Origin IGS: tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatatcgggcatttcttattccatcactttccattcaagtggcagcttgtggcgtcgtagtggaataggttggcacagtaatccgagataaaatatgctccaatca Mask Tandem Repeat Region ================================================ tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta Find is-nt database================================================ Query_seq: TF1634:TF1637|TF1634:TF1637:hypothetical protein:hypothetical protein:->->:1747139..1747245 107 tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1634:TF1637|TF1634:TF1637:hypothetical protein:hypothetical protein:->->:1747139..1747245 107 tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1634:TF1637|TF1634:TF1637:hypothetical protein:hypothetical protein:->->:1747139..1747245 107 tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta Predict ORF larger than 30AA ================================================ tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta 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================================================ tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1634:TF1637|TF1634:TF1637:hypothetical protein:hypothetical protein:->->:1747139..1747245 107 tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: tfor_TF1634_TF1637|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1747139,1747245]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta Inter-species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: pint_PI0378_PI0379|conserved hypothetical protein; possible helicase:conserved hypothetical protein|POSITIVE:POSITIVE|[349600,350011]|412 HSP 1 e-value: 2.0E-47 bit: 188.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 114 Subject End: 220 tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta tgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatatta Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUGGAGCAUAUUUUAUCUCGGAUUACUGUGCCAACCUAUUCCACUACGACGCCACAAGCUGCCACUUGAAUGGAAAGUGAUGGAAUAAGAAAUGCCCGAUAUUA ..(((((.((((..........((((....)).))..(.(((((((.(((....(((((((......))))..)))...))).))))))).)..))))))))).... (-25.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUCGGGCAUUUCUUAUUCCAUCACUUUCCAUUCAAGUGGCAGCUUGUGGCGUCGUAGUGGAAUAGGUUGGCACAGUAAUCCGAGAUAAAAUAUGCUCCAAUCA .......((((((..((((((((((.((...(((..(((((....))))))))....)).))))))))))((((.........))))........)))).))..... (-25.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 66 22 72 28 tfor:TF2225|5end_CTn_excision_protein_2394935..2395165_POSITIVE 348 67 22 201 157 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 329 82 45 55 11 tfor:TF0413|5end_succinyl-diaminopimelate_desuccinylase_430434..430664_POSITIVE 315 69 21 62 15 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 313 67 21 220 164 tfor:TF0022|5end_two-component_system_sensor_histidine_kinase_17295..17525_POSITIVE 312 65 23 210 169 tfor:TF1532|5end_potassium_uptake_system_protein_1637881..1638111_POSITIVE 310 67 30 60 18 tfor:TF2450|5end_outer_membrane_protein_2626471..2626701_POSITIVE 310 67 22 86 39 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 306 66 22 211 166 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 304 65 29 129 96 tfor:TF1009|5end_conserved_hypothetical_protein;_posible_rod-shape_determining_protein,_MreD_1064290..1064520_POSITIVE 303 54 18 72 30 tfor:TF3019|5end_tRNA_and_rRNA_cytosine-C5-methylase_3242164..3242394_POSITIVE 300 91 53 79 35 tfor:TF0228|5end_probable_integral_outer_membrane_protein_253851..254081_POSITIVE 298 65 29 31 2 tfor:TF0307|5end_conserved_hypothetical_protein_332783..333013_POSITIVE 295 99 51 105 53 tfor:TF0394|5end_oxaloacetate_decarboxylase,_alpha_subunit_(pyruvate_carboxylase,_C-terminal_domain)_413268..413498_POSITIVE 291 70 21 76 18 tfor:TF0213|5end_conserved_hypothetical_protein_238921..239151_POSITIVE 288 73 31 43 2 tfor:TF1600|5end_uroporphyrinogen-III_synthase_1713964..1714194_POSITIVE 286 67 23 75 24 tfor:TF1786|5end_hypothetical_protein_1926139..1926369_POSITIVE 285 76 35 207 155 tfor:TF0369|5end_hypothetical_protein_385933..386163_POSITIVE 284 88 41 197 142 tfor:TF0344|5end_hypothetical_protein_366722..366952_POSITIVE 283 60 19 195 157 tfor:TF1291|5end_response_regulator_(fimR__protein)_1371959..1372189_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 86 49 41 8 tfor:TF2224|3end_CTn_excision_protein_2394968..2395118_POSITIVE 310 67 30 50 8 tfor:TF2449|3end_undecaprenyl_diphosphate_synthase_2626541..2626691_POSITIVE 304 65 29 133 100 tfor:TF1008|3end_rod_shape-determining_protein_MreC_1064374..1064524_POSITIVE 303 54 18 69 27 tfor:TF3018|3end_polyphosphate_kinase_3242241..3242391_POSITIVE 303 100 53 115 63 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 299 66 22 123 84 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 291 70 21 76 18 tfor:TF0212|3end_DNA/pantothenate_metabolism_flavoprotein_239001..239151_POSITIVE 288 73 31 53 12 tfor:TF1599|3end_ribonuclease_P_protein_component_1714054..1714204_POSITIVE 282 86 52 55 24 tfor:TF3059|3end_conserved_hypothetical_protein_3283262..3283412_POSITIVE 281 70 24 141 93 tfor:TF0808|3end_cation_efflux_system_protein_865421..865571_POSITIVE 281 67 21 116 66 tfor:TF0271|3end_oxidase/dehydrogenase_298530..298680_POSITIVE 279 68 21 113 71 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 274 66 21 87 52 tfor:TF2006|3end_uracil_permease_2158642..2158792_POSITIVE 273 57 13 132 85 tfor:TF2488|3end_hypothetical_protein_2664478..2664628_POSITIVE 272 69 22 114 73 tfor:TF0448|3end_hypothetical_protein_467911..468061_POSITIVE 272 67 22 48 5 tfor:TF0023|3end_possible_response_element_in_two_component_regulation_20233..20383_POSITIVE 271 76 31 72 16 tfor:TF2340|3end_hypothetical_protein_2500915..2501065_POSITIVE 271 54 21 79 50 tfor:TF2099|3end_D-tyrosyl-tRNA(Tyr)_deacylase_2273419..2273569_POSITIVE 270 78 36 53 6 tfor:TF2468|3end_hypothetical_protein_2646582..2646732_POSITIVE 267 90 45 47 5 tfor:TF2273|3end_conserved_hypothetical_protein_2436708..2436858_POSITIVE