Origin IGS: gagcaatctagtctagacaggctagattttttgatagctatttagaaaaaaaccaaaatacctcttgcttttttgaaagagaagtgttacaatctatttagaagatgttctaattacttcattctgctctgtttaattagtcactgagcaattttttataaaagctatttagaaaaaattctaaatttctctactcaaaaaggaggaaaa .........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 ttttcctcctttttgagtagagaaatttagaattttttctaaatagcttttataaaaaattgctcagtgactaattaaacagagcagaatgaagtaattagaacatcttctaaatagattgtaacacttctctttcaaaaaagcaagaggtattttggtttttttctaaatagctatcaaaaaatctagcctgtctagactagattgctc Mask Tandem Repeat Region ================================================ gagcaatctagtctagacaggctagattttttgatagctatttagaaaaaaaccaaaatacctcttgcttttttgaaagagaagtgttacaatctatttagaagatgttctaattacttcattctgctctgtttaattagtcactgagcaattttttataaaagctatttagaaaaaattctaaatttctctactcaaaaaggaggaaaa Find is-nt database================================================ Query_seq: SSA_0722:SSA_0723|SSA_0722:SSA_0723:hypothetical protein:hypothetical protein:->->:708176..708385 210 gagcaatctagtctagacaggctagattttttgatagctatttagaaaaaaaccaaaatacctcttgcttttttgaaagagaagtgttacaatctatttagaagatgttctaattacttcattctgctctgtttaattagtcactgagcaattttttataaaagctatttagaaaaaattctaaatttctctactcaaaaaggaggaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0722:SSA_0723|SSA_0722:SSA_0723:hypothetical protein:hypothetical protein:->->:708176..708385 210 gagcaatctagtctagacaggctagattttttgatagctatttagaaaaaaaccaaaatacctcttgcttttttgaaagagaagtgttacaatctatttagaagatgttctaattacttcattctgctctgtttaattagtcactgagcaattttttataaaagctatttagaaaaaattctaaatttctctactcaaaaaggaggaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0722:SSA_0723|SSA_0722:SSA_0723:hypothetical protein:hypothetical protein:->->:708176..708385 210 gagcaatctagtctagacaggctagattttttgatagctatttagaaaaaaaccaaaatacctcttgcttttttgaaagagaagtgttacaatctatttagaagatgttctaattacttcattctgctctgtttaattagtcactgagcaattttttataaaagctatttagaaaaaattctaaatttctctactcaaaaaggaggaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagcaatctagtctagacaggctagattttttgatagctatttagaaaaaaaccaaaatacctcttgcttttttgaaagagaagtgttacaatctatttagaagatgttctaattacttcattctgctctgtttaattagtcactgagcaattttttataaaagctatttagaaaaaattctaaatttctctactcaaaaaggaggaaaa Predict ORF larger than 30AA ================================================ gagcaatctagtctagacaggctagattttttgatagctatttagaaaaaaaccaaaatacctcttgcttttttgaaagagaagtgttacaatctatttagaagatgttctaattacttcattctgctctgtttaattagtcactgagcaattttttataaaagctatttagaaaaaattctaaatttctctactcaaaaaggaggaaaa 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: 64 End: 93 ...............................................................CTTGCTTTTTTGAAAGAGAAGTGTTACAAT..................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gagcaatctagtctagacaggctagattttttgatagctatttagaaaaaaaccaaaatacctcttgcttttttgaaagagaagtgttacaatctatttagaagatgttctaattacttcattctgctctgtttaattagtcactgagcaattttttataaaagctatttagaaaaaattctaaatttctctactcaaaaaggaggaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -2.5 Tail_Score: -3.51118 Start: 152 End: 178 Full_Region: TTAGTCACTGAGCAA TTTTTTATAAA AGCTA TTTAGAAAAAA TTCTAAATTTCTCTA .......................................................................................................................................................TTTTTTATAAAAGCTATTTAGAAAAAA................................ Find igs database================================================ Query_seq: SSA_0722:SSA_0723|SSA_0722:SSA_0723:hypothetical protein:hypothetical protein:->->:708176..708385 210 gagcaatctagtctagacaggctagattttttgatagctatttagaaaaaaaccaaaatacctcttgcttttttgaaagagaagtgttacaatctatttagaagatgttctaattacttcattctgctctgtttaattagtcactgagcaattttttataaaagctatttagaaaaaattctaaatttctctactcaaaaaggaggaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 210 Len: 210 Subject: NC_009009_SSA_0722_SSA_0723|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[708176,708385]|210 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 210 Query Start:1 Query End:210 Subject Strand: POSITIVE Subject Start: 1 Subject End: 210 gagcaatctagtctagacaggctagattttttgatagctatttagnnnnnnnccaaaatacctcttgcttttttgaaagagaagtgttacaatctatttagaagatgttctaattacttcattctgctctgtttaattagtcactgagcaattttttataaaagctatttagaaaaaattctaaatttctctactcaaaaaggaggaaaa gagcaatctagtctagacaggctagattttttgatagctatttagaaaaaaaccaaaatacctcttgcttttttgaaagagaagtgttacaatctatttagaagatgttctaattacttcattctgctctgtttaattagtcactgagcaattttttataaaagctatttagaaaaaattctaaatttctctactcaaaaaggaggaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGCAAUCUAGUCUAGACAGGCUAGAUUUUUUGAUAGCUAUUUAGAAAAAAACCAAAAUACCUCUUGCUUUUUUGAAAGAGAAGUGUUACAAUCUAUUUAGAAGAUGUUCUAAUUACUUCAUUCUGCUCUGUUUAAUUAGUCACUGAGCAAUUUUUUAUAAAAGCUAUUUAGAAAAAAUUCUAAAUUUCUCUACUCAAAAAGGAGGAAAA .(((((((((((((....))))))))))........))).....................((((((((((((.((((((((((((((((..((((.......))))....))).))))))....(((((.((..........)).))))).))))))).)))))).((((((((....))))))))..............)))))).... (-44.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCCUCCUUUUUGAGUAGAGAAAUUUAGAAUUUUUUCUAAAUAGCUUUUAUAAAAAAUUGCUCAGUGACUAAUUAAACAGAGCAGAAUGAAGUAAUUAGAACAUCUUCUAAAUAGAUUGUAACACUUCUCUUUCAAAAAAGCAAGAGGUAUUUUGGUUUUUUUCUAAAUAGCUAUCAAAAAAUCUAGCCUGUCUAGACUAGAUUGCUC .........((((((((.((((((((((((((....)))))))).....((((((....((((((.((..........)).))))))..........((((((....)))))).....))))))...)))))))))))))).((...((.(((((.((......)).))))).)).......(((((((.((....)).))))))))).. (-40.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 48 1 88 39 NC_009009:SSA_0701|5end_Cation_transporter_CorA_family,_putative_684368..684598_POSITIVE 254 46 5 171 115 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 252 149 103 57 6 NC_009009:SSA_0678|5end_Transcriptional_regulator,_ArgR_family,_putative_660274..660504_POSITIVE 250 166 121 230 169 NC_009009:SSA_1745|5end_General_stress_response_protein_CsbD,_putative_1732191..1732421_NEGATIVE 247 149 101 56 4 NC_009009:SSA_2328|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_2331483..2331713_POSITIVE 246 160 112 196 148 NC_009009:SSA_0909|5end_Transcriptional_regulator,_AbrB_family_(stationary/sporulation_gene_expression),_putative_920887..921117_POSITIVE 242 150 103 107 59 NC_009009:SSA_0920|5end_hypothetical_protein_930896..931126_POSITIVE 241 150 103 103 41 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 240 39 6 226 190 NC_009009:SSA_0422|5end_Phosphoglycerate_mutase_family_protein,_putative_420157..420387_POSITIVE 238 44 11 94 51 NC_009009:SSA_0205|5end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_202722..202952_POSITIVE 236 49 3 231 172 NC_009009:SSA_0713|5end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_699208..699438_POSITIVE 234 170 126 129 93 NC_009009:SSA_1239|5end_hypothetical_protein_1264689..1264919_NEGATIVE 234 137 92 82 44 NC_009009:SSA_1190|5end_Conserved_uncharacterized_protein_1218137..1218367_NEGATIVE 234 157 118 81 37 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 232 68 21 201 153 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 231 39 2 81 33 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 228 109 61 144 98 NC_009009:SSA_0814|5end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_796835..797065_NEGATIVE 227 150 111 122 76 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 226 110 61 82 28 NC_009009:SSA_2294|5end_hypothetical_protein_2296082..2296312_POSITIVE 226 149 101 207 157 NC_009009:SSA_1822|5end_hypothetical_protein_1811125..1811355_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 46 5 116 60 NC_009009:SSA_0354|3end_Uncharacterized_membrane_protein_346872..347022_POSITIVE 252 149 103 64 13 NC_009009:SSA_0677|3end_rRNA_methylase,_putative_660361..660511_POSITIVE 250 166 121 129 68 NC_009009:SSA_1746|3end_hypothetical_protein_1732292..1732442_NEGATIVE 242 148 103 151 93 NC_009009:SSA_2360|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2362658..2362808_NEGATIVE 242 150 103 76 28 NC_009009:SSA_0918|3end_Conserved_uncharacterized_protein_930945..931095_POSITIVE 238 80 36 90 52 NC_009009:SSA_1504|3end_hypothetical_protein_1506459..1506609_NEGATIVE 238 44 11 127 84 NC_009009:SSA_0204|3end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202835..202985_POSITIVE 232 68 21 145 97 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 227 150 111 110 64 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 225 134 94 83 35 NC_009009:SSA_0653|3end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_637540..637690_POSITIVE 224 44 1 66 19 NC_009009:SSA_0434|3end_Glutamate_formiminotransferase,_putative_435669..435819_NEGATIVE 222 149 102 125 75 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 216 152 114 123 91 NC_009009:SSA_1005|3end_Sugar_ABC_transporter,_permease_protein,_putative_1006941..1007091_POSITIVE 215 140 97 146 100 NC_009009:SSA_2348|3end_Metal_dependent_hydrolase,_putative_2349875..2350025_NEGATIVE 214 34 1 53 21 NC_009009:SSA_0882|3end_Phosphoserine_phosphatase,_putative_877630..877780_POSITIVE 212 39 2 117 86 NC_009009:SSA_1782|3end_hypothetical_protein_1767602..1767752_NEGATIVE 211 151 122 40 3 NC_009009:SSA_1575|3end_Glycosyl_transferase,_putative_1577932..1578082_NEGATIVE 208 150 107 101 54 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 207 190 144 52 3 NC_009009:SSA_0729|3end_hypothetical_protein_714677..714827_POSITIVE 207 165 125 148 101 NC_009009:SSA_0078|3end_N-acetylneuraminate_lyase,_putative_82901..83051_POSITIVE