Origin IGS: aaatctttatgtttttgctgtaattttctatttacataaacggcaattcactgcatttattgagataagaaaaccataaaataatataaaaaagcactcgattgcgaaattatcgctacttttgctctcgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacgagagcaaaagtagcgataatttcgcaatcgagtgcttttttatattattttatggttttcttatctcaataaatgcagtgaattgccgtttatgtaaatagaaaattacagcaaaaacataaagattt Mask Tandem Repeat Region ================================================ aaatctttatgtttttgctgtaattttctatttacataaacggcaattcactgcatttattgagataagaaaaccataaaataatataaaaaagcactcgattgcgaaattatcgctacttttgctctcgtt Find is-nt database================================================ Query_seq: PI0018:PI0019|PI0018:PI0019:hypothetical protein:conserved hypothetical protein:->->:23750..23881 132 aaatctttatgtttttgctgtaattttctatttacataaacggcaattcactgcatttattgagataagaaaaccataaaataatataaaaaagcactcgattgcgaaattatcgctacttttgctctcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0018:PI0019|PI0018:PI0019:hypothetical protein:conserved hypothetical protein:->->:23750..23881 132 aaatctttatgtttttgctgtaattttctatttacataaacggcaattcactgcatttattgagataagaaaaccataaaataatataaaaaagcactcgattgcgaaattatcgctacttttgctctcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0018:PI0019|PI0018:PI0019:hypothetical protein:conserved hypothetical protein:->->:23750..23881 132 aaatctttatgtttttgctgtaattttctatttacataaacggcaattcactgcatttattgagataagaaaaccataaaataatataaaaaagcactcgattgcgaaattatcgctacttttgctctcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatctttatgtttttgctgtaattttctatttacataaacggcaattcactgcatttattgagataagaaaaccataaaataatataaaaaagcactcgattgcgaaattatcgctacttttgctctcgtt Predict ORF larger than 30AA ================================================ aaatctttatgtttttgctgtaattttctatttacataaacggcaattcactgcatttattgagataagaaaaccataaaataatataaaaaagcactcgattgcgaaattatcgctacttttgctctcgtt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatctttatgtttttgctgtaattttctatttacataaacggcaattcactgcatttattgagataagaaaaccataaaataatataaaaaagcactcgattgcgaaattatcgctacttttgctctcgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0018:PI0019|PI0018:PI0019:hypothetical protein:conserved hypothetical protein:->->:23750..23881 132 aaatctttatgtttttgctgtaattttctatttacataaacggcaattcactgcatttattgagataagaaaaccataaaataatataaaaaagcactcgattgcgaaattatcgctacttttgctctcgtt Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: pint_PI0018_PI0019|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[23750,23881]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 aaatctttatgtttttgctgtaattttctatttacataaacggcaattcactgcatttattgagataagaaaaccataaaataatataaaaaagcactcgattgcgaaattatcgctacttttgctctcgtt aaatctttatgtttttgctgtaattttctatttacataaacggcaattcactgcatttattgagataagaaaaccataaaataatataaaaaagcactcgattgcgaaattatcgctacttttgctctcgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCUUUAUGUUUUUGCUGUAAUUUUCUAUUUACAUAAACGGCAAUUCACUGCAUUUAUUGAGAUAAGAAAACCAUAAAAUAAUAUAAAAAAGCACUCGAUUGCGAAAUUAUCGCUACUUUUGCUCUCGUU .....((((((((.((..(((..((((((((((.((......(((......)))......)))))).))))))..))).)).))))))))..((((.......((((.....))))......))))...... (-19.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGAGAGCAAAAGUAGCGAUAAUUUCGCAAUCGAGUGCUUUUUUAUAUUAUUUUAUGGUUUUCUUAUCUCAAUAAAUGCAGUGAAUUGCCGUUUAUGUAAAUAGAAAAUUACAGCAAAAACAUAAAGAUUU ...(((((((...(..((((.....))))...)...)))))))........((((((((((((((.......((((((((((....))).)))))))......)))))))...........))))))).... (-24.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 57 17 168 127 pint:PI1588|5end_DNA_polymerase_III,_epsilon_chain_1516302..1516532_POSITIVE 276 128 84 209 159 pint:PI1528|5end_hypothetical_protein_1449685..1449915_POSITIVE 263 127 89 178 133 pint:PI2170|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2112238..2112468_POSITIVE 231 130 90 95 45 pint:PI0926|5end_hypothetical_protein_856824..857054_POSITIVE 231 85 43 111 74 pint:PI0720|5end_conserved_hypothetical_protein_653949..654179_POSITIVE 227 125 94 35 4 pint:PI1076|5end_hypothetical_protein_998893..999123_POSITIVE 227 129 89 64 20 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 224 55 18 113 70 pint:PI1225|5end_hypothetical_protein_1147758..1147988_POSITIVE 224 78 40 82 48 pint:PI0753|5end_hypothetical_protein_683391..683621_POSITIVE 224 57 20 47 16 pint:PI0392|5end_possible_transcriptional_regulator_358344..358574_POSITIVE 223 130 92 155 122 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 223 130 92 81 48 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 219 127 95 194 159 pint:PI2105|5end_hypothetical_protein_2059357..2059587_POSITIVE 219 127 95 58 23 pint:PI2106|5end_hypothetical_protein_2059221..2059451_POSITIVE 219 125 94 211 171 pint:PI0651|5end_HD_superfamily_hydrolase_592270..592500_POSITIVE 215 55 12 50 3 pint:PI1379|5end_hypothetical_protein_1301817..1302047_POSITIVE 214 127 94 36 5 pint:PI1510|5end_cell_division_protein_1428412..1428642_POSITIVE 214 130 91 208 165 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 213 130 99 192 161 pint:PI1912|5end_possible_DNA_repair_protein_1856364..1856594_POSITIVE 212 130 91 131 93 pint:PI0272|5end_conserved_hypothetical_protein_262621..262851_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 57 17 52 11 pint:PI1587|3end_conserved_hypothetical_protein;_possible_permease_1516266..1516416_POSITIVE 269 129 94 88 55 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE 257 130 91 133 99 pint:PI0365|3end_hypothetical_protein_336118..336268_POSITIVE 246 130 94 123 94 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 245 130 94 89 52 pint:PI0787|3end_glycosyltransferase_725793..725943_POSITIVE 231 126 97 82 58 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE 231 85 43 92 55 pint:PI0719|3end_conserved_hypothetical_protein_654010..654160_POSITIVE 227 125 94 127 96 pint:PI1076|3end_hypothetical_protein_999065..999215_POSITIVE 224 78 40 78 44 pint:PI0752|3end_conserved_hypothetical_protein_683467..683617_POSITIVE 219 127 95 147 112 pint:PI2104|3end_carboxyl-terminal_protease_2059390..2059540_POSITIVE 212 128 88 59 20 pint:PI0932|3end_conserved_hypothetical_protein;_possible_hemin_receptor_865364..865514_POSITIVE 207 54 15 91 53 pint:PI0687|3end_hypothetical_protein_625652..625802_POSITIVE 206 127 94 47 2 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 199 129 100 114 79 pint:PI0729|3end_integrase_661765..661915_POSITIVE 198 128 95 89 62 pint:PI1827|3end_peptidase,_M23/M37_family,_N-terminal_1768602..1768752_POSITIVE 198 124 84 72 30 pint:PI1670|3end_hypothetical_protein_1587026..1587176_POSITIVE 197 60 11 145 82 pint:PI1390|3end_hypothetical_protein_1311329..1311479_POSITIVE 197 128 85 108 62 pint:PI0565|3end_hypothetical_protein_511657..511807_POSITIVE 196 130 93 66 36 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 196 130 94 145 108 pint:PI1815|3end_polyphosphate-selective_porin_O_1754510..1754660_POSITIVE