Origin IGS: tgtaagacctttcgcggtaatttctaacaatttattataacagaaaatggatagaatgaggcagattgttttttaccagaatttttggcgtaaattgtcattggcgtgtcagaatctgtcattttcttgtcggattctgtatcgtataatagtctcatcaatcaaatgaaacaaaagaggaa .........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 ttcctcttttgtttcatttgattgatgagactattatacgatacagaatccgacaagaaaatgacagattctgacacgccaatgacaatttacgccaaaaattctggtaaaaaacaatctgcctcattctatccattttctgttataataaattgttagaaattaccgcgaaaggtcttaca Mask Tandem Repeat Region ================================================ tgtaagacctttcgcggtaatttctaacaatttattataacagaaaatggatagaatgaggcagattgttttttaccagaatttttggcgtaaattgtcattggcgtgtcagaatctgtcattttcttgtcggattctgtatcgtataatagtctcatcaatcaaatgaaacaaaagaggaa Find is-nt database================================================ Query_seq: SSA_0290:SSA_0291|SSA_0290:SSA_0291:hypothetical protein:Oxidoreductase, putative:<-->:285320..285501 182 tgtaagacctttcgcggtaatttctaacaatttattataacagaaaatggatagaatgaggcagattgttttttaccagaatttttggcgtaaattgtcattggcgtgtcagaatctgtcattttcttgtcggattctgtatcgtataatagtctcatcaatcaaatgaaacaaaagaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0290:SSA_0291|SSA_0290:SSA_0291:hypothetical protein:Oxidoreductase, putative:<-->:285320..285501 182 tgtaagacctttcgcggtaatttctaacaatttattataacagaaaatggatagaatgaggcagattgttttttaccagaatttttggcgtaaattgtcattggcgtgtcagaatctgtcattttcttgtcggattctgtatcgtataatagtctcatcaatcaaatgaaacaaaagaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0290:SSA_0291|SSA_0290:SSA_0291:hypothetical protein:Oxidoreductase, putative:<-->:285320..285501 182 tgtaagacctttcgcggtaatttctaacaatttattataacagaaaatggatagaatgaggcagattgttttttaccagaatttttggcgtaaattgtcattggcgtgtcagaatctgtcattttcttgtcggattctgtatcgtataatagtctcatcaatcaaatgaaacaaaagaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtaagacctttcgcggtaatttctaacaatttattataacagaaaatggatagaatgaggcagattgttttttaccagaatttttggcgtaaattgtcattggcgtgtcagaatctgtcattttcttgtcggattctgtatcgtataatagtctcatcaatcaaatgaaacaaaagaggaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 47 End: 166 .............................................. M D R M R Q I V F Y Q N F W R K L S L A C Q N L S F S C R I L Y R I I V S S I K ................ Protein_Len: 45 Strand: - Start: 27 End: 161 .......................... C N I I V S F P Y F S A S Q K K G S N K A Y I T M P T D S D T M K K D S E T D Y L L R M M ..................... tgtaagacctttcgcggtaatttctaacaatttattataacagaaaatggatagaatgaggcagattgttttttaccagaatttttggcgtaaattgtcattggcgtgtcagaatctgtcattttcttgtcggattctgtatcgtataatagtctcatcaatcaaatgaaacaaaagaggaa 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: 121 End: 150 ........................................................................................................................ATTTTCTTGTCGGATTCTGTATCGTATAAT................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtaagacctttcgcggtaatttctaacaatttattataacagaaaatggatagaatgaggcagattgttttttaccagaatttttggcgtaaattgtcattggcgtgtcagaatctgtcattttcttgtcggattctgtatcgtataatagtctcatcaatcaaatgaaacaaaagaggaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -4.2 Tail_Score: -4.78839 Start: 107 End: 121 Full_Region: AAATTGTCATTGGCG TGTCAG AAT CTGTCA TTTTCTTGTCGGATT ..........................................................................................................TGTCAGAATCTGTCA............................................................. TransTerm Strand: + Conf: 62 HP_score: -7.2 Tail_Score: -2.87944 Start: 110 End: 139 Full_Region: TTGTCATTGGCGTGT CAGAATCTGTCA TTTTCT TGTCGGATTCTG TATCGTATAATAGTC .............................................................................................................CAGAATCTGTCATTTTCTTGTCGGATTCTG........................................... TransTerm Strand: + Conf: 47 HP_score: -4.0 Tail_Score: -2.98719 Start: 112 End: 137 Full_Region: GTCATTGGCGTGTCA GAATCTGTCA TTTTCT TGTCGGATTC TGTATCGTATAATAG ...............................................................................................................GAATCTGTCATTTTCTTGTCGGATTC............................................. Find igs database================================================ Query_seq: SSA_0290:SSA_0291|SSA_0290:SSA_0291:hypothetical protein:Oxidoreductase, putative:<-->:285320..285501 182 tgtaagacctttcgcggtaatttctaacaatttattataacagaaaatggatagaatgaggcagattgttttttaccagaatttttggcgtaaattgtcattggcgtgtcagaatctgtcattttcttgtcggattctgtatcgtataatagtctcatcaatcaaatgaaacaaaagaggaa Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: NC_009009_SSA_0290_SSA_0291|hypothetical protein:Oxidoreductase, putative|NEGATIVE:POSITIVE|[285320,285501]|182 HSP 1 e-value: 5.0E-99 bit: 361.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 tgtaagacctttcgcggtaatttctaacaatttattataacagaaaatggatagaatgaggcagattgttttttaccagaatttttggcgtaaattgtcattggcgtgtcagaatctgtcattttcttgtcggattctgtatcgtataatagtctcatcaatcaaatgaaacaaaagaggaa tgtaagacctttcgcggtaatttctaacaatttattataacagaaaatggatagaatgaggcagattgttttttaccagaatttttggcgtaaattgtcattggcgtgtcagaatctgtcattttcttgtcggattctgtatcgtataatagtctcatcaatcaaatgaaacaaaagaggaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAAGACCUUUCGCGGUAAUUUCUAACAAUUUAUUAUAACAGAAAAUGGAUAGAAUGAGGCAGAUUGUUUUUUACCAGAAUUUUUGGCGUAAAUUGUCAUUGGCGUGUCAGAAUCUGUCAUUUUCUUGUCGGAUUCUGUAUCGUAUAAUAGUCUCAUCAAUCAAAUGAAACAAAAGAGGAA .......(((((....((..(((((................)))))...(((.((.((((((.(((.((((....(((((...)))))...)))).)))....(((...(((((((((.((......)).)))))))))...)))......)))))))).))).......))...))))).. (-39.89) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUCUUUUGUUUCAUUUGAUUGAUGAGACUAUUAUACGAUACAGAAUCCGACAAGAAAAUGACAGAUUCUGACACGCCAAUGACAAUUUACGCCAAAAAUUCUGGUAAAAAACAAUCUGCCUCAUUCUAUCCAUUUUCUGUUAUAAUAAAUUGUUAGAAAUUACCGCGAAAGGUCUUACA ..(((.....((((((((.....))))))))............(((((((.(.((......)).).)))))))...(((...((((((((((.((((.......))))....((((........................))))....)))))))))).........)))..)))....... (-27.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 851 140 91 231 182 NC_009009:SSA_0290|5end_hypothetical_protein_285229..285459_NEGATIVE 337 50 3 140 94 NC_009009:SSA_0230|5end_hypothetical_protein_224957..225187_NEGATIVE 290 120 75 218 166 NC_009009:SSA_2093|5end_PTS_system,_membrane_component,_putative_2097462..2097692_NEGATIVE 281 140 95 167 115 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 280 123 86 181 140 NC_009009:SSA_0949|5end_hypothetical_protein_955707..955937_POSITIVE 275 138 92 62 7 NC_009009:SSA_1056|5end_Firmicute_fructose-1,6-bisphosphatase,_putative_1071760..1071990_POSITIVE 275 139 104 162 122 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 273 120 78 153 110 NC_009009:SSA_0471|5end_CbiG_protein,_putative_473600..473830_POSITIVE 271 118 76 210 159 NC_009009:SSA_1558|5end_Hydrolase,_HAD_superfamily_1560862..1561092_NEGATIVE 270 124 95 38 10 NC_009009:SSA_1072|5end_Glutamate_5-kinase,_putative_1089755..1089985_POSITIVE 267 105 64 224 191 NC_009009:SSA_1430|5end_Ribonuclease_Z,_putative_1438036..1438266_NEGATIVE 264 129 85 198 156 NC_009009:SSA_0112|5end_50S_ribosomal_protein_L22,_putative_110965..111195_POSITIVE 261 127 83 71 26 NC_009009:SSA_1685|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1679076..1679306_NEGATIVE 261 129 81 92 33 NC_009009:SSA_1509|5end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1514191..1514421_NEGATIVE 261 113 71 162 115 NC_009009:SSA_1451|5end_Exonuclease_RexA,_putative_1456418..1456648_NEGATIVE 261 139 102 207 170 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 254 125 83 180 137 NC_009009:SSA_1707|5end_Conserved_uncharacterized_protein_1697782..1698012_POSITIVE 252 159 117 49 3 NC_009009:SSA_2258|5end_hypothetical_protein_2254699..2254929_NEGATIVE 252 107 61 194 146 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 250 154 115 208 149 NC_009009:SSA_1924|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1913248..1913478_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 105 66 43 4 NC_009009:SSA_0357|3end_Thioredoxin,_putative_351157..351307_POSITIVE 261 129 81 95 36 NC_009009:SSA_1510|3end_Rhamnosyltransferase,_putative_1514188..1514338_NEGATIVE 261 139 102 151 114 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 256 107 62 140 83 NC_009009:SSA_0779|3end_Glycogen_phosphorylase,_putative_764685..764835_POSITIVE 250 133 105 145 115 NC_009009:SSA_0926|3end_Histone_acetyltransferase_HPA2,_putative_935961..936111_POSITIVE 248 69 21 150 109 NC_009009:SSA_0075|3end_ABC_sugar_transporter,_permease_protein,_putative_79927..80077_POSITIVE 247 90 48 47 7 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 246 109 66 127 84 NC_009009:SSA_0917|3end_Cobalamin-independent_methionine_synthase_II,_putative_929087..929237_NEGATIVE 245 145 101 131 91 NC_009009:SSA_1679|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1672183..1672333_NEGATIVE 245 140 104 59 26 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 240 157 111 134 94 NC_009009:SSA_0793|3end_DNA-entry_nuclease,_putative_775799..775949_POSITIVE 238 144 102 124 80 NC_009009:SSA_0219|3end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215884..216034_POSITIVE 233 130 81 106 35 NC_009009:SSA_1597|3end_hypothetical_protein_1603267..1603417_NEGATIVE 232 157 111 150 95 NC_009009:SSA_0857|3end_hypothetical_protein_845482..845632_POSITIVE 231 138 95 110 65 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 230 130 84 54 7 NC_009009:SSA_1707|3end_Conserved_uncharacterized_protein_1698248..1698398_POSITIVE 229 100 53 80 33 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 228 156 112 78 22 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 228 139 97 46 2 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 228 130 81 69 7 NC_009009:SSA_1380|3end_hypothetical_protein_1398538..1398688_NEGATIVE