Origin IGS: ggcttcagccttctgttgattaccgcgctcggcttcgagttccttgctccagcatctgttgtataaaatgtgataaataccggcgccaaagatttgttgtggttcccaacttttttatacaattgccgtaaaattcgggaattttatgtaagtttgtcacatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgtgacaaacttacataaaattcccgaattttacggcaattgtataaaaaagttgggaaccacaacaaatctttggcgccggtatttatcacattttatacaacagatgctggagcaaggaactcgaagccgagcgcggtaatcaacagaaggctgaagcc Mask Tandem Repeat Region ================================================ ggcttcagccttctgttgattaccgcgctcggcttcgagttccttgctccagcatctgttgtataaaatgtgataaataccggcgccaaagatttgttgtggttcccaacttttttatacaattgccgtaaaattcgggaattttatgtaagtttgtcacatt Find is-nt database================================================ Query_seq: TF0766:TF0767|TF0766:TF0767:hypothetical protein:conserved hypothetical protein:->->:812317..812479 163 ggcttcagccttctgttgattaccgcgctcggcttcgagttccttgctccagcatctgttgtataaaatgtgataaataccggcgccaaagatttgttgtggttcccaacttttttatacaattgccgtaaaattcgggaattttatgtaagtttgtcacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0766:TF0767|TF0766:TF0767:hypothetical protein:conserved hypothetical protein:->->:812317..812479 163 ggcttcagccttctgttgattaccgcgctcggcttcgagttccttgctccagcatctgttgtataaaatgtgataaataccggcgccaaagatttgttgtggttcccaacttttttatacaattgccgtaaaattcgggaattttatgtaagtttgtcacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0766:TF0767|TF0766:TF0767:hypothetical protein:conserved hypothetical protein:->->:812317..812479 163 ggcttcagccttctgttgattaccgcgctcggcttcgagttccttgctccagcatctgttgtataaaatgtgataaataccggcgccaaagatttgttgtggttcccaacttttttatacaattgccgtaaaattcgggaattttatgtaagtttgtcacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggcttcagccttctgttgattaccgcgctcggcttcgagttccttgctccagcatctgttgtataaaatgtgataaataccggcgccaaagatttgttgtggttcccaacttttttatacaattgccgtaaaattcgggaattttatgtaagtttgtcacatt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 70 End: 162 ..................................................................... M I N T G A K D L L W F P T F L Y N C R K I R E F Y V S L S H . Protein_Len: 46 Strand: - Start: 23 End: 160 ...................... R A R S R T G Q E L M Q Q I F H S L Y R R W L N T T T G L K K I C N G Y F E P I K H L N T M ... Protein_Len: 44 Strand: - Start: 3 End: 134 .. K L R R N I V A S P K S N R A G A D T T Y F T I F V P A L S K N H N G V K K Y L Q R L M ............................. Protein_Len: 31 Strand: - Start: 1 End: 93 A E A K Q Q N G R E A E L E K S W C R N Y L I H Y I G A G F M ...................................................................... ggcttcagccttctgttgattaccgcgctcggcttcgagttccttgctccagcatctgttgtataaaatgtgataaataccggcgccaaagatttgttgtggttcccaacttttttatacaattgccgtaaaattcgggaattttatgtaagtttgtcacatt 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================================================ ggcttcagccttctgttgattaccgcgctcggcttcgagttccttgctccagcatctgttgtataaaatgtgataaataccggcgccaaagatttgttgtggttcccaacttttttatacaattgccgtaaaattcgggaattttatgtaagtttgtcacatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 79 HP_score: -4.2 Tail_Score: -5.27923 Start: 96 End: 110 Full_Region: CGGCGCCAAAGATTT GTTGTG GTT CCCAAC TTTTTTATACAATTG ...............................................................................................GTTGTGGTTCCCAAC..................................................... Find igs database================================================ Query_seq: TF0766:TF0767|TF0766:TF0767:hypothetical protein:conserved hypothetical protein:->->:812317..812479 163 ggcttcagccttctgttgattaccgcgctcggcttcgagttccttgctccagcatctgttgtataaaatgtgataaataccggcgccaaagatttgttgtggttcccaacttttttatacaattgccgtaaaattcgggaattttatgtaagtttgtcacatt Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: tfor_TF0766_TF0767|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[812317,812479]|163 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 ggcttcagccttctgttgattaccgcgctcggcttcgagttccttgctccagcatctgttgtataaaatgtgataaataccggcgccaaagatttgttgtggttcccaacttttttatacaattgccgtaaaattcgggaattttatgtaagtttgtcacatt ggcttcagccttctgttgattaccgcgctcggcttcgagttccttgctccagcatctgttgtataaaatgtgataaataccggcgccaaagatttgttgtggttcccaacttttttatacaattgccgtaaaattcgggaattttatgtaagtttgtcacatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCUUCAGCCUUCUGUUGAUUACCGCGCUCGGCUUCGAGUUCCUUGCUCCAGCAUCUGUUGUAUAAAAUGUGAUAAAUACCGGCGCCAAAGAUUUGUUGUGGUUCCCAACUUUUUUAUACAAUUGCCGUAAAAUUCGGGAAUUUUAUGUAAGUUUGUCACAUU (((....)))..........(((.(((....(((..((((.....)))).)))...))).)))...((((((((((((...((.((((...........)))).)).........((((.((((.(((.......))).)))).))))...)))))))))))) (-37.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUGACAAACUUACAUAAAAUUCCCGAAUUUUACGGCAAUUGUAUAAAAAAGUUGGGAACCACAACAAAUCUUUGGCGCCGGUAUUUAUCACAUUUUAUACAACAGAUGCUGGAGCAAGGAACUCGAAGCCGAGCGCGGUAAUCAACAGAAGGCUGAAGCC .((((((.....))))))..((((.(((.......))).))))..........(((((..(((.(......((((((.(.(((((((((.................))))))))).))))))).((((....)))).).)))..)))))....(((....))) (-37.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 48 1 57 9 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 389 50 1 224 162 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 373 46 1 222 173 tfor:TF1801|5end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_1944213..1944443_POSITIVE 372 48 1 166 110 tfor:TF1406|5end_transposase_1481758..1481988_POSITIVE 369 58 12 161 116 tfor:TF3092|5end_30S_ribosomal_protein_S9_3324716..3324946_POSITIVE 368 50 1 212 142 tfor:TF2036|5end_possible_pyruvate_formate-lyase_activating_enzyme_2196302..2196532_POSITIVE 367 53 12 222 174 tfor:TF3027|5end_zinc_metalloprotease_3250223..3250453_POSITIVE 366 37 1 184 148 tfor:TF1785|5end_histidine_ammonia-lyase_1924494..1924724_POSITIVE 362 50 1 214 160 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 361 47 1 185 126 tfor:TF2849|5end_histidinol-phosphate_transaminase_3037288..3037518_POSITIVE 359 47 2 55 8 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 359 47 2 48 1 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 355 49 2 56 1 tfor:TF2817|5end_hypothetical_protein_3007358..3007588_POSITIVE 351 49 3 206 157 tfor:TF1822|5end_outer_membrane_lipoprotein_silC_precursor_1967599..1967829_POSITIVE 351 65 22 61 13 tfor:TF0959|5end_periplasmic_protease_1005218..1005448_POSITIVE 350 49 2 211 155 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 350 49 2 211 155 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 348 49 1 152 97 tfor:TF2674|5end_conserved_hypothetical_protein;_possible_phosphoesterase_2848176..2848406_POSITIVE 348 50 1 153 111 tfor:TF2445|5end_protoporphyrinogen_oxidase_2621457..2621687_POSITIVE 348 47 1 169 131 tfor:TF2348|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2511088..2511318_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 48 1 57 9 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 380 48 2 141 78 tfor:TF2789|3end_enoyl-[acyl-carrier-protein]_reductase_2973365..2973515_POSITIVE 372 48 1 147 91 tfor:TF1405|3end_conserved_hypothetical_protein_1481819..1481969_POSITIVE 360 50 1 137 65 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 348 47 1 93 55 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 346 49 2 121 65 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 342 57 12 151 107 tfor:TF3091|3end_50S_ribosomal_protein_L13_3324787..3324937_POSITIVE 338 49 1 139 94 tfor:TF2787|3end_30S_ribosomal_protein_S1_2972258..2972408_POSITIVE 338 48 2 141 106 tfor:TF1292|3end_sensor_histidine_protein_kinase_1374554..1374704_POSITIVE 329 50 23 37 2 tfor:TF0886|3end_conjugative_transposon_protein_fragment_938152..938302_POSITIVE 329 50 1 85 32 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 328 47 2 140 85 tfor:TF2930|3end_glutamyl-tRNA_synthetase_3134352..3134502_POSITIVE 328 61 23 136 98 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 328 109 68 48 12 tfor:TF1276|3end_acyl-CoA_dehydrogenase_(short_chain_coenzyme_A_dehydrogenase)_1363080..1363230_POSITIVE 327 50 1 112 67 tfor:TF3131|3end_uracil-DNA_glycosylase_3365248..3365398_POSITIVE 320 45 1 65 28 tfor:TF1734|3end_conserved_hypothetical_protein_1860118..1860268_POSITIVE 318 49 1 142 85 tfor:TF3106|3end_hypothetical_protein_3338608..3338758_POSITIVE 317 47 1 48 2 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 316 49 1 135 91 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 316 47 6 148 99 tfor:TF0537|3end_conserved_hypothetical_protein_566836..566986_POSITIVE