Origin IGS: tttacacctcgcattcttttgctgcctctagtttaccataattattattccttttacacttttaacatttttttataccagatatattgttttattttctaatcacttaatgattaacaaatcccat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atgggatttgttaatcattaagtgattagaaaataaaacaatatatctggtataaaaaaatgttaaaagtgtaaaaggaataataattatggtaaactagaggcagcaaaagaatgcgaggtgtaaa Mask Tandem Repeat Region ================================================ tttacacctcgcattcttttgctgcctctagtttaccataattattattccttttacacttttaacatttttttataccagatatattgttttattttctaatcacttaatgattaacaaatcccat Find is-nt database================================================ Query_seq: SSA_1296:SSA_1297|SSA_1296:SSA_1297:hypothetical protein:Nuclease subunit of the excinuclease complex, subunit C, putative:<-<-:1313104..1313230 127 tttacacctcgcattcttttgctgcctctagtttaccataattattattccttttacacttttaacatttttttataccagatatattgttttattttctaatcacttaatgattaacaaatcccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1296:SSA_1297|SSA_1296:SSA_1297:hypothetical protein:Nuclease subunit of the excinuclease complex, subunit C, putative:<-<-:1313104..1313230 127 tttacacctcgcattcttttgctgcctctagtttaccataattattattccttttacacttttaacatttttttataccagatatattgttttattttctaatcacttaatgattaacaaatcccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1296:SSA_1297|SSA_1296:SSA_1297:hypothetical protein:Nuclease subunit of the excinuclease complex, subunit C, putative:<-<-:1313104..1313230 127 tttacacctcgcattcttttgctgcctctagtttaccataattattattccttttacacttttaacatttttttataccagatatattgttttattttctaatcacttaatgattaacaaatcccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttacacctcgcattcttttgctgcctctagtttaccataattattattccttttacacttttaacatttttttataccagatatattgttttattttctaatcacttaatgattaacaaatcccat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 38 End: 127 ..................................... M I I I P F T L L T F F Y T R Y I V L F S N H L M I N K S H tttacacctcgcattcttttgctgcctctagtttaccataattattattccttttacacttttaacatttttttataccagatatattgttttattttctaatcacttaatgattaacaaatcccat 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: 31 End: 60 ..............................GTTTACCATAATTATTATTCCTTTTACACT................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttacacctcgcattcttttgctgcctctagtttaccataattattattccttttacacttttaacatttttttataccagatatattgttttattttctaatcacttaatgattaacaaatcccat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1296:SSA_1297|SSA_1296:SSA_1297:hypothetical protein:Nuclease subunit of the excinuclease complex, subunit C, putative:<-<-:1313104..1313230 127 tttacacctcgcattcttttgctgcctctagtttaccataattattattccttttacacttttaacatttttttataccagatatattgttttattttctaatcacttaatgattaacaaatcccat Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: NC_009009_SSA_1296_SSA_1297|hypothetical protein:Nuclease subunit of the excinuclease complex, subunit C, putative|NEGATIVE:NEGATIVE|[1313104,1313230]|127 HSP 1 e-value: 8.0E-54 bit: 210.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 tttacacctcgcattcttttgctgcctctagtttaccataattattattccttttacacttttaacannnnnnnataccagatatattgttttattttctaatcacttaatgattaacaaatcccat tttacacctcgcattcttttgctgcctctagtttaccataattattattccttttacacttttaacatttttttataccagatatattgttttattttctaatcacttaatgattaacaaatcccat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACACCUCGCAUUCUUUUGCUGCCUCUAGUUUACCAUAAUUAUUAUUCCUUUUACACUUUUAACAUUUUUUUAUACCAGAUAUAUUGUUUUAUUUUCUAAUCACUUAAUGAUUAACAAAUCCCAU ..........(((......)))................(((((((((.............(..((((.....((......)).....))))..).............)))))))))........... ( -6.67) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGGGAUUUGUUAAUCAUUAAGUGAUUAGAAAAUAAAACAAUAUAUCUGGUAUAAAAAAAUGUUAAAAGUGUAAAAGGAAUAAUAAUUAUGGUAAACUAGAGGCAGCAAAAGAAUGCGAGGUGUAAA .((..((((.((((((((...)))))))).))))....)).(((((((.((((.......((((...(((.((.....(((....)))....)).)))...))))........)))).))))))).. (-17.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 809 50 1 141 92 NC_009009:SSA_1296|5end_hypothetical_protein_1313013..1313243_NEGATIVE 274 47 9 179 139 NC_009009:SSA_2194|5end_Nicotinamide_mononucleotide_transporter,_putative_2195663..2195893_NEGATIVE 257 51 11 222 176 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 253 44 7 217 184 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 251 33 8 152 123 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 250 38 5 126 99 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 236 39 4 110 69 NC_009009:SSA_0254|5end_hypothetical_protein_247492..247722_NEGATIVE 233 34 2 42 13 NC_009009:SSA_0677|5end_rRNA_methylase,_putative_659466..659696_POSITIVE 231 62 22 112 71 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 230 56 13 129 97 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 227 48 4 63 12 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 227 41 8 132 98 NC_009009:SSA_1787|5end_Diaminopimelate_decarboxylase,_putative_1771551..1771781_NEGATIVE 225 48 1 143 87 NC_009009:SSA_1984|5end_Cell_surface_SD_repeat_antigen_precursor,_putative_1979035..1979265_NEGATIVE 223 53 16 52 7 NC_009009:SSA_1676|5end_Transcriptional_regulator,_LytTr_family,_putative_1671313..1671543_NEGATIVE 222 50 5 105 49 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 222 30 5 118 89 NC_009009:SSA_0678|5end_Transcriptional_regulator,_ArgR_family,_putative_660274..660504_POSITIVE 222 50 7 68 22 NC_009009:SSA_0395|5end_6-phospho-beta-glucosidase,_putative_391061..391291_POSITIVE 221 32 1 111 78 NC_009009:SSA_1035|5end_Pyrimidine_nucleoside_phosphorylase,_putative_1050174..1050404_POSITIVE 220 38 6 145 115 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 219 40 4 179 144 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 38 5 130 99 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 251 33 8 96 67 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 250 38 5 136 109 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 241 56 11 42 1 NC_009009:SSA_0563|3end_Universal_stress_protein_family,_putative_554947..555097_NEGATIVE 236 39 4 117 76 NC_009009:SSA_0255|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_247485..247635_NEGATIVE 233 34 2 49 20 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 230 56 13 104 72 NC_009009:SSA_1721|3end_DNA_polymerase_III,_delta'_subunit,_putative_1707138..1707288_NEGATIVE 225 38 9 146 117 NC_009009:SSA_2195|3end_ATPase/kinase,_putative_2195685..2195835_NEGATIVE 225 38 5 151 102 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 222 50 5 133 77 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 222 30 5 125 96 NC_009009:SSA_0677|3end_rRNA_methylase,_putative_660361..660511_POSITIVE 221 32 1 109 76 NC_009009:SSA_1034|3end_Conserved_uncharacterized_protein_1050252..1050402_POSITIVE 216 38 5 149 102 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 215 38 1 136 100 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 214 110 68 101 64 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 213 25 7 140 122 NC_009009:SSA_2206|3end_hypothetical_protein_2207275..2207425_POSITIVE 207 50 10 103 54 NC_009009:SSA_0706|3end_RNA_helicase,_putative_692909..693059_POSITIVE 206 38 7 39 8 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 204 38 7 139 105 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE 204 38 5 134 97 NC_009009:SSA_0535|3end_Propanediol_utilization:_dehydratase,_medium_subunit,_putative_531391..531541_POSITIVE