Origin IGS: tgttttcgattttagatgggcagatttctgtgttctaccttatattattattgcaaatatagattttttttttgaaagaaacagtatttgcagaaaaaatattcttttacgcttcattttacaaggtcagaggacacgaaaaaccaaaagagcagtttagacacagcataaggagaaatagcttattttagttaaaaactttagctttttatgacataatgatgtaaaacttcatttttttaaatagtttaaggctaaatattttgtagtttgccaccttattcttaattttacaccgtaaagaaact .........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 agtttctttacggtgtaaaattaagaataaggtggcaaactacaaaatatttagccttaaactatttaaaaaaatgaagttttacatcattatgtcataaaaagctaaagtttttaactaaaataagctatttctccttatgctgtgtctaaactgctcttttggtttttcgtgtcctctgaccttgtaaaatgaagcgtaaaagaatattttttctgcaaatactgtttctttcaaaaaaaaaatctatatttgcaataataatataaggtagaacacagaaatctgcccatctaaaatcgaaaaca Mask Tandem Repeat Region ================================================ tgttttcgattttagatgggcagatttctgtgttctaccttatattattattgcaaatatagattttttttttgaaagaaacagtatttgcagaaaaaatattcttttacgcttcattttacaaggtcagaggacacgaaaaaccaaaagagcagtttagacacagcataaggagaaatagcttattttagttaaaaactttagctttttatgacataatgatgtaaaacttcatttttttaaatagtttaaggctaaatattttgtagtttgccaccttattcttaattttacaccgtaaagaaact Find is-nt database================================================ Query_seq: PI1393:PI1394|PI1393:PI1394:aldose 1-epimerase:glutamate formiminotransferase:->->:1313884..1314191 308 tgttttcgattttagatgggcagatttctgtgttctaccttatattattattgcaaatatagattttttttttgaaagaaacagtatttgcagaaaaaatattcttttacgcttcattttacaaggtcagaggacacgaaaaaccaaaagagcagtttagacacagcataaggagaaatagcttattttagttaaaaactttagctttttatgacataatgatgtaaaacttcatttttttaaatagtttaaggctaaatattttgtagtttgccaccttattcttaattttacaccgtaaagaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1393:PI1394|PI1393:PI1394:aldose 1-epimerase:glutamate formiminotransferase:->->:1313884..1314191 308 tgttttcgattttagatgggcagatttctgtgttctaccttatattattattgcaaatatagattttttttttgaaagaaacagtatttgcagaaaaaatattcttttacgcttcattttacaaggtcagaggacacgaaaaaccaaaagagcagtttagacacagcataaggagaaatagcttattttagttaaaaactttagctttttatgacataatgatgtaaaacttcatttttttaaatagtttaaggctaaatattttgtagtttgccaccttattcttaattttacaccgtaaagaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1393:PI1394|PI1393:PI1394:aldose 1-epimerase:glutamate formiminotransferase:->->:1313884..1314191 308 tgttttcgattttagatgggcagatttctgtgttctaccttatattattattgcaaatatagattttttttttgaaagaaacagtatttgcagaaaaaatattcttttacgcttcattttacaaggtcagaggacacgaaaaaccaaaagagcagtttagacacagcataaggagaaatagcttattttagttaaaaactttagctttttatgacataatgatgtaaaacttcatttttttaaatagtttaaggctaaatattttgtagtttgccaccttattcttaattttacaccgtaaagaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttttcgattttagatgggcagatttctgtgttctaccttatattattattgcaaatatagattttttttttgaaagaaacagtatttgcagaaaaaatattcttttacgcttcattttacaaggtcagaggacacgaaaaaccaaaagagcagtttagacacagcataaggagaaatagcttattttagttaaaaactttagctttttatgacataatgatgtaaaacttcatttttttaaatagtttaaggctaaatattttgtagtttgccaccttattcttaattttacaccgtaaagaaact Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 44 End: 157 ........................................... M I I A N I D F F F E R N S I C R K N I L L R F I L Q G Q R T R K T K R A V ....................................................................................................................................................... Protein_Len: 42 Strand: + Start: 63 End: 188 .............................................................. M F F L K E T V F A E K I F F Y A S F Y K V R G H E K P K E Q F R H S I R R N S L F ........................................................................................................................ tgttttcgattttagatgggcagatttctgtgttctaccttatattattattgcaaatatagattttttttttgaaagaaacagtatttgcagaaaaaatattcttttacgcttcattttacaaggtcagaggacacgaaaaaccaaaagagcagtttagacacagcataaggagaaatagcttattttagttaaaaactttagctttttatgacataatgatgtaaaacttcatttttttaaatagtttaaggctaaatattttgtagtttgccaccttattcttaattttacaccgtaaagaaact 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: 71 End: 100 ......................................................................TTTGAAAGAAACAGTATTTGCAGAAAAAAT................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 191 End: 220 ..............................................................................................................................................................................................GTTAAAAACTTTAGCTTTTTATGACATAAT........................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgttttcgattttagatgggcagatttctgtgttctaccttatattattattgcaaatatagattttttttttgaaagaaacagtatttgcagaaaaaatattcttttacgcttcattttacaaggtcagaggacacgaaaaaccaaaagagcagtttagacacagcataaggagaaatagcttattttagttaaaaactttagctttttatgacataatgatgtaaaacttcatttttttaaatagtttaaggctaaatattttgtagtttgccaccttattcttaattttacaccgtaaagaaact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -2.8 Tail_Score: -5.49729 Start: 220 End: 234 Full_Region: CTTTTTATGACATAA TGATGT AAA ACTTCA TTTTTTTAAATAGTT ...........................................................................................................................................................................................................................TGATGTAAAACTTCA.......................................................................... Find igs database================================================ Query_seq: PI1393:PI1394|PI1393:PI1394:aldose 1-epimerase:glutamate formiminotransferase:->->:1313884..1314191 308 tgttttcgattttagatgggcagatttctgtgttctaccttatattattattgcaaatatagattttttttttgaaagaaacagtatttgcagaaaaaatattcttttacgcttcattttacaaggtcagaggacacgaaaaaccaaaagagcagtttagacacagcataaggagaaatagcttattttagttaaaaactttagctttttatgacataatgatgtaaaacttcatttttttaaatagtttaaggctaaatattttgtagtttgccaccttattcttaattttacaccgtaaagaaact Intra-Species Hit: Count: 1 Min: 1 Max: 308 Len: 308 Subject: pint_PI1393_PI1394|aldose 1-epimerase:glutamate formiminotransferase|POSITIVE:POSITIVE|[1313884, 1314191]|308 HSP 1 e-value: 1.0E-143 bit: 509.0 Len: 308 Query Start:1 Query End:308 Subject Strand: POSITIVE Subject Start: 1 Subject End: 308 tgttttcgattttagatgggcagatttctgtgttctaccttatattattattgcaaatatagannnnnnnnnngaaagaaacagtatttgcagaaaaaatattcttttacgcttcattttacaaggtcagaggacacgaaaaaccaaaagagcagtttagacacagcataaggagaaatagcttattttagttaaaaactttagctttttatgacataatgatgtaaaacttcannnnnnnaaatagtttaaggctaaatattttgtagtttgccaccttattcttaattttacaccgtaaagaaact tgttttcgattttagatgggcagatttctgtgttctaccttatattattattgcaaatatagattttttttttgaaagaaacagtatttgcagaaaaaatattcttttacgcttcattttacaaggtcagaggacacgaaaaaccaaaagagcagtttagacacagcataaggagaaatagcttattttagttaaaaactttagctttttatgacataatgatgtaaaacttcatttttttaaatagtttaaggctaaatattttgtagtttgccaccttattcttaattttacaccgtaaagaaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUCGAUUUUAGAUGGGCAGAUUUCUGUGUUCUACCUUAUAUUAUUAUUGCAAAUAUAGAUUUUUUUUUUGAAAGAAACAGUAUUUGCAGAAAAAAUAUUCUUUUACGCUUCAUUUUACAAGGUCAGAGGACACGAAAAACCAAAAGAGCAGUUUAGACACAGCAUAAGGAGAAAUAGCUUAUUUUAGUUAAAAACUUUAGCUUUUUAUGACAUAAUGAUGUAAAACUUCAUUUUUUUAAAUAGUUUAAGGCUAAAUAUUUUGUAGUUUGCCACCUUAUUCUUAAUUUUACACCGUAAAGAAACU .......((....((...((((((((..((((((((((((((((((.((.((((((((((.(.(((((((....)))))))).)))))))))).)).)))))....................)))))...))))))))......(((((.(((...((((((...((((((((((...(((((......)))))..........))))))))).)..(((((.(.....).)))))..........)))))).))).....))))).))))))))..))...))....((((((...))))))..... (-53.57) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUCUUUACGGUGUAAAAUUAAGAAUAAGGUGGCAAACUACAAAAUAUUUAGCCUUAAACUAUUUAAAAAAAUGAAGUUUUACAUCAUUAUGUCAUAAAAAGCUAAAGUUUUUAACUAAAAUAAGCUAUUUCUCCUUAUGCUGUGUCUAAACUGCUCUUUUGGUUUUUCGUGUCCUCUGACCUUGUAAAAUGAAGCGUAAAAGAAUAUUUUUUCUGCAAAUACUGUUUCUUUCAAAAAAAAAAUCUAUAUUUGCAAUAAUAAUAUAAGGUAGAACACAGAAAUCUGCCCAUCUAAAAUCGAAAACA (((((...((((((((((.....((((....((((((..........((..(((.......)))..))....(((((.(.....).))))).))))))....((((...(((((.....))))).))))..))))..))))))))))...)))))....((((((((((..(((...((((.(((((((..............((((......))))(((((((..((((.(((....))).))))...)))))))........)))))))))))...(((....)))..)))..))))))))))... (-50.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 179 134 72 20 pint:PI0455|5end_hypothetical_protein_427361..427591_POSITIVE 275 41 1 91 54 pint:PI2085|5end_conserved_hypothetical_protein_2041100..2041330_POSITIVE 264 167 121 167 110 pint:PI0784|5end_possible_amidase_enhancer_precursor_721892..722122_POSITIVE 262 168 124 143 104 pint:PI0654|5end_K+-dependent_Na+/Ca+_exchanger_related-protein_596283..596513_POSITIVE 246 182 148 77 36 pint:PI0245|5end_possible_mobilization_protein_242946..243176_POSITIVE 241 183 143 172 135 pint:PI0405|5end_hypothetical_protein_372534..372764_POSITIVE 240 40 2 220 167 pint:PI2087|5end_dihydropicolinate_reductase_2043423..2043653_POSITIVE 237 300 251 131 74 pint:PI0114|5end_hypothetical_protein_108139..108369_POSITIVE 233 60 12 217 172 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 231 46 6 189 157 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 230 175 137 201 161 pint:PI0346|5end_hypothetical_protein_320834..321064_POSITIVE 229 59 12 117 72 pint:PI0967|5end_conserved_hypothetical_protein_895424..895654_POSITIVE 228 276 232 156 102 pint:PI1436|5end_hypothetical_protein_1355961..1356191_POSITIVE 228 164 123 175 138 pint:PI0595|5end_conserved_hypothetical_protein_545571..545801_POSITIVE 227 168 121 181 128 pint:PI0101|5end_lauroyl/myristoyl_acyltransferase_96729..96959_POSITIVE 224 300 258 119 82 pint:PI1623|5end_hypothetical_protein_1547163..1547393_POSITIVE 223 45 1 92 31 pint:PI1734|5end_possible_carboxyl-terminal_protease-related_protein_1652409..1652639_POSITIVE 223 35 4 230 205 pint:PI1078|5end_conserved_hypothetical_protein_999500..999730_POSITIVE 222 41 7 173 130 pint:PI1547|5end_hypothetical_protein_1465808..1466038_POSITIVE 221 169 124 220 167 pint:PI1233|5end_conserved_hypothetical_protein;_possible__MazG_family_protein_1153334..1153564_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 167 121 122 65 pint:PI0782|3end_beta-lactamase_induction_signal_transducer,_AmpG_protein_721927..722077_POSITIVE 244 173 136 87 54 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 241 183 143 84 47 pint:PI0404|3end_integrase_372526..372676_POSITIVE 237 300 251 124 67 pint:PI0112|3end_hypothetical_protein_108212..108362_POSITIVE 235 157 111 74 26 pint:PI0286|3end_ISPg3-related_transposase_272065..272215_POSITIVE 230 175 137 96 56 pint:PI0345|3end_conserved_hypothetical_protein_320809..320959_POSITIVE 227 168 121 98 45 pint:PI0100|3end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_96726..96876_POSITIVE 224 300 258 106 69 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE 218 168 126 45 3 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE 218 138 107 64 32 pint:PI1358|3end_phospho-N-acetylmuramoyl-pentapeptide-transferase__1275516..1275666_POSITIVE 217 300 268 133 101 pint:PI0241|3end_possible_tetracycline_resistance_element_/mobilization_regulatory_protein_240036..240186_POSITIVE 215 138 102 111 72 pint:PI1848|3end_hypothetical_protein_1795015..1795165_POSITIVE 213 173 151 63 40 pint:PI1122|3end_pyridoxal-phosphate-dependent_aminotransferase_1048059..1048209_POSITIVE 213 161 121 60 2 pint:PI0403|3end_probable_integrase_371125..371275_POSITIVE 213 175 131 131 83 pint:PI0086|3end_possible_uroporphyrinogen-III_synthase_85770..85920_POSITIVE 211 48 19 125 93 pint:PI2117|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066684..2066834_POSITIVE 211 168 121 61 6 pint:PI1806|3end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1742191..1742341_POSITIVE 211 138 91 64 13 pint:PI1231|3end_hypothetical_protein_1153464..1153614_POSITIVE 211 208 162 92 41 pint:PI1187|3end_conserved_hypothetical_protein_1107245..1107395_POSITIVE 210 59 16 81 41 pint:PI1839|3end_hypothetical_protein_1782500..1782650_POSITIVE