Origin IGS: agctaaaataaattctcgggattcacattctttagaggcttaaaagtgcggatttaacatgaattaaacaagtcgttccttcaacatctgcttcgttttcgatctcgttacgaagaattgtgtaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattacacaattcttcgtaacgagatcgaaaacgaagcagatgttgaaggaacgacttgtttaattcatgttaaatccgcacttttaagcctctaaagaatgtgaatcccgagaatttattttagct Mask Tandem Repeat Region ================================================ agctaaaataaattctcgggattcacattctttagaggcttaaaagtgcggatttaacatgaattaaacaagtcgttccttcaacatctgcttcgttttcgatctcgttacgaagaattgtgtaatt Find is-nt database================================================ Query_seq: TF1940:TF1941|TF1940:TF1941:TPR-repeat-containing protein:3-phosphoshikimate-1-carboxyvinyltransferase:->->:2088875..2089001 127 agctaaaataaattctcgggattcacattctttagaggcttaaaagtgcggatttaacatgaattaaacaagtcgttccttcaacatctgcttcgttttcgatctcgttacgaagaattgtgtaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1940:TF1941|TF1940:TF1941:TPR-repeat-containing protein:3-phosphoshikimate-1-carboxyvinyltransferase:->->:2088875..2089001 127 agctaaaataaattctcgggattcacattctttagaggcttaaaagtgcggatttaacatgaattaaacaagtcgttccttcaacatctgcttcgttttcgatctcgttacgaagaattgtgtaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1940:TF1941|TF1940:TF1941:TPR-repeat-containing protein:3-phosphoshikimate-1-carboxyvinyltransferase:->->:2088875..2089001 127 agctaaaataaattctcgggattcacattctttagaggcttaaaagtgcggatttaacatgaattaaacaagtcgttccttcaacatctgcttcgttttcgatctcgttacgaagaattgtgtaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctaaaataaattctcgggattcacattctttagaggcttaaaagtgcggatttaacatgaattaaacaagtcgttccttcaacatctgcttcgttttcgatctcgttacgaagaattgtgtaatt Predict ORF larger than 30AA ================================================ agctaaaataaattctcgggattcacattctttagaggcttaaaagtgcggatttaacatgaattaaacaagtcgttccttcaacatctgcttcgttttcgatctcgttacgaagaattgtgtaatt 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================================================ agctaaaataaattctcgggattcacattctttagaggcttaaaagtgcggatttaacatgaattaaacaagtcgttccttcaacatctgcttcgttttcgatctcgttacgaagaattgtgtaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1940:TF1941|TF1940:TF1941:TPR-repeat-containing protein:3-phosphoshikimate-1-carboxyvinyltransferase:->->:2088875..2089001 127 agctaaaataaattctcgggattcacattctttagaggcttaaaagtgcggatttaacatgaattaaacaagtcgttccttcaacatctgcttcgttttcgatctcgttacgaagaattgtgtaatt Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: tfor_TF1940_TF1941|TPR-repeat-containing protein:3-phosphoshikimate-1- carboxyvinyltransferase|POSITIVE:POSITIVE|[2088875, 2089001]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 agctaaaataaattctcgggattcacattctttagaggcttaaaagtgcggatttaacatgaattaaacaagtcgttccttcaacatctgcttcgttttcgatctcgttacgaagaattgtgtaatt agctaaaataaattctcgggattcacattctttagaggcttaaaagtgcggatttaacatgaattaaacaagtcgttccttcaacatctgcttcgttttcgatctcgttacgaagaattgtgtaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUAAAAUAAAUUCUCGGGAUUCACAUUCUUUAGAGGCUUAAAAGUGCGGAUUUAACAUGAAUUAAACAAGUCGUUCCUUCAACAUCUGCUUCGUUUUCGAUCUCGUUACGAAGAAUUGUGUAAUU ..........(((((...((((((.((((.(((((....))))))))).)))))).....)))))..................((((...((((((...((....))..))))))....)))).... (-20.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUACACAAUUCUUCGUAACGAGAUCGAAAACGAAGCAGAUGUUGAAGGAACGACUUGUUUAAUUCAUGUUAAAUCCGCACUUUUAAGCCUCUAAAGAAUGUGAAUCCCGAGAAUUUAUUUUAGCU ............((((((..((....))...)))))).....(((((((......((((....(((((((((......((........))........)))))))))..))))......))))))). (-19.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 108 65 156 116 tfor:TF2331|5end_conserved_hypothetical_protein_2491073..2491303_POSITIVE 324 120 73 85 35 tfor:TF0239|5end_conserved_hypothetical_protein_268894..269124_POSITIVE 310 120 71 190 146 tfor:TF0727|5end_ABC_transporter,_ATP-binding_protein_779178..779408_POSITIVE 305 113 79 122 83 tfor:TF0296|5end_hypothetical_protein_321941..322171_POSITIVE 301 115 71 82 33 tfor:TF2226|5end_CTn_excision_protein_2395529..2395759_POSITIVE 288 112 71 218 162 tfor:TF2807|5end_possible_chloride_channel_protein_2996637..2996867_POSITIVE 288 115 78 141 99 tfor:TF0780|5end_alpha-L-arabinofuranosidase,_precursor_A_831944..832174_POSITIVE 286 113 71 187 143 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 285 110 69 210 161 tfor:TF1315|5end_purine_nucleoside_phosphorylase_1390236..1390466_POSITIVE 280 116 72 130 83 tfor:TF0658|5end_2-amino-3-ketobutyrate_coenzyme_A_ligase_703912..704142_POSITIVE 279 113 74 184 142 tfor:TF2161|5end_conserved_hypothetical_protein_2336972..2337202_POSITIVE 269 120 77 33 3 tfor:TF2333|5end_signal_peptidase_I_2492560..2492790_POSITIVE 269 120 85 162 130 tfor:TF2264|5end_transfer_region-related_protein,_TraO_2432890..2433120_POSITIVE 269 113 91 205 181 tfor:TF1628|5end_conserved_hypothetical_protein_1740627..1740857_POSITIVE 267 109 62 204 157 tfor:TF1914|5end_conserved_hypothetical_protein_2066599..2066829_POSITIVE 265 117 73 166 126 tfor:TF1896|5end_conserved_hypothetical_protein;_possible_phage-related_protein_2047858..2048088_POSITIVE 265 97 60 166 125 tfor:TF1406|5end_transposase_1481758..1481988_POSITIVE 259 109 69 185 151 tfor:TF0118|5end_5-keto-D-gluconate_5-reductase_129768..129998_POSITIVE 257 115 73 55 21 tfor:TF1873|5end_possible_hemolysin_secretion_protein_2026745..2026975_POSITIVE 257 115 73 55 21 tfor:TF1131|5end_membrane-fusion_protein;_possible_hemolysin_secretion_protein_1207611..1207841_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 108 65 112 72 tfor:TF2330|3end_conserved_hypothetical_protein_2491109..2491259_POSITIVE 324 120 73 68 18 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 301 115 71 75 26 tfor:TF2225|3end_CTn_excision_protein_2395602..2395752_POSITIVE 286 113 71 123 79 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 266 120 71 52 7 tfor:TF0007|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_3599..3749_POSITIVE 265 97 60 147 106 tfor:TF1405|3end_conserved_hypothetical_protein_1481819..1481969_POSITIVE 259 109 69 145 111 tfor:TF0117|3end_2-dehydro-3-deoxygluconokinase_129808..129958_POSITIVE 257 115 73 41 7 tfor:TF1872|3end_ABC_transporter,_ATP-binding/permease_component_2026811..2026961_POSITIVE 257 115 73 41 7 tfor:TF1130|3end_ABC_transporter_ATP-binding_protein/permease_component_1207677..1207827_POSITIVE 253 109 70 110 66 tfor:TF1698|3end_mobilization_protein_1819782..1819932_POSITIVE 253 112 71 112 72 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 251 106 70 52 13 tfor:TF2280|3end_hypothetical_protein_2439474..2439624_POSITIVE 250 117 71 151 99 tfor:TF1001|3end_penicillin-binding_protein_1A_1056600..1056750_POSITIVE 247 53 13 56 10 tfor:TF0258|3end_hypothetical_protein_289534..289684_POSITIVE 246 118 71 58 5 tfor:TF2751|3end_phenylalanyl-tRNA_synthetase,_alpha_subunit_2936815..2936965_POSITIVE 246 111 72 140 100 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 245 88 44 65 21 tfor:TF2830|3end_ABC_transporter,_ATP-binding_protein_3021419..3021569_POSITIVE 245 115 85 151 124 tfor:TF2263|3end_transfer_region-related_protein,_TraN_2432964..2433114_POSITIVE 244 111 76 48 1 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 244 56 15 101 63 tfor:TF2815|3end_meso-diaminopimelate_D-dehydrogenase_3006420..3006570_POSITIVE