Origin IGS: tcttactgttttccaattatattattgttactaacgcttaaacttaaaaaatattttaatgttttaccacttatttcactttatacacaataaaagcaaaggaaacgtgttatgtaattaaacttgttaagaaactttgaaacaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttgtttcaaagtttcttaacaagtttaattacataacacgtttcctttgcttttattgtgtataaagtgaaataagtggtaaaacattaaaatattttttaagtttaagcgttagtaacaataatataattggaaaacagtaaga Mask Tandem Repeat Region ================================================ tcttactgttttccaattatattattgttactaacgcttaaacttaaaaaatattttaatgttttaccacttatttcactttatacacaataaaagcaaaggaaacgtgttatgtaattaaacttgttaagaaactttgaaacaaac Find is-nt database================================================ Query_seq: PI1357:PI1358|PI1357:PI1358:glycosyltransferase:phospho-N-acetylmuramoyl-pentapeptide-transferase :->->:1274320..1274466 147 tcttactgttttccaattatattattgttactaacgcttaaacttaaaaaatattttaatgttttaccacttatttcactttatacacaataaaagcaaaggaaacgtgttatgtaattaaacttgttaagaaactttgaaacaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1357:PI1358|PI1357:PI1358:glycosyltransferase:phospho-N-acetylmuramoyl-pentapeptide-transferase :->->:1274320..1274466 147 tcttactgttttccaattatattattgttactaacgcttaaacttaaaaaatattttaatgttttaccacttatttcactttatacacaataaaagcaaaggaaacgtgttatgtaattaaacttgttaagaaactttgaaacaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1357:PI1358|PI1357:PI1358:glycosyltransferase:phospho-N-acetylmuramoyl-pentapeptide-transferase :->->:1274320..1274466 147 tcttactgttttccaattatattattgttactaacgcttaaacttaaaaaatattttaatgttttaccacttatttcactttatacacaataaaagcaaaggaaacgtgttatgtaattaaacttgttaagaaactttgaaacaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttactgttttccaattatattattgttactaacgcttaaacttaaaaaatattttaatgttttaccacttatttcactttatacacaataaaagcaaaggaaacgtgttatgtaattaaacttgttaagaaactttgaaacaaac Predict ORF larger than 30AA ================================================ tcttactgttttccaattatattattgttactaacgcttaaacttaaaaaatattttaatgttttaccacttatttcactttatacacaataaaagcaaaggaaacgtgttatgtaattaaacttgttaagaaactttgaaacaaac 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================================================ tcttactgttttccaattatattattgttactaacgcttaaacttaaaaaatattttaatgttttaccacttatttcactttatacacaataaaagcaaaggaaacgtgttatgtaattaaacttgttaagaaactttgaaacaaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1357:PI1358|PI1357:PI1358:glycosyltransferase:phospho-N-acetylmuramoyl-pentapeptide-transferase :->->:1274320..1274466 147 tcttactgttttccaattatattattgttactaacgcttaaacttaaaaaatattttaatgttttaccacttatttcactttatacacaataaaagcaaaggaaacgtgttatgtaattaaacttgttaagaaactttgaaacaaac Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: pint_PI1357_PI1358|glycosyltransferase:phospho-N-acetylmuramoyl- pentapeptide-transferase |POSITIVE:POSITIVE|[1274320,1274466]|147 HSP 1 e-value: 3.0E-78 bit: 291.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 tcttactgttttccaattatattattgttactaacgcttaaacttaaaaaatattttaatgttttaccacttatttcactttatacacaataaaagcaaaggaaacgtgttatgtaattaaacttgttaagaaactttgaaacaaac tcttactgttttccaattatattattgttactaacgcttaaacttaaaaaatattttaatgttttaccacttatttcactttatacacaataaaagcaaaggaaacgtgttatgtaattaaacttgttaagaaactttgaaacaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUACUGUUUUCCAAUUAUAUUAUUGUUACUAACGCUUAAACUUAAAAAAUAUUUUAAUGUUUUACCACUUAUUUCACUUUAUACACAAUAAAAGCAAAGGAAACGUGUUAUGUAAUUAAACUUGUUAAGAAACUUUGAAACAAAC ..(((..(((((..(((.........(((((((((((..((((((((((....)))))).)))).........((((.((((...............)))))))).)))))).))))).......)))..)))))..)))....... (-15.05) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUGUUUCAAAGUUUCUUAACAAGUUUAAUUACAUAACACGUUUCCUUUGCUUUUAUUGUGUAUAAAGUGAAAUAAGUGGUAAAACAUUAAAAUAUUUUUUAAGUUUAAGCGUUAGUAACAAUAAUAUAAUUGGAAAACAGUAAGA ((((..(((((.(((....)))........((((.((((.(....((((((.(((((((........))))))))))).))..((((.((((((....))))))))))..).))))))))...........)))))))))....... (-16.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 217 79 35 230 197 pint:PI0028|5end_aminopeptidase_31559..31789_POSITIVE 207 108 69 169 122 pint:PI0521|5end_hypothetical_protein_478886..479116_POSITIVE 204 101 61 213 174 pint:PI2095|5end_hypothetical_protein_2049195..2049425_POSITIVE 204 101 61 208 169 pint:PI2093|5end_hypothetical_protein_2049190..2049420_POSITIVE 204 101 61 198 159 pint:PI2092|5end_hypothetical_protein_2049180..2049410_POSITIVE 202 108 68 178 129 pint:PI0190|5end_3-dehydroquinate_dehydratase_II_180618..180848_POSITIVE 195 138 94 118 76 pint:PI0081|5end_hypothetical_protein_80423..80653_POSITIVE 188 49 1 197 154 pint:PI0957|5end_conserved_hypothetical_protein_888789..889019_POSITIVE 186 126 85 188 148 pint:PI0284|5end_flavoprotein_A_268848..269078_POSITIVE 183 115 93 158 133 pint:PI0853|5end_glycosyl_transferase,_group_2_family_protein_785515..785745_POSITIVE 182 110 66 170 126 pint:PI0127|5end_conserved_hypothetical_protein_118683..118913_POSITIVE 181 114 72 185 152 pint:PI1438|5end_penicillin_tolerance_protein/steroid_biosynthesis_1356263..1356493_POSITIVE 181 97 54 193 139 pint:PI0812|5end_conserved_hypothetical_protein;_possible_ferredoxin_750185..750415_POSITIVE 178 37 1 89 44 pint:PI1688|5end_possible_GTPase_1602882..1603112_POSITIVE 177 111 77 40 6 pint:PI1529|5end_cytosine/adenosine_deaminase_1449887..1450117_POSITIVE 173 140 99 63 13 pint:PI1803|5end_conserved_hypothetical_protein_1735081..1735311_POSITIVE 170 108 76 162 135 pint:PI2151|5end_conserved_hypothetical_protein_2097573..2097803_POSITIVE 170 115 71 192 145 pint:PI0430|5end_periplasmic_protease;_MdsD_protein_399830..400060_POSITIVE 169 128 88 170 137 pint:PI0027|5end_aminopeptidase_C_30468..30698_POSITIVE 168 111 76 228 195 pint:PI1914|5end_RNA_polymerase,_ECF-type_sigma_factor_1858025..1858255_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 215 110 65 66 6 pint:PI1231|3end_hypothetical_protein_1153464..1153614_POSITIVE 205 106 69 149 107 pint:PI0520|3end_hypothetical_protein_478951..479101_POSITIVE 188 137 93 84 29 pint:PI1379|3end_hypothetical_protein_1302292..1302442_POSITIVE 188 49 1 64 21 pint:PI0956|3end_conserved_hypothetical_protein_888736..888886_POSITIVE 186 126 85 141 101 pint:PI0283|3end_Zn-dependent_peptidase_268881..269031_POSITIVE 181 114 72 74 41 pint:PI1436|3end_hypothetical_protein_1356232..1356382_POSITIVE 180 110 90 29 8 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 168 111 76 131 98 pint:PI1913|3end_conserved_hypothetical_protein_1858008..1858158_POSITIVE 168 80 52 130 94 pint:PI0580|3end_Holliday_junction_DNA_helicase_524902..525052_POSITIVE 168 118 86 84 48 pint:PI0409|3end_3-deoxy-D-manno-octulosonic-acid_transferase_(kdotransferase)_375969..376119_POSITIVE 166 132 94 80 47 pint:PI0100|3end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_96726..96876_POSITIVE 165 109 67 49 2 pint:PI0992|3end_RNA_polymerase_sigma-70_factor_917222..917372_POSITIVE 165 131 94 129 80 pint:PI0276|3end_anti-restriction_protein_265021..265171_POSITIVE 164 85 47 57 15 pint:PI0926|3end_hypothetical_protein_857047..857197_POSITIVE 162 129 86 109 77 pint:PI1204|3end_hypothetical_protein_1124635..1124785_POSITIVE 162 114 89 112 90 pint:PI1188|3end_hypothetical_protein_1108895..1109045_POSITIVE 159 39 6 108 74 pint:PI1627|3end_hypothetical_protein_1551157..1551307_POSITIVE 159 140 94 68 15 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 157 106 62 61 16 pint:PI0981|3end_outer_membrane_protein,_TonB_dependent_receptor_909390..909540_POSITIVE 157 99 62 50 14 pint:PI0836|3end_conserved_hypothetical_protein_772373..772523_POSITIVE