Origin IGS: atatattcttaattctctaccttgttgtcaaggctttatataatgcaaagataataaaacttaatggataagtaggctaactcctatttattttgtacatttgcacctaatattaatgataaagaactaaacaaatgcagaatttagttatatataatacgctgcatcggcagaaggaacgcttccaaccgatagctgctcccaatgtagga .........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 tcctacattgggagcagctatcggttggaagcgttccttctgccgatgcagcgtattatatataactaaattctgcatttgtttagttctttatcattaatattaggtgcaaatgtacaaaataaataggagttagcctacttatccattaagttttattatctttgcattatataaagccttgacaacaaggtagagaattaagaatatat Mask Tandem Repeat Region ================================================ atatattcttaattctctaccttgttgtcaaggctttatataatgcaaagataataaaacttaatggataagtaggctaactcctatttattttgtacatttgcacctaatattaatgataaagaactaaacaaatgcagaatttagttatatataatacgctgcatcggcagaaggaacgcttccaaccgatagctgctcccaatgtagga Find is-nt database================================================ Query_seq: PI2138:PI2139|PI2138:PI2139:nicotinate phosphoribosyltransferase:cysteinyl-tRNA synthetase:->->:2085194..2085405 212 atatattcttaattctctaccttgttgtcaaggctttatataatgcaaagataataaaacttaatggataagtaggctaactcctatttattttgtacatttgcacctaatattaatgataaagaactaaacaaatgcagaatttagttatatataatacgctgcatcggcagaaggaacgcttccaaccgatagctgctcccaatgtagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2138:PI2139|PI2138:PI2139:nicotinate phosphoribosyltransferase:cysteinyl-tRNA synthetase:->->:2085194..2085405 212 atatattcttaattctctaccttgttgtcaaggctttatataatgcaaagataataaaacttaatggataagtaggctaactcctatttattttgtacatttgcacctaatattaatgataaagaactaaacaaatgcagaatttagttatatataatacgctgcatcggcagaaggaacgcttccaaccgatagctgctcccaatgtagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2138:PI2139|PI2138:PI2139:nicotinate phosphoribosyltransferase:cysteinyl-tRNA synthetase:->->:2085194..2085405 212 atatattcttaattctctaccttgttgtcaaggctttatataatgcaaagataataaaacttaatggataagtaggctaactcctatttattttgtacatttgcacctaatattaatgataaagaactaaacaaatgcagaatttagttatatataatacgctgcatcggcagaaggaacgcttccaaccgatagctgctcccaatgtagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatattcttaattctctaccttgttgtcaaggctttatataatgcaaagataataaaacttaatggataagtaggctaactcctatttattttgtacatttgcacctaatattaatgataaagaactaaacaaatgcagaatttagttatatataatacgctgcatcggcagaaggaacgcttccaaccgatagctgctcccaatgtagga Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 116 End: 205 ................................................................................................................... H Y L V L C I C F K T I Y L V S C R C F S R K W G I A A G M ....... atatattcttaattctctaccttgttgtcaaggctttatataatgcaaagataataaaacttaatggataagtaggctaactcctatttattttgtacatttgcacctaatattaatgataaagaactaaacaaatgcagaatttagttatatataatacgctgcatcggcagaaggaacgcttccaaccgatagctgctcccaatgtagga 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: 51 End: 80 ..................................................TTAGCCTACTTATCCATTAAGTTTTATTAT.................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatattcttaattctctaccttgttgtcaaggctttatataatgcaaagataataaaacttaatggataagtaggctaactcctatttattttgtacatttgcacctaatattaatgataaagaactaaacaaatgcagaatttagttatatataatacgctgcatcggcagaaggaacgcttccaaccgatagctgctcccaatgtagga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 62 HP_score: -3.8 Tail_Score: -4.51196 Start: 69 End: 90 Full_Region: ATAAAACTTAATGGA TAAGTAGG CTAACT CCTATTTA TTTTGTACATTTGCA ....................................................................TAAGTAGGCTAACTCCTATTTA.......................................................................................................................... Find igs database================================================ Query_seq: PI2138:PI2139|PI2138:PI2139:nicotinate phosphoribosyltransferase:cysteinyl-tRNA synthetase:->->:2085194..2085405 212 atatattcttaattctctaccttgttgtcaaggctttatataatgcaaagataataaaacttaatggataagtaggctaactcctatttattttgtacatttgcacctaatattaatgataaagaactaaacaaatgcagaatttagttatatataatacgctgcatcggcagaaggaacgcttccaaccgatagctgctcccaatgtagga Intra-Species Hit: Count: 1 Min: 1 Max: 212 Len: 212 Subject: pint_PI2138_PI2139|nicotinate phosphoribosyltransferase:cysteinyl-tRNA synthetase|POSITIVE:POSITIVE|[2085194,2085405]|212 HSP 1 e-value: 1.0E-117 bit: 420.0 Len: 212 Query Start:1 Query End:212 Subject Strand: POSITIVE Subject Start: 1 Subject End: 212 atatattcttaattctctaccttgttgtcaaggctttatataatgcaaagataataaaacttaatggataagtaggctaactcctatttattttgtacatttgcacctaatattaatgataaagaactaaacaaatgcagaatttagttatatataatacgctgcatcggcagaaggaacgcttccaaccgatagctgctcccaatgtagga atatattcttaattctctaccttgttgtcaaggctttatataatgcaaagataataaaacttaatggataagtaggctaactcctatttattttgtacatttgcacctaatattaatgataaagaactaaacaaatgcagaatttagttatatataatacgctgcatcggcagaaggaacgcttccaaccgatagctgctcccaatgtagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAUUCUUAAUUCUCUACCUUGUUGUCAAGGCUUUAUAUAAUGCAAAGAUAAUAAAACUUAAUGGAUAAGUAGGCUAACUCCUAUUUAUUUUGUACAUUUGCACCUAAUAUUAAUGAUAAAGAACUAAACAAAUGCAGAAUUUAGUUAUAUAUAAUACGCUGCAUCGGCAGAAGGAACGCUUCCAACCGAUAGCUGCUCCCAAUGUAGGA ((((((.((.((((((...(((((....)))))((((((....((((((.((((............((((((((((......))))))))))))))...)))))).............))))))..............)))))).))..)))))).....((.(((((((..((((.....))))...))))).)).))..((......)). (-41.13) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUACAUUGGGAGCAGCUAUCGGUUGGAAGCGUUCCUUCUGCCGAUGCAGCGUAUUAUAUAUAACUAAAUUCUGCAUUUGUUUAGUUCUUUAUCAUUAAUAUUAGGUGCAAAUGUACAAAAUAAAUAGGAGUUAGCCUACUUAUCCAUUAAGUUUUAUUAUCUUUGCAUUAUAUAAAGCCUUGACAACAAGGUAGAGAAUUAAGAAUAUAU .....((..((((((.(((.((.....)))))))))))..))..(((((((.((.(((........))))).)))))))..(((((((((((.............((((((((.(((.(((((.....(((...((....))..))).....)))))..))).)))))))).......((((((....)))))))))))))))))....... (-44.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 209 162 110 46 pint:PI1475|5end_possible_short_chain_dehydrogenase_1397142..1397372_POSITIVE 378 200 154 61 12 pint:PI1058|5end_possible_FHA_domain_protein_977577..977807_POSITIVE 352 200 159 211 173 pint:PI0251|5end_hypothetical_protein_247551..247781_POSITIVE 348 209 164 76 29 pint:PI0953|5end_hypothetical_protein_885119..885349_POSITIVE 346 210 168 74 31 pint:PI1230|5end_probable_metallo-beta-lactamase_family_protein_1151840..1152070_POSITIVE 336 193 157 54 12 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 332 209 161 85 34 pint:PI1829|5end_hypothetical_protein_1769255..1769485_POSITIVE 324 209 161 85 26 pint:PI1346|5end_hypothetical_protein_1260814..1261044_POSITIVE 324 209 161 134 75 pint:PI0055|5end_hypothetical_protein_54815..55045_POSITIVE 321 199 168 69 37 pint:PI0929|5end_copper_homeostasis_protein_860294..860524_POSITIVE 319 207 161 167 126 pint:PI2121|5end_glucose_inhibited_division_protein_A_2069889..2070119_POSITIVE 312 210 166 51 5 pint:PI0139|5end_pyridoxine_biosynthesis_protein_131835..132065_POSITIVE 310 208 163 126 72 pint:PI2162|5end_conserved_hypothetical_protein_2108796..2109026_POSITIVE 310 209 163 85 33 pint:PI2153|5end_hypothetical_protein_2099392..2099622_POSITIVE 310 197 159 81 29 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 310 209 163 211 159 pint:PI0788|5end_3-methyladenine_DNA_glycosylase_(DNA-3-methyladenine_glycosylase_I)_726152..726382_POSITIVE 310 209 163 216 164 pint:PI0771|5end_conserved_hypothetical_protein_706524..706754_POSITIVE 309 205 165 131 93 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 309 207 161 59 1 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 307 208 162 173 126 pint:PI0203|5end_conserved_hypothetical_protein_195109..195339_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 202 161 139 72 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 324 209 161 127 68 pint:PI1141|3end_hypothetical_protein_1069713..1069863_POSITIVE 324 196 161 150 121 pint:PI0911|3end_tyrosine_phenol-lyase_841209..841359_POSITIVE 324 209 161 68 9 pint:PI0054|3end_hypothetical_protein_54829..54979_POSITIVE 310 197 159 61 9 pint:PI1635|3end_hypothetical_protein_1554306..1554456_POSITIVE 309 205 165 134 96 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 304 200 156 145 107 pint:PI1587|3end_conserved_hypothetical_protein;_possible_permease_1516266..1516416_POSITIVE 302 201 161 74 29 pint:PI0634|3end_conserved_hypothetical_protein_581121..581271_POSITIVE 301 208 162 47 4 pint:PI2108|3end_cell_surface_protein;_possible_cell_surface_antigen_BspA_2060625..2060775_POSITIVE 299 207 162 139 88 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 298 202 161 105 72 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 297 210 167 59 1 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 296 191 155 134 89 pint:PI1973|3end_conserved_hypothetical_protein_1931171..1931321_POSITIVE 295 202 167 103 69 pint:PI1178|3end_histidyl-tRNA_synthetase_1100564..1100714_POSITIVE 293 209 161 68 9 pint:PI0996|3end_hypothetical_protein_920660..920810_POSITIVE 288 207 162 98 37 pint:PI0539|3end_hypothetical_protein_493728..493878_POSITIVE 288 200 157 48 10 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 287 204 161 53 6 pint:PI1363|3end_hypothetical_protein_1281922..1282072_POSITIVE 286 200 160 95 54 pint:PI0057|3end_conserved_hypothetical_protein_56512..56662_POSITIVE 285 199 158 85 28 pint:PI1366|3end_conserved_hypothetical_protein;_possible_hydrolase,_HAD_superfamily_1286647..1286797_POSITIVE