Origin IGS: atgattacctctatccttctacattttatttttaaacattctactgtatgaaaatgcgaatgtcaagagaaattttaatatttattaaaataaaagcgttttatcgatttttattcaaaatcaatatattatatactggactcaaaataagaaaaaagagtccgtcaagactcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggagtcttgacggactcttttttcttattttgagtccagtatataatatattgattttgaataaaaatcgataaaacgcttttattttaataaatattaaaatttctcttgacattcgcattttcatacagtagaatgtttaaaaataaaatgtagaaggatagaggtaatcat Mask Tandem Repeat Region ================================================ atgattacctctatccttctacattttatttttaaacattctactgtatgaaaatgcgaatgtcaagagaaattttaatatttattaaaataaaagcgttttatcgatttttattcaaaatcaatatattatatactggactcaaaataagaaaaaagagtccgtcaagactcc Find is-nt database================================================ Query_seq: SSA_2142:SSA_2143|SSA_2142:SSA_2143:Argininosuccinate synthase, putative:Conserved uncharacterized protein:<-<-:2143506..2143679 174 atgattacctctatccttctacattttatttttaaacattctactgtatgaaaatgcgaatgtcaagagaaattttaatatttattaaaataaaagcgttttatcgatttttattcaaaatcaatatattatatactggactcaaaataagaaaaaagagtccgtcaagactcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2142:SSA_2143|SSA_2142:SSA_2143:Argininosuccinate synthase, putative:Conserved uncharacterized protein:<-<-:2143506..2143679 174 atgattacctctatccttctacattttatttttaaacattctactgtatgaaaatgcgaatgtcaagagaaattttaatatttattaaaataaaagcgttttatcgatttttattcaaaatcaatatattatatactggactcaaaataagaaaaaagagtccgtcaagactcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2142:SSA_2143|SSA_2142:SSA_2143:Argininosuccinate synthase, putative:Conserved uncharacterized protein:<-<-:2143506..2143679 174 atgattacctctatccttctacattttatttttaaacattctactgtatgaaaatgcgaatgtcaagagaaattttaatatttattaaaataaaagcgttttatcgatttttattcaaaatcaatatattatatactggactcaaaataagaaaaaagagtccgtcaagactcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgattacctctatccttctacattttatttttaaacattctactgtatgaaaatgcgaatgtcaagagaaattttaatatttattaaaataaaagcgttttatcgatttttattcaaaatcaatatattatatactggactcaaaataagaaaaaagagtccgtcaagactcc Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 48 End: 173 ............................................... M K M R M S R E I L I F I K I K A F Y R F L F K I N I L Y T G L K I R K K S P S R L . atgattacctctatccttctacattttatttttaaacattctactgtatgaaaatgcgaatgtcaagagaaattttaatatttattaaaataaaagcgttttatcgatttttattcaaaatcaatatattatatactggactcaaaataagaaaaaagagtccgtcaagactcc 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: 88 Start: 38 End: 67 .....................................CTTGACATTCGCATTTTCATACAGTAGAAT........................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 128 End: 157 ...............................................................................................................................TTTTTTCTTATTTTGAGTCCAGTATATAAT................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgattacctctatccttctacattttatttttaaacattctactgtatgaaaatgcgaatgtcaagagaaattttaatatttattaaaataaaagcgttttatcgatttttattcaaaatcaatatattatatactggactcaaaataagaaaaaagagtccgtcaagactcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -3.0 Tail_Score: -3.34902 Start: 102 End: 126 Full_Region: AAAATAAAAGCGTTT TATCGATTTT TATTC AAAATCAATA TATTATATACTGGAC .....................................................................................................TATCGATTTTTATTCAAAATCAATA................................................ Find igs database================================================ Query_seq: SSA_2142:SSA_2143|SSA_2142:SSA_2143:Argininosuccinate synthase, putative:Conserved uncharacterized protein:<-<-:2143506..2143679 174 atgattacctctatccttctacattttatttttaaacattctactgtatgaaaatgcgaatgtcaagagaaattttaatatttattaaaataaaagcgttttatcgatttttattcaaaatcaatatattatatactggactcaaaataagaaaaaagagtccgtcaagactcc Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: NC_009009_SSA_2142_SSA_2143|Argininosuccinate synthase, putative:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[2143506,2143679]|174 HSP 1 e-value: 1.0E-31 bit: 137.0 Len: 69 Query Start:1 Query End:69 Subject Strand: POSITIVE Subject Start: 1 Subject End: 69 atgattacctctatccttctacattttatttttaaacattctactgtatgaaaatgcgaatgtcaagag......................................................................................................... atgattacctctatccttctacattttatttttaaacattctactgtatgaaaatgcgaatgtcaagag......................................................................................................... HSP 2 e-value: 1.0E-13 bit: 77.8 Len: 39 Query Start:136 Query End:174 Subject Strand: POSITIVE Subject Start: 136 Subject End: 174 .......................................................................................................................................ctggactcaaaataagaaaaaagagtccgtcaagactcc .......................................................................................................................................ctggactcaaaataagaaaaaagagtccgtcaagactcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAUUACCUCUAUCCUUCUACAUUUUAUUUUUAAACAUUCUACUGUAUGAAAAUGCGAAUGUCAAGAGAAAUUUUAAUAUUUAUUAAAAUAAAAGCGUUUUAUCGAUUUUUAUUCAAAAUCAAUAUAUUAUAUACUGGACUCAAAAUAAGAAAAAAGAGUCCGUCAAGACUCC ................((((((((((((((((((.(((......))).)))))))).))))))..))))..((((((((....))))))))......(((((...((((((.....))))))...............((((((..............))))))...)))))... (-26.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAGUCUUGACGGACUCUUUUUUCUUAUUUUGAGUCCAGUAUAUAAUAUAUUGAUUUUGAAUAAAAAUCGAUAAAACGCUUUUAUUUUAAUAAAUAUUAAAAUUUCUCUUGACAUUCGCAUUUUCAUACAGUAGAAUGUUUAAAAAUAAAAUGUAGAAGGAUAGAGGUAAUCAU (((((((....)))))))......(((((((..((((...........((((((((((.....))))))))))..(((.(((((((((...((((......)))).....(((((((................)))))))..))))))))))))....)))).))))))).... (-31.39) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 719 50 1 141 92 NC_009009:SSA_2142|5end_Argininosuccinate_synthase,_putative_2143415..2143645_NEGATIVE 277 45 8 144 99 NC_009009:SSA_1327|5end_hypothetical_protein_1344301..1344531_NEGATIVE 250 59 11 138 88 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 236 50 1 141 90 NC_009009:SSA_1978|5end_Dihydroxyacetone_kinase_family_protein_(Dak2_domain),_putative_1973933..1974163_NEGATIVE 220 75 39 55 17 NC_009009:SSA_0257|5end_N-acetylmuramidase/lysin,_putative_248878..249108_POSITIVE 212 72 41 70 37 NC_009009:SSA_0897|5end_Two_component_system_histidine_kinase,_putative_888358..888588_POSITIVE 205 71 37 162 135 NC_009009:SSA_0740|5end_C4-dicarboxylate_anaerobic_carrier,_possible_arginine_transporter,_putative_722240..722470_POSITIVE 195 140 93 107 61 NC_009009:SSA_0517|5end_Sensor_histidine_kinase,_putative_515060..515290_POSITIVE 194 59 11 121 75 NC_009009:SSA_0678|5end_Transcriptional_regulator,_ArgR_family,_putative_660274..660504_POSITIVE 194 59 14 142 95 NC_009009:SSA_0016|5end_ComX1,_transcriptional_regulator_of_competence-specific_genes,_putative_15487..15717_POSITIVE 190 58 13 164 124 NC_009009:SSA_0716|5end_Competence_protein,_putative_701390..701620_POSITIVE 189 71 42 160 131 NC_009009:SSA_0243|5end_Cyclo-nucleotide_phosphodiesterase,_putative_238235..238465_NEGATIVE 188 44 9 227 192 NC_009009:SSA_0818|5end_SPX_domain-like_protein,_putative_799675..799905_POSITIVE 181 140 94 163 114 NC_009009:SSA_1941|5end_hypothetical_protein_1927452..1927682_NEGATIVE 180 166 135 149 117 NC_009009:SSA_0967|5end_hypothetical_protein_975872..976102_POSITIVE 178 70 21 183 133 NC_009009:SSA_2094|5end_Conserved_uncharacterized_protein_2098247..2098477_NEGATIVE 178 72 45 157 127 NC_009009:SSA_1615|5end_Alanine_dehydrogenase,_putative_1618126..1618356_POSITIVE 176 49 8 143 102 NC_009009:SSA_0993|5end_hypothetical_protein_994064..994294_POSITIVE 176 60 14 144 98 NC_009009:SSA_0309|5end_Glyoxalase/Bleomycin_resistance_protein/dioxygenase_domain,_putative_304894..305124_POSITIVE 175 99 56 157 115 NC_009009:SSA_0561|5end_RNA:NAD_2'-phosphotransferase,_putative_553630..553860_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 45 8 103 58 NC_009009:SSA_1328|3end_hypothetical_protein_1344342..1344492_NEGATIVE 250 59 11 128 78 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 245 69 44 34 3 NC_009009:SSA_1323|3end_hypothetical_protein_1339788..1339938_NEGATIVE 240 106 62 97 56 NC_009009:SSA_0883|3end_Glycerate_kinase,_putative_878758..878908_POSITIVE 236 50 1 138 87 NC_009009:SSA_1979|3end_Alkaline-shock_protein,_putative_1973936..1974086_NEGATIVE 212 72 41 73 40 NC_009009:SSA_0896|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_888441..888591_POSITIVE 198 162 135 61 36 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 195 140 93 107 61 NC_009009:SSA_0516|3end_AmiR_two-component_response_regulator_with_transcriptional_antiterminator_output_domain,_putative_515140..515290_POSITIVE 194 59 11 128 82 NC_009009:SSA_0677|3end_rRNA_methylase,_putative_660361..660511_POSITIVE 190 170 133 89 49 NC_009009:SSA_2256|3end_hypothetical_protein_2251235..2251385_POSITIVE 182 170 135 79 43 NC_009009:SSA_1130|3end_Iron-dependent_peroxidase,_putative_1157090..1157240_POSITIVE 176 49 8 146 105 NC_009009:SSA_0992|3end_hypothetical_protein_994147..994297_POSITIVE 176 60 14 54 8 NC_009009:SSA_0308|3end_hypothetical_protein_304884..305034_POSITIVE 174 50 1 79 34 NC_009009:SSA_2305|3end_hypothetical_protein_2306326..2306476_NEGATIVE 174 31 1 34 4 NC_009009:SSA_0936|3end_FAD_synthase,_putative_946151..946301_POSITIVE 171 70 22 79 33 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 171 45 8 61 24 NC_009009:SSA_0971|3end_Conserved_uncharacterized_protein_980069..980219_POSITIVE 170 34 8 29 6 NC_009009:SSA_0552|3end_Cof_family_protein,_putative_548901..549051_POSITIVE 169 41 7 119 87 NC_009009:SSA_0911|3end_hypothetical_protein_922898..923048_POSITIVE 168 167 126 84 42 NC_009009:SSA_2272|3end_hypothetical_protein_2272577..2272727_NEGATIVE