Origin IGS: tccgtcattatactacaaatactcctatttttctatctttttttgatgagaatattcacaaaattctaaagcaatatccttgcatatgatactatttattggtaaaatattgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacaatattttaccaataaatagtatcatatgcaaggatattgctttagaattttgtgaatattctcatcaaaaaaagatagaaaaataggagtatttgtagtataatgacgga Mask Tandem Repeat Region ================================================ tccgtcattatactacaaatactcctatttttctatctttttttgatgagaatattcacaaaattctaaagcaatatccttgcatatgatactatttattggtaaaatattgtt Find is-nt database================================================ Query_seq: SSA_1384:SSA_1385|SSA_1384:SSA_1385:hypothetical protein:Multiple antibiotic resistance operon transcription repressor (MarR), putative:<-->:1402294..1402407 114 tccgtcattatactacaaatactcctatttttctatctttttttgatgagaatattcacaaaattctaaagcaatatccttgcatatgatactatttattggtaaaatattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1384:SSA_1385|SSA_1384:SSA_1385:hypothetical protein:Multiple antibiotic resistance operon transcription repressor (MarR), putative:<-->:1402294..1402407 114 tccgtcattatactacaaatactcctatttttctatctttttttgatgagaatattcacaaaattctaaagcaatatccttgcatatgatactatttattggtaaaatattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1384:SSA_1385|SSA_1384:SSA_1385:hypothetical protein:Multiple antibiotic resistance operon transcription repressor (MarR), putative:<-->:1402294..1402407 114 tccgtcattatactacaaatactcctatttttctatctttttttgatgagaatattcacaaaattctaaagcaatatccttgcatatgatactatttattggtaaaatattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccgtcattatactacaaatactcctatttttctatctttttttgatgagaatattcacaaaattctaaagcaatatccttgcatatgatactatttattggtaaaatattgtt Predict ORF larger than 30AA ================================================ tccgtcattatactacaaatactcctatttttctatctttttttgatgagaatattcacaaaattctaaagcaatatccttgcatatgatactatttattggtaaaatattgtt 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: 86 Start: 7 End: 36 ......ATAGAAAAATAGGAGTATTTGTAGTATAAT.............................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 79 End: 108 ..............................................................................CTTGCATATGATACTATTTATTGGTAAAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tccgtcattatactacaaatactcctatttttctatctttttttgatgagaatattcacaaaattctaaagcaatatccttgcatatgatactatttattggtaaaatattgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1384:SSA_1385|SSA_1384:SSA_1385:hypothetical protein:Multiple antibiotic resistance operon transcription repressor (MarR), putative:<-->:1402294..1402407 114 tccgtcattatactacaaatactcctatttttctatctttttttgatgagaatattcacaaaattctaaagcaatatccttgcatatgatactatttattggtaaaatattgtt Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_009009_SSA_1384_SSA_1385|hypothetical protein:Multiple antibiotic resistance operon transcription repressor (MarR), putative|NEGATIVE:POSITIVE|[1402294,1402407]|114 HSP 1 e-value: 4.0E-46 bit: 184.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 tccgtcattatactacaaatactcctatttttctatcnnnnnnngatgagaatattcacaaaattctaaagcaatatccttgcatatgatactatttattggtaaaatattgtt tccgtcattatactacaaatactcctatttttctatctttttttgatgagaatattcacaaaattctaaagcaatatccttgcatatgatactatttattggtaaaatattgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGUCAUUAUACUACAAAUACUCCUAUUUUUCUAUCUUUUUUUGAUGAGAAUAUUCACAAAAUUCUAAAGCAAUAUCCUUGCAUAUGAUACUAUUUAUUGGUAAAAUAUUGUU ............................(((((.(((.......)))))))).................((((((((..((((..((((......))))..)))).)))))))) (-11.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAUAUUUUACCAAUAAAUAGUAUCAUAUGCAAGGAUAUUGCUUUAGAAUUUUGUGAAUAUUCUCAUCAAAAAAAGAUAGAAAAAUAGGAGUAUUUGUAGUAUAAUGACGGA ............((..(((((((((((.........))))))).)))).....(((..(((((((..((.................))..)))))))..))).........)). (-13.43) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 737 50 1 141 92 NC_009009:SSA_1384|5end_hypothetical_protein_1402203..1402433_NEGATIVE 224 68 34 131 97 NC_009009:SSA_0876|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870233..870463_POSITIVE 221 45 1 228 187 NC_009009:SSA_1021|5end_Conserved_uncharacterized_protein_1036144..1036374_POSITIVE 218 50 1 136 91 NC_009009:SSA_0523|5end_Aldehyde_dehydrogenase,_putative_521637..521867_POSITIVE 216 59 16 192 147 NC_009009:SSA_0649|5end_Ribosomal_small_subunit_pseudouridine_synthase_A,_putative_632545..632775_NEGATIVE 199 58 35 56 34 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 198 49 21 212 184 NC_009009:SSA_0324|5end_Conserved_uncharacterized_protein_317019..317249_POSITIVE 197 95 64 66 40 NC_009009:SSA_1253|5end_hypothetical_protein_1281245..1281475_NEGATIVE 195 84 41 221 174 NC_009009:SSA_2371|5end_Zn-dependent_peptidase,_putative_2373681..2373911_NEGATIVE 191 78 37 92 43 NC_009009:SSA_1405|5end_Copper_homeostasis_protein_CutC,_putative_1419393..1419623_NEGATIVE 190 48 22 120 97 NC_009009:SSA_0130|5end_30S_ribosomal_protein_S13,_putative_120332..120562_POSITIVE 189 48 1 132 68 NC_009009:SSA_0529|5end_Ethanolamine_utilization_protein,_putative_525945..526175_POSITIVE 183 50 3 121 80 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 182 90 57 212 174 NC_009009:SSA_0701|5end_Cation_transporter_CorA_family,_putative_684368..684598_POSITIVE 182 102 65 51 15 NC_009009:SSA_0581|5end_Conserved_uncharacterized_protein_573329..573559_POSITIVE 182 58 17 210 177 NC_009009:SSA_0454|5end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_457015..457245_NEGATIVE 181 46 14 181 153 NC_009009:SSA_1376|5end_Transport_protein,_putative_1396111..1396341_NEGATIVE 181 80 33 65 18 NC_009009:SSA_0077|5end_Oxidoreductase,_putative_80738..80968_POSITIVE 180 80 31 148 99 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 180 101 64 178 146 NC_009009:SSA_1223|5end_30S_ribosomal_protein_S1,_putative_1246872..1247102_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 68 34 58 24 NC_009009:SSA_0875|3end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_870240..870390_POSITIVE 221 45 1 108 67 NC_009009:SSA_1020|3end_hypothetical_protein_1036104..1036254_POSITIVE 218 50 1 129 84 NC_009009:SSA_0522|3end_Ethanolamine_utilization_protein,_putative_521710..521860_POSITIVE 203 104 68 151 110 NC_009009:SSA_2032|3end_Integrase/recombinase,_phage_integrase_family,_putative_2038307..2038457_POSITIVE 199 58 35 45 23 NC_009009:SSA_1469|3end_Shikimate_dehydrogenase,_putative_1475463..1475613_NEGATIVE 197 95 64 69 43 NC_009009:SSA_1254|3end_hypothetical_protein_1281242..1281392_NEGATIVE 193 49 1 151 102 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 193 36 1 102 76 NC_009009:SSA_1474|3end_Lipoprotein,_putative_1479067..1479217_NEGATIVE 190 72 32 131 94 NC_009009:SSA_0805|3end_Collagen-binding_surface_protein,_putative_789232..789382_POSITIVE 190 48 22 102 79 NC_009009:SSA_2392|3end_50S_ribosomal_protein_L36,_putative_120394..120544_POSITIVE 189 48 1 117 53 NC_009009:SSA_0528|3end_Conserved_uncharacterized_protein_526010..526160_POSITIVE 186 90 57 41 8 NC_009009:SSA_1406|3end_Histone_acetyltransferase_HPA2,_putative_1419455..1419605_NEGATIVE 185 106 69 105 70 NC_009009:SSA_1942|3end_Enoyl-CoA_hydratase/carnithine_racemase,_putative_1927705..1927855_NEGATIVE 183 50 3 47 6 NC_009009:SSA_2146|3end_Metallo-beta-lactamase,_putative_2146732..2146882_NEGATIVE 182 102 65 41 5 NC_009009:SSA_0580|3end_Isochorismatase_family_protein,_putative_573399..573549_POSITIVE 181 70 22 126 81 NC_009009:SSA_1312|3end_RADC-like_protein,_putative_1328737..1328887_NEGATIVE 180 90 49 86 47 NC_009009:SSA_0548|3end_Alanine_racemase,_putative_543529..543679_POSITIVE 178 50 1 146 104 NC_009009:SSA_2219|3end_UDP-glucose_4-epimerase,_putative_2219967..2220117_NEGATIVE 176 85 48 54 19 NC_009009:SSA_2066|3end_DNA_polymerase_III_polC-type,_putative_2065749..2065899_NEGATIVE 172 49 23 116 89 NC_009009:SSA_1804|3end_NADPH-flavin_oxidoreductase,_putative_1787952..1788102_NEGATIVE