Origin IGS: aaagttattttatcataagataatttgaatgaaaacggatttatcggatgagacaatcattcttttctaatggttgatagattagaaagtagctaggtatactattttaaaaaagaaagaacgagatttac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtaaatctcgttctttcttttttaaaatagtatacctagctactttctaatctatcaaccattagaaaagaatgattgtctcatccgataaatccgttttcattcaaattatcttatgataaaataacttt Mask Tandem Repeat Region ================================================ aaagttattttatcataagataatttgaatgaaaacggatttatcggatgagacaatcattcttttctaatggttgatagattagaaagtagctaggtatactattttaaaaaagaaagaacgagatttac Find is-nt database================================================ Query_seq: SSA_0413:SSA_0414|SSA_0413:SSA_0414:Anthranilate/para-aminobenzoate synthases component I/ Chorismate binding enzyme, putative:hypothetical protein:<-->:410127..410257 131 aaagttattttatcataagataatttgaatgaaaacggatttatcggatgagacaatcattcttttctaatggttgatagattagaaagtagctaggtatactattttaaaaaagaaagaacgagatttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0413:SSA_0414|SSA_0413:SSA_0414:Anthranilate/para-aminobenzoate synthases component I/ Chorismate binding enzyme, putative:hypothetical protein:<-->:410127..410257 131 aaagttattttatcataagataatttgaatgaaaacggatttatcggatgagacaatcattcttttctaatggttgatagattagaaagtagctaggtatactattttaaaaaagaaagaacgagatttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0413:SSA_0414|SSA_0413:SSA_0414:Anthranilate/para-aminobenzoate synthases component I/ Chorismate binding enzyme, putative:hypothetical protein:<-->:410127..410257 131 aaagttattttatcataagataatttgaatgaaaacggatttatcggatgagacaatcattcttttctaatggttgatagattagaaagtagctaggtatactattttaaaaaagaaagaacgagatttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagttattttatcataagataatttgaatgaaaacggatttatcggatgagacaatcattcttttctaatggttgatagattagaaagtagctaggtatactattttaaaaaagaaagaacgagatttac Predict ORF larger than 30AA ================================================ aaagttattttatcataagataatttgaatgaaaacggatttatcggatgagacaatcattcttttctaatggttgatagattagaaagtagctaggtatactattttaaaaaagaaagaacgagatttac 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: 83 Start: 7 End: 36 ......GTTTTCATTCAAATTATCTTATGATAAAAT............................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagttattttatcataagataatttgaatgaaaacggatttatcggatgagacaatcattcttttctaatggttgatagattagaaagtagctaggtatactattttaaaaaagaaagaacgagatttac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 58 HP_score: -3.0 Tail_Score: -4.51097 Start: 46 End: 62 Full_Region: GAAAACGGATTTATC GGATGA GACAA TCATTC TTTTCTAATGGTTGA .............................................GGATGAGACAATCATTC..................................................................... Find igs database================================================ Query_seq: SSA_0413:SSA_0414|SSA_0413:SSA_0414:Anthranilate/para-aminobenzoate synthases component I/ Chorismate binding enzyme, putative:hypothetical protein:<-->:410127..410257 131 aaagttattttatcataagataatttgaatgaaaacggatttatcggatgagacaatcattcttttctaatggttgatagattagaaagtagctaggtatactattttaaaaaagaaagaacgagatttac Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: NC_009009_SSA_0413_SSA_0414|Anthranilate/para-aminobenzoate synthases component I/ Chorismate binding enzyme, putative:hypothetical protein|NEGATIVE:POSITIVE|[410127,410257]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 aaagttattttatcataagataatttgaatgaaaacggatttatcggatgagacaatcattcttttctaatggttgatagattagaaagtagctaggtatactattttaaaaaagaaagaacgagatttac aaagttattttatcataagataatttgaatgaaaacggatttatcggatgagacaatcattcttttctaatggttgatagattagaaagtagctaggtatactattttaaaaaagaaagaacgagatttac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUUAUUUUAUCAUAAGAUAAUUUGAAUGAAAACGGAUUUAUCGGAUGAGACAAUCAUUCUUUUCUAAUGGUUGAUAGAUUAGAAAGUAGCUAGGUAUACUAUUUUAAAAAAGAAAGAACGAGAUUUAC ..(((((((((.((((..(((((((((........)))).)))))..))))..((((((((.......)))))))).........)))))))))..................................... (-20.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAAUCUCGUUCUUUCUUUUUUAAAAUAGUAUACCUAGCUACUUUCUAAUCUAUCAACCAUUAGAAAAGAAUGAUUGUCUCAUCCGAUAAAUCCGUUUUCAUUCAAAUUAUCUUAUGAUAAAAUAACUUU .......((((((..............((((.......)))).((((((((.........)))))))).))))))(((((......))))).................(((((....)))))......... (-13.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 796 80 31 171 122 NC_009009:SSA_0413|5end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_410036..410266_NEGATIVE 261 66 32 197 163 NC_009009:SSA_1543|5end_hypothetical_protein_1547835..1548065_POSITIVE 252 84 47 60 27 NC_009009:SSA_2220|5end_Galactosyltransferase,_putative_2221439..2221669_NEGATIVE 236 80 31 158 122 NC_009009:SSA_0083|5end_hypothetical_protein_85437..85667_POSITIVE 234 67 27 209 165 NC_009009:SSA_2285|5end_hypothetical_protein_2287404..2287634_POSITIVE 225 116 71 219 163 NC_009009:SSA_0767|5end_Diacylglycerol_kinase_catalytic_domain_protein,_putative_747087..747317_POSITIVE 223 96 56 133 92 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 217 75 35 80 44 NC_009009:SSA_1782|5end_hypothetical_protein_1768123..1768353_NEGATIVE 210 98 51 54 4 NC_009009:SSA_2213|5end_Nucleotide_sugar_dehydratase,_putative_2215111..2215341_NEGATIVE 208 100 52 156 102 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 208 68 36 99 66 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 208 100 56 181 140 NC_009009:SSA_0431|5end_hypothetical_protein_433275..433505_NEGATIVE 207 66 24 104 60 NC_009009:SSA_0737|5end_Arginine_deiminase,_putative_718624..718854_POSITIVE 205 78 36 57 23 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 205 100 56 130 95 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 204 115 72 64 25 NC_009009:SSA_1750|5end_Extracellular_nuclease,_putative_1737922..1738152_NEGATIVE 204 98 51 149 93 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 204 77 31 216 163 NC_009009:SSA_0183|5end_hypothetical_protein_187646..187876_POSITIVE 202 117 73 82 32 NC_009009:SSA_0614|5end_Transporter,_putative_607974..608204_NEGATIVE 199 66 34 87 44 NC_009009:SSA_1013|5end_Phosphatidylserine_synthase,_putative_1017221..1017451_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 84 47 44 11 NC_009009:SSA_2221|3end_Cps9E,_putative_2221455..2221605_NEGATIVE 218 96 58 144 100 NC_009009:SSA_0729|3end_hypothetical_protein_714677..714827_POSITIVE 217 75 35 101 65 NC_009009:SSA_1783|3end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1768102..1768252_NEGATIVE 214 66 28 74 37 NC_009009:SSA_0999|3end_Biotin--[acetyl-CoA-carboxylase]_ligase,_putative_998781..998931_NEGATIVE 210 98 51 52 2 NC_009009:SSA_2214|3end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215113..2215263_NEGATIVE 208 100 52 98 44 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 208 99 57 126 95 NC_009009:SSA_1971|3end_hypothetical_protein_1967597..1967747_POSITIVE 208 68 36 51 18 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 205 100 56 113 78 NC_009009:SSA_0278|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_272382..272532_POSITIVE 204 109 67 85 47 NC_009009:SSA_0698|3end_Peptide_chain_release_factor_3,_putative_682007..682157_POSITIVE 203 97 59 130 100 NC_009009:SSA_0453|3end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_455993..456143_POSITIVE 199 69 30 36 3 NC_009009:SSA_1383|3end_Aspartate_aminotransferase,_putative_1400537..1400687_NEGATIVE 199 66 34 100 57 NC_009009:SSA_1012|3end_Phosphoenolpyruvate_synthase,_putative_1017314..1017464_POSITIVE 198 97 62 134 103 NC_009009:SSA_2145|3end_Tributyrin_esterase,_putative_2145879..2146029_NEGATIVE 198 83 45 126 80 NC_009009:SSA_0356|3end_Dipeptidase,_putative_350757..350907_POSITIVE 194 101 74 33 4 NC_009009:SSA_0960|3end_Sensor_protein_ciaH,_putative_969977..970127_POSITIVE 193 80 43 83 41 NC_009009:SSA_1204|3end_Phosphoglucomutase_1229585..1229735_POSITIVE 193 97 54 145 111 NC_009009:SSA_1173|3end_Lipoate_protein_ligase_A,_putative_1200092..1200242_NEGATIVE 193 93 53 54 23 NC_009009:SSA_0293|3end_hypothetical_protein_287356..287506_NEGATIVE 192 97 66 32 4 NC_009009:SSA_2076|3end_Conserved_uncharacterized_protein_2079390..2079540_NEGATIVE