Origin IGS: taaaagtgaagcatagagtaagtatatctattaaaagaaaaacaaataagataactataaaaactgctaatggtaacactaataccattggcagtttttattatataagaatattttattgtgaatcagaacatctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagatgttctgattcacaataaaatattcttatataataaaaactgccaatggtattagtgttaccattagcagtttttatagttatcttatttgtttttcttttaatagatatacttactctatgcttcactttta Mask Tandem Repeat Region ================================================ taaaagtgaagcatagagtaagtatatctattaaaagaaaaacaaataagataactataaaaactgctaatggtaacactaataccattggcagtttttattatataagaatattttattgtgaatcagaacatctta Find is-nt database================================================ Query_seq: PI1011:PI1012|PI1011:PI1012:cytochrome c biogenesis protein CycY:DNA-binding protein, histone-like family:->->:933050..933187 138 taaaagtgaagcatagagtaagtatatctattaaaagaaaaacaaataagataactataaaaactgctaatggtaacactaataccattggcagtttttattatataagaatattttattgtgaatcagaacatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1011:PI1012|PI1011:PI1012:cytochrome c biogenesis protein CycY:DNA-binding protein, histone-like family:->->:933050..933187 138 taaaagtgaagcatagagtaagtatatctattaaaagaaaaacaaataagataactataaaaactgctaatggtaacactaataccattggcagtttttattatataagaatattttattgtgaatcagaacatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1011:PI1012|PI1011:PI1012:cytochrome c biogenesis protein CycY:DNA-binding protein, histone-like family:->->:933050..933187 138 taaaagtgaagcatagagtaagtatatctattaaaagaaaaacaaataagataactataaaaactgctaatggtaacactaataccattggcagtttttattatataagaatattttattgtgaatcagaacatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagtgaagcatagagtaagtatatctattaaaagaaaaacaaataagataactataaaaactgctaatggtaacactaataccattggcagtttttattatataagaatattttattgtgaatcagaacatctta Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 6 End: 137 ..... M K H R V S I S I K R K T N K I T I K T A N G N T N T I G S F Y Y I R I F Y C E S E H L . Protein_Len: 39 Strand: - Start: 3 End: 119 .. F H L M S Y T Y R N F S F C I L Y S Y F S S I T V S I G N A T K I I Y S Y K M ................... Protein_Len: 31 Strand: - Start: 2 End: 94 . F T F C L T L I D I L L F V F L I V I F V A L P L V L V M P M ............................................ taaaagtgaagcatagagtaagtatatctattaaaagaaaaacaaataagataactataaaaactgctaatggtaacactaataccattggcagtttttattatataagaatattttattgtgaatcagaacatctta 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================================================ taaaagtgaagcatagagtaagtatatctattaaaagaaaaacaaataagataactataaaaactgctaatggtaacactaataccattggcagtttttattatataagaatattttattgtgaatcagaacatctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.6 Tail_Score: -5.24796 Start: 64 End: 94 Full_Region: AGATAACTATAAAAA CTGCTAATGGTA ACACTAA TACCATTGGCAG TTTTTATTATATAAG ...............................................................CTGCTAATGGTAACACTAATACCATTGGCAG............................................ TransTerm Strand: - Conf: 91 HP_score: -8.4 Tail_Score: -5.02439 Start: 64 End: 94 Full_Region: cttatataataaaaa ctgccaatggta ttagtgt taccattagcag tttttatagttatct ...............................................................ctgccaatggtattagtgttaccattagcag............................................ Find igs database================================================ Query_seq: PI1011:PI1012|PI1011:PI1012:cytochrome c biogenesis protein CycY:DNA-binding protein, histone-like family:->->:933050..933187 138 taaaagtgaagcatagagtaagtatatctattaaaagaaaaacaaataagataactataaaaactgctaatggtaacactaataccattggcagtttttattatataagaatattttattgtgaatcagaacatctta Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: pint_PI1011_PI1012|cytochrome c biogenesis protein CycY:DNA-binding protein, histone-like family|POSITIVE:POSITIVE|[933050,933187]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 taaaagtgaagcatagagtaagtatatctattaaaagaaaaacaaataagataactataaaaactgctaatggtaacactaataccattggcagtttttattatataagaatattttattgtgaatcagaacatctta taaaagtgaagcatagagtaagtatatctattaaaagaaaaacaaataagataactataaaaactgctaatggtaacactaataccattggcagtttttattatataagaatattttattgtgaatcagaacatctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGUGAAGCAUAGAGUAAGUAUAUCUAUUAAAAGAAAAACAAAUAAGAUAACUAUAAAAACUGCUAAUGGUAACACUAAUACCAUUGGCAGUUUUUAUUAUAUAAGAAUAUUUUAUUGUGAAUCAGAACAUCUUA ......(((..(((((...((((((.(((......)))............(((...(((((((((((((((((((.......)))))))))))))))))))..)))....))))))..)))))..))).......... (-31.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAUGUUCUGAUUCACAAUAAAAUAUUCUUAUAUAAUAAAAACUGCCAAUGGUAUUAGUGUUACCAUUAGCAGUUUUUAUAGUUAUCUUAUUUGUUUUUCUUUUAAUAGAUAUACUUACUCUAUGCUUCACUUUUA ...((.((...((........................(((((((((((.(((((((.......))))))).)))))))))))........((((((((........)))))))).......))...)).))....... (-26.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 99 62 83 45 pint:PI1671|5end_hypothetical_protein_1586397..1586627_POSITIVE 229 93 62 74 44 pint:PI0460|5end_50S_ribosomal_protein_L3_432471..432701_POSITIVE 208 95 64 28 1 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 207 93 66 47 15 pint:PI1743|5end_stationary-phase_survival_protein_1663948..1664178_POSITIVE 207 70 28 116 74 pint:PI0884|5end_hypothetical_protein_817302..817532_POSITIVE 207 70 28 94 52 pint:PI0885|5end_hypothetical_protein_817280..817510_POSITIVE 203 51 13 135 94 pint:PI1540|5end_hypothetical_protein_1461362..1461592_POSITIVE 202 102 66 209 176 pint:PI1476|5end_acyl-CoA_synthase/O-succinylbenzoic_acid-CoA_ligase_1397699..1397929_POSITIVE 202 101 64 71 22 pint:PI0385|5end_hypothetical_protein_353968..354198_POSITIVE 199 87 46 156 114 pint:PI0664|5end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_606891..607121_POSITIVE 198 99 63 71 36 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 198 94 56 174 136 pint:PI0493|5end_surface_antigen_BspA_452844..453074_POSITIVE 196 96 63 81 54 pint:PI1908|5end_transcriptional_regulator,_AraC_family_1852261..1852491_POSITIVE 196 42 2 225 176 pint:PI1080|5end_conserved_hypothetical_protein;_possible_outer_membrane_lipoprotein_1000264..1000494_POSITIVE 193 107 66 110 70 pint:PI1891|5end_hypothetical_protein_1835196..1835426_POSITIVE 189 104 64 73 22 pint:PI1330|5end_WxcM-like,_C-terminal_family_protein_1247936..1248166_POSITIVE 186 101 65 142 110 pint:PI0141|5end_glutamine_amidotransferase_involved_in_pyridoxine_biosynthesis_132710..132940_POSITIVE 185 123 89 199 168 pint:PI0294|5end_conserved_hypothetical_protein_276223..276453_POSITIVE 183 102 63 109 62 pint:PI0570|5end_exsB_protein;_possible_aluminum_resistance_protein_514665..514895_POSITIVE 182 94 65 167 138 pint:PI1448|5end_hypothetical_protein_1371579..1371809_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 240 120 71 46 4 pint:PI1011|3end_cytochrome_c_biogenesis_protein_CycY_932989..933139_POSITIVE 210 94 62 97 61 pint:PI0892|3end_acyl-ACP_thioesterase_823939..824089_POSITIVE 200 102 63 143 103 pint:PI1568|3end_OmpA_family_protein_1491043..1491193_POSITIVE 186 101 65 76 44 pint:PI0139|3end_pyridoxine_biosynthesis_protein_132724..132874_POSITIVE 183 96 63 78 44 pint:PI1378|3end_GTP-binding_protein_lepA_1301651..1301801_POSITIVE 179 110 63 70 15 pint:PI0096|3end_glycerol-3-phosphate_cytidylyltransferase_93305..93455_POSITIVE 178 92 64 105 73 pint:PI0652|3end_conserved_hypothetical_protein_595792..595942_POSITIVE 177 94 54 50 14 pint:PI2151|3end_conserved_hypothetical_protein_2098252..2098402_POSITIVE 177 110 70 137 91 pint:PI1147|3end_conserved_hypothetical_protein_1074769..1074919_POSITIVE 174 101 75 131 106 pint:PI0423|3end_hypothetical_protein_388432..388582_POSITIVE 173 109 71 43 10 pint:PI0286|3end_ISPg3-related_transposase_272065..272215_POSITIVE 172 97 63 34 2 pint:PI1896|3end_hypothetical_protein_1841188..1841338_POSITIVE 172 97 63 81 49 pint:PI1897|3end_conserved_hypothetical_protein_1841235..1841385_POSITIVE 171 97 70 78 49 pint:PI1250|3end_RNA_polymerase_ECF-type_sigma_70_factor_1174781..1174931_POSITIVE 169 95 66 85 61 pint:PI1857|3end_guanylate_kinase_1804396..1804546_POSITIVE 169 95 62 139 107 pint:PI1111|3end_ISPg3-related_transposase_1036404..1036554_POSITIVE 169 104 63 123 84 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 168 73 44 74 38 pint:PI0769|3end_phosphomannomutase_706172..706322_POSITIVE 167 96 61 107 81 pint:PI0538|3end_transcriptional_regulator_492925..493075_POSITIVE 163 97 66 146 115 pint:PI2146|3end_prolipoprotein_diacylglyceryl_transferase_2093321..2093471_POSITIVE