Origin IGS: ttttcatctttcagcgttgtataataagtatttaatgatactcataaagactttaatttaaacgcaaagttataaaaaaaatgagaaatagatatgtctttcttcaagaattactatttggtagttcatttaattctatgatcgaaaacctcgatacatacaaaactgacttatgaaatcagttttgcactatcggtataaagacattatatcgacttcacattactttacaaacaaagaaaaactaaattatttgatatggttttaagattattatgaagttgttttacacgtttctggtttacctttaagaaaggttcgacagtaaattatgggagatttgatttccttcttcttattgttggtagatacagaaaaactttttagctttgtaaagattattcattagaaaaatgacaatttcgat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcgaaattgtcatttttctaatgaataatctttacaaagctaaaaagtttttctgtatctaccaacaataagaagaaggaaatcaaatctcccataatttactgtcgaacctttcttaaaggtaaaccagaaacgtgtaaaacaacttcataataatcttaaaaccatatcaaataatttagtttttctttgtttgtaaagtaatgtgaagtcgatataatgtctttataccgatagtgcaaaactgatttcataagtcagttttgtatgtatcgaggttttcgatcatagaattaaatgaactaccaaatagtaattcttgaagaaagacatatctatttctcattttttttataactttgcgtttaaattaaagtctttatgagtatcattaaatacttattatacaacgctgaaagatgaaaa Mask Tandem Repeat Region ================================================ ttttcatctttcagcgttgtataataagtatttaatgatactcataaagactttaatttaaacgcaaagttataaaaaaaatgagaaatagatatgtctttcttcaagaattactatttggtagttcatttaattctatgatcgaaaacctcgatacatacaaaactgacttatgaaatcagttttgcactatcggtataaagacattatatcgacttcacattactttacaaacaaagaaaaactaaattatttgatatggttttaagattattatgaagttgttttacacgtttctggtttacctttaagaaaggttcgacagtaaattatgggagatttgatttccttcttcttattgttggtagatacagaaaaactttttagctttgtaaagattattcattagaaaaatgacaatttcgat Find is-nt database================================================ Query_seq: PI1435:PI1436|PI1435:PI1436:D12 class N6 adenine-specific DNA methyltransferase:hypothetical protein:->->:1355674..1356100 427 ttttcatctttcagcgttgtataataagtatttaatgatactcataaagactttaatttaaacgcaaagttataaaaaaaatgagaaatagatatgtctttcttcaagaattactatttggtagttcatttaattctatgatcgaaaacctcgatacatacaaaactgacttatgaaatcagttttgcactatcggtataaagacattatatcgacttcacattactttacaaacaaagaaaaactaaattatttgatatggttttaagattattatgaagttgttttacacgtttctggtttacctttaagaaaggttcgacagtaaattatgggagatttgatttccttcttcttattgttggtagatacagaaaaactttttagctttgtaaagattattcattagaaaaatgacaatttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1435:PI1436|PI1435:PI1436:D12 class N6 adenine-specific DNA methyltransferase:hypothetical protein:->->:1355674..1356100 427 ttttcatctttcagcgttgtataataagtatttaatgatactcataaagactttaatttaaacgcaaagttataaaaaaaatgagaaatagatatgtctttcttcaagaattactatttggtagttcatttaattctatgatcgaaaacctcgatacatacaaaactgacttatgaaatcagttttgcactatcggtataaagacattatatcgacttcacattactttacaaacaaagaaaaactaaattatttgatatggttttaagattattatgaagttgttttacacgtttctggtttacctttaagaaaggttcgacagtaaattatgggagatttgatttccttcttcttattgttggtagatacagaaaaactttttagctttgtaaagattattcattagaaaaatgacaatttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1435:PI1436|PI1435:PI1436:D12 class N6 adenine-specific DNA methyltransferase:hypothetical protein:->->:1355674..1356100 427 ttttcatctttcagcgttgtataataagtatttaatgatactcataaagactttaatttaaacgcaaagttataaaaaaaatgagaaatagatatgtctttcttcaagaattactatttggtagttcatttaattctatgatcgaaaacctcgatacatacaaaactgacttatgaaatcagttttgcactatcggtataaagacattatatcgacttcacattactttacaaacaaagaaaaactaaattatttgatatggttttaagattattatgaagttgttttacacgtttctggtttacctttaagaaaggttcgacagtaaattatgggagatttgatttccttcttcttattgttggtagatacagaaaaactttttagctttgtaaagattattcattagaaaaatgacaatttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcatctttcagcgttgtataataagtatttaatgatactcataaagactttaatttaaacgcaaagttataaaaaaaatgagaaatagatatgtctttcttcaagaattactatttggtagttcatttaattctatgatcgaaaacctcgatacatacaaaactgacttatgaaatcagttttgcactatcggtataaagacattatatcgacttcacattactttacaaacaaagaaaaactaaattatttgatatggttttaagattattatgaagttgttttacacgtttctggtttacctttaagaaaggttcgacagtaaattatgggagatttgatttccttcttcttattgttggtagatacagaaaaactttttagctttgtaaagattattcattagaaaaatgacaatttcgat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 72 End: 173 ....................................................................... M K K M R N R Y V F L Q E L L F G S S F N S M I E N L D T Y K T D L .............................................................................................................................................................................................................................................................. Protein_Len: 31 Strand: + Start: 173 End: 265 ............................................................................................................................................................................ M K S V L H Y R Y K D I I S T S H Y F T N K E K L N Y L I W F .................................................................................................................................................................. Protein_Len: 42 Strand: - Start: 277 End: 402 .................................................................................................................................................................................................................................................................................... S T T K C T E P K G K L F T R C Y I I P S K I E K K K N N T S V S F S K L K T F I M ......................... ttttcatctttcagcgttgtataataagtatttaatgatactcataaagactttaatttaaacgcaaagttataaaaaaaatgagaaatagatatgtctttcttcaagaattactatttggtagttcatttaattctatgatcgaaaacctcgatacatacaaaactgacttatgaaatcagttttgcactatcggtataaagacattatatcgacttcacattactttacaaacaaagaaaaactaaattatttgatatggttttaagattattatgaagttgttttacacgtttctggtttacctttaagaaaggttcgacagtaaattatgggagatttgatttccttcttcttattgttggtagatacagaaaaactttttagctttgtaaagattattcattagaaaaatgacaatttcgat 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: 206 End: 235 .............................................................................................................................................................................................................GTTTGTAAAGTAATGTGAAGTCGATATAAT................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcatctttcagcgttgtataataagtatttaatgatactcataaagactttaatttaaacgcaaagttataaaaaaaatgagaaatagatatgtctttcttcaagaattactatttggtagttcatttaattctatgatcgaaaacctcgatacatacaaaactgacttatgaaatcagttttgcactatcggtataaagacattatatcgacttcacattactttacaaacaaagaaaaactaaattatttgatatggttttaagattattatgaagttgttttacacgtttctggtttacctttaagaaaggttcgacagtaaattatgggagatttgatttccttcttcttattgttggtagatacagaaaaactttttagctttgtaaagattattcattagaaaaatgacaatttcgat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 90 HP_score: -11.8 Tail_Score: -3.00215 Start: 161 End: 187 Full_Region: tttataccgatagtg caaaactgattt cat aagtcagttttg tatgtatcgaggttt ................................................................................................................................................................caaaactgatttcataagtcagttttg................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 73 HP_score: -5.9 Tail_Score: -4.64844 Start: 166 End: 182 Full_Region: accgatagtgcaaaa ctgattt cat aagtcag ttttgtatgtatcga .....................................................................................................................................................................ctgatttcataagtcag..................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1435:PI1436|PI1435:PI1436:D12 class N6 adenine-specific DNA methyltransferase:hypothetical protein:->->:1355674..1356100 427 ttttcatctttcagcgttgtataataagtatttaatgatactcataaagactttaatttaaacgcaaagttataaaaaaaatgagaaatagatatgtctttcttcaagaattactatttggtagttcatttaattctatgatcgaaaacctcgatacatacaaaactgacttatgaaatcagttttgcactatcggtataaagacattatatcgacttcacattactttacaaacaaagaaaaactaaattatttgatatggttttaagattattatgaagttgttttacacgtttctggtttacctttaagaaaggttcgacagtaaattatgggagatttgatttccttcttcttattgttggtagatacagaaaaactttttagctttgtaaagattattcattagaaaaatgacaatttcgat Intra-Species Hit: Count: 1 Min: 1 Max: 427 Len: 427 Subject: pint_PI1435_PI1436|D12 class N6 adenine-specific DNA methyltransferase:hypothetical protein|POSITIVE:POSITIVE|[1355674,1356100]|427 HSP 1 e-value: 0.0 bit: 799.0 Len: 427 Query Start:1 Query End:427 Subject Strand: POSITIVE Subject Start: 1 Subject End: 427 ttttcatctttcagcgttgtataataagtatttaatgatactcataaagactttaatttaaacgcaaagttatnnnnnnnntgagaaatagatatgtctttcttcaagaattactatttggtagttcatttaattctatgatcgaaaacctcgatacatacaaaactgacttatgaaatcagttttgcactatcggtataaagacattatatcgacttcacattactttacaaacaaagaaaaactaaattatttgatatggttttaagattattatgaagttgttttacacgtttctggtttacctttaagaaaggttcgacagtaaattatgggagatttgatttccttcttcttattgttggtagatacagaaaaactttttagctttgtaaagattattcattagaaaaatgacaatttcgat ttttcatctttcagcgttgtataataagtatttaatgatactcataaagactttaatttaaacgcaaagttataaaaaaaatgagaaatagatatgtctttcttcaagaattactatttggtagttcatttaattctatgatcgaaaacctcgatacatacaaaactgacttatgaaatcagttttgcactatcggtataaagacattatatcgacttcacattactttacaaacaaagaaaaactaaattatttgatatggttttaagattattatgaagttgttttacacgtttctggtttacctttaagaaaggttcgacagtaaattatgggagatttgatttccttcttcttattgttggtagatacagaaaaactttttagctttgtaaagattattcattagaaaaatgacaatttcgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCAUCUUUCAGCGUUGUAUAAUAAGUAUUUAAUGAUACUCAUAAAGACUUUAAUUUAAACGCAAAGUUAUAAAAAAAAUGAGAAAUAGAUAUGUCUUUCUUCAAGAAUUACUAUUUGGUAGUUCAUUUAAUUCUAUGAUCGAAAACCUCGAUACAUACAAAACUGACUUAUGAAAUCAGUUUUGCACUAUCGGUAUAAAGACAUUAUAUCGACUUCACAUUACUUUACAAACAAAGAAAAACUAAAUUAUUUGAUAUGGUUUUAAGAUUAUUAUGAAGUUGUUUUACACGUUUCUGGUUUACCUUUAAGAAAGGUUCGACAGUAAAUUAUGGGAGAUUUGAUUUCCUUCUUCUUAUUGUUGGUAGAUACAGAAAAACUUUUUAGCUUUGUAAAGAUUAUUCAUUAGAAAAAUGACAAUUUCGAU ...((((.((((.(((((.......((((.((((.((.....)))))).)))).......)))))...(((.((((...((((.(((...(((((((((((..((..((((((((....)))))))).........(((((((((.....))))).))))(((((((((.........))))))))).......))...)))))))...))))...))).))))..))))..))).....(((((((.(((....))).)))))))..((((.(((..((((((.........((((((....(((((.....)))))((((((((((.....(((((((...))))))).....))))))))))......)))))).......))))))..))).))))........)))).)))).......... (-87.13) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGAAAUUGUCAUUUUUCUAAUGAAUAAUCUUUACAAAGCUAAAAAGUUUUUCUGUAUCUACCAACAAUAAGAAGAAGGAAAUCAAAUCUCCCAUAAUUUACUGUCGAACCUUUCUUAAAGGUAAACCAGAAACGUGUAAAACAACUUCAUAAUAAUCUUAAAACCAUAUCAAAUAAUUUAGUUUUUCUUUGUUUGUAAAGUAAUGUGAAGUCGAUAUAAUGUCUUUAUACCGAUAGUGCAAAACUGAUUUCAUAAGUCAGUUUUGUAUGUAUCGAGGUUUUCGAUCAUAGAAUUAAAUGAACUACCAAAUAGUAAUUCUUGAAGAAAGACAUAUCUAUUUCUCAUUUUUUUUAUAACUUUGCGUUUAAAUUAAAGUCUUUAUGAGUAUCAUUAAAUACUUAUUAUACAACGCUGAAAGAUGAAAA ..........(((((((((...........(((((.(((((((((...((((..(((........)))..)))).((((.......................(((....(((((.....)))))....)))....((.....))..))))............................)))))))))..((((..((((((((((((.(((((.((((...(((((((....(((((((((((((((((((.....)))))))))))))).)))))..........(((.(((((((..((......)).....))))))))))..))))))))))).))))).)))).........))))))))..)))).))))).....((((((((......))))))))...........)))))))))... (-80.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 378 331 159 111 pint:PI1325|5end_conserved_hypothetical_protein_1243415..1243645_POSITIVE 271 340 292 72 23 pint:PI1200|5end_carbon-nitrogen_hydrolase/beta-alanine_synthase_1115662..1115892_POSITIVE 269 399 351 202 148 pint:PI1392|5end_hypothetical_protein_1311901..1312131_POSITIVE 265 356 314 109 73 pint:PI1185|5end_hypothetical_protein_1106076..1106306_POSITIVE 262 326 287 142 102 pint:PI1739|5end_Na+-driven_multidrug_efflux_pump,_MATE_efflux_family_protein_1660177..1660407_POSITIVE 260 417 372 130 84 pint:PI1870|5end_hypothetical_protein_1815302..1815532_POSITIVE 253 371 338 140 107 pint:PI2013|5end_hypothetical_protein_1972329..1972559_POSITIVE 243 371 332 149 112 pint:PI0056|5end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_54967..55197_POSITIVE 237 370 331 195 155 pint:PI0459|5end_30S_ribosomal_protein_S10_432085..432315_POSITIVE 234 372 344 126 96 pint:PI1484|5end_conserved_hypothetical_protein_1404619..1404849_POSITIVE 234 216 172 221 175 pint:PI1172|5end_sensor_histidine_kinase_1091850..1092080_POSITIVE 234 352 311 60 14 pint:PI0888|5end_hypothetical_protein_817751..817981_POSITIVE 232 380 331 205 154 pint:PI0140|5end_conserved_hypothetical_protein_131643..131873_POSITIVE 231 220 180 211 173 pint:PI1068|5end_nucleolar_protein,_Sun_(Fmu)_family_protein;_tRNA/rRNA_cytosine-C5-methylase_984743..984973_POSITIVE 231 399 351 169 116 pint:PI0407|5end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_372973..373203_POSITIVE 223 339 291 202 161 pint:PI0492|5end_hypothetical_protein_451701..451931_POSITIVE 222 218 181 43 11 pint:PI2074|5end_conserved_hypothetical_protein_2033660..2033890_POSITIVE 220 390 344 87 24 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 220 126 83 175 138 pint:PI1465|5end_conserved_hypothetical_protein_1390081..1390311_POSITIVE 219 378 334 180 138 pint:PI1734|5end_possible_carboxyl-terminal_protease-related_protein_1652409..1652639_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 340 292 76 27 pint:PI1199|3end_possible_acetyltransferase_1115746..1115896_POSITIVE 265 356 314 116 80 pint:PI1184|3end_conserved_hypothetical_protein_1106163..1106313_POSITIVE 243 371 332 146 109 pint:PI0055|3end_hypothetical_protein_55044..55194_POSITIVE 237 370 331 101 61 pint:PI0458|3end_translation_elongation_factor_G_(EF-G)/tetracycline_resistance_factor_Q_432071..432221_POSITIVE 234 372 344 101 71 pint:PI1483|3end_hypothetical_protein_1404674..1404824_POSITIVE 234 372 344 72 42 pint:PI1482|3end_hypothetical_protein_1404645..1404795_POSITIVE 234 216 172 127 81 pint:PI1171|3end_hypothetical_protein_1091836..1091986_POSITIVE 232 410 362 125 78 pint:PI1346|3end_hypothetical_protein_1261028..1261178_POSITIVE 223 374 332 120 80 pint:PI1653|3end_hypothetical_protein_1565714..1565864_POSITIVE 222 347 311 83 47 pint:PI2083|3end_hypothetical_protein_2040661..2040811_POSITIVE 220 126 83 150 113 pint:PI1464|3end_zinc_protease_1390136..1390286_POSITIVE 219 378 334 128 86 pint:PI1733|3end_hypothetical_protein_1652437..1652587_POSITIVE 219 152 112 84 43 pint:PI0474|3end_30S_ribosomal_protein_S8_439515..439665_POSITIVE 218 301 276 46 20 pint:PI1958|3end_hypothetical_protein_1917369..1917519_POSITIVE 217 375 331 84 19 pint:PI0847|3end_thiamine_biosynthesis_lipoprotein,_ApbE_782232..782382_POSITIVE 213 307 261 130 78 pint:PI1105|3end_hypothetical_protein_1030235..1030385_POSITIVE 213 340 291 74 9 pint:PI0519|3end_5'-nucleotidase/2',3'-cyclic_phosphodiesterase_478809..478959_POSITIVE 212 410 361 78 23 pint:PI1922|3end_hypothetical_protein_1865454..1865604_POSITIVE 212 43 12 79 46 pint:PI1884|3end_conserved_hypothetical_protein_1827457..1827607_POSITIVE 212 417 372 74 28 pint:PI0182|3end_hypothetical_protein_174277..174427_POSITIVE