Origin IGS: ttgtttttcctccttcttttttgtttttcgactgtttatcttgtcgtcttcaaacaaacgacaaataaaatgccactggtaagaatatgacaaaatggcggttgttggccggtaaaccgataatgatttgacaggaggaagaattcgcaatctgcccgtatgtatttttactcgttgggtacatcattttcgatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatcgaaaatgatgtacccaacgagtaaaaatacatacgggcagattgcgaattcttcctcctgtcaaatcattatcggtttaccggccaacaaccgccattttgtcatattcttaccagtggcattttatttgtcgtttgtttgaagacgacaagataaacagtcgaaaaacaaaaaagaaggaggaaaaacaa Mask Tandem Repeat Region ================================================ ttgtttttcctccttcttttttgtttttcgactgtttatcttgtcgtcttcaaacaaacgacaaataaaatgccactggtaagaatatgacaaaatggcggttgttggccggtaaaccgataatgatttgacaggaggaagaattcgcaatctgcccgtatgtatttttactcgttgggtacatcattttcgatttt Find is-nt database================================================ Query_seq: TF0019:TF0020|TF0019:TF0020:heat shock protein ClpB:possible glycoprotein endopeptidase:->->:15176..15372 197 ttgtttttcctccttcttttttgtttttcgactgtttatcttgtcgtcttcaaacaaacgacaaataaaatgccactggtaagaatatgacaaaatggcggttgttggccggtaaaccgataatgatttgacaggaggaagaattcgcaatctgcccgtatgtatttttactcgttgggtacatcattttcgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0019:TF0020|TF0019:TF0020:heat shock protein ClpB:possible glycoprotein endopeptidase:->->:15176..15372 197 ttgtttttcctccttcttttttgtttttcgactgtttatcttgtcgtcttcaaacaaacgacaaataaaatgccactggtaagaatatgacaaaatggcggttgttggccggtaaaccgataatgatttgacaggaggaagaattcgcaatctgcccgtatgtatttttactcgttgggtacatcattttcgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0019:TF0020|TF0019:TF0020:heat shock protein ClpB:possible glycoprotein endopeptidase:->->:15176..15372 197 ttgtttttcctccttcttttttgtttttcgactgtttatcttgtcgtcttcaaacaaacgacaaataaaatgccactggtaagaatatgacaaaatggcggttgttggccggtaaaccgataatgatttgacaggaggaagaattcgcaatctgcccgtatgtatttttactcgttgggtacatcattttcgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtttttcctccttcttttttgtttttcgactgtttatcttgtcgtcttcaaacaaacgacaaataaaatgccactggtaagaatatgacaaaatggcggttgttggccggtaaaccgataatgatttgacaggaggaagaattcgcaatctgcccgtatgtatttttactcgttgggtacatcattttcgatttt Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: - Start: 53 End: 187 .................................................... V F S L Y F A V P L F I V F H R N N A P L G I I I Q C S S S N A I Q G Y T N K S T P Y M M .......... Protein_Len: 41 Strand: - Start: 39 End: 161 ...................................... R T T K L C V V F L I G S T L I H C F P P Q Q G T F R Y H N S L L F F E C D A R M .................................... Protein_Len: 55 Strand: - Start: 1 End: 165 Q K E E K K K T K R S N I K D D E F L R C I F H W Q Y S Y S L I A T T P R Y V S L S K V P P L I R L R G T H M ................................ ttgtttttcctccttcttttttgtttttcgactgtttatcttgtcgtcttcaaacaaacgacaaataaaatgccactggtaagaatatgacaaaatggcggttgttggccggtaaaccgataatgatttgacaggaggaagaattcgcaatctgcccgtatgtatttttactcgttgggtacatcattttcgatttt 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================================================ ttgtttttcctccttcttttttgtttttcgactgtttatcttgtcgtcttcaaacaaacgacaaataaaatgccactggtaagaatatgacaaaatggcggttgttggccggtaaaccgataatgatttgacaggaggaagaattcgcaatctgcccgtatgtatttttactcgttgggtacatcattttcgatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0019:TF0020|TF0019:TF0020:heat shock protein ClpB:possible glycoprotein endopeptidase:->->:15176..15372 197 ttgtttttcctccttcttttttgtttttcgactgtttatcttgtcgtcttcaaacaaacgacaaataaaatgccactggtaagaatatgacaaaatggcggttgttggccggtaaaccgataatgatttgacaggaggaagaattcgcaatctgcccgtatgtatttttactcgttgggtacatcattttcgatttt Intra-Species Hit: Count: 1 Min: 29 Max: 197 Len: 169 Subject: tfor_TF0019_TF0020|heat shock protein ClpB:possible glycoprotein endopeptidase|POSITIVE:POSITIVE|[15176,15372]|197 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 169 Query Start:29 Query End:197 Subject Strand: POSITIVE Subject Start: 29 Subject End: 197 ............................cgactgtttatcttgtcgtcttcaaacaaacgacaaataaaatgccactggtaagaatatgacaaaatggcggttgttggccggtaaaccgataatgatttgacaggaggaagaattcgcaatctgcccgtatgtatttttactcgttgggtacatcattttcgatttt ............................cgactgtttatcttgtcgtcttcaaacaaacgacaaataaaatgccactggtaagaatatgacaaaatggcggttgttggccggtaaaccgataatgatttgacaggaggaagaattcgcaatctgcccgtatgtatttttactcgttgggtacatcattttcgatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGACUGUUUAUCUUGUCGUCUUCAAACAAACGACAAAUAAAAUGCCACUGGUAAGAAUAUGACAAAAUGGCGGUUGUUGGCCGGUAAACCGAUAAUGAUUUGACAGGAGGAAGAAUUCGCAAUCUGCCCGUAUGUAUUUUUACUCGUUGGGUACAUCAUUUUCGAUUUU (((.(.(((.((((((((...(((......((((((......(((((...((.........))....))))).))))))..(((....)))....)))..)))))))).))).)..........((((((...(((....)))....))))))........)))..... (-36.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCGAAAAUGAUGUACCCAACGAGUAAAAAUACAUACGGGCAGAUUGCGAAUUCUUCCUCCUGUCAAAUCAUUAUCGGUUUACCGGCCAACAACCGCCAUUUUGUCAUAUUCUUACCAGUGGCAUUUUAUUUGUCGUUUGUUUGAAGACGACAAGAUAAACAGUCG .(((((((.((((((...........(((....))).....(((((...(.((.....)))..)))))..)))))).)))))))..((((........((((((................))))))..((((((((((((((......))))))).)))))))..)))) (-37.49) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 86 44 71 26 tfor:TF2647|5end_transcriptional_regulator,_possible_arylsulfatase_regulator_2816796..2817026_POSITIVE 335 90 42 71 15 tfor:TF1970|5end_oxaloacetate_decarboxylase,_beta_subunit_2116804..2117034_POSITIVE 327 110 61 227 172 tfor:TF1910|5end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase_2064001..2064231_POSITIVE 322 90 43 129 73 tfor:TF1181|5end_methylated-DNA--[protein]-cysteine_S-methyltransferase_1267522..1267752_POSITIVE 316 90 43 59 4 tfor:TF1011|5end_cell_division_protein;_rod_shape-determining_protein_1066647..1066877_POSITIVE 311 109 65 180 131 tfor:TF0664|5end_small_protein_B_(SMPB)_709029..709259_POSITIVE 310 85 43 219 178 tfor:TF1462|5end_erythronate-4-phosphate_dehydrogenase_1552184..1552414_POSITIVE 310 100 60 58 18 tfor:TF1200|5end_conserved_hypothetical_protein_1282717..1282947_POSITIVE 308 129 82 204 160 tfor:TF2880|5end_phenylalanyl-tRNA_synthetase,_beta_subunit_3069052..3069282_POSITIVE 304 137 96 40 6 tfor:TF2186|5end_outer_membrane_protein_2360291..2360521_POSITIVE 304 157 111 173 137 tfor:TF1044|5end_Mg(2)+_transport-related_protein,__MgtC_family_1106561..1106791_POSITIVE 302 130 81 74 13 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 302 149 104 122 59 tfor:TF0851|5end_helicase_SNF2_family_899486..899716_POSITIVE 301 107 61 177 129 tfor:TF2247|5end_transfer_region-related_protein,_TraA_2421463..2421693_POSITIVE 301 130 82 50 3 tfor:TF2165|5end_hypothetical_protein_2341654..2341884_POSITIVE 300 84 41 150 111 tfor:TF0995|5end_conserved_hypothetical_protein_1049695..1049925_POSITIVE 296 107 61 149 114 tfor:TF2333|5end_signal_peptidase_I_2492560..2492790_POSITIVE 296 129 83 172 133 tfor:TF0810|5end_possible_outer_membrane_efflux_protein_868438..868668_POSITIVE 295 130 81 196 159 tfor:TF2200|5end_outer_membrane_protein,_TonB_dependent_receptor_2376495..2376725_POSITIVE 293 118 72 89 40 tfor:TF3112|5end_Na+/H+_anitporter_3346775..3347005_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 92 68 149 125 tfor:TF2913|3end_conserved_hypothetical_protein_3109117..3109267_POSITIVE 316 90 43 66 11 tfor:TF1010|3end_penicillin_binding_protein_2_1066734..1066884_POSITIVE 313 116 71 100 33 tfor:TF1422|3end_GLCNAC_transferase_(UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)-pyr_ophosphoryl-undecaprenol_N-acetylglucosamine_transferase)_1505823..1505973_POSITIVE 310 100 60 58 18 tfor:TF1199|3end_dephospho-CoA_kinase_1282797..1282947_POSITIVE 308 129 82 80 36 tfor:TF2879|3end_tRNA_(guanine-N-1)-methyltransferase_3069008..3069158_POSITIVE 303 110 62 148 97 tfor:TF3122|3end_ABC_transporter,_ATP-binding_protein_3357743..3357893_POSITIVE 296 107 61 122 87 tfor:TF2332|3end_signal_peptidase_I_2492613..2492763_POSITIVE 295 89 44 151 109 tfor:TF0780|3end_alpha-L-arabinofuranosidase,_precursor_A_834441..834591_POSITIVE 293 118 72 70 21 tfor:TF3111|3end_hypothetical_protein_3346836..3346986_POSITIVE 293 91 52 135 84 tfor:TF0375|3end_thioredoxin_reductase_394338..394488_POSITIVE 292 145 106 115 73 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 289 107 68 135 104 tfor:TF1497|3end_GTP-binding_protein,_Era/ThdF_family_1597519..1597669_POSITIVE 289 108 69 73 29 tfor:TF0114|3end_conserved_hypothetical_protein_125224..125374_POSITIVE 288 119 71 73 37 tfor:TF2462|3end_hypothetical_protein_2642076..2642226_POSITIVE 288 99 59 143 107 tfor:TF1528|3end_malate_dehydrogenase_1634362..1634512_POSITIVE 288 119 71 75 11 tfor:TF0060|3end_conserved_hypothetical_protein_62863..63013_POSITIVE 287 150 104 116 76 tfor:TF0844|3end_transposase,_IS3_family_896099..896249_POSITIVE 286 87 45 136 97 tfor:TF3022|3end_chorismate_synthase_3247301..3247451_POSITIVE 286 110 66 55 4 tfor:TF0224|3end_N-acetylglucosamine-6-phosphate_deacetylase_251547..251697_POSITIVE 284 133 96 65 24 tfor:TF1301|3end_hypothetical_protein_1383487..1383637_POSITIVE