Origin IGS: gatgaaaagcagtgggccaagttaaagatttttaattcttggttctaagctcttttcatttacaaagtatgatagatgcttaatatttcttcctggactatgctagttccttgaaaggagaaagaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttctttctcctttcaaggaactagcatagtccaggaagaaatattaagcatctatcatactttgtaaatgaaaagagcttagaaccaagaattaaaaatctttaacttggcccactgcttttcatc Mask Tandem Repeat Region ================================================ gatgaaaagcagtgggccaagttaaagatttttaattcttggttctaagctcttttcatttacaaagtatgatagatgcttaatatttcttcctggactatgctagttccttgaaaggagaaagaaa Find is-nt database================================================ Query_seq: SSA_0002:SSA_2390|SSA_0002:SSA_2390:DNA polymerase III, beta chain, putative:hypothetical protein:->->:2862..2988 127 gatgaaaagcagtgggccaagttaaagatttttaattcttggttctaagctcttttcatttacaaagtatgatagatgcttaatatttcttcctggactatgctagttccttgaaaggagaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0002:SSA_2390|SSA_0002:SSA_2390:DNA polymerase III, beta chain, putative:hypothetical protein:->->:2862..2988 127 gatgaaaagcagtgggccaagttaaagatttttaattcttggttctaagctcttttcatttacaaagtatgatagatgcttaatatttcttcctggactatgctagttccttgaaaggagaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0002:SSA_2390|SSA_0002:SSA_2390:DNA polymerase III, beta chain, putative:hypothetical protein:->->:2862..2988 127 gatgaaaagcagtgggccaagttaaagatttttaattcttggttctaagctcttttcatttacaaagtatgatagatgcttaatatttcttcctggactatgctagttccttgaaaggagaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgaaaagcagtgggccaagttaaagatttttaattcttggttctaagctcttttcatttacaaagtatgatagatgcttaatatttcttcctggactatgctagttccttgaaaggagaaagaaa Predict ORF larger than 30AA ================================================ gatgaaaagcagtgggccaagttaaagatttttaattcttggttctaagctcttttcatttacaaagtatgatagatgcttaatatttcttcctggactatgctagttccttgaaaggagaaagaaa 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================================================ gatgaaaagcagtgggccaagttaaagatttttaattcttggttctaagctcttttcatttacaaagtatgatagatgcttaatatttcttcctggactatgctagttccttgaaaggagaaagaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0002:SSA_2390|SSA_0002:SSA_2390:DNA polymerase III, beta chain, putative:hypothetical protein:->->:2862..2988 127 gatgaaaagcagtgggccaagttaaagatttttaattcttggttctaagctcttttcatttacaaagtatgatagatgcttaatatttcttcctggactatgctagttccttgaaaggagaaagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: NC_009009_SSA_0002_SSA_2390|DNA polymerase III, beta chain, putative:hypothetical protein|POSITIVE:POSITIVE|[2862,2988]|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 gatgaaaagcagtgggccaagttaaagatttttaattcttggttctaagctcttttcatttacaaagtatgatagatgcttaatatttcttcctggactatgctagttccttgaaaggagaaagaaa gatgaaaagcagtgggccaagttaaagatttttaattcttggttctaagctcttttcatttacaaagtatgatagatgcttaatatttcttcctggactatgctagttccttgaaaggagaaagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAAAAGCAGUGGGCCAAGUUAAAGAUUUUUAAUUCUUGGUUCUAAGCUCUUUUCAUUUACAAAGUAUGAUAGAUGCUUAAUAUUUCUUCCUGGACUAUGCUAGUUCCUUGAAAGGAGAAAGAAA (((((((((.((((((((((((((((....)))))..))))))))...))))))))))))....((((((.....))))))....(((((.(((((((((...))))))......)))))))).... (-30.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUUCUCCUUUCAAGGAACUAGCAUAGUCCAGGAAGAAAUAUUAAGCAUCUAUCAUACUUUGUAAAUGAAAAGAGCUUAGAACCAAGAAUUAAAAAUCUUUAACUUGGCCCACUGCUUUUCAUC (((((((((........(((.(((...)))))))))))))))..((((((.(((.((((.........))))..)))))))))..(((((..(((((....))))))))))................ (-20.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 120 80 121 66 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 253 57 13 103 57 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 246 79 36 50 9 NC_009009:SSA_1736|5end_L-cysteine_desulfhydrase,_putative_1722619..1722849_NEGATIVE 246 75 36 49 18 NC_009009:SSA_1537|5end_Conserved_uncharacterized_protein_1544441..1544671_NEGATIVE 242 112 75 103 65 NC_009009:SSA_1601|5end_VacB-like_protein,_putative_1607059..1607289_NEGATIVE 236 115 77 178 142 NC_009009:SSA_1040|5end_Sugar_ABC_transporter,_permease_protein,_putative_1055302..1055532_POSITIVE 232 119 72 131 90 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 232 50 11 60 16 NC_009009:SSA_0053|5end_Beta-galactosidase,_putative_56748..56978_POSITIVE 231 114 74 75 31 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 230 108 68 125 82 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 230 108 61 170 115 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 228 46 4 84 40 NC_009009:SSA_2139|5end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2140324..2140554_NEGATIVE 228 118 91 210 186 NC_009009:SSA_1508|5end_ABC-type_lipopolysaccharide_transport_system,_permease_component,_putative_1513250..1513480_NEGATIVE 228 60 11 61 16 NC_009009:SSA_0833|5end_Accessory_secretory_protein_Asp1,_putative_817940..818170_POSITIVE 227 79 32 217 153 NC_009009:SSA_2329|5end_hypothetical_protein_2332262..2332492_POSITIVE 226 50 9 70 15 NC_009009:SSA_1280|5end_hypothetical_protein_1301596..1301826_NEGATIVE 225 105 61 65 17 NC_009009:SSA_1837|5end_hypothetical_protein_1832243..1832473_POSITIVE 225 119 76 214 165 NC_009009:SSA_0220|5end_PTS_system,_mannose-specific_IIB_component,_putative_215848..216078_POSITIVE 223 113 71 56 22 NC_009009:SSA_1253|5end_hypothetical_protein_1281245..1281475_NEGATIVE 222 114 74 125 82 NC_009009:SSA_1636|5end_ABC-type_antibiotic_exporter,_ATPase_component,_putative_1640905..1641135_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 59 14 89 46 NC_009009:SSA_0002|3end_DNA_polymerase_III,_beta_chain,_putative_2801..2951_POSITIVE 302 118 75 58 12 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 289 56 11 92 43 NC_009009:SSA_1595|3end_Tellurite_resistance,_putative_1600951..1601101_NEGATIVE 261 120 86 139 99 NC_009009:SSA_1020|3end_hypothetical_protein_1036104..1036254_POSITIVE 253 57 13 116 70 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 251 120 74 124 76 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 247 50 5 109 64 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 246 79 36 48 7 NC_009009:SSA_1737|3end_Cystathionine_gamma-synthase,_putative_1722621..1722771_NEGATIVE 242 51 13 105 56 NC_009009:SSA_1487|3end_Conserved_uncharacterized_protein_1493483..1493633_NEGATIVE 232 119 72 122 81 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 231 114 74 78 34 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 230 108 68 135 92 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 228 46 4 100 56 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE 228 60 11 52 7 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 226 50 9 58 3 NC_009009:SSA_1281|3end_Uracil-DNA_glycosylase,_putative_1301608..1301758_NEGATIVE 223 113 71 59 25 NC_009009:SSA_1254|3end_hypothetical_protein_1281242..1281392_NEGATIVE 217 23 1 75 51 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 215 104 70 146 108 NC_009009:SSA_0577|3end_Ancient_RNA-binding_IF3-C_fold_(CRS1/YhbY_domain),_putative_571644..571794_POSITIVE 213 120 72 80 30 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 211 113 71 117 71 NC_009009:SSA_1073|3end_Gamma-glutamyl_phosphate_reductase,_putative_1092228..1092378_POSITIVE