Origin IGS: gttctatattatcaaaaattactcttattttcaagatagctatctaattcttctacaaagtttaaattatccattagttaagattcagatcttcaactgatagaatattttattacaccattagctctttgctgtcatcaaattttggaggtattattaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattaataatacctccaaaatttgatgacagcaaagagctaatggtgtaataaaatattctatcagttgaagatctgaatcttaactaatggataatttaaactttgtagaagaattagatagctatcttgaaaataagagtaatttttgataatatagaac Mask Tandem Repeat Region ================================================ gttctatattatcaaaaattactcttattttcaagatagctatctaattcttctacaaagtttaaattatccattagttaagattcagatcttcaactgatagaatattttattacaccattagctctttgctgtcatcaaattttggaggtattattaatt Find is-nt database================================================ Query_seq: TDE0126:TDE0127|TDE0126:TDE0127:hypothetical protein:DNA-binding protein:<-->:145728..145889 162 gttctatattatcaaaaattactcttattttcaagatagctatctaattcttctacaaagtttaaattatccattagttaagattcagatcttcaactgatagaatattttattacaccattagctctttgctgtcatcaaattttggaggtattattaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0126:TDE0127|TDE0126:TDE0127:hypothetical protein:DNA-binding protein:<-->:145728..145889 162 gttctatattatcaaaaattactcttattttcaagatagctatctaattcttctacaaagtttaaattatccattagttaagattcagatcttcaactgatagaatattttattacaccattagctctttgctgtcatcaaattttggaggtattattaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0126:TDE0127|TDE0126:TDE0127:hypothetical protein:DNA-binding protein:<-->:145728..145889 162 gttctatattatcaaaaattactcttattttcaagatagctatctaattcttctacaaagtttaaattatccattagttaagattcagatcttcaactgatagaatattttattacaccattagctctttgctgtcatcaaattttggaggtattattaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttctatattatcaaaaattactcttattttcaagatagctatctaattcttctacaaagtttaaattatccattagttaagattcagatcttcaactgatagaatattttattacaccattagctctttgctgtcatcaaattttggaggtattattaatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 8 End: 97 ....... M I K N Y S Y F Q D S Y L I L L Q S L N Y P L V K I Q I F N ................................................................. gttctatattatcaaaaattactcttattttcaagatagctatctaattcttctacaaagtttaaattatccattagttaagattcagatcttcaactgatagaatattttattacaccattagctctttgctgtcatcaaattttggaggtattattaatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 6 End: 35 .....CTTGAAAATAAGAGTAATTTTTGATAATAT............................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 128 End: 157 ...............................................................................................................................TTTGCTGTCATCAAATTTTGGAGGTATTAT..... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttctatattatcaaaaattactcttattttcaagatagctatctaattcttctacaaagtttaaattatccattagttaagattcagatcttcaactgatagaatattttattacaccattagctctttgctgtcatcaaattttggaggtattattaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0126:TDE0127|TDE0126:TDE0127:hypothetical protein:DNA-binding protein:<-->:145728..145889 162 gttctatattatcaaaaattactcttattttcaagatagctatctaattcttctacaaagtttaaattatccattagttaagattcagatcttcaactgatagaatattttattacaccattagctctttgctgtcatcaaattttggaggtattattaatt Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: NC_002967_TDE0126_TDE0127|hypothetical protein:DNA-binding protein|NEGATIVE:POSITIVE|[145728,145889]|162 HSP 1 e-value: 4.0E-87 bit: 321.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 gttctatattatcaaaaattactcttattttcaagatagctatctaattcttctacaaagtttaaattatccattagttaagattcagatcttcaactgatagaatattttattacaccattagctctttgctgtcatcaaattttggaggtattattaatt gttctatattatcaaaaattactcttattttcaagatagctatctaattcttctacaaagtttaaattatccattagttaagattcagatcttcaactgatagaatattttattacaccattagctctttgctgtcatcaaattttggaggtattattaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCUAUAUUAUCAAAAAUUACUCUUAUUUUCAAGAUAGCUAUCUAAUUCUUCUACAAAGUUUAAAUUAUCCAUUAGUUAAGAUUCAGAUCUUCAACUGAUAGAAUAUUUUAUUACACCAUUAGCUCUUUGCUGUCAUCAAAUUUUGGAGGUAUUAUUAAUU ................(((((....((((((((((((......................((.((((.((((.((((((((((((....))))).))))))).).))).))))..)).....((((.....)))).......))))))))))))....))))) (-23.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAUAAUACCUCCAAAAUUUGAUGACAGCAAAGAGCUAAUGGUGUAAUAAAAUAUUCUAUCAGUUGAAGAUCUGAAUCUUAACUAAUGGAUAAUUUAAACUUUGUAGAAGAAUUAGAUAGCUAUCUUGAAAAUAAGAGUAAUUUUUGAUAAUAUAGAAC .(((((.(((..(((.....((..(.((.(((....((((.((((.(((......))).)))).))))....((((((.((((..(((..((..........))...))))))).)))))).))).)))..)).....)))..))).))))).......... (-22.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 791 140 91 231 182 NC_002967:TDE0126|5end_hypothetical_protein_145637..145867_NEGATIVE 253 151 115 198 164 NC_002967:TDE1219|5end_flagellar_protein_FliJ,_putative_1251871..1252101_POSITIVE 252 100 51 199 154 NC_002967:TDE1272|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1306976..1307206_NEGATIVE 248 72 35 117 83 NC_002967:TDE0451|5end_arginine_deiminase_508653..508883_POSITIVE 244 152 116 57 22 NC_002967:TDE2474|5end_acetyltransferase,_GNAT_family_2497096..2497326_NEGATIVE 237 137 92 125 79 NC_002967:TDE2545|5end_hypothetical_protein_2571814..2572044_NEGATIVE 235 158 120 95 55 NC_002967:TDE0254|5end_hypothetical_protein_288654..288884_POSITIVE 234 149 108 140 99 NC_002967:TDE2416|5end_hypothetical_protein_2442799..2443029_NEGATIVE 226 154 115 211 167 NC_002967:TDE1747|5end_nicotinate_(nicotinamide)_nucleotide_adenylyltransferase_1801935..1802165_NEGATIVE 226 57 22 120 78 NC_002967:TDE0263|5end_spermidine_N1-acetyltransferase,_putative_296942..297172_NEGATIVE 224 66 23 114 74 NC_002967:TDE2281|5end_LysM_domain_protein_2318493..2318723_NEGATIVE 222 153 115 60 18 NC_002967:TDE2404|5end_RNA_polymerase_sigma-54_factor,_putative_2430704..2430934_NEGATIVE 222 135 108 129 103 NC_002967:TDE0292|5end_hypothetical_protein_322014..322244_NEGATIVE 222 151 118 60 28 NC_002967:TDE0009|5end_hypothetical_protein_14545..14775_NEGATIVE 220 148 116 129 89 NC_002967:TDE1380|5end_hypothetical_protein_1421284..1421514_NEGATIVE 219 98 51 71 10 NC_002967:TDE0986|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1013061..1013291_POSITIVE 216 151 113 186 151 NC_002967:TDE2614|5end_ApbE_family_protein_2657133..2657363_NEGATIVE 215 157 115 51 10 NC_002967:TDE0818|5end_ABC_transporter,_ATP-binding/permease_protein_841647..841877_NEGATIVE 214 160 121 66 24 NC_002967:TDE1242|5end_hypothetical_protein_1274565..1274795_POSITIVE 211 160 119 37 1 NC_002967:TDE0868|5end_oxidoreductase,_FAD/FMN-binding_890385..890615_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 148 104 137 95 NC_002967:TDE1278|3end_conserved_hypothetical_protein_TIGR01440_1312228..1312378_NEGATIVE 252 100 51 146 101 NC_002967:TDE1273|3end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1307029..1307179_NEGATIVE 237 137 92 62 16 NC_002967:TDE2546|3end_hypothetical_protein_2571877..2572027_NEGATIVE 235 158 120 86 46 NC_002967:TDE0253|3end_hypothetical_protein_288725..288875_POSITIVE 234 149 108 127 86 NC_002967:TDE2417|3end_nitroimidazole_resistance_protein,_putative_2442812..2442962_NEGATIVE 222 153 115 48 6 NC_002967:TDE2405|3end_hypothetical_protein_2430716..2430866_NEGATIVE 222 135 108 125 99 NC_002967:TDE0293|3end_MATE_efflux_family_protein_322018..322168_NEGATIVE 220 148 116 125 85 NC_002967:TDE1381|3end_V-type_ATP_synthase_subunit_E_1421288..1421438_NEGATIVE 215 157 115 49 8 NC_002967:TDE0819|3end_ABC_transporter,_ATP-binding/permease_protein_841649..841799_NEGATIVE 214 160 121 73 31 NC_002967:TDE1241|3end_HD_domain_protein_1274652..1274802_POSITIVE 207 153 121 79 49 NC_002967:TDE2482|3end_hypothetical_protein_2505822..2505972_POSITIVE 204 148 123 129 98 NC_002967:TDE2126|3end_hypothetical_protein_2159843..2159993_POSITIVE 199 140 99 46 9 NC_002967:TDE2360|3end_dihydroxyacetone_kinase_family_protein_2394792..2394942_NEGATIVE 199 40 2 117 71 NC_002967:TDE0813|3end_ABC_transporter,_ATP-binding_protein/permease_835707..835857_POSITIVE 198 128 83 99 58 NC_002967:TDE0196|3end_hypothetical_protein_232845..232995_POSITIVE 197 154 118 42 4 NC_002967:TDE2500|3end_DJ-1_family_protein_2523952..2524102_NEGATIVE 197 125 90 97 63 NC_002967:TDE1567|3end_hypothetical_protein_1619591..1619741_POSITIVE 197 155 123 50 17 NC_002967:TDE1132|3end_chorismate_synthase_1164580..1164730_POSITIVE 196 150 121 65 25 NC_002967:TDE0750|3end_magnesium_chelatase,_subunit_D/I_family_788204..788354_NEGATIVE 196 153 116 100 63 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE