Origin IGS: caaaataaatcacatttaaaaaaacagattttctaactgaagatttgttttttatttttttagtaaaaatgaacagtattttcaggctgttcaaaaacatgatgatttcagccttcaaagatatatttttaagcaaaagcattgaatttttgtaggaaattctgtaaaattttaagagattattatatgaagaaaagggaattatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataattcccttttcttcatataataatctcttaaaattttacagaatttcctacaaaaattcaatgcttttgcttaaaaatatatctttgaaggctgaaatcatcatgtttttgaacagcctgaaaatactgttcatttttactaaaaaaataaaaaacaaatcttcagttagaaaatctgtttttttaaatgtgatttattttg Mask Tandem Repeat Region ================================================ caaaataaatcacatttaaaaaaacagattttctaactgaagatttgttttttatttttttagtaaaaatgaacagtattttcaggctgttcaaaaacatgatgatttcagccttcaaagatatatttttaagcaaaagcattgaatttttgtaggaaattctgtaaaattttaagagattattatatgaagaaaagggaattatt Find is-nt database================================================ Query_seq: SSA_1017:SSA_1018|SSA_1017:SSA_1018:hypothetical protein:Zinc metalloprotease zmpC precursor, putative:->->:1023280..1023485 206 caaaataaatcacatttaaaaaaacagattttctaactgaagatttgttttttatttttttagtaaaaatgaacagtattttcaggctgttcaaaaacatgatgatttcagccttcaaagatatatttttaagcaaaagcattgaatttttgtaggaaattctgtaaaattttaagagattattatatgaagaaaagggaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1017:SSA_1018|SSA_1017:SSA_1018:hypothetical protein:Zinc metalloprotease zmpC precursor, putative:->->:1023280..1023485 206 caaaataaatcacatttaaaaaaacagattttctaactgaagatttgttttttatttttttagtaaaaatgaacagtattttcaggctgttcaaaaacatgatgatttcagccttcaaagatatatttttaagcaaaagcattgaatttttgtaggaaattctgtaaaattttaagagattattatatgaagaaaagggaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1017:SSA_1018|SSA_1017:SSA_1018:hypothetical protein:Zinc metalloprotease zmpC precursor, putative:->->:1023280..1023485 206 caaaataaatcacatttaaaaaaacagattttctaactgaagatttgttttttatttttttagtaaaaatgaacagtattttcaggctgttcaaaaacatgatgatttcagccttcaaagatatatttttaagcaaaagcattgaatttttgtaggaaattctgtaaaattttaagagattattatatgaagaaaagggaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaaataaatcacatttaaaaaaacagattttctaactgaagatttgttttttatttttttagtaaaaatgaacagtattttcaggctgttcaaaaacatgatgatttcagccttcaaagatatatttttaagcaaaagcattgaatttttgtaggaaattctgtaaaattttaagagattattatatgaagaaaagggaattatt Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 9 End: 152 ........ M T F K K T D F L T E D L F F I F L V K M N S I F R L F K N M M I S A F K D I F L S K S I E F L ...................................................... Protein_Len: 60 Strand: - Start: 2 End: 205 . S K R V S S K N K I K K T F I F L I K L S N L F M I I E A K L S I N K L L L M S N K Y S I R Y F K L L N N Y S S F P I M . caaaataaatcacatttaaaaaaacagattttctaactgaagatttgttttttatttttttagtaaaaatgaacagtattttcaggctgttcaaaaacatgatgatttcagccttcaaagatatatttttaagcaaaagcattgaatttttgtaggaaattctgtaaaattttaagagattattatatgaagaaaagggaattatt 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: 84 Start: 141 End: 170 ............................................................................................................................................ATTGAATTTTTGTAGGAAATTCTGTAAAAT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caaaataaatcacatttaaaaaaacagattttctaactgaagatttgttttttatttttttagtaaaaatgaacagtattttcaggctgttcaaaaacatgatgatttcagccttcaaagatatatttttaagcaaaagcattgaatttttgtaggaaattctgtaaaattttaagagattattatatgaagaaaagggaattatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 56 HP_score: -2.5 Tail_Score: -4.72272 Start: 70 End: 93 Full_Region: aaatcatcatgtttt tgaacag cctgaaaata ctgttca tttttactaaaaaaa .....................................................................tgaacagcctgaaaatactgttca................................................................................................................. Find igs database================================================ Query_seq: SSA_1017:SSA_1018|SSA_1017:SSA_1018:hypothetical protein:Zinc metalloprotease zmpC precursor, putative:->->:1023280..1023485 206 caaaataaatcacatttaaaaaaacagattttctaactgaagatttgttttttatttttttagtaaaaatgaacagtattttcaggctgttcaaaaacatgatgatttcagccttcaaagatatatttttaagcaaaagcattgaatttttgtaggaaattctgtaaaattttaagagattattatatgaagaaaagggaattatt Intra-Species Hit: Count: 1 Min: 1 Max: 206 Len: 206 Subject: NC_009009_SSA_1017_SSA_1018|hypothetical protein:Zinc metalloprotease zmpC precursor, putative|POSITIVE:POSITIVE|[1023280,1023485]|206 HSP 1 e-value: 7.0E-77 bit: 287.0 Len: 145 Query Start:62 Query End:206 Subject Strand: POSITIVE Subject Start: 62 Subject End: 206 .............................................................agtaaaaatgaacagtattttcaggctgttcaaaaacatgatgatttcagccttcaaagatatatttttaagcaaaagcattgaatttttgtaggaaattctgtaaaattttaagagattattatatgaagaaaagggaattatt .............................................................agtaaaaatgaacagtattttcaggctgttcaaaaacatgatgatttcagccttcaaagatatatttttaagcaaaagcattgaatttttgtaggaaattctgtaaaattttaagagattattatatgaagaaaagggaattatt HSP 2 e-value: 7.0E-6 bit: 52.0 Len: 47 Query Start:1 Query End:47 Subject Strand: POSITIVE Subject Start: 1 Subject End: 47 caaaataaatcacatttnnnnnnncagattttctaactgaagatttg............................................................................................................................................................... caaaataaatcacatttaaaaaaacagattttctaactgaagatttg............................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAAUAAAUCACAUUUAAAAAAACAGAUUUUCUAACUGAAGAUUUGUUUUUUAUUUUUUUAGUAAAAAUGAACAGUAUUUUCAGGCUGUUCAAAAACAUGAUGAUUUCAGCCUUCAAAGAUAUAUUUUUAAGCAAAAGCAUUGAAUUUUUGUAGGAAAUUCUGUAAAAUUUUAAGAGAUUAUUAUAUGAAGAAAAGGGAAUUAUU ...(((((.((.......(((((((((((((((.....))))))))))))))).((((((((.......((((((((........)))))))).....(((((((((((.......................((....))..((((.(((((((((....))))))))).)))).))))))))))).))))))))...)).))))) (-43.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUUCCCUUUUCUUCAUAUAAUAAUCUCUUAAAAUUUUACAGAAUUUCCUACAAAAAUUCAAUGCUUUUGCUUAAAAAUAUAUCUUUGAAGGCUGAAAUCAUCAUGUUUUUGAACAGCCUGAAAAUACUGUUCAUUUUUACUAAAAAAAUAAAAAACAAAUCUUCAGUUAGAAAAUCUGUUUUUUUAAAUGUGAUUUAUUUUG ................((((((.........((((((....(((((.((((..((.....((((..((((((..................)))))))))).......(((((((((((((..(....)..)))))).(((((....)))))...)))))))........))..)))).)))))..))))))))))))......... (-28.27) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 89 41 223 174 NC_009009:SSA_0624|5end_hypothetical_protein_615079..615309_POSITIVE 247 121 83 106 64 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 244 117 71 59 8 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 239 117 82 211 168 NC_009009:SSA_2265|5end_Maltodextrin_phosphorylase,_putative_2264197..2264427_NEGATIVE 234 144 106 167 120 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 232 118 74 103 56 NC_009009:SSA_0726|5end_FmtA-like_protein,_putative_710905..711135_POSITIVE 230 110 68 227 174 NC_009009:SSA_0297|5end_Malolactic_enzyme,_putative_289706..289936_POSITIVE 227 119 78 53 15 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 221 188 142 183 137 NC_009009:SSA_0028|5end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_31883..32113_POSITIVE 217 116 73 210 164 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 213 114 83 197 161 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 212 116 74 224 185 NC_009009:SSA_1698|5end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690648..1690878_NEGATIVE 212 117 77 141 102 NC_009009:SSA_0675|5end_Exodeoxyribonuclease_VII_small_subunit,_putative_658389..658619_POSITIVE 209 120 72 109 53 NC_009009:SSA_0571|5end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B,_putative_565381..565611_POSITIVE 208 125 84 92 53 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 208 200 151 225 177 NC_009009:SSA_1970|5end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1966915..1967145_NEGATIVE 208 116 76 213 170 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 204 120 74 161 110 NC_009009:SSA_0605|5end_Methyltransferase_gidB,_putative_593707..593937_NEGATIVE 202 114 74 209 162 NC_009009:SSA_2154|5end_Conserved_uncharacterized_protein_2155259..2155489_NEGATIVE 202 115 78 100 57 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 89 41 144 95 NC_009009:SSA_0623|3end_hypothetical_protein_615080..615230_POSITIVE 252 116 83 90 62 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 244 117 71 66 15 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 241 125 84 52 16 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 234 144 106 142 95 NC_009009:SSA_1721|3end_DNA_polymerase_III,_delta'_subunit,_putative_1707138..1707288_NEGATIVE 226 120 73 106 62 NC_009009:SSA_2005|3end_Chaperone_protein_dnaJ,_putative_2005251..2005401_NEGATIVE 222 125 84 147 104 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE 213 53 19 72 38 NC_009009:SSA_1017|3end_hypothetical_protein_1023219..1023369_POSITIVE 212 130 81 115 76 NC_009009:SSA_2059|3end_16S_rRNA_uridine-516_pseudouridylate_synthase,_putative_2060494..2060644_NEGATIVE 209 120 72 109 53 NC_009009:SSA_0570|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_565461..565611_POSITIVE 208 115 75 140 93 NC_009009:SSA_1487|3end_Conserved_uncharacterized_protein_1493483..1493633_NEGATIVE 204 120 74 79 28 NC_009009:SSA_0606|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_593789..593939_NEGATIVE 202 114 74 61 14 NC_009009:SSA_2155|3end_hypothetical_protein_2155407..2155557_NEGATIVE 201 114 84 86 58 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE 196 120 85 149 120 NC_009009:SSA_2073|3end_Undecaprenyl_pyrophosphate_synthetase,_putative_2075622..2075772_NEGATIVE 194 154 111 68 8 NC_009009:SSA_2066|3end_DNA_polymerase_III_polC-type,_putative_2065749..2065899_NEGATIVE 193 166 134 66 31 NC_009009:SSA_2085|3end_Glyoxylate_reductase,_NADH-dependent,_putative_2089448..2089598_NEGATIVE 193 127 85 77 28 NC_009009:SSA_2046|3end_Uridine_phosphorylase,_putative_2048957..2049107_NEGATIVE 192 115 74 146 105 NC_009009:SSA_2283|3end_Conserved_uncharacterized_protein_2285537..2285687_NEGATIVE 192 118 82 69 31 NC_009009:SSA_1066|3end_ABC-type_oligopeptide_transport_system,_putative_1086376..1086526_POSITIVE