Origin IGS: atcacacctcctatgtaacgttttaaaagttacacacagtataccagatgaaatcgagaaaagcaagttctttattgaatattgttatttccagcaagagtgtggtaaactgtaggaaggaatataatcaggaggtagagag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctctctacctcctgattatattccttcctacagtttaccacactcttgctggaaataacaatattcaataaagaacttgcttttctcgatttcatctggtatactgtgtgtaacttttaaaacgttacataggaggtgtgat Mask Tandem Repeat Region ================================================ atcacacctcctatgtaacgttttaaaagttacacacagtataccagatgaaatcgagaaaagcaagttctttattgaatattgttatttccagcaagagtgtggtaaactgtaggaaggaatataatcaggaggtagagag Find is-nt database================================================ Query_seq: SSA_0622:SSA_0623|SSA_0622:SSA_0623:Transcriptional regulator (XRE family), SOS-response transcriptional repressors (RecA-mediated autopeptidases), putative:hypothetical protein:<-->:614510..614651 142 atcacacctcctatgtaacgttttaaaagttacacacagtataccagatgaaatcgagaaaagcaagttctttattgaatattgttatttccagcaagagtgtggtaaactgtaggaaggaatataatcaggaggtagagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0622:SSA_0623|SSA_0622:SSA_0623:Transcriptional regulator (XRE family), SOS-response transcriptional repressors (RecA-mediated autopeptidases), putative:hypothetical protein:<-->:614510..614651 142 atcacacctcctatgtaacgttttaaaagttacacacagtataccagatgaaatcgagaaaagcaagttctttattgaatattgttatttccagcaagagtgtggtaaactgtaggaaggaatataatcaggaggtagagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0622:SSA_0623|SSA_0622:SSA_0623:Transcriptional regulator (XRE family), SOS-response transcriptional repressors (RecA-mediated autopeptidases), putative:hypothetical protein:<-->:614510..614651 142 atcacacctcctatgtaacgttttaaaagttacacacagtataccagatgaaatcgagaaaagcaagttctttattgaatattgttatttccagcaagagtgtggtaaactgtaggaaggaatataatcaggaggtagagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcacacctcctatgtaacgttttaaaagttacacacagtataccagatgaaatcgagaaaagcaagttctttattgaatattgttatttccagcaagagtgtggtaaactgtaggaaggaatataatcaggaggtagagag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 48 End: 140 ............................................... M K S R K A S S L L N I V I S S K S V V N C R K E Y N Q E V E .. atcacacctcctatgtaacgttttaaaagttacacacagtataccagatgaaatcgagaaaagcaagttctttattgaatattgttatttccagcaagagtgtggtaaactgtaggaaggaatataatcaggaggtagagag 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: 38 End: 67 .....................................CTTGCTTTTCTCGATTTCATCTGGTATACT........................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcacacctcctatgtaacgttttaaaagttacacacagtataccagatgaaatcgagaaaagcaagttctttattgaatattgttatttccagcaagagtgtggtaaactgtaggaaggaatataatcaggaggtagagag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0622:SSA_0623|SSA_0622:SSA_0623:Transcriptional regulator (XRE family), SOS-response transcriptional repressors (RecA-mediated autopeptidases), putative:hypothetical protein:<-->:614510..614651 142 atcacacctcctatgtaacgttttaaaagttacacacagtataccagatgaaatcgagaaaagcaagttctttattgaatattgttatttccagcaagagtgtggtaaactgtaggaaggaatataatcaggaggtagagag Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_009009_SSA_0622_SSA_0623|Transcriptional regulator (XRE family), SOS-response transcriptional repressors (RecA-mediated autopeptidases), putative:hypothetical protein|NEGATIVE:POSITIVE|[614510,614651]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 atcacacctcctatgtaacgttttaaaagttacacacagtataccagatgaaatcgagaaaagcaagttctttattgaatattgttatttccagcaagagtgtggtaaactgtaggaaggaatataatcaggaggtagagag atcacacctcctatgtaacgttttaaaagttacacacagtataccagatgaaatcgagaaaagcaagttctttattgaatattgttatttccagcaagagtgtggtaaactgtaggaaggaatataatcaggaggtagagag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCACACCUCCUAUGUAACGUUUUAAAAGUUACACACAGUAUACCAGAUGAAAUCGAGAAAAGCAAGUUCUUUAUUGAAUAUUGUUAUUUCCAGCAAGAGUGUGGUAAACUGUAGGAAGGAAUAUAAUCAGGAGGUAGAGAG .((.((((((((.((((((.........)))))).(((((.(((((.((.....(..(((((((((((((......)))).))))).))))..).....)).))))).)))))................))))))).).)). (-37.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUCUACCUCCUGAUUAUAUUCCUUCCUACAGUUUACCACACUCUUGCUGGAAAUAACAAUAUUCAAUAAAGAACUUGCUUUUCUCGAUUUCAUCUGGUAUACUGUGUGUAACUUUUAAAACGUUACAUAGGAGGUGUGAU ...(((((((((((..............((((((.(((((........(.(((((...(((..(((......))).)))..))))).)........))))).)))))).(((((.........))))).))))))))).)). (-33.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 922 140 91 231 182 NC_009009:SSA_0622|5end_Transcriptional_regulator_(XRE_family),_SOS-response_transcriptional_repressors_(RecA-mediated_autopeptidases),_putative_614419..614649_NEGATIVE 283 64 28 53 20 NC_009009:SSA_0696|5end_hypothetical_protein_679154..679384_POSITIVE 274 138 91 56 6 NC_009009:SSA_1764|5end_hypothetical_protein_1750868..1751098_POSITIVE 270 119 74 49 7 NC_009009:SSA_0720|5end_hypothetical_protein_705106..705336_POSITIVE 258 120 79 147 103 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 246 137 91 90 46 NC_009009:SSA_1957|5end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1954670..1954900_NEGATIVE 243 132 91 144 103 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 243 140 92 81 28 NC_009009:SSA_0203|5end_hypothetical_protein_201322..201552_POSITIVE 239 140 91 152 96 NC_009009:SSA_1166|5end_hypothetical_protein_1191929..1192159_POSITIVE 238 105 62 53 8 NC_009009:SSA_0651|5end_hypothetical_protein_634548..634778_POSITIVE 237 109 67 213 170 NC_009009:SSA_1791|5end_Acylphosphatase,_putative_1773676..1773906_POSITIVE 233 130 83 202 147 NC_009009:SSA_1946|5end_Oligopeptide_transport_system_permease_protein,_putative_1938624..1938854_NEGATIVE 230 138 91 193 120 NC_009009:SSA_1360|5end_Arginine/histidine_ABC_transporter,_ATPase_component,_putative_1376350..1376580_POSITIVE 228 140 94 52 5 NC_009009:SSA_1744|5end_Iron_compound_ABC_transporter,_permease_protein,_putative_1730915..1731145_POSITIVE 228 127 89 78 40 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 227 106 61 121 65 NC_009009:SSA_0968|5end_hypothetical_protein_976699..976929_POSITIVE 227 139 92 58 5 NC_009009:SSA_0186|5end_Competence_protein_ComYC,_putative_190061..190291_POSITIVE 226 120 88 231 204 NC_009009:SSA_2380|5end_hypothetical_protein_2386144..2386374_NEGATIVE 226 140 91 174 117 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 225 139 93 153 107 NC_009009:SSA_0662|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_648302..648532_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 64 28 34 1 NC_009009:SSA_0695|3end_hypothetical_protein_679215..679365_POSITIVE 274 138 91 59 9 NC_009009:SSA_1763|3end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750951..1751101_POSITIVE 258 120 79 137 93 NC_009009:SSA_0745|3end_hypothetical_protein_726814..726964_NEGATIVE 246 137 91 99 55 NC_009009:SSA_1958|3end_Adapter_protein_mecA,_putative_1954661..1954811_NEGATIVE 243 132 91 47 6 NC_009009:SSA_1606|3end_Dephospho-CoA_kinase,_putative_1611829..1611979_NEGATIVE 243 140 92 81 28 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 242 131 94 75 30 NC_009009:SSA_1349|3end_Transcriptional_regulator,_biotin_repressor_family,_putative_1366513..1366663_POSITIVE 236 122 82 139 91 NC_009009:SSA_2080|3end_hypothetical_protein_2084598..2084748_NEGATIVE 236 138 93 73 32 NC_009009:SSA_2079|3end_Acetyltransferase,_putative_2084599..2084749_POSITIVE 228 140 94 62 15 NC_009009:SSA_1743|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1731005..1731155_POSITIVE 227 139 92 58 5 NC_009009:SSA_0185|3end_Competence_protein_ComYB,_putative_190141..190291_POSITIVE 224 121 93 109 78 NC_009009:SSA_0981|3end_3-isopropylmalate_dehydratase_small_subunit,_putative_986066..986216_POSITIVE 222 135 99 43 1 NC_009009:SSA_2132|3end_Ure_cluster_protein,_putative_2135665..2135815_POSITIVE 222 74 37 87 51 NC_009009:SSA_0730|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_715167..715317_POSITIVE 219 120 81 144 101 NC_009009:SSA_0329|3end_Glycerol_uptake_facilitator/aquaporin_protein,_putative_323815..323965_POSITIVE 217 105 61 121 76 NC_009009:SSA_2285|3end_hypothetical_protein_2287825..2287975_POSITIVE 217 108 62 78 35 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 215 139 91 38 2 NC_009009:SSA_1205|3end_Bta,_putative_1230057..1230207_POSITIVE 215 133 91 79 41 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 212 77 43 45 6 NC_009009:SSA_2211|3end_Transmembrane_protein,_putative_2211499..2211649_NEGATIVE