Origin IGS: tttaagttgaatatgataatctggcggcaaaagtagctattttttgcggataaaaaaagcatgtaaggcgcttaatatttcgtgcaaatatttgtataaaagtaaatatttttcttgtataatgatgattaagtacgaatcttttatattttatgcttatttttgtctcgagaaaagaaatcatgtccatacaaaataaaatcaaatatagcg .........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 cgctatatttgattttattttgtatggacatgatttcttttctcgagacaaaaataagcataaaatataaaagattcgtacttaatcatcattatacaagaaaaatatttacttttatacaaatatttgcacgaaatattaagcgccttacatgctttttttatccgcaaaaaatagctacttttgccgccagattatcatattcaacttaaa Mask Tandem Repeat Region ================================================ tttaagttgaatatgataatctggcggcaaaagtagctattttttgcggataaaaaaagcatgtaaggcgcttaatatttcgtgcaaatatttgtataaaagtaaatatttttcttgtataatgatgattaagtacgaatcttttatattttatgcttatttttgtctcgagaaaagaaatcatgtccatacaaaataaaatcaaatatagcg Find is-nt database================================================ Query_seq: TF3031:TF3032|TF3031:TF3032:conserved hypothetical protein:thiamin biosynthesis protein:->->:3255147..3255359 213 tttaagttgaatatgataatctggcggcaaaagtagctattttttgcggataaaaaaagcatgtaaggcgcttaatatttcgtgcaaatatttgtataaaagtaaatatttttcttgtataatgatgattaagtacgaatcttttatattttatgcttatttttgtctcgagaaaagaaatcatgtccatacaaaataaaatcaaatatagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3031:TF3032|TF3031:TF3032:conserved hypothetical protein:thiamin biosynthesis protein:->->:3255147..3255359 213 tttaagttgaatatgataatctggcggcaaaagtagctattttttgcggataaaaaaagcatgtaaggcgcttaatatttcgtgcaaatatttgtataaaagtaaatatttttcttgtataatgatgattaagtacgaatcttttatattttatgcttatttttgtctcgagaaaagaaatcatgtccatacaaaataaaatcaaatatagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3031:TF3032|TF3031:TF3032:conserved hypothetical protein:thiamin biosynthesis protein:->->:3255147..3255359 213 tttaagttgaatatgataatctggcggcaaaagtagctattttttgcggataaaaaaagcatgtaaggcgcttaatatttcgtgcaaatatttgtataaaagtaaatatttttcttgtataatgatgattaagtacgaatcttttatattttatgcttatttttgtctcgagaaaagaaatcatgtccatacaaaataaaatcaaatatagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaagttgaatatgataatctggcggcaaaagtagctattttttgcggataaaaaaagcatgtaaggcgcttaatatttcgtgcaaatatttgtataaaagtaaatatttttcttgtataatgatgattaagtacgaatcttttatattttatgcttatttttgtctcgagaaaagaaatcatgtccatacaaaataaaatcaaatatagcg Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 44 End: 196 ........................................... M R I K K A C K A L N I S C K Y L Y K S K Y F S C I M M I K Y E S F I F Y A Y F C L E K R N H V H T K ................. Protein_Len: 36 Strand: - Start: 40 End: 147 ....................................... K K R I F F A H L A S L I E H L Y K Y L L L Y K E Q I I I I L Y S D K M .................................................................. Protein_Len: 60 Strand: - Start: 5 End: 205 .... A F T A I K Q P Y F F C T L R K I N R A F I Q I F T F I K R T Y H H N L V F R K Y K I S I K T E L F S I M D M C F L I M ........ tttaagttgaatatgataatctggcggcaaaagtagctattttttgcggataaaaaaagcatgtaaggcgcttaatatttcgtgcaaatatttgtataaaagtaaatatttttcttgtataatgatgattaagtacgaatcttttatattttatgcttatttttgtctcgagaaaagaaatcatgtccatacaaaataaaatcaaatatagcg 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================================================ tttaagttgaatatgataatctggcggcaaaagtagctattttttgcggataaaaaaagcatgtaaggcgcttaatatttcgtgcaaatatttgtataaaagtaaatatttttcttgtataatgatgattaagtacgaatcttttatattttatgcttatttttgtctcgagaaaagaaatcatgtccatacaaaataaaatcaaatatagcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3031:TF3032|TF3031:TF3032:conserved hypothetical protein:thiamin biosynthesis protein:->->:3255147..3255359 213 tttaagttgaatatgataatctggcggcaaaagtagctattttttgcggataaaaaaagcatgtaaggcgcttaatatttcgtgcaaatatttgtataaaagtaaatatttttcttgtataatgatgattaagtacgaatcttttatattttatgcttatttttgtctcgagaaaagaaatcatgtccatacaaaataaaatcaaatatagcg Intra-Species Hit: Count: 1 Min: 1 Max: 213 Len: 213 Subject: tfor_TF3031_TF3032|conserved hypothetical protein:thiamin biosynthesis protein|POSITIVE:POSITIVE|[3255147,3255359]|213 HSP 1 e-value: 1.0E-105 bit: 381.0 Len: 213 Query Start:1 Query End:213 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 tttaagttgaatatgataatctggcggcaaaagtagctattttttgcggatnnnnnnngcatgtaaggcgcttaatatttcgtgcaaatatttgtataaaagtaaatatttttcttgtataatgatgattaagtacgaatcttttatattttatgcttatttttgtctcgagaaaagaaatcatgtccatacaaaataaaatcaaatatagcg tttaagttgaatatgataatctggcggcaaaagtagctattttttgcggataaaaaaagcatgtaaggcgcttaatatttcgtgcaaatatttgtataaaagtaaatatttttcttgtataatgatgattaagtacgaatcttttatattttatgcttatttttgtctcgagaaaagaaatcatgtccatacaaaataaaatcaaatatagcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAGUUGAAUAUGAUAAUCUGGCGGCAAAAGUAGCUAUUUUUUGCGGAUAAAAAAAGCAUGUAAGGCGCUUAAUAUUUCGUGCAAAUAUUUGUAUAAAAGUAAAUAUUUUUCUUGUAUAAUGAUGAUUAAGUACGAAUCUUUUAUAUUUUAUGCUUAUUUUUGUCUCGAGAAAAGAAAUCAUGUCCAUACAAAAUAAAAUCAAAUAUAGCG .....((((.(((((((....((((.((....)).))))(((((((.((((((((((((((((....((((..........))))........(((((((((....(((((.((............))..))))).....)))))))))..))))))).))))))))))))))))....))))))).)).))..................... (-38.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCUAUAUUUGAUUUUAUUUUGUAUGGACAUGAUUUCUUUUCUCGAGACAAAAAUAAGCAUAAAAUAUAAAAGAUUCGUACUUAAUCAUCAUUAUACAAGAAAAAUAUUUACUUUUAUACAAAUAUUUGCACGAAAUAUUAAGCGCCUUACAUGCUUUUUUUAUCCGCAAAAAAUAGCUACUUUUGCCGCCAGAUUAUCAUAUUCAACUUAAA .((.(((((((......((((((((((..((((((........((((.(.......................).)))).....))))))..))))))))))...(((........))).)))))))..))..((...(((..(((.(......(((.(((((.......))))).))).......).)))..)))..)).............. (-23.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 69 21 123 65 tfor:TF0392|5end_hypothetical_protein_412335..412565_POSITIVE 337 69 21 72 14 tfor:TF0393|5end_conserved_hypothetical_protein_412284..412514_POSITIVE 298 50 5 223 173 tfor:TF0342|5end_hypothetical_protein_366189..366419_POSITIVE 291 70 22 126 82 tfor:TF0062|5end_conserved_hypothetical_protein_64916..65146_POSITIVE 290 96 57 215 181 tfor:TF0595|5end_hypothetical_protein_627820..628050_POSITIVE 288 60 19 97 57 tfor:TF0372|5end_transcriptional_regulator_390538..390768_POSITIVE 286 50 13 63 28 tfor:TF2803|5end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2991909..2992139_POSITIVE 283 70 22 143 96 tfor:TF2271|5end_conserved_hypothetical_protein_2435802..2436032_POSITIVE 281 50 20 139 107 tfor:TF0228|5end_probable_integral_outer_membrane_protein_253851..254081_POSITIVE 273 50 13 185 144 tfor:TF2780|5end_hypothetical_protein_2966060..2966290_POSITIVE 271 51 21 225 188 tfor:TF1049|5end_cobyrinic_acid_a,c-diamide_synthase_1110140..1110370_POSITIVE 269 47 14 150 114 tfor:TF2113|5end_phosphoribosylaminoimidazole_carboxylase_2282503..2282733_POSITIVE 267 50 6 56 9 tfor:TF1494|5end_cobinamide_kinase/cobinamide_phosphate_guanylyltransferase_1594016..1594246_POSITIVE 265 60 11 139 90 tfor:TF0283|5end_possible_nicotinamide_mononucleotide_transporter_311335..311565_POSITIVE 263 70 21 71 14 tfor:TF1801|5end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_1944213..1944443_POSITIVE 263 49 4 194 143 tfor:TF0432|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_452531..452761_POSITIVE 263 84 48 127 89 tfor:TF0240|5end_conserved_hypothetical_protein;_possible_gycosyltransferase_I_family_protein_270086..270316_POSITIVE 261 69 21 66 26 tfor:TF0778|5end_outer_membrane_protein,_TonB_dependent_receptor_827284..827514_POSITIVE 260 50 6 78 26 tfor:TF1682|5end_hydrolase_1796409..1796639_POSITIVE 256 69 22 195 142 tfor:TF1645|5end_conserved_hypothetical_protein_1755427..1755657_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 70 22 136 92 tfor:TF0061|3end_hypothetical_protein_65006..65156_POSITIVE 281 50 20 55 23 tfor:TF0226|3end_hypothetical_protein_253847..253997_POSITIVE 278 46 7 151 112 tfor:TF1611|3end_conserved_hypothetical_protein;_possible_glycosyl_transferase_1730797..1730947_POSITIVE 273 50 13 132 91 tfor:TF2781|3end_hypothetical_protein_2966087..2966237_POSITIVE 269 47 14 140 104 tfor:TF2112|3end_glycine_cleavage_H_protein_2282573..2282723_POSITIVE 265 60 11 100 51 tfor:TF0282|3end_probable_tonB-linked_outer_membrane_receptor_311376..311526_POSITIVE 263 49 4 53 2 tfor:TF0431|3end_hypothetical_protein_452470..452620_POSITIVE 263 49 4 86 35 tfor:TF0430|3end_hypothetical_protein_452503..452653_POSITIVE 260 50 6 100 48 tfor:TF1683|3end_conserved_hypothetical_protein_1796511..1796661_POSITIVE 248 174 133 130 77 tfor:TF0475|3end_possible_transcriptional_regulator,_AraC_family_494825..494975_POSITIVE 244 70 21 151 107 tfor:TF2618|3end_integral_membrane_protein,_possible_zinc_transporter_2796113..2796263_POSITIVE 241 82 41 105 65 tfor:TF0098|3end_permease_109280..109430_POSITIVE 240 70 23 137 107 tfor:TF2578|3end_30S_ribosomal_protein_S11_2747164..2747314_POSITIVE 239 50 6 149 108 tfor:TF0589|3end_anti-sigma_factor_624603..624753_POSITIVE 238 49 3 86 31 tfor:TF0385|3end_conserved_hypothetical_protein_406980..407130_POSITIVE 235 84 44 63 17 tfor:TF1281|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_(3-deoxy-D-manno-2-octulosonate-8-phosphate_synthase)_(KDO-8-phosphate_synthetase)_(KDO_8-P_synthase)_1366487..1366637_POSITIVE 234 49 13 116 77 tfor:TF3068|3end_flavodoxin_A_3293383..3293533_POSITIVE 234 70 34 101 58 tfor:TF2778|3end_outer_membrane_protein,__TonB_dependent_receptor_2964251..2964401_POSITIVE 233 157 118 128 87 tfor:TF2720|3end_conserved_hypothetical_protein_2894941..2895091_POSITIVE 233 88 46 54 23 tfor:TF2379|3end_phosphoribosylformylglycinamidine_cyclo-ligase_(AIR_synthase)_2545092..2545242_POSITIVE