Origin IGS: gacattgtatcggttacaaaattaatacctatgcaaatgtagtttcttttttggaaacatgcaacacccgcatcttttttataaatttgcacaaaggaacataaccctctaataagataaatattatacgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcgtataatatttatcttattagagggttatgttcctttgtgcaaatttataaaaaagatgcgggtgttgcatgtttccaaaaaagaaactacatttgcataggtattaattttgtaaccgatacaatgtc Mask Tandem Repeat Region ================================================ gacattgtatcggttacaaaattaatacctatgcaaatgtagtttcttttttggaaacatgcaacacccgcatcttttttataaatttgcacaaaggaacataaccctctaataagataaatattatacgc Find is-nt database================================================ Query_seq: TF2798:TF2799|TF2798:TF2799:conserved hypothetical protein:RNA polymerase ECF-type sigma factor:->->:2984394..2984524 131 gacattgtatcggttacaaaattaatacctatgcaaatgtagtttcttttttggaaacatgcaacacccgcatcttttttataaatttgcacaaaggaacataaccctctaataagataaatattatacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2798:TF2799|TF2798:TF2799:conserved hypothetical protein:RNA polymerase ECF-type sigma factor:->->:2984394..2984524 131 gacattgtatcggttacaaaattaatacctatgcaaatgtagtttcttttttggaaacatgcaacacccgcatcttttttataaatttgcacaaaggaacataaccctctaataagataaatattatacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2798:TF2799|TF2798:TF2799:conserved hypothetical protein:RNA polymerase ECF-type sigma factor:->->:2984394..2984524 131 gacattgtatcggttacaaaattaatacctatgcaaatgtagtttcttttttggaaacatgcaacacccgcatcttttttataaatttgcacaaaggaacataaccctctaataagataaatattatacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacattgtatcggttacaaaattaatacctatgcaaatgtagtttcttttttggaaacatgcaacacccgcatcttttttataaatttgcacaaaggaacataaccctctaataagataaatattatacgc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 9 End: 101 ........ M G Y K I N T Y A N V V S F L E T C N T R I F F I N L H K G T .............................. Protein_Len: 32 Strand: - Start: 32 End: 127 ............................... A F T T E K K S V H L V R M K K I F K C L P V Y G E L L I F I M .... Protein_Len: 40 Strand: - Start: 3 End: 122 .. M T D T V F N I G I C I Y N R K Q F C A V G A D K K Y I Q V F S C L G R I L Y M ......... gacattgtatcggttacaaaattaatacctatgcaaatgtagtttcttttttggaaacatgcaacacccgcatcttttttataaatttgcacaaaggaacataaccctctaataagataaatattatacgc 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================================================ gacattgtatcggttacaaaattaatacctatgcaaatgtagtttcttttttggaaacatgcaacacccgcatcttttttataaatttgcacaaaggaacataaccctctaataagataaatattatacgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2798:TF2799|TF2798:TF2799:conserved hypothetical protein:RNA polymerase ECF-type sigma factor:->->:2984394..2984524 131 gacattgtatcggttacaaaattaatacctatgcaaatgtagtttcttttttggaaacatgcaacacccgcatcttttttataaatttgcacaaaggaacataaccctctaataagataaatattatacgc Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: tfor_TF2798_TF2799|conserved hypothetical protein:RNA polymerase ECF-type sigma factor|POSITIVE:POSITIVE|[2984394,2984524]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 gacattgtatcggttacaaaattaatacctatgcaaatgtagtttcttttttggaaacatgcaacacccgcatcttttttataaatttgcacaaaggaacataaccctctaataagataaatattatacgc gacattgtatcggttacaaaattaatacctatgcaaatgtagtttcttttttggaaacatgcaacacccgcatcttttttataaatttgcacaaaggaacataaccctctaataagataaatattatacgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAUUGUAUCGGUUACAAAAUUAAUACCUAUGCAAAUGUAGUUUCUUUUUUGGAAACAUGCAACACCCGCAUCUUUUUUAUAAAUUUGCACAAAGGAACAUAACCCUCUAAUAAGAUAAAUAUUAUACGC .(((((((((.(((............))).)))).))))).((((((((..((....))..........(((..(((.....)))..)))..))))))))............................... (-20.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGUAUAAUAUUUAUCUUAUUAGAGGGUUAUGUUCCUUUGUGCAAAUUUAUAAAAAAGAUGCGGGUGUUGCAUGUUUCCAAAAAAGAAACUACAUUUGCAUAGGUAUUAAUUUUGUAACCGAUACAAUGUC .......(((((((((....(((((((......)))))))((((((.(((........((((((((((.....(((((.......))))).))))))))))......))).))))))...)))).))))). (-26.44) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 76 31 230 185 tfor:TF0251|5end_conserved_hypothetical_protein;_possible_exporter_279955..280185_POSITIVE 253 109 61 98 49 tfor:TF0289|5end_conserved_hypothetical_protein_318015..318245_POSITIVE 251 70 28 32 1 tfor:TF1241|5end_prolyl-tRNA_synthetase_1324711..1324941_POSITIVE 247 99 53 229 190 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 246 90 41 170 112 tfor:TF1971|5end_biotin_carboxyl_carrier_protein_2117976..2118206_POSITIVE 241 50 5 66 19 tfor:TF1812|5end_tryptophan_synthase,_beta_chain_1952696..1952926_POSITIVE 240 76 32 197 164 tfor:TF2344|5end_ATP/GTP_binding_protein_2507422..2507652_POSITIVE 237 71 33 48 13 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 234 71 56 230 215 tfor:TF3158|5end_inner_membrane_protein_3393729..3393959_POSITIVE 233 71 33 179 129 tfor:TF0211|5end_DNA_polymerase_III,_epsilon_subunit_236905..237135_POSITIVE 221 80 32 119 70 tfor:TF2974|5end_conserved_hypothetical_protein;_possible_hydrolase_3181418..3181648_POSITIVE 221 73 31 82 39 tfor:TF1822|5end_outer_membrane_lipoprotein_silC_precursor_1967599..1967829_POSITIVE 221 111 89 192 172 tfor:TF0685|5end_hypothetical_protein_730852..731082_POSITIVE 219 70 28 141 98 tfor:TF1753|5end_topoisomerase_IV_subunit_A_1888130..1888360_POSITIVE 219 77 37 135 94 tfor:TF1315|5end_purine_nucleoside_phosphorylase_1390236..1390466_POSITIVE 217 66 31 50 9 tfor:TF2845|5end_hypothetical_protein_3034414..3034644_POSITIVE 216 79 33 105 55 tfor:TF1838|5end_tRNA/rRNA_methyltransferase_1987904..1988134_POSITIVE 216 71 50 29 4 tfor:TF1465|5end_modulator_of_DNA_gyrase_1554148..1554378_POSITIVE 215 73 37 218 185 tfor:TF0014|5end_beta-glucosidase_(beta-D-glucoside_glucohydrolase),_periplasmic_7233..7463_POSITIVE 214 80 33 225 175 tfor:TF3091|5end_50S_ribosomal_protein_L13_3324213..3324443_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 109 61 102 53 tfor:TF0288|3end_conserved_hypothetical_protein_318099..318249_POSITIVE 241 50 5 66 19 tfor:TF1811|3end_hypothetical_protein_1952776..1952926_POSITIVE 237 71 33 52 17 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 227 110 61 130 84 tfor:TF1660|3end_hypothetical_protein_1775600..1775750_POSITIVE 223 130 88 97 58 tfor:TF3000|3end_hypothetical_protein_3216740..3216890_POSITIVE 221 73 31 48 5 tfor:TF1821|3end_cation_efflux_system_protein_1967645..1967795_POSITIVE 219 70 28 103 60 tfor:TF1752|3end_hypothetical_protein_1888172..1888322_POSITIVE 219 77 37 121 80 tfor:TF1314|3end_conserved_hypothetical_protein_1390302..1390452_POSITIVE 217 77 47 144 110 tfor:TF1540|3end_possible_ATPase_1645987..1646137_POSITIVE 217 107 69 119 85 tfor:TF0530|3end_hypothetical_protein_with_TPR_domain_556859..557009_POSITIVE 215 80 31 145 91 tfor:TF1970|3end_oxaloacetate_decarboxylase,_beta_subunit_2118044..2118194_POSITIVE 214 80 33 72 22 tfor:TF3089|3end_ISPg2_(PGIS2)_transposase_3324140..3324290_POSITIVE 211 99 53 77 41 tfor:TF0860|3end_conserved_hypothetical_protein_913369..913519_POSITIVE 205 111 86 38 12 tfor:TF1980|3end_conserved_hypothetical_protein_2130860..2131010_POSITIVE 203 104 62 83 30 tfor:TF3095|3end_ABC_transporter,_ATP-binding_protein_3328033..3328183_POSITIVE 203 79 37 47 1 tfor:TF1837|3end_conserved_hypothetical_protein;_possible_outer_membrane_protein_1987926..1988076_POSITIVE 203 73 38 113 73 tfor:TF0651|3end_hypothetical_protein_694353..694503_POSITIVE 202 109 73 121 80 tfor:TF2660|3end_hypothetical_protein_2833540..2833690_POSITIVE 202 55 11 84 37 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 201 76 31 83 40 tfor:TF3132|3end_conserved_hypothetical_protein_3368047..3368197_POSITIVE