Origin IGS: tgtcttttctttttggttgcaaaattaaacatgaaagagcctaaccctgctatgcaaaatatagagcagtagagcaacagcaacggatgcacggaaaaccgctgtttttctcctctttgacggaggtgattaccttgctttcgggtaacgatttgaaaacctttctgtcgcaataatccgcatattactgcctcgtggcaggtggcggattttctgcagtttgcgccgtatgtccttaataatcaagcccaattgcgttaaactgccgattttatgcgaatattacagcgattttaagttactttgcaatcgtaaaaaatatagagaattggaaaacaac .........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 gttgttttccaattctctatattttttacgattgcaaagtaacttaaaatcgctgtaatattcgcataaaatcggcagtttaacgcaattgggcttgattattaaggacatacggcgcaaactgcagaaaatccgccacctgccacgaggcagtaatatgcggattattgcgacagaaaggttttcaaatcgttacccgaaagcaaggtaatcacctccgtcaaagaggagaaaaacagcggttttccgtgcatccgttgctgttgctctactgctctatattttgcatagcagggttaggctctttcatgtttaattttgcaaccaaaaagaaaagaca Mask Tandem Repeat Region ================================================ tgtcttttctttttggttgcaaaattaaacatgaaagagcctaaccctgctatgcaaaatatagagcagtagagcaacagcaacggatgcacggaaaaccgctgtttttctcctctttgacggaggtgattaccttgctttcgggtaacgatttgaaaacctttctgtcgcaataatccgcatattactgcctcgtggcaggtggcggattttctgcagtttgcgccgtatgtccttaataatcaagcccaattgcgttaaactgccgattttatgcgaatattacagcgattttaagttactttgcaatcgtaaaaaatatagagaattggaaaacaac Find is-nt database================================================ Query_seq: PG1113:PG1114|PG1113:PG1114:integrase:aspartate 1-decarboxylase precursor:<-->:1186837..1187176 340 tgtcttttctttttggttgcaaaattaaacatgaaagagcctaaccctgctatgcaaaatatagagcagtagagcaacagcaacggatgcacggaaaaccgctgtttttctcctctttgacggaggtgattaccttgctttcgggtaacgatttgaaaacctttctgtcgcaataatccgcatattactgcctcgtggcaggtggcggattttctgcagtttgcgccgtatgtccttaataatcaagcccaattgcgttaaactgccgattttatgcgaatattacagcgattttaagttactttgcaatcgtaaaaaatatagagaattggaaaacaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1113:PG1114|PG1113:PG1114:integrase:aspartate 1-decarboxylase precursor:<-->:1186837..1187176 340 tgtcttttctttttggttgcaaaattaaacatgaaagagcctaaccctgctatgcaaaatatagagcagtagagcaacagcaacggatgcacggaaaaccgctgtttttctcctctttgacggaggtgattaccttgctttcgggtaacgatttgaaaacctttctgtcgcaataatccgcatattactgcctcgtggcaggtggcggattttctgcagtttgcgccgtatgtccttaataatcaagcccaattgcgttaaactgccgattttatgcgaatattacagcgattttaagttactttgcaatcgtaaaaaatatagagaattggaaaacaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1113:PG1114|PG1113:PG1114:integrase:aspartate 1-decarboxylase precursor:<-->:1186837..1187176 340 tgtcttttctttttggttgcaaaattaaacatgaaagagcctaaccctgctatgcaaaatatagagcagtagagcaacagcaacggatgcacggaaaaccgctgtttttctcctctttgacggaggtgattaccttgctttcgggtaacgatttgaaaacctttctgtcgcaataatccgcatattactgcctcgtggcaggtggcggattttctgcagtttgcgccgtatgtccttaataatcaagcccaattgcgttaaactgccgattttatgcgaatattacagcgattttaagttactttgcaatcgtaaaaaatatagagaattggaaaacaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtcttttctttttggttgcaaaattaaacatgaaagagcctaaccctgctatgcaaaatatagagcagtagagcaacagcaacggatgcacggaaaaccgctgtttttctcctctttgacggaggtgattaccttgctttcgggtaacgatttgaaaacctttctgtcgcaataatccgcatattactgcctcgtggcaggtggcggattttctgcagtttgcgccgtatgtccttaataatcaagcccaattgcgttaaactgccgattttatgcgaatattacagcgattttaagttactttgcaatcgtaaaaaatatagagaattggaaaacaac Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 173 End: 340 ............................................................................................................................................................................ M I R I L L P R G R W R I F C S L R R M S L I I K P N C V K L P I L C E Y Y S D F K L L C N R K K Y R E L E N N Protein_Len: 46 Strand: - Start: 133 End: 270 .................................................................................................................................... R A K P Y R N S F R E T A I I R M N S G R P L H R I K Q L K R R I D K I I L G L Q T L S G M ...................................................................... Protein_Len: 60 Strand: - Start: 3 End: 185 .. K K K T A F N F M F S G L G A I C F I S C Y L L L L P H V S F R Q K E G R Q R L H N G Q K R T V I Q F G K Q R L L G C M ........................................................................................................................................................... tgtcttttctttttggttgcaaaattaaacatgaaagagcctaaccctgctatgcaaaatatagagcagtagagcaacagcaacggatgcacggaaaaccgctgtttttctcctctttgacggaggtgattaccttgctttcgggtaacgatttgaaaacctttctgtcgcaataatccgcatattactgcctcgtggcaggtggcggattttctgcagtttgcgccgtatgtccttaataatcaagcccaattgcgttaaactgccgattttatgcgaatattacagcgattttaagttactttgcaatcgtaaaaaatatagagaattggaaaacaac 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================================================ tgtcttttctttttggttgcaaaattaaacatgaaagagcctaaccctgctatgcaaaatatagagcagtagagcaacagcaacggatgcacggaaaaccgctgtttttctcctctttgacggaggtgattaccttgctttcgggtaacgatttgaaaacctttctgtcgcaataatccgcatattactgcctcgtggcaggtggcggattttctgcagtttgcgccgtatgtccttaataatcaagcccaattgcgttaaactgccgattttatgcgaatattacagcgattttaagttactttgcaatcgtaaaaaatatagagaattggaaaacaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1113:PG1114|PG1113:PG1114:integrase:aspartate 1-decarboxylase precursor:<-->:1186837..1187176 340 tgtcttttctttttggttgcaaaattaaacatgaaagagcctaaccctgctatgcaaaatatagagcagtagagcaacagcaacggatgcacggaaaaccgctgtttttctcctctttgacggaggtgattaccttgctttcgggtaacgatttgaaaacctttctgtcgcaataatccgcatattactgcctcgtggcaggtggcggattttctgcagtttgcgccgtatgtccttaataatcaagcccaattgcgttaaactgccgattttatgcgaatattacagcgattttaagttactttgcaatcgtaaaaaatatagagaattggaaaacaac Intra-Species Hit: Count: 1 Min: 1 Max: 340 Len: 340 Subject: NC_002950_PG1113_PG1114|integrase:aspartate 1-decarboxylase precursor|NEGATIVE:POSITIVE|[1186837,1187176]|340 HSP 1 e-value: 0.0 bit: 674.0 Len: 340 Query Start:1 Query End:340 Subject Strand: POSITIVE Subject Start: 1 Subject End: 340 tgtcttttctttttggttgcaaaattaaacatgaaagagcctaaccctgctatgcaaaatatagagcagtagagcaacagcaacggatgcacggaaaaccgctgtttttctcctctttgacggaggtgattaccttgctttcgggtaacgatttgaaaacctttctgtcgcaataatccgcatattactgcctcgtggcaggtggcggattttctgcagtttgcgccgtatgtccttaataatcaagcccaattgcgttaaactgccgattttatgcgaatattacagcgattttaagttactttgcaatcgtaaaaaatatagagaattggaaaacaac tgtcttttctttttggttgcaaaattaaacatgaaagagcctaaccctgctatgcaaaatatagagcagtagagcaacagcaacggatgcacggaaaaccgctgtttttctcctctttgacggaggtgattaccttgctttcgggtaacgatttgaaaacctttctgtcgcaataatccgcatattactgcctcgtggcaggtggcggattttctgcagtttgcgccgtatgtccttaataatcaagcccaattgcgttaaactgccgattttatgcgaatattacagcgattttaagttactttgcaatcgtaaaaaatatagagaattggaaaacaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUUUUCUUUUUGGUUGCAAAAUUAAACAUGAAAGAGCCUAACCCUGCUAUGCAAAAUAUAGAGCAGUAGAGCAACAGCAACGGAUGCACGGAAAACCGCUGUUUUUCUCCUCUUUGACGGAGGUGAUUACCUUGCUUUCGGGUAACGAUUUGAAAACCUUUCUGUCGCAAUAAUCCGCAUAUUACUGCCUCGUGGCAGGUGGCGGAUUUUCUGCAGUUUGCGCCGUAUGUCCUUAAUAAUCAAGCCCAAUUGCGUUAAACUGCCGAUUUUAUGCGAAUAUUACAGCGAUUUUAAGUUACUUUGCAAUCGUAAAAAAUAUAGAGAAUUGGAAAACAAC ..(((.((((((.((((((((((....(((.(((((..((...((((.(((.(((..........)))....)))...(((((.((..((((((....))).)))...((.(((((.....))))).))...)))))))...)))).....................(((((..(((((((......(((((....)))))...))))))).((.(((((((((((.((.((..(((.......)))..)))).))).)))))))).)).....)))))........))..))))).)))..))))))))))..........))))))..)))....... (-92.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUGUUUUCCAAUUCUCUAUAUUUUUUACGAUUGCAAAGUAACUUAAAAUCGCUGUAAUAUUCGCAUAAAAUCGGCAGUUUAACGCAAUUGGGCUUGAUUAUUAAGGACAUACGGCGCAAACUGCAGAAAAUCCGCCACCUGCCACGAGGCAGUAAUAUGCGGAUUAUUGCGACAGAAAGGUUUUCAAAUCGUUACCCGAAAGCAAGGUAAUCACCUCCGUCAAAGAGGAGAAAAACAGCGGUUUUCCGUGCAUCCGUUGCUGUUGCUCUACUGCUCUAUAUUUUGCAUAGCAGGGUUAGGCUCUUUCAUGUUUAAUUUUGCAACCAAAAAGAAAAGACA (((.(((((.......................(((((((((....(((((((((((.....(((((.....((.(((((((..(((...((..(((((...)))))..))....))).))))))).)).(((((((...(((((....)))))......)))))))..)))))........(((((.....(((((((....)...))))))..((((.......)))).))))))))))))))))..(.(((......((....)).....))).)..)))))))))..((((((((((((........)))))))))))).........)))))))). (-94.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 977 130 81 221 172 NC_002950:PG1113|5end_integrase_1186746..1186976_NEGATIVE 487 130 81 114 50 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 476 232 191 68 25 NC_002950:PG0691|5end_NifU-related_protein_747469..747699_NEGATIVE 448 229 188 71 19 NC_002950:PG0753|5end_protease_798301..798531_POSITIVE 414 170 121 225 182 NC_002950:PG0215|5end_hypothetical_protein_251460..251690_POSITIVE 411 120 71 211 169 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 407 205 162 207 158 NC_002950:PG0739|5end_ribonuclease_Z_786947..787177_POSITIVE 395 239 193 220 176 NC_002950:PG0923|5end_ribosome-binding_factor_A_982814..983044_NEGATIVE 379 115 74 163 123 NC_002950:PG2114|5end_hypothetical_protein_2224158..2224388_NEGATIVE 375 145 101 157 112 NC_002950:PG0926|5end_hypothetical_protein_984634..984864_NEGATIVE 373 235 192 67 12 NC_002950:PG1979|5end_hypothetical_protein_2067272..2067502_POSITIVE 368 128 87 205 168 NC_002950:PG0375|5end_50S_ribosomal_protein_L13_405934..406164_POSITIVE 365 148 101 156 114 NC_002950:PG1459|5end_hypothetical_protein_1539769..1539999_NEGATIVE 363 129 84 48 6 NC_002950:PG1859|5end_glycerate_kinase_family_protein_1958334..1958564_NEGATIVE 361 226 191 136 92 NC_002950:PG0877|5end_hypothetical_protein_941545..941775_NEGATIVE 358 228 188 191 140 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 358 209 166 99 58 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 356 228 185 213 173 NC_002950:PG1487|5end_hypothetical_protein_1561468..1561698_POSITIVE 355 209 165 99 43 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 352 150 101 149 93 NC_002950:PG2032|5end_primosomal_protein_N'_2133381..2133611_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 487 130 81 130 66 NC_002950:PG0157|3end_regulatory_protein_RecX_180271..180421_POSITIVE 448 229 188 87 35 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 415 206 163 150 112 NC_002950:PG0004|3end_NAD-dependent_deacetylase_3752..3902_POSITIVE 369 150 113 148 112 NC_002950:PG1697|3end_type_II_restriction_endonuclease,_putative_1785074..1785224_POSITIVE 368 117 71 105 52 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 358 228 188 112 61 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 352 150 101 115 59 NC_002950:PG2033|3end_glutamate_synthase,_small_subunit_2133415..2133565_NEGATIVE 350 235 192 53 5 NC_002950:PG2027|3end_hypothetical_protein_2126098..2126248_POSITIVE 346 205 161 72 15 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 340 229 188 135 85 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 338 228 188 106 60 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 335 210 161 64 12 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 334 120 75 57 1 NC_002950:PG0579|3end_cell_division_protein_FtsW,_putative_637180..637330_POSITIVE 333 148 101 136 76 NC_002950:PG1556|3end_hypothetical_protein_1637001..1637151_POSITIVE 332 230 188 58 24 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 332 232 192 145 99 NC_002950:PG0445|3end_peptidase_T_486549..486699_POSITIVE 330 137 98 46 4 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 330 104 63 124 76 NC_002950:PG1066|3end_butyrate-acetoacetate_CoA-transferase,_subunit_A_1134245..1134395_POSITIVE 329 208 163 79 35 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 327 207 167 67 33 NC_002950:PG1963|3end_Sua5/YciO/YrdC/YwlC_family_protein_2052993..2053143_POSITIVE