Origin IGS: tcctctgaattgctgttatgccaaaattattgtataatgtttaagagcatgcagtacacttctgaaggtttaaaatcatgaagaaggtttactaaattggaagaaaaacaaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctttgtttttcttccaatttagtaaaccttcttcatgattttaaaccttcagaagtgtactgcatgctcttaaacattatacaataattttggcataacagcaattcagagga Mask Tandem Repeat Region ================================================ tcctctgaattgctgttatgccaaaattattgtataatgtttaagagcatgcagtacacttctgaaggtttaaaatcatgaagaaggtttactaaattggaagaaaaacaaaga Find is-nt database================================================ Query_seq: SSA_0514:SSA_0515|SSA_0514:SSA_0515:PduQ protein, putative:Propanediol utilization protein PduU, putative:->->:514160..514273 114 tcctctgaattgctgttatgccaaaattattgtataatgtttaagagcatgcagtacacttctgaaggtttaaaatcatgaagaaggtttactaaattggaagaaaaacaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0514:SSA_0515|SSA_0514:SSA_0515:PduQ protein, putative:Propanediol utilization protein PduU, putative:->->:514160..514273 114 tcctctgaattgctgttatgccaaaattattgtataatgtttaagagcatgcagtacacttctgaaggtttaaaatcatgaagaaggtttactaaattggaagaaaaacaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0514:SSA_0515|SSA_0514:SSA_0515:PduQ protein, putative:Propanediol utilization protein PduU, putative:->->:514160..514273 114 tcctctgaattgctgttatgccaaaattattgtataatgtttaagagcatgcagtacacttctgaaggtttaaaatcatgaagaaggtttactaaattggaagaaaaacaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcctctgaattgctgttatgccaaaattattgtataatgtttaagagcatgcagtacacttctgaaggtttaaaatcatgaagaaggtttactaaattggaagaaaaacaaaga Predict ORF larger than 30AA ================================================ tcctctgaattgctgttatgccaaaattattgtataatgtttaagagcatgcagtacacttctgaaggtttaaaatcatgaagaaggtttactaaattggaagaaaaacaaaga 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: 86 Start: 9 End: 38 ........ATTGCTGTTATGCCAAAATTATTGTATAAT............................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcctctgaattgctgttatgccaaaattattgtataatgtttaagagcatgcagtacacttctgaaggtttaaaatcatgaagaaggtttactaaattggaagaaaaacaaaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0514:SSA_0515|SSA_0514:SSA_0515:PduQ protein, putative:Propanediol utilization protein PduU, putative:->->:514160..514273 114 tcctctgaattgctgttatgccaaaattattgtataatgtttaagagcatgcagtacacttctgaaggtttaaaatcatgaagaaggtttactaaattggaagaaaaacaaaga Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_009009_SSA_0514_SSA_0515|PduQ protein, putative:Propanediol utilization protein PduU, putative|POSITIVE:POSITIVE|[514160,514273]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 tcctctgaattgctgttatgccaaaattattgtataatgtttaagagcatgcagtacacttctgaaggtttaaaatcatgaagaaggtttactaaattggaagaaaaacaaaga tcctctgaattgctgttatgccaaaattattgtataatgtttaagagcatgcagtacacttctgaaggtttaaaatcatgaagaaggtttactaaattggaagaaaaacaaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUCUGAAUUGCUGUUAUGCCAAAAUUAUUGUAUAAUGUUUAAGAGCAUGCAGUACACUUCUGAAGGUUUAAAAUCAUGAAGAAGGUUUACUAAAUUGGAAGAAAAACAAAGA ((.((..(..((((((.(((((.....((((....)))).....).))))))))))..(((((...(((.....)))....)))))..........)..)).)).......... (-16.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUGUUUUUCUUCCAAUUUAGUAAACCUUCUUCAUGAUUUUAAACCUUCAGAAGUGUACUGCAUGCUCUUAAACAUUAUACAAUAAUUUUGGCAUAACAGCAAUUCAGAGGA ((((((..............(((((......((((.(((..........)))))))..)))))..((((.(((..((..((......))..))...))).))))...)))))). (-14.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 73 32 189 146 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 250 90 48 102 59 NC_009009:SSA_1540|5end_hypothetical_protein_1545268..1545498_NEGATIVE 236 88 49 230 188 NC_009009:SSA_0448|5end_Excinuclease_ATPase_subunit_A,_putative_446480..446710_POSITIVE 235 80 39 82 40 NC_009009:SSA_0734|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_716895..717125_POSITIVE 231 83 44 218 172 NC_009009:SSA_0666|5end_hypothetical_protein_649788..650018_NEGATIVE 222 88 44 193 139 NC_009009:SSA_1772|5end_hypothetical_protein_1759545..1759775_NEGATIVE 222 48 1 79 33 NC_009009:SSA_0316|5end_hypothetical_protein_310576..310806_POSITIVE 217 89 43 85 24 NC_009009:SSA_0137|5end_ABC_transporter_(permease),_Zn_porter,_putative_131717..131947_POSITIVE 216 87 45 230 186 NC_009009:SSA_0313|5end_Conserved_uncharacterized_protein_308619..308849_NEGATIVE 211 78 32 72 28 NC_009009:SSA_1337|5end_hypothetical_protein_1351091..1351321_NEGATIVE 209 50 5 91 40 NC_009009:SSA_2385|5end_hypothetical_protein_1752542..1752772_POSITIVE 207 80 37 73 30 NC_009009:SSA_1834|5end_30S_ribosomal_interface_protein_S30EA,_putative_1830194..1830424_NEGATIVE 205 87 45 53 10 NC_009009:SSA_2121|5end_Cell_wall_surface_anchor_family_protein,_putative_2126907..2127137_NEGATIVE 202 68 27 161 118 NC_009009:SSA_1892|5end_hypothetical_protein_1889262..1889492_NEGATIVE 201 64 44 131 110 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 200 59 11 184 130 NC_009009:SSA_1302|5end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1322484..1322714_NEGATIVE 198 71 38 43 9 NC_009009:SSA_1356|5end_Helicase_subunit_of_the_DNA_excision_repair_complex,_subunit_B,_putative_1371915..1372145_NEGATIVE 196 87 46 160 117 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 195 69 43 225 183 NC_009009:SSA_1632|5end_Surface_protein,_putative_1634045..1634275_NEGATIVE 195 100 56 173 115 NC_009009:SSA_0667|5end_Transcriptional_regulator,_putative_649778..650008_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 103 61 129 79 NC_009009:SSA_2170|3end_hypothetical_protein_2169557..2169707_NEGATIVE 250 90 48 59 16 NC_009009:SSA_1541|3end_Peptidase,_U32_family,_putative_1545311..1545461_NEGATIVE 235 80 39 44 2 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE 222 48 1 69 23 NC_009009:SSA_0315|3end_Transcriptional_regulator,_MarR_family,_putative_310646..310796_POSITIVE 217 89 43 92 31 NC_009009:SSA_0136|3end_ABC_transporter,_Zn_porter,_putative_131804..131954_POSITIVE 209 50 1 138 95 NC_009009:SSA_2213|3end_Nucleotide_sugar_dehydratase,_putative_2214047..2214197_NEGATIVE 206 70 21 133 85 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE 202 90 53 44 1 NC_009009:SSA_0872|3end_Zn-dependent_hydrolases,_including_glyoxylases,_putative_864667..864817_NEGATIVE 201 64 44 131 110 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 200 25 2 43 20 NC_009009:SSA_0604|3end_hypothetical_protein_592992..593142_POSITIVE 195 26 1 40 14 NC_009009:SSA_0190|3end_hypothetical_protein_191905..192055_POSITIVE 193 26 4 117 96 NC_009009:SSA_2385|3end_hypothetical_protein_1752996..1753146_POSITIVE 193 90 46 90 41 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE 192 69 40 149 113 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 191 90 43 56 10 NC_009009:SSA_0358|3end_hypothetical_protein_351288..351438_NEGATIVE 190 79 38 143 92 NC_009009:SSA_1577|3end_Proline_dipeptidase,_putative_1581456..1581606_POSITIVE 188 32 1 47 18 NC_009009:SSA_2184|3end_hypothetical_protein_2183284..2183434_NEGATIVE 188 88 44 97 50 NC_009009:SSA_0741|3end_Acetylornithine_deacetylase/Succinyl-diaminopimelate_desuccinylase,_putative_725190..725340_POSITIVE 188 23 1 60 37 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 187 69 44 146 117 NC_009009:SSA_1216|3end_AT-rich_DNA-binding_protein,_possible_redox-sensing_transcriptional_repressor,_putative_1239019..1239169_POSITIVE