Origin IGS: tgcagtaagtatttatattctattccatgttataaatataagtctgacagtatatttttctcttctgacgtcgcatttttccgttctgacgatatattttttcgatctgacatcgcatttacctttccggcattgcattttacccttttgacatgccgtgatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatcacggcatgtcaaaagggtaaaatgcaatgccggaaaggtaaatgcgatgtcagatcgaaaaaatatatcgtcagaacggaaaaatgcgacgtcagaagagaaaaatatactgtcagacttatatttataacatggaatagaatataaatacttactgca Mask Tandem Repeat Region ================================================ tgcagtaagtatttatattctattccatgttataaatataagtctgacagtatatttttctctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacctttccggcattgcattttacccttttgacatgccgtgatta Find is-nt database================================================ Query_seq: TF1175:TF1176|TF1175:TF1176:membrane-fusion protein:outer membrane protein:->->:1259531..1259694 164 tgcagtaagtatttatattctattccatgttataaatataagtctgacagtatatttttctcttctgacgtcgcatttttccgttctgacgatatattttttcgatctgacatcgcatttacctttccggcattgcattttacccttttgacatgccgtgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1175:TF1176|TF1175:TF1176:membrane-fusion protein:outer membrane protein:->->:1259531..1259694 164 tgcagtaagtatttatattctattccatgttataaatataagtctgacagtatatttttctcttctgacgtcgcatttttccgttctgacgatatattttttcgatctgacatcgcatttacctttccggcattgcattttacccttttgacatgccgtgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1175:TF1176|TF1175:TF1176:membrane-fusion protein:outer membrane protein:->->:1259531..1259694 164 tgcagtaagtatttatattctattccatgttataaatataagtctgacagtatatttttctcttctgacgtcgcatttttccgttctgacgatatattttttcgatctgacatcgcatttacctttccggcattgcattttacccttttgacatgccgtgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcagtaagtatttatattctattccatgttataaatataagtctgacagtatatttttctcttctgacgtcgcatttttccgttctgacgatatattttttcgatctgacatcgcatttacctttccggcattgcattttacccttttgacatgccgtgatta Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 11 End: 148 .......... M Y I L F H V I N I S L T V Y F S L L T S H F S V L T I Y F F D L T S H L P F R H C I L P F ................ Protein_Len: 47 Strand: + Start: 22 End: 162 ..................... M P C Y K Y K S D S I F F S S D V A F F R S D D I F F R S D I A F T F P A L H F T L L T C R D .. Protein_Len: 32 Strand: - Start: 23 End: 118 ...................... E M N Y I Y T Q C Y I K R K Q R R M K G N Q R Y I K E I Q C R M .............................................. Protein_Len: 49 Strand: - Start: 16 End: 162 ............... I R N W T I F I L R V T Y K E R R V D C K E T R V I Y K K S R V D C K G K R C Q M K G K Q C A T M .. tgcagtaagtatttatattctattccatgttataaatataagtctgacagtatatttttctcttctgacgtcgcatttttccgttctgacgatatattttttcgatctgacatcgcatttacctttccggcattgcattttacccttttgacatgccgtgatta 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================================================ tgcagtaagtatttatattctattccatgttataaatataagtctgacagtatatttttctcttctgacgtcgcatttttccgttctgacgatatattttttcgatctgacatcgcatttacctttccggcattgcattttacccttttgacatgccgtgatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1175:TF1176|TF1175:TF1176:membrane-fusion protein:outer membrane protein:->->:1259531..1259694 164 tgcagtaagtatttatattctattccatgttataaatataagtctgacagtatatttttctcttctgacgtcgcatttttccgttctgacgatatattttttcgatctgacatcgcatttacctttccggcattgcattttacccttttgacatgccgtgatta Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: tfor_TF1175_TF1176|membrane-fusion protein:outer membrane protein|POSITIVE:POSITIVE|[1259531,1259694]|164 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 tgcagtaagtatttatattctattccatgttataaatataagtctgacagtatatttttctcttctgacgtcgcatttttccgttctgacgatatattttttcgatctgacatcgcatttacctttccggcattgcattttacccttttgacatgccgtgatta tgcagtaagtatttatattctattccatgttataaatataagtctgacagtatatttttctcttctgacgtcgcatttttccgttctgacgatatattttttcgatctgacatcgcatttacctttccggcattgcattttacccttttgacatgccgtgatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAGUAAGUAUUUAUAUUCUAUUCCAUGUUAUAAAUAUAAGUCUGACAGUAUAUUUUUCUCUUCUGACGUCGCAUUUUUCCGUUCUGACGAUAUAUUUUUUCGAUCUGACAUCGCAUUUACCUUUCCGGCAUUGCAUUUUACCCUUUUGACAUGCCGUGAUUA (((.....(((((((((..(........).)))))))))..(((.(((((..............))).(((((.............)))))..............)).)))...)))........((((((((..((...........))..)))))).))... (-23.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCACGGCAUGUCAAAAGGGUAAAAUGCAAUGCCGGAAAGGUAAAUGCGAUGUCAGAUCGAAAAAAUAUAUCGUCAGAACGGAAAAAUGCGACGUCAGAAGAGAAAAAUAUACUGUCAGACUUAUAUUUAUAACAUGGAAUAGAAUAUAAAUACUUACUGCA ...((.((((((...................))))))))..(((((....((((((.((.(((.........)))))....((......)).))))))...........((((.(((((....((((....))))....).)))).))))......)))))... (-22.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 160 113 53 6 tfor:TF0944|5end_TonB-dependent_receptor_986340..986570_POSITIVE 348 130 82 126 64 tfor:TF1740|5end_hypothetical_protein_1868645..1868875_POSITIVE 335 157 112 60 6 tfor:TF2709|5end_hypothetical_protein_2882160..2882390_POSITIVE 316 158 112 155 113 tfor:TF0236|5end_multidrug_resistance_protein_261779..262009_POSITIVE 315 91 59 193 150 tfor:TF3071|5end_integral_membrane_protein,_possible_MotA/TolQ/ExbB_proton_channel_family_3294703..3294933_POSITIVE 307 88 44 50 13 tfor:TF2846|5end_cobyric_acid_synthase_3034896..3035126_POSITIVE 306 110 63 203 164 tfor:TF2832|5end_possible_proton/sodium:glutamate_symporter_protein_3022660..3022890_POSITIVE 304 109 69 64 23 tfor:TF2328|5end_conserved_hypothetical_protein_2487184..2487414_POSITIVE 303 159 112 164 111 tfor:TF1925|5end_hypothetical_protein_2074458..2074688_POSITIVE 303 159 112 121 68 tfor:TF1926|5end_hypothetical_protein_2074415..2074645_POSITIVE 301 160 111 44 2 tfor:TF1493|5end_thioredoxin_family_protein_1592883..1593113_POSITIVE 298 93 55 175 138 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 296 158 112 62 11 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 293 158 122 177 140 tfor:TF3141|5end_NADH:_ubiquinone_oxidoreductase,_subunit_A_3374667..3374897_POSITIVE 290 130 81 70 14 tfor:TF0380|5end_conserved_hypothetical_protein_400762..400992_POSITIVE 287 89 45 108 63 tfor:TF2569|5end_50S_ribosomal_protein_L6_2741622..2741852_POSITIVE 287 140 99 106 48 tfor:TF1667|5end_biotin_acetyl-CoA_carboxylase_ligase/biotin_operon_repressor_bifunctional_protein_1779809..1780039_POSITIVE 286 130 81 230 173 tfor:TF2419|5end_conserved_hypothetical_protein;_possible_DNA_uptake-related_protein_2598358..2598588_POSITIVE 286 159 111 178 129 tfor:TF2261|5end_transfer_region-related_protein,_TraM_2430496..2430726_POSITIVE 286 130 82 230 166 tfor:TF1617|5end_conserved_hypothetical_protein;_possible_methyltransferase_1733150..1733380_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 158 112 145 103 tfor:TF0235|3end_hypothetical_protein_261849..261999_POSITIVE 307 88 44 59 22 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 306 110 63 134 95 tfor:TF2831|3end_ABC_transporter,_permease_component_3022671..3022821_POSITIVE 303 159 112 143 90 tfor:TF1915|3end_NAD-dependent_protein_deacetylase,_SIR2_family_2068489..2068639_POSITIVE 298 93 55 149 112 tfor:TF2560|3end_30S_ribosomal_protein_S3_2738747..2738897_POSITIVE 287 89 45 85 40 tfor:TF2568|3end_30S_ribosomal_protein_S8_2741679..2741829_POSITIVE 285 116 71 140 83 tfor:TF3124|3end_dTDP-glucose_4,6-dehydratase_3359883..3360033_POSITIVE 285 159 112 134 94 tfor:TF2660|3end_hypothetical_protein_2833540..2833690_POSITIVE 284 108 64 113 69 tfor:TF2789|3end_enoyl-[acyl-carrier-protein]_reductase_2973365..2973515_POSITIVE 281 117 73 62 11 tfor:TF2245|3end_conserved_hypothetical_protein_2421291..2421441_POSITIVE 281 160 123 33 1 tfor:TF1818|3end_conserved_hypothetical_protein_1958754..1958904_POSITIVE 280 144 102 83 31 tfor:TF0810|3end_possible_outer_membrane_efflux_protein_869696..869846_POSITIVE 278 160 114 133 82 tfor:TF2173|3end_hypothetical_protein_2346063..2346213_POSITIVE 278 160 114 133 82 tfor:TF0346|3end_hypothetical_protein_367316..367466_POSITIVE 277 159 111 140 94 tfor:TF1540|3end_possible_ATPase_1645987..1646137_POSITIVE 273 160 113 120 56 tfor:TF2008|3end_DNA_polymerase_I_2162183..2162333_POSITIVE 272 136 96 150 115 tfor:TF2433|3end_possible_UDP-2,3-diacylglucosamine_hydrolase_2614043..2614193_POSITIVE 271 129 81 47 1 tfor:TF1488|3end_conserved_hypothetical_protein_1588975..1589125_POSITIVE 270 157 112 59 6 tfor:TF0336|3end_Xaa-Pro_aminopeptidase_361868..362018_POSITIVE 268 131 100 131 100 tfor:TF2937|3end_translation_elongation_factor_Tu_3140502..3140652_POSITIVE