Origin IGS: agaagactcctcaaattttatgactaaaattatatactcttttttttattttatcaatagaattgttgatttaaaatcaattcttttaaaatatagtttttttaaataagctataaaggcggtttcatgggctttgtagatattattacattttctttacattttcgctgatttattctctccttgctggtataatctatttggaaaagataggttttttaggagactaatca .........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 tgattagtctcctaaaaaacctatcttttccaaatagattataccagcaaggagagaataaatcagcgaaaatgtaaagaaaatgtaataatatctacaaagcccatgaaaccgcctttatagcttatttaaaaaaactatattttaaaagaattgattttaaatcaacaattctattgataaaataaaaaaaagagtatataattttagtcataaaatttgaggagtcttct Mask Tandem Repeat Region ================================================ agaagactcctcaaattttatgactaaaattatatactcttttttttattttatcaatagaattgttgatttaaaatcaattcttttaaaatatagtttttttaaataagctataaaggcggtttcatgggctttgtagatattattacattttctttacattttcgctgatttattctctccttgctggtataatctatttggaaaagataggttttttaggagactaatca Find is-nt database================================================ Query_seq: SSA_0171:SSA_0172|SSA_0171:SSA_0172:Cro-like transcriptional repressor, XRE family, putative:Transcriptional regulator, XRE family, putative:<-->:169047..169279 233 agaagactcctcaaattttatgactaaaattatatactcttttttttattttatcaatagaattgttgatttaaaatcaattcttttaaaatatagtttttttaaataagctataaaggcggtttcatgggctttgtagatattattacattttctttacattttcgctgatttattctctccttgctggtataatctatttggaaaagataggttttttaggagactaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0171:SSA_0172|SSA_0171:SSA_0172:Cro-like transcriptional repressor, XRE family, putative:Transcriptional regulator, XRE family, putative:<-->:169047..169279 233 agaagactcctcaaattttatgactaaaattatatactcttttttttattttatcaatagaattgttgatttaaaatcaattcttttaaaatatagtttttttaaataagctataaaggcggtttcatgggctttgtagatattattacattttctttacattttcgctgatttattctctccttgctggtataatctatttggaaaagataggttttttaggagactaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0171:SSA_0172|SSA_0171:SSA_0172:Cro-like transcriptional repressor, XRE family, putative:Transcriptional regulator, XRE family, putative:<-->:169047..169279 233 agaagactcctcaaattttatgactaaaattatatactcttttttttattttatcaatagaattgttgatttaaaatcaattcttttaaaatatagtttttttaaataagctataaaggcggtttcatgggctttgtagatattattacattttctttacattttcgctgatttattctctccttgctggtataatctatttggaaaagataggttttttaggagactaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaagactcctcaaattttatgactaaaattatatactcttttttttattttatcaatagaattgttgatttaaaatcaattcttttaaaatatagtttttttaaataagctataaaggcggtttcatgggctttgtagatattattacattttctttacattttcgctgatttattctctccttgctggtataatctatttggaaaagataggttttttaggagactaatca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 140 End: 232 ........................................................................................................................................... M L L H F L Y I F A D L F S P C W Y N L F G K D R F F R R L I . Protein_Len: 31 Strand: - Start: 49 End: 141 ................................................ K I L L I T S K F D I R K F Y L K K L Y A I F A T E H A K Y M ............................................................................................ agaagactcctcaaattttatgactaaaattatatactcttttttttattttatcaatagaattgttgatttaaaatcaattcttttaaaatatagtttttttaaataagctataaaggcggtttcatgggctttgtagatattattacattttctttacattttcgctgatttattctctccttgctggtataatctatttggaaaagataggttttttaggagactaatca 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: 87 Start: 29 End: 58 ............................ATTGATAAAATAAAAAAAAGAGTATATAAT............................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 167 End: 196 ......................................................................................................................................................................GCTGATTTATTCTCTCCTTGCTGGTATAAT..................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaagactcctcaaattttatgactaaaattatatactcttttttttattttatcaatagaattgttgatttaaaatcaattcttttaaaatatagtttttttaaataagctataaaggcggtttcatgggctttgtagatattattacattttctttacattttcgctgatttattctctccttgctggtataatctatttggaaaagataggttttttaggagactaatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0171:SSA_0172|SSA_0171:SSA_0172:Cro-like transcriptional repressor, XRE family, putative:Transcriptional regulator, XRE family, putative:<-->:169047..169279 233 agaagactcctcaaattttatgactaaaattatatactcttttttttattttatcaatagaattgttgatttaaaatcaattcttttaaaatatagtttttttaaataagctataaaggcggtttcatgggctttgtagatattattacattttctttacattttcgctgatttattctctccttgctggtataatctatttggaaaagataggttttttaggagactaatca Intra-Species Hit: Count: 1 Min: 1 Max: 233 Len: 233 Subject: NC_009009_SSA_0171_SSA_0172|Cro-like transcriptional repressor, XRE family, putative:Transcriptional regulator, XRE family, putative|NEGATIVE:POSITIVE|[169047,169279]|233 HSP 1 e-value: 1.0E-102 bit: 373.0 Len: 233 Query Start:1 Query End:233 Subject Strand: POSITIVE Subject Start: 1 Subject End: 233 agaagactcctcaaattttatgactaaaattatatactcnnnnnnnnattttatcaatagaattgttgatttaaaatcaattcttttaaaatatagnnnnnnnaaataagctataaaggcggtttcatgggctttgtagatattattacattttctttacattttcgctgatttattctctccttgctggtataatctatttggaaaagataggttttttaggagactaatca agaagactcctcaaattttatgactaaaattatatactcttttttttattttatcaatagaattgttgatttaaaatcaattcttttaaaatatagtttttttaaataagctataaaggcggtttcatgggctttgtagatattattacattttctttacattttcgctgatttattctctccttgctggtataatctatttggaaaagataggttttttaggagactaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAGACUCCUCAAAUUUUAUGACUAAAAUUAUAUACUCUUUUUUUUAUUUUAUCAAUAGAAUUGUUGAUUUAAAAUCAAUUCUUUUAAAAUAUAGUUUUUUUAAAUAAGCUAUAAAGGCGGUUUCAUGGGCUUUGUAGAUAUUAUUACAUUUUCUUUACAUUUUCGCUGAUUUAUUCUCUCCUUGCUGGUAUAAUCUAUUUGGAAAAGAUAGGUUUUUUAGGAGACUAAUCA ((((((((.....(((((((....)))))))...............(((((((.....(((((((............)))))))..))))))).))))))))..(((((.((((((((.(.((...)).).))))))))...)))))......................((((.....((((((.........(((((((((.....)))))))))....))))))..)))). (-38.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUAGUCUCCUAAAAAACCUAUCUUUUCCAAAUAGAUUAUACCAGCAAGGAGAGAAUAAAUCAGCGAAAAUGUAAAGAAAAUGUAAUAAUAUCUACAAAGCCCAUGAAACCGCCUUUAUAGCUUAUUUAAAAAAACUAUAUUUUAAAAGAAUUGAUUUUAAAUCAACAAUUCUAUUGAUAAAAUAAAAAAAAGAGUAUAUAAUUUUAGUCAUAAAAUUUGAGGAGUCUUCU .....((.(((((..........((((((....((((......((.....))......(((((.(((.....(((((((....((((........))))..((..........)))))))))))).)))))......))))...((((.(((((((............))))))).))))..........))))))......(((((((....)))))))..))))).))... (-28.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 768 140 91 231 182 NC_009009:SSA_0171|5end_Cro-like_transcriptional_repressor,_XRE_family,_putative_168956..169186_NEGATIVE 277 160 118 199 142 NC_009009:SSA_2047|5end_hypothetical_protein_2049953..2050183_NEGATIVE 275 189 146 106 49 NC_009009:SSA_1383|5end_Aspartate_aminotransferase,_putative_1401718..1401948_NEGATIVE 270 189 147 107 57 NC_009009:SSA_0200|5end_Bifunctional_folate_synthesis_protein,_putative_198918..199148_POSITIVE 261 139 93 228 174 NC_009009:SSA_0588|5end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_579800..580030_POSITIVE 259 209 162 192 148 NC_009009:SSA_0863|5end_Cof_family_protein,_putative_855015..855245_NEGATIVE 254 156 117 96 47 NC_009009:SSA_0695|5end_hypothetical_protein_678449..678679_POSITIVE 253 160 115 102 59 NC_009009:SSA_1851|5end_Guanylate_kinase,_putative_1846682..1846912_NEGATIVE 253 212 178 50 6 NC_009009:SSA_1841|5end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1835822..1836052_NEGATIVE 252 226 181 203 153 NC_009009:SSA_1685|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1679076..1679306_NEGATIVE 252 206 167 174 129 NC_009009:SSA_0939|5end_Inositol_monophosphatase_(Mg++_dependent),_putative_946810..947040_POSITIVE 251 190 150 110 72 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 247 220 179 227 181 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 246 169 121 198 157 NC_009009:SSA_2314|5end_hypothetical_protein_2316335..2316565_NEGATIVE 246 192 153 114 72 NC_009009:SSA_0897|5end_Two_component_system_histidine_kinase,_putative_888358..888588_POSITIVE 245 200 151 144 81 NC_009009:SSA_0799|5end_hypothetical_protein_781970..782200_NEGATIVE 243 223 182 51 11 NC_009009:SSA_0998|5end_hypothetical_protein_998487..998717_POSITIVE 243 157 120 171 135 NC_009009:SSA_0946|5end_Phosphate_transport_system_regulatory_protein,_putative_953393..953623_POSITIVE 242 137 96 122 79 NC_009009:SSA_2294|5end_hypothetical_protein_2296082..2296312_POSITIVE 242 194 162 116 77 NC_009009:SSA_0349|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_341110..341340_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 189 146 109 52 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 261 139 93 109 55 NC_009009:SSA_0587|3end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_579761..579911_POSITIVE 246 169 121 46 5 NC_009009:SSA_2315|3end_Conserved_uncharacterized_protein_2316487..2316637_NEGATIVE 246 192 153 117 75 NC_009009:SSA_0896|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_888441..888591_POSITIVE 245 200 151 125 62 NC_009009:SSA_0800|3end_Glutamine_amidotransferase,_putative_781989..782139_NEGATIVE 244 135 95 135 87 NC_009009:SSA_2152|3end_ABC-type_transporter_(uncharacterized),_ATPase_component,_putative_2153043..2153193_NEGATIVE 244 191 161 132 98 NC_009009:SSA_0727|3end_Metal-dependent_membrane_protease,_putative_713639..713789_POSITIVE 242 194 162 40 1 NC_009009:SSA_0348|3end_CAAX_amino_terminal_protease_family,_putative_341114..341264_POSITIVE 240 134 91 144 97 NC_009009:SSA_1469|3end_Shikimate_dehydrogenase,_putative_1475463..1475613_NEGATIVE 239 203 165 123 80 NC_009009:SSA_1020|3end_hypothetical_protein_1036104..1036254_POSITIVE 234 158 115 126 83 NC_009009:SSA_0884|3end_hypothetical_protein_878725..878875_NEGATIVE 233 140 93 122 68 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 231 139 109 133 106 NC_009009:SSA_2287|3end_50S_ribosomal_protein_L32,_putative_2290083..2290233_POSITIVE 227 130 107 74 53 NC_009009:SSA_1239|3end_hypothetical_protein_1263151..1263301_NEGATIVE 225 134 96 48 9 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 225 137 106 120 79 NC_009009:SSA_1093|3end_ATP-dependent_Clp_protease_ATP-binding_subunit_clpX,_putative_1111645..1111795_POSITIVE 225 228 194 48 12 NC_009009:SSA_0746|3end_Glucosamine-6-phosphate_deaminase,_putative_727865..728015_POSITIVE 225 140 108 72 39 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 222 163 121 43 5 NC_009009:SSA_2324|3end_hypothetical_protein_2328847..2328997_NEGATIVE 221 192 151 138 99 NC_009009:SSA_1957|3end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1953504..1953654_NEGATIVE