Origin IGS: cccgtattacatgataaaccgccgcaaagctacgaaaaaaaacttcatcgggaaaagttggatatatcaagaaaatgactacctttgcaccgcaaattttaaaacagtaacattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatgttactgttttaaaatttgcggtgcaaaggtagtcattttcttgatatatccaacttttcccgatgaagttttttttcgtagctttgcggcggtttatcatgtaatacggg Mask Tandem Repeat Region ================================================ cccgtattacatgataaaccgccgcaaagctacgaaaaaaaacttcatcgggaaaagttggatatatcaagaaaatgactacctttgcaccgcaaattttaaaacagtaacattt Find is-nt database================================================ Query_seq: TF1015:TF1016|TF1015:TF1016:conserved hypothetical protein:30S ribosomal protein S6:->->:1074176..1074290 115 cccgtattacatgataaaccgccgcaaagctacgaaaaaaaacttcatcgggaaaagttggatatatcaagaaaatgactacctttgcaccgcaaattttaaaacagtaacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1015:TF1016|TF1015:TF1016:conserved hypothetical protein:30S ribosomal protein S6:->->:1074176..1074290 115 cccgtattacatgataaaccgccgcaaagctacgaaaaaaaacttcatcgggaaaagttggatatatcaagaaaatgactacctttgcaccgcaaattttaaaacagtaacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1015:TF1016|TF1015:TF1016:conserved hypothetical protein:30S ribosomal protein S6:->->:1074176..1074290 115 cccgtattacatgataaaccgccgcaaagctacgaaaaaaaacttcatcgggaaaagttggatatatcaagaaaatgactacctttgcaccgcaaattttaaaacagtaacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cccgtattacatgataaaccgccgcaaagctacgaaaaaaaacttcatcgggaaaagttggatatatcaagaaaatgactacctttgcaccgcaaattttaaaacagtaacattt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 11 End: 115 .......... M I N R R K A T K K N F I G K S W I Y Q E N D Y L C T A N F K T V T F Protein_Len: 32 Strand: - Start: 2 End: 97 . R I V H Y V A A F S R F F V E D P F T P Y I L F I V V K A G C M .................. cccgtattacatgataaaccgccgcaaagctacgaaaaaaaacttcatcgggaaaagttggatatatcaagaaaatgactacctttgcaccgcaaattttaaaacagtaacattt 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================================================ cccgtattacatgataaaccgccgcaaagctacgaaaaaaaacttcatcgggaaaagttggatatatcaagaaaatgactacctttgcaccgcaaattttaaaacagtaacattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1015:TF1016|TF1015:TF1016:conserved hypothetical protein:30S ribosomal protein S6:->->:1074176..1074290 115 cccgtattacatgataaaccgccgcaaagctacgaaaaaaaacttcatcgggaaaagttggatatatcaagaaaatgactacctttgcaccgcaaattttaaaacagtaacattt Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: tfor_TF1015_TF1016|conserved hypothetical protein:30S ribosomal protein S6|POSITIVE:POSITIVE|[1074176,1074290]|115 HSP 1 e-value: 6.0E-45 bit: 180.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 cccgtattacatgataaaccgccgcaaagctacgnnnnnnnncttcatcgggaaaagttggatatatcaagaaaatgactacctttgcaccgcaaattttaaaacagtaacattt cccgtattacatgataaaccgccgcaaagctacgaaaaaaaacttcatcgggaaaagttggatatatcaagaaaatgactacctttgcaccgcaaattttaaaacagtaacattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGUAUUACAUGAUAAACCGCCGCAAAGCUACGAAAAAAAACUUCAUCGGGAAAAGUUGGAUAUAUCAAGAAAAUGACUACCUUUGCACCGCAAAUUUUAAAACAGUAACAUUU ((((................((......))...(((.......)))..))))....((((......(((......))).....(((((...)))))...........)))).... (-10.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUGUUACUGUUUUAAAAUUUGCGGUGCAAAGGUAGUCAUUUUCUUGAUAUAUCCAACUUUUCCCGAUGAAGUUUUUUUUCGUAGCUUUGCGGCGGUUUAUCAUGUAAUACGGG ...((((((((...((((.....((.(((((((...((((......)))).................((((((.....))))))..))))))).)).)))).)).)))))).... (-21.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 60 19 44 6 tfor:TF0089|5end_conserved_hypothetical_protein_95437..95667_POSITIVE 323 50 1 93 33 tfor:TF1323|5end_metallo-beta-lactamase_superfamily_protein_1402650..1402880_POSITIVE 290 90 43 200 159 tfor:TF1497|5end_GTP-binding_protein,_Era/ThdF_family_1596129..1596359_POSITIVE 279 57 19 230 185 tfor:TF0189|5end_phosphatidate_cytidylytransferase_(CDP-diglyceride_synthetase)_203162..203392_POSITIVE 272 46 5 179 132 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 270 57 21 86 47 tfor:TF0697|5end_glycerol-3-phosphate_cytidyltransferase_740667..740897_POSITIVE 255 79 40 161 120 tfor:TF1876|5end_hypothetical_protein_2029744..2029974_POSITIVE 255 55 20 200 170 tfor:TF0757|5end_50S_ribosomal_protein_L25;_general_stress_protein_804554..804784_POSITIVE 254 36 1 178 148 tfor:TF0098|5end_permease_108103..108333_POSITIVE 253 33 2 207 180 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 251 60 12 71 18 tfor:TF1200|5end_conserved_hypothetical_protein_1282717..1282947_POSITIVE 250 49 1 121 78 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 248 62 22 225 181 tfor:TF2503|5end_conserved_hypothetical_protein_2678430..2678660_POSITIVE 248 34 1 194 144 tfor:TF0194|5end_hypothetical_protein_215193..215423_POSITIVE 247 94 68 72 46 tfor:TF0029|5end_hypothetical_protein_24824..25054_POSITIVE 245 90 42 75 23 tfor:TF2668|5end_hypothetical_protein_2842471..2842701_POSITIVE 243 47 2 113 67 tfor:TF0879|5end_TraG_family_protein_932023..932253_POSITIVE 241 53 18 184 151 tfor:TF1990|5end_outer_membrane_protein_2141320..2141550_POSITIVE 240 68 21 105 53 tfor:TF0627|5end_conserved_hypothetical_protein_662743..662973_POSITIVE 238 96 51 67 20 tfor:TF2176|5end_hypothetical_protein_2348911..2349141_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 90 43 60 19 tfor:TF1496|3end_tyrosyl-tRNA_synthetase_1596069..1596219_POSITIVE 283 50 2 139 83 tfor:TF0001|3end_hypothetical_protein_158..308_POSITIVE 272 46 5 147 100 tfor:TF2127|3end_hypothetical_protein_2304306..2304456_POSITIVE 270 57 21 80 41 tfor:TF0696|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_740741..740891_POSITIVE 253 107 80 78 52 tfor:TF2583|3end_possible_ABC_transporter,__permease_component_2751026..2751176_POSITIVE 251 60 12 71 18 tfor:TF1199|3end_dephospho-CoA_kinase_1282797..1282947_POSITIVE 246 100 58 76 33 tfor:TF2027|3end_conserved_hypothetical_protein_2184176..2184326_POSITIVE 244 71 31 147 107 tfor:TF3030|3end_16S_rRNA_processing_protein_3254296..3254446_POSITIVE 237 89 63 138 113 tfor:TF2362|3end_conserved_hypothetical_protein_2529168..2529318_POSITIVE 236 31 1 88 62 tfor:TF0145|3end_glutamine_synthetase_154718..154868_POSITIVE 234 55 18 81 46 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 231 34 2 121 85 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 230 30 1 43 9 tfor:TF2374|3end_UDP-3-O-(R-3-hydoxymyristoyl)-glucosamine-N-acylt_ransferase_2540892..2541042_POSITIVE 230 36 1 62 28 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 230 63 21 141 111 tfor:TF1062|3end_glycosyltransferase_1132739..1132889_POSITIVE 227 52 18 77 32 tfor:TF3022|3end_chorismate_synthase_3247301..3247451_POSITIVE 227 88 46 55 17 tfor:TF2590|3end_transposase_2757566..2757716_POSITIVE 226 104 83 88 64 tfor:TF3160|3end_conserved_hypothetical_protein_3396258..3396408_POSITIVE 226 93 51 52 9 tfor:TF0947|3end_extracellular_protease_993550..993700_POSITIVE 222 102 70 81 53 tfor:TF1242|3end_3-methyl-2-oxobutanoate_hydroxymethyltransferase_1327114..1327264_POSITIVE