Origin IGS: ataaaaaaggactgctctggacaatcctttttccaatgttcttcataaactatcagatactgaattcgcttttcagtttaagtcaatacaactaaaataacaagccaaaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtttggcttgttattttagttgtattgacttaaactgaaaagcgaattcagtatctgatagtttatgaagaacattggaaaaaggattgtccagagcagtccttttttat Mask Tandem Repeat Region ================================================ ataaaaaaggactgctctggacaatcctttttccaatgttcttcataaactatcagatactgaattcgcttttcagtttaagtcaatacaactaaaataacaagccaaaca Find is-nt database================================================ Query_seq: SSA_1191:SSA_1192|SSA_1191:SSA_1192:hypothetical protein:hypothetical protein:<-<-:1218414..1218524 111 ataaaaaaggactgctctggacaatcctttttccaatgttcttcataaactatcagatactgaattcgcttttcagtttaagtcaatacaactaaaataacaagccaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1191:SSA_1192|SSA_1191:SSA_1192:hypothetical protein:hypothetical protein:<-<-:1218414..1218524 111 ataaaaaaggactgctctggacaatcctttttccaatgttcttcataaactatcagatactgaattcgcttttcagtttaagtcaatacaactaaaataacaagccaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1191:SSA_1192|SSA_1191:SSA_1192:hypothetical protein:hypothetical protein:<-<-:1218414..1218524 111 ataaaaaaggactgctctggacaatcctttttccaatgttcttcataaactatcagatactgaattcgcttttcagtttaagtcaatacaactaaaataacaagccaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaaaaaggactgctctggacaatcctttttccaatgttcttcataaactatcagatactgaattcgcttttcagtttaagtcaatacaactaaaataacaagccaaaca Predict ORF larger than 30AA ================================================ ataaaaaaggactgctctggacaatcctttttccaatgttcttcataaactatcagatactgaattcgcttttcagtttaagtcaatacaactaaaataacaagccaaaca 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: 82 Start: 69 End: 98 ....................................................................CTTTTCAGTTTAAGTCAATACAACTAAAAT............. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataaaaaaggactgctctggacaatcctttttccaatgttcttcataaactatcagatactgaattcgcttttcagtttaagtcaatacaactaaaataacaagccaaaca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.3 Tail_Score: -3.6682 Start: 60 End: 76 Full_Region: ATAAACTATCAGATA CTGAA TTCGCTT TTCAG TTTAAGTCAATACAA ...........................................................CTGAATTCGCTTTTCAG................................... Find igs database================================================ Query_seq: SSA_1191:SSA_1192|SSA_1191:SSA_1192:hypothetical protein:hypothetical protein:<-<-:1218414..1218524 111 ataaaaaaggactgctctggacaatcctttttccaatgttcttcataaactatcagatactgaattcgcttttcagtttaagtcaatacaactaaaataacaagccaaaca Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_009009_SSA_1191_SSA_1192|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1218414,1218524]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 ataaaaaaggactgctctggacaatcctttttccaatgttcttcataaactatcagatactgaattcgcttttcagtttaagtcaatacaactaaaataacaagccaaaca ataaaaaaggactgctctggacaatcctttttccaatgttcttcataaactatcagatactgaattcgcttttcagtttaagtcaatacaactaaaataacaagccaaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAAAGGACUGCUCUGGACAAUCCUUUUUCCAAUGUUCUUCAUAAACUAUCAGAUACUGAAUUCGCUUUUCAGUUUAAGUCAAUACAACUAAAAUAACAAGCCAAACA ...((((((((.(((....).)).)))))))).......................(((((((((.......))))))....)))........................... (-13.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUGGCUUGUUAUUUUAGUUGUAUUGACUUAAACUGAAAAGCGAAUUCAGUAUCUGAUAGUUUAUGAAGAACAUUGGAAAAAGGAUUGUCCAGAGCAGUCCUUUUUUAU (((((..(........((((..(((((((.((...((....))..)).)))))))))))........)..)))))...(((((((((((((.....))))))))))))).. (-26.09) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 829 60 11 151 102 NC_009009:SSA_1191|5end_hypothetical_protein_1218323..1218553_NEGATIVE 324 56 12 188 142 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 261 44 10 98 57 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 246 70 25 138 99 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 245 50 5 78 32 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 245 35 8 206 174 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 237 68 22 172 123 NC_009009:SSA_0679|5end_DNA_repair_and_genetic_recombination,_putative_660714..660944_POSITIVE 232 54 14 178 138 NC_009009:SSA_0997|5end_DNA-directed_DNA_polymerase_III_chain,_putative_996779..997009_POSITIVE 231 80 33 56 3 NC_009009:SSA_1249|5end_hypothetical_protein_1273985..1274215_NEGATIVE 229 65 25 118 65 NC_009009:SSA_0158|5end_hypothetical_protein_153801..154031_POSITIVE 226 70 25 150 97 NC_009009:SSA_1474|5end_Lipoprotein,_putative_1479741..1479971_NEGATIVE 226 56 12 194 143 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 226 42 9 42 2 NC_009009:SSA_0601|5end_Phosphorylase,_Pnp/Udp_family,_putative_589147..589377_POSITIVE 226 55 11 52 4 NC_009009:SSA_0183|5end_hypothetical_protein_187646..187876_POSITIVE 225 36 7 34 9 NC_009009:SSA_1648|5end_hypothetical_protein_1647909..1648139_NEGATIVE 224 44 7 223 192 NC_009009:SSA_0776|5end_Glucose-1-phosphate_adenylyltransferase,_putative_758298..758528_POSITIVE 224 60 14 69 10 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 223 38 11 230 207 NC_009009:SSA_0465|5end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_469185..469415_POSITIVE 223 49 8 94 48 NC_009009:SSA_0036|5end_Secreted_protein,_possible_function_in_cell-wall_metabolism_(amidase),_putative_43999..44229_NEGATIVE 222 43 2 225 182 NC_009009:SSA_2339|5end_Microcin_C7_resistance_protein,_putative_2340456..2340686_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 56 12 142 96 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 246 70 25 134 95 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 243 44 8 142 106 NC_009009:SSA_1764|3end_hypothetical_protein_1752510..1752660_POSITIVE 231 80 33 59 6 NC_009009:SSA_1250|3end_Conserved_uncharacterized_protein,_putative_1273982..1274132_NEGATIVE 229 65 25 114 61 NC_009009:SSA_0157|3end_hypothetical_protein_153877..154027_POSITIVE 225 36 7 37 12 NC_009009:SSA_1649|3end_hypothetical_protein_1647906..1648056_NEGATIVE 222 43 2 81 38 NC_009009:SSA_2338|3end_Conserved_uncharacterized_protein_2340392..2340542_POSITIVE 222 47 6 58 12 NC_009009:SSA_0457|3end_Fructokinase,_putative_461642..461792_POSITIVE 221 46 6 123 78 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 217 90 41 131 87 NC_009009:SSA_0905|3end_CshA-like_fibrillar_surface_protein_B_909060..909210_POSITIVE 216 37 11 53 27 NC_009009:SSA_1493|3end_hypothetical_protein_1498929..1499079_NEGATIVE 213 85 41 68 31 NC_009009:SSA_1292|3end_hypothetical_protein_1311099..1311249_NEGATIVE 212 54 22 129 103 NC_009009:SSA_0928|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938525..938675_POSITIVE 210 70 21 134 75 NC_009009:SSA_2013|3end_hypothetical_protein_2013470..2013620_NEGATIVE 209 52 12 124 79 NC_009009:SSA_2271|3end_hypothetical_protein_2272238..2272388_NEGATIVE 208 44 6 44 1 NC_009009:SSA_0688|3end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_672132..672282_POSITIVE 206 45 12 113 83 NC_009009:SSA_0994|3end_Peptidase_E,_putative_995390..995540_POSITIVE 205 42 5 88 55 NC_009009:SSA_2192|3end_Conserved_uncharacterized_protein_2193093..2193243_NEGATIVE 205 52 12 93 61 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 205 40 12 27 2 NC_009009:SSA_0560|3end_hypothetical_protein_553717..553867_POSITIVE