Origin IGS: ccttttctaaatatactagcttcattttatcatattttgtaagagtttgcagaagtttttcacagaggagtttttcattccttcgcaaataagctcaattttcaaaata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tattttgaaaattgagcttatttgcgaaggaatgaaaaactcctctgtgaaaaacttctgcaaactcttacaaaatatgataaaatgaagctagtatatttagaaaagg Mask Tandem Repeat Region ================================================ ccttttctaaatatactagcttcattttatcatattttgtaagagtttgcagaagtttttcacagaggagtttttcattccttcgcaaataagctcaattttcaaaata Find is-nt database================================================ Query_seq: SSA_1283:SSA_1284|SSA_1283:SSA_1284:Nitroreductase, putative:hypothetical protein:<-<-:1304427..1304535 109 ccttttctaaatatactagcttcattttatcatattttgtaagagtttgcagaagtttttcacagaggagtttttcattccttcgcaaataagctcaattttcaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1283:SSA_1284|SSA_1283:SSA_1284:Nitroreductase, putative:hypothetical protein:<-<-:1304427..1304535 109 ccttttctaaatatactagcttcattttatcatattttgtaagagtttgcagaagtttttcacagaggagtttttcattccttcgcaaataagctcaattttcaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1283:SSA_1284|SSA_1283:SSA_1284:Nitroreductase, putative:hypothetical protein:<-<-:1304427..1304535 109 ccttttctaaatatactagcttcattttatcatattttgtaagagtttgcagaagtttttcacagaggagtttttcattccttcgcaaataagctcaattttcaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccttttctaaatatactagcttcattttatcatattttgtaagagtttgcagaagtttttcacagaggagtttttcattccttcgcaaataagctcaattttcaaaata Predict ORF larger than 30AA ================================================ ccttttctaaatatactagcttcattttatcatattttgtaagagtttgcagaagtttttcacagaggagtttttcattccttcgcaaataagctcaattttcaaaata 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: 81 Start: 4 End: 33 ...TTTCTAAATATACTAGCTTCATTTTATCAT............................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ccttttctaaatatactagcttcattttatcatattttgtaagagtttgcagaagtttttcacagaggagtttttcattccttcgcaaataagctcaattttcaaaata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1283:SSA_1284|SSA_1283:SSA_1284:Nitroreductase, putative:hypothetical protein:<-<-:1304427..1304535 109 ccttttctaaatatactagcttcattttatcatattttgtaagagtttgcagaagtttttcacagaggagtttttcattccttcgcaaataagctcaattttcaaaata Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_009009_SSA_1283_SSA_1284|Nitroreductase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1304427,1304535]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 ccttttctaaatatactagcttcattttatcatattttgtaagagtttgcagaagtttttcacagaggagtttttcattccttcgcaaataagctcaattttcaaaata ccttttctaaatatactagcttcattttatcatattttgtaagagtttgcagaagtttttcacagaggagtttttcattccttcgcaaataagctcaattttcaaaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUUUCUAAAUAUACUAGCUUCAUUUUAUCAUAUUUUGUAAGAGUUUGCAGAAGUUUUUCACAGAGGAGUUUUUCAUUCCUUCGCAAAUAAGCUCAAUUUUCAAAAUA ................................(((((((...((((((((.(((....)))...(((((((.....))))))).))))....))))......))))))) (-14.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUUGAAAAUUGAGCUUAUUUGCGAAGGAAUGAAAAACUCCUCUGUGAAAAACUUCUGCAAACUCUUACAAAAUAUGAUAAAAUGAAGCUAGUAUAUUUAGAAAAGG ..(((((((.((..(((((.(((((((((.........((......))......)))).)))))......((.....))........)))))...)).))))))).... (-14.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 822 90 41 181 132 NC_009009:SSA_1283|5end_Nitroreductase,_putative_1304336..1304566_NEGATIVE 341 97 55 202 156 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 281 55 17 169 129 NC_009009:SSA_1703|5end_Methionyl-tRNA_synthetase,_putative_1695640..1695870_NEGATIVE 272 87 49 90 58 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 267 69 21 141 87 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 265 60 13 139 88 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 259 89 45 218 178 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 252 80 33 181 139 NC_009009:SSA_1656|5end_Nisin_resistance_protein,_putative_1652890..1653120_NEGATIVE 247 90 43 107 61 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 240 68 21 176 112 NC_009009:SSA_1111|5end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1136532..1136762_POSITIVE 234 48 1 148 100 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 233 87 46 188 150 NC_009009:SSA_1801|5end_hypothetical_protein_1783314..1783544_NEGATIVE 231 86 43 163 128 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 231 69 21 184 121 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 229 90 41 67 8 NC_009009:SSA_1279|5end_Oxidoreductase,_putative_1300832..1301062_NEGATIVE 227 85 41 191 155 NC_009009:SSA_2220|5end_Galactosyltransferase,_putative_2221439..2221669_NEGATIVE 227 93 59 81 46 NC_009009:SSA_0713|5end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_699208..699438_POSITIVE 223 86 44 102 50 NC_009009:SSA_1787|5end_Diaminopimelate_decarboxylase,_putative_1771551..1771781_NEGATIVE 223 86 43 116 63 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 223 82 45 56 25 NC_009009:SSA_0757|5end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_739596..739826_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 84 50 148 106 NC_009009:SSA_1664|3end_Phosphatidylethanolamine_N-methyltransferase,_putative_1664449..1664599_NEGATIVE 272 87 49 74 42 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 270 55 18 40 1 NC_009009:SSA_1704|3end_Conserved_uncharacterized_protein_1695769..1695919_NEGATIVE 267 69 21 81 27 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 265 60 13 139 88 NC_009009:SSA_1660|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1656819..1656969_NEGATIVE 262 71 35 61 23 NC_009009:SSA_0259|3end_Thiol_peroxidase,_putative_253013..253163_NEGATIVE 258 70 29 134 84 NC_009009:SSA_1205|3end_Bta,_putative_1230057..1230207_POSITIVE 252 80 33 109 67 NC_009009:SSA_1657|3end_hypothetical_protein_1652962..1653112_NEGATIVE 233 87 46 133 95 NC_009009:SSA_1802|3end_Snf2_family_protein,_putative_1783369..1783519_NEGATIVE 225 98 74 114 90 NC_009009:SSA_2269|3end_hypothetical_protein_2269392..2269542_NEGATIVE 223 86 43 116 63 NC_009009:SSA_1531|3end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_1538778..1538928_NEGATIVE 216 86 41 105 56 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 213 86 44 145 93 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 213 75 41 79 49 NC_009009:SSA_1327|3end_hypothetical_protein_1343750..1343900_NEGATIVE 210 97 56 52 5 NC_009009:SSA_1624|3end_hypothetical_protein_1626497..1626647_POSITIVE 210 94 64 51 9 NC_009009:SSA_1567|3end_Polar_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_1571267..1571417_POSITIVE 209 69 24 59 2 NC_009009:SSA_0586|3end_Conserved_uncharacterized_protein_578243..578393_POSITIVE 208 89 43 66 23 NC_009009:SSA_2330|3end_Acetyltransferase,_putative_2333170..2333320_NEGATIVE 205 87 43 47 3 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 204 67 21 119 73 NC_009009:SSA_2174|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2171991..2172141_NEGATIVE