Origin IGS: tttttaacagaattatctttacaaaataagagcgaaaactcccctttattccattaagggaattgcattttttaaagacgatttaggcttttccatttaaagataatcccacagatgttcttgtgttattaggctttttttcagactgcaataaagaataagaaaagtattggttattgttgtttctttcaataatagtcctatacttttgcacaaattaaaaaaaaaggttatatttgcaaccagatagctaaacaattaattaattaatcaaaatgcccctgcctcggtaaggcgtttccctttacgcaaagggattatggagaggcgcgtttagaaca .........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 tgttctaaacgcgcctctccataatccctttgcgtaaagggaaacgccttaccgaggcaggggcattttgattaattaattaattgtttagctatctggttgcaaatataacctttttttttaatttgtgcaaaagtataggactattattgaaagaaacaacaataaccaatacttttcttattctttattgcagtctgaaaaaaagcctaataacacaagaacatctgtgggattatctttaaatggaaaagcctaaatcgtctttaaaaaatgcaattcccttaatggaataaaggggagttttcgctcttattttgtaaagataattctgttaaaaa Mask Tandem Repeat Region ================================================ tttttaacagaattatctttacaaaataagagcgaaaactcccctttattccattaagggaattgcattttttaaagacgatttaggcttttccatttaaagataatcccacagatgttcttgtgttattaggctttttttcagactgcaataaagaataagaaaagtattggttattgttgtttctttcaataatagtcctatacttttgcacaaattaaaaaaaaaggttatatttgcaaccagatagctaaacaattaattaattaatcaaaatgcccctgcctcggtaaggcgtttccctttacgcaaagggattatggagaggcgcgtttagaaca Find is-nt database================================================ Query_seq: PI0755:PI0756|PI0755:PI0756:hypothetical protein:50S ribosomal protein L7/L12:->->:686945..687285 341 tttttaacagaattatctttacaaaataagagcgaaaactcccctttattccattaagggaattgcattttttaaagacgatttaggcttttccatttaaagataatcccacagatgttcttgtgttattaggctttttttcagactgcaataaagaataagaaaagtattggttattgttgtttctttcaataatagtcctatacttttgcacaaattaaaaaaaaaggttatatttgcaaccagatagctaaacaattaattaattaatcaaaatgcccctgcctcggtaaggcgtttccctttacgcaaagggattatggagaggcgcgtttagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0755:PI0756|PI0755:PI0756:hypothetical protein:50S ribosomal protein L7/L12:->->:686945..687285 341 tttttaacagaattatctttacaaaataagagcgaaaactcccctttattccattaagggaattgcattttttaaagacgatttaggcttttccatttaaagataatcccacagatgttcttgtgttattaggctttttttcagactgcaataaagaataagaaaagtattggttattgttgtttctttcaataatagtcctatacttttgcacaaattaaaaaaaaaggttatatttgcaaccagatagctaaacaattaattaattaatcaaaatgcccctgcctcggtaaggcgtttccctttacgcaaagggattatggagaggcgcgtttagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0755:PI0756|PI0755:PI0756:hypothetical protein:50S ribosomal protein L7/L12:->->:686945..687285 341 tttttaacagaattatctttacaaaataagagcgaaaactcccctttattccattaagggaattgcattttttaaagacgatttaggcttttccatttaaagataatcccacagatgttcttgtgttattaggctttttttcagactgcaataaagaataagaaaagtattggttattgttgtttctttcaataatagtcctatacttttgcacaaattaaaaaaaaaggttatatttgcaaccagatagctaaacaattaattaattaatcaaaatgcccctgcctcggtaaggcgtttccctttacgcaaagggattatggagaggcgcgtttagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttaacagaattatctttacaaaataagagcgaaaactcccctttattccattaagggaattgcattttttaaagacgatttaggcttttccatttaaagataatcccacagatgttcttgtgttattaggctttttttcagactgcaataaagaataagaaaagtattggttattgttgtttctttcaataatagtcctatacttttgcacaaattaaaaaaaaaggttatatttgcaaccagatagctaaacaattaattaattaatcaaaatgcccctgcctcggtaaggcgtttccctttacgcaaagggattatggagaggcgcgtttagaaca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 158 End: 247 ............................................................................................................................................................. M R K V L V I V V S F N N S P I L L H K L K K K V I F A T R .............................................................................................. Protein_Len: 53 Strand: - Start: 100 End: 258 ................................................................................................... L Y D W L H E Q T I L S K K L S C Y L I L F T N T I T T E K L L L G I S K C L N F F F T I N A V L Y S F M ................................................................................... Protein_Len: 43 Strand: - Start: 86 End: 214 ..................................................................................... A K G N L S L G V S T R T N N P K K E S Q L L S Y S F Y Q N N N N R E I I T R Y K Q M ............................................................................................................................... tttttaacagaattatctttacaaaataagagcgaaaactcccctttattccattaagggaattgcattttttaaagacgatttaggcttttccatttaaagataatcccacagatgttcttgtgttattaggctttttttcagactgcaataaagaataagaaaagtattggttattgttgtttctttcaataatagtcctatacttttgcacaaattaaaaaaaaaggttatatttgcaaccagatagctaaacaattaattaattaatcaaaatgcccctgcctcggtaaggcgtttccctttacgcaaagggattatggagaggcgcgtttagaaca 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: 208 End: 237 ...............................................................................................................................................................................................................TTTGCACAAATTAAAAAAAAAGGTTATATT........................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttaacagaattatctttacaaaataagagcgaaaactcccctttattccattaagggaattgcattttttaaagacgatttaggcttttccatttaaagataatcccacagatgttcttgtgttattaggctttttttcagactgcaataaagaataagaaaagtattggttattgttgtttctttcaataatagtcctatacttttgcacaaattaaaaaaaaaggttatatttgcaaccagatagctaaacaattaattaattaatcaaaatgcccctgcctcggtaaggcgtttccctttacgcaaagggattatggagaggcgcgtttagaaca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 72 HP_score: -8.5 Tail_Score: -3.28712 Start: 300 End: 317 Full_Region: CCTCGGTAAGGCGTT TCCCTTT ACGC AAAGGGA TTATGGAGAGGCGCG ...........................................................................................................................................................................................................................................................................................................TCCCTTTACGCAAAGGGA........................ Find igs database================================================ Query_seq: PI0755:PI0756|PI0755:PI0756:hypothetical protein:50S ribosomal protein L7/L12:->->:686945..687285 341 tttttaacagaattatctttacaaaataagagcgaaaactcccctttattccattaagggaattgcattttttaaagacgatttaggcttttccatttaaagataatcccacagatgttcttgtgttattaggctttttttcagactgcaataaagaataagaaaagtattggttattgttgtttctttcaataatagtcctatacttttgcacaaattaaaaaaaaaggttatatttgcaaccagatagctaaacaattaattaattaatcaaaatgcccctgcctcggtaaggcgtttccctttacgcaaagggattatggagaggcgcgtttagaaca Intra-Species Hit: Count: 1 Min: 1 Max: 341 Len: 341 Subject: pint_PI0755_PI0756|hypothetical protein:50S ribosomal protein L7/L12|POSITIVE:POSITIVE|[686945,687285]|341 HSP 1 e-value: 1.0E-165 bit: 581.0 Len: 341 Query Start:1 Query End:341 Subject Strand: POSITIVE Subject Start: 1 Subject End: 341 tttttaacagaattatctttacaaaataagagcgaaaactcccctttattccattaagggaattgcattttttaaagacgatttaggcttttccatttaaagataatcccacagatgttcttgtgttattaggcnnnnnnncagactgcaataaagaataagaaaagtattggttattgttgtttctttcaataatagtcctatacttttgcacaaattnnnnnnnnnggttatatttgcaaccagatagctaaacaattaattaattaatcaaaatgcccctgcctcggtaaggcgtttccctttacgcaaagggattatggagaggcgcgtttagaaca tttttaacagaattatctttacaaaataagagcgaaaactcccctttattccattaagggaattgcattttttaaagacgatttaggcttttccatttaaagataatcccacagatgttcttgtgttattaggctttttttcagactgcaataaagaataagaaaagtattggttattgttgtttctttcaataatagtcctatacttttgcacaaattaaaaaaaaaggttatatttgcaaccagatagctaaacaattaattaattaatcaaaatgcccctgcctcggtaaggcgtttccctttacgcaaagggattatggagaggcgcgtttagaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAACAGAAUUAUCUUUACAAAAUAAGAGCGAAAACUCCCCUUUAUUCCAUUAAGGGAAUUGCAUUUUUUAAAGACGAUUUAGGCUUUUCCAUUUAAAGAUAAUCCCACAGAUGUUCUUGUGUUAUUAGGCUUUUUUUCAGACUGCAAUAAAGAAUAAGAAAAGUAUUGGUUAUUGUUGUUUCUUUCAAUAAUAGUCCUAUACUUUUGCACAAAUUAAAAAAAAAGGUUAUAUUUGCAACCAGAUAGCUAAACAAUUAAUUAAUUAAUCAAAAUGCCCCUGCCUCGGUAAGGCGUUUCCCUUUACGCAAAGGGAUUAUGGAGAGGCGCGUUUAGAACA ((((.(((.((((..((((((.(((((..(((......))).((((((......))))))......))))).))))))..))))..(((((((((........(((((((.....(((((((.(((..((.((.......)).))..)))...)))))))..((((((((.(((((((((((.......))))))))).)).))))))))...............(((((...((((((....))))))........................(((((((..(((....))).))))))).))))).......))))))))))))))))..))).)))).. (-75.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCUAAACGCGCCUCUCCAUAAUCCCUUUGCGUAAAGGGAAACGCCUUACCGAGGCAGGGGCAUUUUGAUUAAUUAAUUAAUUGUUUAGCUAUCUGGUUGCAAAUAUAACCUUUUUUUUUAAUUUGUGCAAAAGUAUAGGACUAUUAUUGAAAGAAACAACAAUAACCAAUACUUUUCUUAUUCUUUAUUGCAGUCUGAAAAAAAGCCUAAUAACACAAGAACAUCUGUGGGAUUAUCUUUAAAUGGAAAAGCCUAAAUCGUCUUUAAAAAAUGCAAUUCCCUUAAUGGAAUAAAGGGGAGUUUUCGCUCUUAUUUUGUAAAGAUAAUUCUGUUAAAAA ((((((......(((((.......(((((((....)))))))...(((((...))))).)))))...................(((((..(((....(((((......)))))..((((((((..(((((..((((.((((((..(.(((((.................))))).)..)))))).))))..)))))..)))))))))))..)))))....))))))...(..((((((((((((.....((.(((..(((((.((((((..........((((......)))))))))).)).)))..))).))......))))))))))))..)...... (-74.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 329 283 78 26 pint:PI1240|5end_probable_Xaa-Pro_dipeptidase_(aminopeptidase_P)_1164798..1165028_POSITIVE 356 128 87 168 127 pint:PI0820|5end_hypothetical_protein_759694..759924_POSITIVE 343 330 283 56 7 pint:PI0621|5end_conserved_hypothetical_protein_570770..571000_POSITIVE 336 339 293 86 34 pint:PI1983|5end_possible_xylanase_1939151..1939381_POSITIVE 335 316 274 159 104 pint:PI0213|5end_conserved_hypothetical_protein_207065..207295_POSITIVE 328 327 282 110 62 pint:PI1691|5end_hypothetical_protein_1605504..1605734_POSITIVE 325 49 1 202 146 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 320 330 281 63 4 pint:PI0272|5end_conserved_hypothetical_protein_262621..262851_POSITIVE 319 330 282 224 175 pint:PI1070|5end_peptidoglycan-associated_lipoprotein_986110..986340_POSITIVE 319 327 285 200 160 pint:PI0122|5end_outer_membrane_protein,_ompH_family_113319..113549_POSITIVE 316 330 283 47 7 pint:PI0256|5end_conjugative_transposon_protein,_TraE_249044..249274_POSITIVE 313 317 276 201 169 pint:PI2115|5end_hypothetical_protein_2064966..2065196_POSITIVE 312 330 281 59 3 pint:PI0602|5end_conserved_hypothetical_protein_549099..549329_POSITIVE 311 330 284 181 115 pint:PI2166|5end_hypothetical_protein_2111394..2111624_POSITIVE 311 330 284 73 7 pint:PI2168|5end_hypothetical_protein_2111286..2111516_POSITIVE 309 330 281 202 154 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 308 328 287 89 44 pint:PI1870|5end_hypothetical_protein_1815302..1815532_POSITIVE 305 316 274 75 22 pint:PI1313|5end_possible_POT_family_(proton-dependent_oligopeptide_transport_family)_1229710..1229940_POSITIVE 304 311 271 144 112 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 304 331 292 170 127 pint:PI0815|5end_hypothetical_protein_754475..754705_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 497 329 281 52 2 pint:PI1245|3end_hypothetical_protein_1171492..1171642_POSITIVE 497 316 276 41 1 pint:PI1246|3end_conserved_hypothetical_protein;_possible_lipoprotein_1171496..1171646_POSITIVE 371 49 1 60 7 pint:PI1379|3end_hypothetical_protein_1302292..1302442_POSITIVE 356 128 87 53 12 pint:PI0818|3end_alpha-amylase_759659..759809_POSITIVE 352 330 281 136 85 pint:PI1178|3end_histidyl-tRNA_synthetase_1100564..1100714_POSITIVE 338 316 274 66 21 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 336 339 293 63 11 pint:PI1982|3end_conserved_hypothetical_protein_1939208..1939358_POSITIVE 322 330 282 71 15 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 311 150 107 133 82 pint:PI0335|3end_hypothetical_protein_314420..314570_POSITIVE 308 328 287 133 88 pint:PI1869|3end_hypothetical_protein_1815426..1815576_POSITIVE 301 336 293 91 45 pint:PI0031|3end_peptidylprolyl_isomerase_36131..36281_POSITIVE 300 339 293 129 59 pint:PI1541|3end_hypothetical_protein_1461884..1462034_POSITIVE 298 326 283 97 54 pint:PI0672|3end_conserved_hypothetical_protein_612230..612380_POSITIVE 296 313 275 38 3 pint:PI2028|3end_shikimate_kinase_1982802..1982952_POSITIVE 295 330 283 142 92 pint:PI2083|3end_hypothetical_protein_2040661..2040811_POSITIVE 292 330 286 121 75 pint:PI0769|3end_phosphomannomutase_706172..706322_POSITIVE 289 322 281 92 50 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 286 329 282 90 52 pint:PI0427|3end_conserved_hypothetical_protein_393088..393238_POSITIVE 284 328 283 150 96 pint:PI0409|3end_3-deoxy-D-manno-octulosonic-acid_transferase_(kdotransferase)_375969..376119_POSITIVE 283 150 108 52 9 pint:PI2035|3end_Holliday_junction_DNA_helicase_ruvB_1989323..1989473_POSITIVE