Origin IGS: aattttatccctcctataccattttactttttctgtctgaaataagctagaaaatagcccggaatttttactaaaaaagtttacacattgttaaatggaaaaatttttagtttaatttctggacatcatgtctgtttaaaaactggacgatttcacaaaaatgtacataaatcaagccgataattcttttattttaacaagttaatatgataaaataataaaaaatcttatcagaagtcaaatagaaagtgtagtttaaagattacctaatctgaaagatttatgggaggtttgactggactttttattaagggttactgatcgggataataaactatgttcaggggagaataaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttattctcccctgaacatagtttattatcccgatcagtaacccttaataaaaagtccagtcaaacctcccataaatctttcagattaggtaatctttaaactacactttctatttgacttctgataagattttttattattttatcatattaacttgttaaaataaaagaattatcggcttgatttatgtacatttttgtgaaatcgtccagtttttaaacagacatgatgtccagaaattaaactaaaaatttttccatttaacaatgtgtaaacttttttagtaaaaattccgggctattttctagcttatttcagacagaaaaagtaaaatggtataggagggataaaatt Mask Tandem Repeat Region ================================================ aattttatccctcctataccattttactttttctgtctgaaataagctagaaaatagcccggaatttttactaaaaaagtttacacattgttaaatggaaaaatttttagtttaatttctggacatcatgtctgtttaaaaactggacgatttcacaaaaatgtacataaatcaagccgataattcttttattttaacaagttaatatgataaaataataaaaaatcttatcagaagtcaaatagaaagtgtagtttaaagattacctaatctgaaagatttatgggaggtttgactggactttttattaagggttactgatcgggataataaactatgttcaggggagaataaa Find is-nt database================================================ Query_seq: SSA_0145:SSA_0146|SSA_0145:SSA_0146:Transcriptional regulator, TetR family, putative:DNA repair ATPase, putative:<-->:139471..139825 355 aattttatccctcctataccattttactttttctgtctgaaataagctagaaaatagcccggaatttttactaaaaaagtttacacattgttaaatggaaaaatttttagtttaatttctggacatcatgtctgtttaaaaactggacgatttcacaaaaatgtacataaatcaagccgataattcttttattttaacaagttaatatgataaaataataaaaaatcttatcagaagtcaaatagaaagtgtagtttaaagattacctaatctgaaagatttatgggaggtttgactggactttttattaagggttactgatcgggataataaactatgttcaggggagaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0145:SSA_0146|SSA_0145:SSA_0146:Transcriptional regulator, TetR family, putative:DNA repair ATPase, putative:<-->:139471..139825 355 aattttatccctcctataccattttactttttctgtctgaaataagctagaaaatagcccggaatttttactaaaaaagtttacacattgttaaatggaaaaatttttagtttaatttctggacatcatgtctgtttaaaaactggacgatttcacaaaaatgtacataaatcaagccgataattcttttattttaacaagttaatatgataaaataataaaaaatcttatcagaagtcaaatagaaagtgtagtttaaagattacctaatctgaaagatttatgggaggtttgactggactttttattaagggttactgatcgggataataaactatgttcaggggagaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0145:SSA_0146|SSA_0145:SSA_0146:Transcriptional regulator, TetR family, putative:DNA repair ATPase, putative:<-->:139471..139825 355 aattttatccctcctataccattttactttttctgtctgaaataagctagaaaatagcccggaatttttactaaaaaagtttacacattgttaaatggaaaaatttttagtttaatttctggacatcatgtctgtttaaaaactggacgatttcacaaaaatgtacataaatcaagccgataattcttttattttaacaagttaatatgataaaataataaaaaatcttatcagaagtcaaatagaaagtgtagtttaaagattacctaatctgaaagatttatgggaggtttgactggactttttattaagggttactgatcgggataataaactatgttcaggggagaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttatccctcctataccattttactttttctgtctgaaataagctagaaaatagcccggaatttttactaaaaaagtttacacattgttaaatggaaaaatttttagtttaatttctggacatcatgtctgtttaaaaactggacgatttcacaaaaatgtacataaatcaagccgataattcttttattttaacaagttaatatgataaaataataaaaaatcttatcagaagtcaaatagaaagtgtagtttaaagattacctaatctgaaagatttatgggaggtttgactggactttttattaagggttactgatcgggataataaactatgttcaggggagaataaa Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 64 End: 180 ............................................................... M F T K K V Y T L L N G K I F S L I S G H H V C L K T G R F H K N V H K S S R ............................................................................................................................................................................... aattttatccctcctataccattttactttttctgtctgaaataagctagaaaatagcccggaatttttactaaaaaagtttacacattgttaaatggaaaaatttttagtttaatttctggacatcatgtctgtttaaaaactggacgatttcacaaaaatgtacataaatcaagccgataattcttttattttaacaagttaatatgataaaataataaaaaatcttatcagaagtcaaatagaaagtgtagtttaaagattacctaatctgaaagatttatgggaggtttgactggactttttattaagggttactgatcgggataataaactatgttcaggggagaataaa 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: 87 End: 116 ......................................................................................ATTGTTAAATGGAAAAATTTTTAGTTTAAT............................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattttatccctcctataccattttactttttctgtctgaaataagctagaaaatagcccggaatttttactaaaaaagtttacacattgttaaatggaaaaatttttagtttaatttctggacatcatgtctgtttaaaaactggacgatttcacaaaaatgtacataaatcaagccgataattcttttattttaacaagttaatatgataaaataataaaaaatcttatcagaagtcaaatagaaagtgtagtttaaagattacctaatctgaaagatttatgggaggtttgactggactttttattaagggttactgatcgggataataaactatgttcaggggagaataaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0145:SSA_0146|SSA_0145:SSA_0146:Transcriptional regulator, TetR family, putative:DNA repair ATPase, putative:<-->:139471..139825 355 aattttatccctcctataccattttactttttctgtctgaaataagctagaaaatagcccggaatttttactaaaaaagtttacacattgttaaatggaaaaatttttagtttaatttctggacatcatgtctgtttaaaaactggacgatttcacaaaaatgtacataaatcaagccgataattcttttattttaacaagttaatatgataaaataataaaaaatcttatcagaagtcaaatagaaagtgtagtttaaagattacctaatctgaaagatttatgggaggtttgactggactttttattaagggttactgatcgggataataaactatgttcaggggagaataaa Intra-Species Hit: Count: 1 Min: 1 Max: 355 Len: 355 Subject: NC_009009_SSA_0145_SSA_0146|Transcriptional regulator, TetR family, putative:DNA repair ATPase, putative|NEGATIVE:POSITIVE|[139471,139825]|355 HSP 1 e-value: 0.0 bit: 704.0 Len: 355 Query Start:1 Query End:355 Subject Strand: POSITIVE Subject Start: 1 Subject End: 355 aattttatccctcctataccattttactttttctgtctgaaataagctagaaaatagcccggaatttttactaaaaaagtttacacattgttaaatggaaaaatttttagtttaatttctggacatcatgtctgtttaaaaactggacgatttcacaaaaatgtacataaatcaagccgataattcttttattttaacaagttaatatgataaaataataaaaaatcttatcagaagtcaaatagaaagtgtagtttaaagattacctaatctgaaagatttatgggaggtttgactggactttttattaagggttactgatcgggataataaactatgttcaggggagaataaa aattttatccctcctataccattttactttttctgtctgaaataagctagaaaatagcccggaatttttactaaaaaagtttacacattgttaaatggaaaaatttttagtttaatttctggacatcatgtctgtttaaaaactggacgatttcacaaaaatgtacataaatcaagccgataattcttttattttaacaagttaatatgataaaataataaaaaatcttatcagaagtcaaatagaaagtgtagtttaaagattacctaatctgaaagatttatgggaggtttgactggactttttattaagggttactgatcgggataataaactatgttcaggggagaataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUAUCCCUCCUAUACCAUUUUACUUUUUCUGUCUGAAAUAAGCUAGAAAAUAGCCCGGAAUUUUUACUAAAAAAGUUUACACAUUGUUAAAUGGAAAAAUUUUUAGUUUAAUUUCUGGACAUCAUGUCUGUUUAAAAACUGGACGAUUUCACAAAAAUGUACAUAAAUCAAGCCGAUAAUUCUUUUAUUUUAACAAGUUAAUAUGAUAAAAUAAUAAAAAAUCUUAUCAGAAGUCAAAUAGAAAGUGUAGUUUAAAGAUUACCUAAUCUGAAAGAUUUAUGGGAGGUUUGACUGGACUUUUUAUUAAGGGUUACUGAUCGGGAUAAUAAACUAUGUUCAGGGGAGAAUAAA .......((.(((((....((((((...(((((((.((......)).)))))))..(.((((((.((..((((((((..(((...((((....)))).)))..))))))))..)).)))))).)....((((((((....))).)))))........)))))).(((((...................((((((((.((........)).))))))))......((((((((((.(..(.((((((((((.(((((...((((..(((((((.....)))...))))..))))))))).))))))))))...)..).))))).))))).......)))))..))))).))..... (-72.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUUCUCCCCUGAACAUAGUUUAUUAUCCCGAUCAGUAACCCUUAAUAAAAAGUCCAGUCAAACCUCCCAUAAAUCUUUCAGAUUAGGUAAUCUUUAAACUACACUUUCUAUUUGACUUCUGAUAAGAUUUUUUAUUAUUUUAUCAUAUUAACUUGUUAAAAUAAAAGAAUUAUCGGCUUGAUUUAUGUACAUUUUUGUGAAAUCGUCCAGUUUUUAAACAGACAUGAUGUCCAGAAAUUAAACUAAAAAUUUUUCCAUUUAACAAUGUGUAAACUUUUUUAGUAAAAAUUCCGGGCUAUUUUCUAGCUUAUUUCAGACAGAAAAAGUAAAAUGGUAUAGGAGGGAUAAAAUU ((((((((..((((.((....((((((..((((...................(((((.((((...........(((((((((((((((((((...................)))))))..))))).)))))))....((((((((.((........)).))))))))..........)))).)))))......(((((((.((.(((((...((((......))))))))).)))))))))...((((((((..(((.(((........))).)))..))))))))........))))...((((((..((......))..))))))))))))...)).)))).))))))))... (-60.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 803 60 11 151 102 NC_009009:SSA_0145|5end_Transcriptional_regulator,_TetR_family,_putative_139380..139610_NEGATIVE 287 159 111 149 94 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 256 50 8 147 95 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 253 150 104 56 10 NC_009009:SSA_0178|5end_UDP-N-acetylglucosamine_2-epimerase,_putative_182816..183046_POSITIVE 252 297 253 199 155 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 245 60 11 156 99 NC_009009:SSA_2278|5end_Ukp_protein,_putative_2281669..2281899_NEGATIVE 244 329 284 191 143 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 243 301 264 78 36 NC_009009:SSA_0846|5end_DNA-polymerase_III_alpha-chain,_putative_830078..830308_POSITIVE 242 60 11 113 59 NC_009009:SSA_0687|5end_hypothetical_protein_670467..670697_POSITIVE 241 329 285 221 181 NC_009009:SSA_1381|5end_hypothetical_protein_1399565..1399795_NEGATIVE 240 64 28 144 105 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 236 322 284 200 164 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 235 329 291 160 117 NC_009009:SSA_1015|5end_4-hydroxybenzoate_octaprenyltransferase,_putative_1018703..1018933_POSITIVE 235 302 265 124 94 NC_009009:SSA_0967|5end_hypothetical_protein_975872..976102_POSITIVE 234 322 282 55 19 NC_009009:SSA_2361|5end_L-serine_dehydratase_beta_subunit_2364028..2364258_POSITIVE 233 153 113 190 137 NC_009009:SSA_1981|5end_hypothetical_protein_1975421..1975651_NEGATIVE 233 139 95 224 178 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 232 326 283 200 157 NC_009009:SSA_1268|5end_Chorismate_mutase/prephenate_dehydratase,_putative_1291610..1291840_NEGATIVE 231 325 284 198 161 NC_009009:SSA_0548|5end_Alanine_racemase,_putative_542340..542570_POSITIVE 230 279 231 195 146 NC_009009:SSA_1419|5end_hypothetical_protein_1429675..1429905_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 159 111 137 82 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 259 60 11 145 80 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE 256 50 8 69 17 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 252 297 253 48 4 NC_009009:SSA_0746|3end_Glucosamine-6-phosphate_deaminase,_putative_727865..728015_POSITIVE 243 50 2 119 70 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 240 64 28 147 108 NC_009009:SSA_0097|3end_Multi_antimicrobial_extrusion_(MATE)_family_transporter,_putative_99505..99655_POSITIVE 231 348 312 48 8 NC_009009:SSA_1400|3end_Pyridoxal_kinase,_putative_1412206..1412356_NEGATIVE 230 59 11 118 82 NC_009009:SSA_1497|3end_DCMP_deaminase,_putative_1503068..1503218_NEGATIVE 229 316 281 126 91 NC_009009:SSA_0836|3end_SecA-like_protein,_putative_823969..824119_POSITIVE 229 329 288 135 95 NC_009009:SSA_0813|3end_Thioredoxin_reductase,_putative_794438..794588_NEGATIVE 226 329 290 73 30 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 226 326 281 147 104 NC_009009:SSA_0886|3end_Enolase,_putative_881057..881207_POSITIVE 225 60 13 120 74 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE 225 64 37 56 27 NC_009009:SSA_0425|3end_Glycosyltransferase,_putative_422230..422380_NEGATIVE 222 60 12 103 56 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 222 38 1 129 88 NC_009009:SSA_1361|3end_ORFA,_transposon_ISSsa2_1377784..1377934_POSITIVE 222 325 287 78 41 NC_009009:SSA_0829|3end_Platelet-binding_glycoprotein_812165..812315_POSITIVE 222 188 142 72 19 NC_009009:SSA_0776|3end_Glucose-1-phosphate_adenylyltransferase,_putative_759520..759670_POSITIVE 222 38 1 129 88 NC_009009:SSA_0265|3end_ORFA,_transposon_ISSsa1_260007..260157_POSITIVE 222 299 260 134 88 NC_009009:SSA_0157|3end_hypothetical_protein_153877..154027_POSITIVE