Origin IGS: tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgtatgaagatagagaaattcaaggtgttgctctacctgaaaaagagcagacccgacaagtcgggcaaagccccgatc .........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 gatcggggctttgcccgacttgtcgggtctgctctttttcaggtagagcaacaccttgaatttctctatcttcatacgctttaactttatgggcaaaattacccgttatcaaagcgttctctgatacgcaaaatattgataaacagataagaagaaaccgtatgagaaaaattcttccaataatcattacctca Mask Tandem Repeat Region ================================================ tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgtatgaagatagagaaattcaaggtgttgctctacctgaaaaagagcagacccgacaagtcgggcaaagccccgatc Find is-nt database================================================ Query_seq: PI0387:PI0388|PI0387:PI0388:hypothetical protein:integrase:->->:354873..355066 194 tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgtatgaagatagagaaattcaaggtgttgctctacctgaaaaagagcagacccgacaagtcgggcaaagccccgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0387:PI0388|PI0387:PI0388:hypothetical protein:integrase:->->:354873..355066 194 tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgtatgaagatagagaaattcaaggtgttgctctacctgaaaaagagcagacccgacaagtcgggcaaagccccgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0387:PI0388|PI0387:PI0388:hypothetical protein:integrase:->->:354873..355066 194 tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgtatgaagatagagaaattcaaggtgttgctctacctgaaaaagagcagacccgacaagtcgggcaaagccccgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgtatgaagatagagaaattcaaggtgttgctctacctgaaaaagagcagacccgacaagtcgggcaaagccccgatc Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 8 End: 193 ....... M I I G R I F L I R F L L I C L S I F C V S E N A L I T G N F A H K V K A Y E D R E I Q G V A L P E K E Q T R Q V G Q S . Protein_Len: 33 Strand: + Start: 96 End: 194 ............................................................................................... M L P I K L K R M K I E K F K V L L Y L K K S R P D K S G K A P I Protein_Len: 45 Strand: - Start: 1 End: 135 S T I I I P L I K R M R N R R I Q K D I N Q T D S F A K I V P L K A W L T L A Y S S L S M ........................................................... tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgtatgaagatagagaaattcaaggtgttgctctacctgaaaaagagcagacccgacaagtcgggcaaagccccgatc 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================================================ tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgtatgaagatagagaaattcaaggtgttgctctacctgaaaaagagcagacccgacaagtcgggcaaagccccgatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0387:PI0388|PI0387:PI0388:hypothetical protein:integrase:->->:354873..355066 194 tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgtatgaagatagagaaattcaaggtgttgctctacctgaaaaagagcagacccgacaagtcgggcaaagccccgatc Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: pint_PI0387_PI0388|hypothetical protein:integrase|POSITIVE:POSITIVE|[354873,355066]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgtatgaagatagagaaattcaaggtgttgctctacctgaaaaagagcagacccgacaagtcgggcaaagccccgatc tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgtatgaagatagagaaattcaaggtgttgctctacctgaaaaagagcagacccgacaagtcgggcaaagccccgatc Inter-species Hit: Count: 2 Min: 1 Max: 119 Len: 119 Subject: NC_002950_PG1454_PG1457|integrase:hypothetical protein|NEGATIVE:POSITIVE|[1538197,1538789]|593 HSP 1 e-value: 5.0E-59 bit: 228.0 Len: 119 Query Start:1 Query End:119 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 119 tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgt........................................................................... tgaggtaatgattattggaagaatttttctcatacggtttctttttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgt........................................................................... Subject: NC_002950_PG0816_PG0819|hypothetical protein:integrase|NEGATIVE:POSITIVE|[876950,877465]|516 HSP 1 e-value: 5.0E-59 bit: 228.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 398 Subject End: 516 tgaggtaatgattattggaagaatttttctcatacggtttcttcttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgt........................................................................... tgaggtaatgattattggaagaatttttctcatacggtttctttttatctgtttatcaatattttgcgtatcagagaacgctttgataacgggtaattttgcccataaagttaaagcgt........................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGGUAAUGAUUAUUGGAAGAAUUUUUCUCAUACGGUUUCUUCUUAUCUGUUUAUCAAUAUUUUGCGUAUCAGAGAACGCUUUGAUAACGGGUAAUUUUGCCCAUAAAGUUAAAGCGU ...(((((.(((....(((((((....((......)).))))))).)))...)))))....................((((((((((...(((((....))))).....)))))))))) (-26.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGCUUUAACUUUAUGGGCAAAAUUACCCGUUAUCAAAGCGUUCUCUGAUACGCAAAAUAUUGAUAAACAGAUAAGAAGAAACCGUAUGAGAAAAAUUCUUCCAAUAAUCAUUACCUCA (((((((......(((((........)))))....)))))))..((((.....(((....))).....))))...((((((...............))))))................. (-18.36) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 546 109 62 92 45 pint:PI0405|5end_hypothetical_protein_372534..372764_POSITIVE 289 102 64 225 187 pint:PI0047|5end_phosphomethylpyrimidine_kinase_45964..46194_POSITIVE 271 108 61 202 154 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 267 104 66 117 83 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 266 70 22 153 109 pint:PI1820|5end_hypothetical_protein_1759962..1760192_POSITIVE 260 108 61 192 127 pint:PI0462|5end_50S_ribosomal_protein_L23_433707..433937_POSITIVE 258 110 72 182 139 pint:PI1011|5end_cytochrome_c_biogenesis_protein_CycY_932115..932345_POSITIVE 250 46 1 212 169 pint:PI0373|5end_hypothetical_protein_344293..344523_POSITIVE 239 108 62 200 143 pint:PI0356|5end_hypothetical_protein_326642..326872_POSITIVE 238 110 61 183 127 pint:PI1620|5end__two-component_system_sensor_protein_1543956..1544186_POSITIVE 237 103 66 123 78 pint:PI0737|5end_hypothetical_protein_671182..671412_POSITIVE 237 102 71 52 10 pint:PI0473|5end_30S_ribosomal_protein_S14_438634..438864_POSITIVE 236 104 71 105 66 pint:PI1267|5end_probable_integrase_1186105..1186335_POSITIVE 233 94 51 225 191 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 232 46 4 104 60 pint:PI0268|5end_lysozyme-related_protein_259198..259428_POSITIVE 231 102 62 100 54 pint:PI1578|5end_rod_shape-determining_protein_1504188..1504418_POSITIVE 230 100 56 203 156 pint:PI1200|5end_carbon-nitrogen_hydrolase/beta-alanine_synthase_1115662..1115892_POSITIVE 228 95 58 152 113 pint:PI1913|5end_conserved_hypothetical_protein_1857104..1857334_POSITIVE 228 110 62 116 57 pint:PI1604|5end_hypothetical_protein_1534017..1534247_POSITIVE 225 106 61 195 163 pint:PI1310|5end_LysM_domain_protein_1227262..1227492_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 109 62 63 17 pint:PI1560|3end_integrase_1478265..1478415_POSITIVE 277 104 66 51 1 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 259 102 61 150 101 pint:PI0461|3end_50S_ribosomal_protein_L4_433761..433911_POSITIVE 250 110 62 102 47 pint:PI0365|3end_hypothetical_protein_336118..336268_POSITIVE 237 103 66 132 87 pint:PI0736|3end_transcriptional_regulator,_TetR_family_671271..671421_POSITIVE 237 102 71 43 1 pint:PI0472|3end_50S_ribosomal_protein_L5_438705..438855_POSITIVE 234 96 60 149 110 pint:PI1368|3end_enolase_(phosphopyruvate_hydratase)_1289507..1289657_POSITIVE 233 106 63 81 27 pint:PI0982|3end_hypothetical_protein_909649..909799_POSITIVE 232 46 4 117 73 pint:PI0267|3end_conjugative_transposon_protein,_TraQ_259291..259441_POSITIVE 231 104 62 151 119 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 228 95 58 134 95 pint:PI1912|3end_possible_DNA_repair_protein_1857166..1857316_POSITIVE 222 103 66 115 79 pint:PI0576|3end_helicase,_UvrD/Rep_521724..521874_POSITIVE 219 80 33 125 89 pint:PI1873|3end_hypothetical_protein_1818419..1818569_POSITIVE 215 100 51 74 19 pint:PI0361|3end_hypothetical_protein_333426..333576_POSITIVE 215 100 51 120 65 pint:PI0360|3end_conserved_hypothetical_protein_333472..333622_POSITIVE 212 103 67 128 84 pint:PI0006|3end_hypothetical_protein_8268..8418_POSITIVE 210 98 52 142 98 pint:PI0035|3end_NAD-dependent_protein_deacetylase,_SIR2_family_38642..38792_POSITIVE 209 48 2 68 12 pint:PI0815|3end_hypothetical_protein_754677..754827_POSITIVE 208 57 21 102 65 pint:PI1330|3end_WxcM-like,_C-terminal_family_protein_1248423..1248573_POSITIVE 208 91 66 145 122 pint:PI1132|3end_DnaJ_heat_shock_protein_(Hsp40)_1059668..1059818_POSITIVE