Origin IGS: aggtttagttcaatctagaattcagctggattagcttgcgaaatatttagaaatctgttagaatgaaatataactaaatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagtaaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccgcttatggagattggcgcgctttttattttggagggaaa .........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 tttccctccaaaataaaaagcgcgccaatctccataagcggagcgttgacacgcggtaccatccgttttttatctggcaagccagaccttacttatcaatcccatagcaagtgaattcgcctagctttcatctagagagctttcagtcgctggctcccctccctgttaaacttcccctaggttactggtcttgcggattgctatttagttatatttcattctaacagatttctaaatatttcgcaagctaatccagctgaattctagattgaactaaacct Mask Tandem Repeat Region ================================================ aggtttagttcaatctagaattcagctggattagcttgcgaaatatttagaaatctgttagaatgaaatataactaaatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagtaaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccgcttatggagattggcgcgctttttattttggagggaaa Find is-nt database================================================ Query_seq: SSA_0911:SSA_0912|SSA_0911:SSA_0912:hypothetical protein:Phenylalanyl-tRNA synthetase alpha chain, putative:->->:922959..923239 281 aggtttagttcaatctagaattcagctggattagcttgcgaaatatttagaaatctgttagaatgaaatataactaaatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagtaaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccgcttatggagattggcgcgctttttattttggagggaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0911:SSA_0912|SSA_0911:SSA_0912:hypothetical protein:Phenylalanyl-tRNA synthetase alpha chain, putative:->->:922959..923239 281 aggtttagttcaatctagaattcagctggattagcttgcgaaatatttagaaatctgttagaatgaaatataactaaatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagtaaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccgcttatggagattggcgcgctttttattttggagggaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0911:SSA_0912|SSA_0911:SSA_0912:hypothetical protein:Phenylalanyl-tRNA synthetase alpha chain, putative:->->:922959..923239 281 aggtttagttcaatctagaattcagctggattagcttgcgaaatatttagaaatctgttagaatgaaatataactaaatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagtaaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccgcttatggagattggcgcgctttttattttggagggaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggtttagttcaatctagaattcagctggattagcttgcgaaatatttagaaatctgttagaatgaaatataactaaatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagtaaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccgcttatggagattggcgcgctttttattttggagggaaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 171 End: 269 .......................................................................................................................................................................... K S H S Q Y T L D P K G S L F R I T G R T L A G S I S I P A S K M ............ Protein_Len: 37 Strand: - Start: 61 End: 171 ............................................................ F S I Y S F L L G C S W Y G L P L K V P L P A L S Q F S E L H F S P S N M .............................................................................................................. aggtttagttcaatctagaattcagctggattagcttgcgaaatatttagaaatctgttagaatgaaatataactaaatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagtaaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccgcttatggagattggcgcgctttttattttggagggaaa 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: 85 Start: 35 End: 64 ..................................CTTGCGAAATATTTAGAAATCTGTTAGAAT......................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggtttagttcaatctagaattcagctggattagcttgcgaaatatttagaaatctgttagaatgaaatataactaaatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagtaaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccgcttatggagattggcgcgctttttattttggagggaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 90 HP_score: -5.7 Tail_Score: -5.45802 Start: 228 End: 262 Full_Region: AAAACGGATGGTACC GCGTGTCAACGCTCCG CTTA TGGAGATTGGCGCGC TTTTTATTTTGGAGG ...................................................................................................................................................................................................................................GCGTGTCAACGCTCCGCTTATGGAGATTGGCGCGC................... Find igs database================================================ Query_seq: SSA_0911:SSA_0912|SSA_0911:SSA_0912:hypothetical protein:Phenylalanyl-tRNA synthetase alpha chain, putative:->->:922959..923239 281 aggtttagttcaatctagaattcagctggattagcttgcgaaatatttagaaatctgttagaatgaaatataactaaatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagtaaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccgcttatggagattggcgcgctttttattttggagggaaa Intra-Species Hit: Count: 1 Min: 1 Max: 281 Len: 281 Subject: NC_009009_SSA_0911_SSA_0912|hypothetical protein:Phenylalanyl-tRNA synthetase alpha chain, putative|POSITIVE:POSITIVE|[922959,923239]|281 HSP 1 e-value: 1.0E-158 bit: 557.0 Len: 281 Query Start:1 Query End:281 Subject Strand: POSITIVE Subject Start: 1 Subject End: 281 aggtttagttcaatctagaattcagctggattagcttgcgaaatatttagaaatctgttagaatgaaatataactaaatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagtaaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccgcttatggagattggcgcgctttttattttggagggaaa aggtttagttcaatctagaattcagctggattagcttgcgaaatatttagaaatctgttagaatgaaatataactaaatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagtaaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccgcttatggagattggcgcgctttttattttggagggaaa Inter-species Hit: Count: 3 Min: 77 Max: 243 Len: 167 Subject: smit_SMT_1685_SMT_1686|phenylalanyl-tRNA synthetase alpha chain:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:POSITIVE|[1668936,1670314]|1379 HSP 1 e-value: 1.0E-23 bit: 111.0 Len: 167 Query Start:77 Query End:243 Subject Strand: NEGATIVE Subject Start: 16 Subject End: 181 ............................................................................aatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagt-aaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccg...................................... ............................................................................aatagaaatccgcaagactagtagcctaagggaagtatatcagggaggagagcc-gtgactgcaagctctctatatgaaagctgggtgaattcacttgcgcatggatttagaaatgaaggtctgacttgtcagat-gaaaacggatggtaccgcgtgtcaacgctccg...................................... Subject: NC_008533_SPD_0503_SPD_0504|6-phospho-beta- glucosidase:phenylalanyl-tRNA synthetase, alpha subunit|POSITIVE:POSITIVE|[512526,513116]|591 HSP 1 e-value: 2.0E-16 bit: 87.7 Len: 167 Query Start:77 Query End:243 Subject Strand: POSITIVE Subject Start: 369 Subject End: 534 ............................................................................aatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagt-aaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccg...................................... ............................................................................aatagaaatctgaaagactagtagcccaagggaagtatatcagggaggagagcc-gtgactgcaagctctctatatgaaagctgggtgaattcacttgcgcatggatttagaaatgaaggtctgacttgtcagatgaaaa-cggatggtaccgcgtgtcaacgctccg...................................... Subject: NC_003028_SP_0578_SP_0579|6-phospho-beta-glucosidase:phenylalanyl- tRNA synthetase alpha subunit|POSITIVE:POSITIVE|[547288,547768]|481 HSP 1 e-value: 2.0E-16 bit: 87.7 Len: 167 Query Start:77 Query End:243 Subject Strand: POSITIVE Subject Start: 259 Subject End: 424 ............................................................................aatagcaatccgcaagaccagtaacctaggggaagtttaacagggaggggagccagcgactgaaagctctctagatgaaagctaggcgaattcacttgctatgggattgataagt-aaggtctggcttgccagataaaaaacggatggtaccgcgtgtcaacgctccg...................................... ............................................................................aataggaatctgaaagactagtagcccaagggaagtatatcagggaggagagcc-gtgactgcaagctctctatatgaaagctgggtgaattcacttgcgcatggatttagaaatgaaggtctgacttgtcagatgaaaa-cggatggtaccgcgtgtcaacgctccg...................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAGCAAUCCGCAAGACCAGUAACCUAGGGGAAGUUUAACAGGGAGGGGAGCCAGCGACUGAAAGCUCUCUAGAUGAAAGCUAGGCGAAUUCACUUGCUAUGGGAUUGAUAAGUAAGGUCUGGCUUGCCAGAUAAAAAACGGAUGGUACCGCGUGUCAACGCUCCG ....((.((((((((..(((.....((((((..(((((..(((...((....)).....))).))))))))))).....(((.(((.(....).)))))).)))..))).........((((((....))))))......))))).))...((((....)))).... (-43.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGAGCGUUGACACGCGGUACCAUCCGUUUUUUAUCUGGCAAGCCAGACCUUACUUAUCAAUCCCAUAGCAAGUGAAUUCGCCUAGCUUUCAUCUAGAGAGCUUUCAGUCGCUGGCUCCCCUCCCUGUUAAACUUCCCCUAGGUUACUGGUCUUGCGGAUUGCUAUU ...(((........((((......)))).....(((((.((((((((....................(((.(((((........(((((((.....))))))).....))))).)))......((((............))))...)))).))))))))).)))... (-40.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 90 43 118 69 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 373 87 41 178 125 NC_009009:SSA_2098|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103617..2103847_NEGATIVE 360 86 41 217 166 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 360 89 42 76 15 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 349 89 41 74 17 NC_009009:SSA_0498|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_systems,_permease_components,_putative_497910..498140_POSITIVE 335 87 51 72 42 NC_009009:SSA_0281|5end_hypothetical_protein_273404..273634_POSITIVE 334 88 41 55 4 NC_009009:SSA_1467|5end_Chorismate_synthase,_putative_1474293..1474523_NEGATIVE 324 87 50 231 187 NC_009009:SSA_0491|5end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_490961..491191_POSITIVE 321 90 41 67 16 NC_009009:SSA_0252|5end_hypothetical_protein_245839..246069_NEGATIVE 319 86 41 140 105 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 318 99 60 152 105 NC_009009:SSA_2185|5end_Adenylosuccinate_synthetase,_putative_2185290..2185520_NEGATIVE 315 60 13 204 139 NC_009009:SSA_2339|5end_Microcin_C7_resistance_protein,_putative_2340456..2340686_POSITIVE 312 64 26 145 108 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 311 57 11 63 11 NC_009009:SSA_1004|5end_ABC_transporter_membrane-spanning_permease-multiple_sugars,_putative_1005148..1005378_POSITIVE 310 85 42 227 175 NC_009009:SSA_1401|5end_Transcriptional_regulator_GntR_family_1413062..1413292_POSITIVE 309 89 49 189 140 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 307 150 101 174 118 NC_009009:SSA_0634|5end_Anthranilate_phosphoribosyltransferase,_putative_623387..623617_POSITIVE 307 98 51 172 115 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 303 99 51 136 83 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 300 98 55 228 184 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 90 43 121 72 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 375 69 24 63 6 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 360 86 41 112 61 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 360 89 42 86 25 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 335 86 42 150 106 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 320 99 51 149 93 NC_009009:SSA_1746|3end_hypothetical_protein_1732292..1732442_NEGATIVE 312 64 26 145 108 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 307 98 51 97 40 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 303 99 51 54 1 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 302 58 11 62 21 NC_009009:SSA_2077|3end_hypothetical_protein_2081352..2081502_NEGATIVE 301 57 15 49 12 NC_009009:SSA_1003|3end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1005214..1005364_POSITIVE 301 85 46 65 13 NC_009009:SSA_0715|3end_DNA_uptake_protein,_putative_701486..701636_POSITIVE 299 86 42 65 23 NC_009009:SSA_1777|3end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1764427..1764577_NEGATIVE 297 88 42 89 25 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 297 159 114 79 43 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 295 58 26 48 19 NC_009009:SSA_2276|3end_hypothetical_protein_2275587..2275737_NEGATIVE 294 94 54 134 94 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE 292 55 18 140 106 NC_009009:SSA_1512|3end_hypothetical_protein_1516701..1516851_NEGATIVE 292 113 71 149 109 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE 292 57 11 78 15 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE