical protein:hypothetical protein:->->:3403778..3404036 259 tttttttgttgttataaagaattaatatagaaaaagtattgttcgcaggtatgatcgtcacagattatggggtgacggagacaggaaaatattatatagaggctctttcgtttctgttatactcaatggggaaagaacattccaatgatatagattcatttttgctataatattgaattacggcgcaaaaataaatgatttttttaaaacaacaattctttgataaaaaaacacaaagagaaaaacgaatgatgcgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3163:TF3164|TF3163:TF3164:conserved hypothetical protein:hypothetical protein:->->:3403778..3404036 259 tttttttgttgttataaagaattaatatagaaaaagtattgttcgcaggtatgatcgtcacagattatggggtgacggagacaggaaaatattatatagaggctctttcgtttctgttatactcaatggggaaagaacattccaatgatatagattcatttttgctataatattgaattacggcgcaaaaataaatgatttttttaaaacaacaattctttgataaaaaaacacaaagagaaaaacgaatgatgcgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3163:TF3164|TF3163:TF3164:conserved hypothetical protein:hypothetical protein:->->:3403778..3404036 259 tttttttgttgttataaagaattaatatagaaaaagtattgttcgcaggtatgatcgtcacagattatggggtgacggagacaggaaaatattatatagaggctctttcgtttctgttatactcaatggggaaagaacattccaatgatatagattcatttttgctataatattgaattacggcgcaaaaataaatgatttttttaaaacaacaattctttgataaaaaaacacaaagagaaaaacgaatgatgcgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttttgttgttataaagaattaatatagaaaaagtattgttcgcaggtatgatcgtcacagattatggggtgacggagacaggaaaatattatatagaggctctttcgtttctgttatactcaatggggaaagaacattccaatgatatagattcatttttgctataatattgaattacggcgcaaaaataaatgatttttttaaaacaacaattctttgataaaaaaacacaaagagaaaaacgaatgatgcgttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 38 End: 145 ..................................... M V R R Y D R H R L W G D G D R K I L Y R G S F V S V I L N G E R T F Q .................................................................................................................. Protein_Len: 49 Strand: + Start: 21 End: 167 .................... M N I E K V L F A G M I V T D Y G V T E T G K Y Y I E A L S F L L Y S M G K E H S N D I D S F L L ............................................................................................ Protein_Len: 53 Strand: - Start: 95 End: 253 .............................................................................................. I S A R E N R N Y E I P F S C E L S I S E N K S Y Y Q I V A C F Y I I K K F C C N K S L F V C L S F R I M ...... Protein_Len: 37 Strand: - Start: 61 End: 171 ............................................................ L N H P S P S L F I N Y L P E K T E T I S L P S L V N W H Y L N M K A I M ........................................................................................ tttttttgttgttataaagaattaatatagaaaaagtattgttcgcaggtatgatcgtcacagattatggggtgacggagacaggaaaatattatatagaggctctttcgtttctgttatactcaatggggaaagaacattccaatgatatagattcatttttgctataatattgaattacggcgcaaaaataaatgatttttttaaaacaacaattctttgataaaaaaacacaaagagaaaaacgaatgatgcgttt 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================================================ tttttttgttgttataaagaattaatatagaaaaagtattgttcgcaggtatgatcgtcacagattatggggtgacggagacaggaaaatattatatagaggctctttcgtttctgttatactcaatggggaaagaacattccaatgatatagattcatttttgctataatattgaattacggcgcaaaaataaatgatttttttaaaacaacaattctttgataaaaaaacacaaagagaaaaacgaatgatgcgttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3163:TF3164|TF3163:TF3164:conserved hypothetical protein:hypothetical protein:->->:3403778..3404036 259 tttttttgttgttataaagaattaatatagaaaaagtattgttcgcaggtatgatcgtcacagattatggggtgacggagacaggaaaatattatatagaggctctttcgtttctgttatactcaatggggaaagaacattccaatgatatagattcatttttgctataatattgaattacggcgcaaaaataaatgatttttttaaaacaacaattctttgataaaaaaacacaaagagaaaaacgaatgatgcgttt Intra-Species Hit: Count: 1 Min: 8 Max: 185 Len: 178 Subject: tfor_TF3163_TF3164|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3403778,3404036]|259 HSP 1 e-value: 2.0E-96 bit: 353.0 Len: 178 Query Start:8 Query End:185 Subject Strand: POSITIVE Subject Start: 8 Subject End: 185 .......gttgttataaagaattaatatagaaaaagtattgttcgcaggtatgatcgtcacagattatggggtgacggagacaggaaaatattatatagaggctctttcgtttctgttatactcaatggggaaagaacattccaatgatatagattcatttttgctataatattgaattacggcg.......................................................................... .......gttgttataaagaattaatatagaaaaagtattgttcgcaggtatgatcgtcacagattatggggtgacggagacaggaaaatattatatagaggctctttcgtttctgttatactcaatggggaaagaacattccaatgatatagattcatttttgctataatattgaattacggcg.......................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUGUUAUAAAGAAUUAAUAUAGAAAAAGUAUUGUUCGCAGGUAUGAUCGUCACAGAUUAUGGGGUGACGGAGACAGGAAAAUAUUAUAUAGAGGCUCUUUCGUUUCUGUUAUACUCAAUGGGGAAAGAACAUUCCAAUGAUAUAGAUUCAUUUUUGCUAUAAUAUUGAAUUACGGCG (((((......................((((((((..(((((.((((((((((.......(((((((((((((((.((((..................))))))))))))))).))))....((((......))))..))))...)).)))).))))).)))))))).....))))). (-34.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCCGUAAUUCAAUAUUAUAGCAAAAAUGAAUCUAUAUCAUUGGAAUGUUCUUUCCCCAUUGAGUAUAACAGAAACGAAAGAGCCUCUAUAUAAUAUUUUCCUGUCUCCGUCACCCCAUAAUCUGUGACGAUCAUACCUGCGAACAAUACUUUUUCUAUAUUAAUUCUUUAUAACAAC (((.(((....(((((((((...........((((......))))..((((((((....(((.......)))....)))))))).....)))))))))..........((((((..........))))))....)))..))).................................... (-25.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 78 31 83 32 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 341 78 32 183 133 tfor:TF0377|5end_FtsK/SpoIIIE_family_cell_division_protein_394944..395174_POSITIVE 305 80 32 76 30 tfor:TF2086|5end_transglutaminase-related_protein_2253931..2254161_POSITIVE 304 71 31 209 157 tfor:TF0881|5end_conserved_hypothetical_protein_934459..934689_POSITIVE 303 70 22 46 1 tfor:TF0557|5end_conserved_hypothetical_protein_589069..589299_POSITIVE 301 78 38 231 191 tfor:TF0706|5end_possible_outer_membrane_transport_protein_749304..749534_POSITIVE 300 78 31 223 177 tfor:TF1903|5end_hypothetical_protein_2057392..2057622_POSITIVE 300 77 33 74 24 tfor:TF1236|5end_L-rhamnose_isomerase_1320743..1320973_POSITIVE 300 72 31 75 20 tfor:TF0981|5end_possible_hydrolase_1038112..1038342_POSITIVE 299 80 38 48 4 tfor:TF2918|5end_hypothetical_protein_3114084..3114314_POSITIVE 299 77 32 86 43 tfor:TF1925|5end_hypothetical_protein_2074458..2074688_POSITIVE 299 77 32 186 143 tfor:TF1916|5end_conserved_hypothetical_protein;_possible_ATPase_2068530..2068760_POSITIVE 296 78 34 203 160 tfor:TF0969|5end_oxidoreductase_1019550..1019780_POSITIVE 294 76 35 209 159 tfor:TF0858|5end_conserved_hypothetical_protein_910326..910556_POSITIVE 294 80 33 155 102 tfor:TF0620|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_654711..654941_POSITIVE 293 76 31 86 24 tfor:TF1476|5end_outer_membrane_protein_P49_1569723..1569953_POSITIVE 292 78 31 155 109 tfor:TF2747|5end_heat_shock_protein,_HSP90_family_2928279..2928509_POSITIVE 285 78 32 187 143 tfor:TF2188|5end_conserved_hypothetical_protein_2362652..2362882_POSITIVE 285 77 41 43 10 tfor:TF1926|5end_hypothetical_protein_2074415..2074645_POSITIVE 284 74 33 70 25 tfor:TF0440|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_2_463655..463885_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 70 22 46 1 tfor:TF0556|3end_Bacteroides_aerotolerance_protein,_BatA_589149..589299_POSITIVE 302 78 36 49 1 tfor:TF2039|3end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199835..2199985_POSITIVE 299 80 38 45 1 tfor:TF2917|3end_conserved_hypothetical_protein_3114161..3114311_POSITIVE 299 77 32 65 22 tfor:TF1915|3end_NAD-dependent_protein_deacetylase,_SIR2_family_2068489..2068639_POSITIVE 294 76 35 151 101 tfor:TF0857|3end_hypothetical_protein_910348..910498_POSITIVE 294 80 33 145 92 tfor:TF0619|3end_ubiquinone_biosynthesis_methyltransferase_654781..654931_POSITIVE 286 78 37 65 31 tfor:TF0365|3end_hypothetical_protein_383152..383302_POSITIVE 283 89 41 58 1 tfor:TF1931|3end_ATPase/GTPase_2078622..2078772_POSITIVE 279 79 37 72 31 tfor:TF1129|3end_possible_lantibiotic_biosynthesis_protein_1205477..1205627_POSITIVE 279 72 34 96 42 tfor:TF0326|3end_hypothetical_protein_354317..354467_POSITIVE 278 110 61 91 31 tfor:TF2018|3end_hypothetical_protein_2175315..2175465_POSITIVE 278 79 37 47 4 tfor:TF0471|3end_conserved_hypothetical_protein_487886..488036_POSITIVE 276 79 42 129 92 tfor:TF0467|3end_acetyltransferase-related_protein_486543..486693_POSITIVE 276 79 33 85 35 tfor:TF0320|3end_dihydroorotase_347518..347668_POSITIVE 275 79 31 62 11 tfor:TF1479|3end_ABC_transporter,_permease_component_1573592..1573742_POSITIVE 273 74 37 151 110 tfor:TF2643|3end_possible_O-antigen_transporter_2813071..2813221_POSITIVE 270 70 28 106 69 tfor:TF0183|3end_conserved_hypothetical_protein_196567..196717_POSITIVE 268 78 31 59 6 tfor:TF1205|3end_beta-glucanase/beta-glucan_synthetase;_endoglucanase_related_1288580..1288730_POSITIVE 265 79 43 122 76 tfor:TF2705|3end_conserved_hypothetical_protein;_possible_SufE_Fe/S-cluster-related_protein_2877364..2877514_POSITIVE 263 74 32 119 77 tfor:TF2900|3end_conserved_hypothetical_protein_3090029..3090179_POSITIVE