Origin IGS: gtgatttctcaacataaccttctaagtttaaaagtctgatttgtattcagactttttcttttttctctctttatgataaagctctataggtaatatttcctgtataattttaagtaagaaatattataaaaaggaggtgaaaaaggattgtccaatatcctaagtaaacatagaatcaaacaaactgaaaccggaaagtat .........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 atactttccggtttcagtttgtttgattctatgtttacttaggatattggacaatcctttttcacctcctttttataatatttcttacttaaaattatacaggaaatattacctatagagctttatcataaagagagaaaaaagaaaaagtctgaatacaaatcagacttttaaacttagaaggttatgttgagaaatcac Mask Tandem Repeat Region ================================================ gtgatttctcaacataaccttctaagtttaaaagtctgatttgtattcagactttttcttttttctctctttatgataaagctctataggtaatatttcctgtataattttaagtaagaaatattataaaaaggaggtgaaaaaggattgtccaatatcctaagtaaacatagaatcaaacaaactgaaaccggaaagtat Find is-nt database================================================ Query_seq: SSA_0167:SSA_0168|SSA_0167:SSA_0168:Hypothetical protein (Asparagine/proline-rich):hypothetical protein:->->:166396..166596 201 gtgatttctcaacataaccttctaagtttaaaagtctgatttgtattcagactttttcttttttctctctttatgataaagctctataggtaatatttcctgtataattttaagtaagaaatattataaaaaggaggtgaaaaaggattgtccaatatcctaagtaaacatagaatcaaacaaactgaaaccggaaagtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0167:SSA_0168|SSA_0167:SSA_0168:Hypothetical protein (Asparagine/proline-rich):hypothetical protein:->->:166396..166596 201 gtgatttctcaacataaccttctaagtttaaaagtctgatttgtattcagactttttcttttttctctctttatgataaagctctataggtaatatttcctgtataattttaagtaagaaatattataaaaaggaggtgaaaaaggattgtccaatatcctaagtaaacatagaatcaaacaaactgaaaccggaaagtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0167:SSA_0168|SSA_0167:SSA_0168:Hypothetical protein (Asparagine/proline-rich):hypothetical protein:->->:166396..166596 201 gtgatttctcaacataaccttctaagtttaaaagtctgatttgtattcagactttttcttttttctctctttatgataaagctctataggtaatatttcctgtataattttaagtaagaaatattataaaaaggaggtgaaaaaggattgtccaatatcctaagtaaacatagaatcaaacaaactgaaaccggaaagtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgatttctcaacataaccttctaagtttaaaagtctgatttgtattcagactttttcttttttctctctttatgataaagctctataggtaatatttcctgtataattttaagtaagaaatattataaaaaggaggtgaaaaaggattgtccaatatcctaagtaaacatagaatcaaacaaactgaaaccggaaagtat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 87 End: 179 ...................................................................................... L Y Y K R Y L K L Y S I N Y F P P S F P N D L I R L L C L I M ...................... gtgatttctcaacataaccttctaagtttaaaagtctgatttgtattcagactttttcttttttctctctttatgataaagctctataggtaatatttcctgtataattttaagtaagaaatattataaaaaggaggtgaaaaaggattgtccaatatcctaagtaaacatagaatcaaacaaactgaaaccggaaagtat 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: 147 End: 176 ..................................................................................................................................................ATTGTCCAATATCCTAAGTAAACATAGAAT......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgatttctcaacataaccttctaagtttaaaagtctgatttgtattcagactttttcttttttctctctttatgataaagctctataggtaatatttcctgtataattttaagtaagaaatattataaaaaggaggtgaaaaaggattgtccaatatcctaagtaaacatagaatcaaacaaactgaaaccggaaagtat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0167:SSA_0168|SSA_0167:SSA_0168:Hypothetical protein (Asparagine/proline-rich):hypothetical protein:->->:166396..166596 201 gtgatttctcaacataaccttctaagtttaaaagtctgatttgtattcagactttttcttttttctctctttatgataaagctctataggtaatatttcctgtataattttaagtaagaaatattataaaaaggaggtgaaaaaggattgtccaatatcctaagtaaacatagaatcaaacaaactgaaaccggaaagtat Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: NC_009009_SSA_0167_SSA_0168|Hypothetical protein (Asparagine/proline-rich):hypothetical protein|POSITIVE:POSITIVE|[166396,166596]|201 HSP 1 e-value: 8.0E-89 bit: 327.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 gtgatttctcaacataaccttctaagtttaaaagtctgatttgtattcagacnnnnnnnnnnnnctctctttatgataaagctctataggtaatatttcctgtataattttaagtaagaaatattataaaaaggaggtgaaaaaggattgtccaatatcctaagtaaacatagaatcaaacaaactgaaaccggaaagtat gtgatttctcaacataaccttctaagtttaaaagtctgatttgtattcagactttttcttttttctctctttatgataaagctctataggtaatatttcctgtataattttaagtaagaaatattataaaaaggaggtgaaaaaggattgtccaatatcctaagtaaacatagaatcaaacaaactgaaaccggaaagtat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGAUUUCUCAACAUAACCUUCUAAGUUUAAAAGUCUGAUUUGUAUUCAGACUUUUUCUUUUUUCUCUCUUUAUGAUAAAGCUCUAUAGGUAAUAUUUCCUGUAUAAUUUUAAGUAAGAAAUAUUAUAAAAAGGAGGUGAAAAAGGAUUGUCCAAUAUCCUAAGUAAACAUAGAAUCAAACAAACUGAAACCGGAAAGUAU .((.((((...........(((((.((((((((((((((.......))))))))).((((((((((((((((((((((......((((((........))))))...((((....))))..))))))))...))))).))))))))).................))))).)))))...........)))).))........ (-38.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACUUUCCGGUUUCAGUUUGUUUGAUUCUAUGUUUACUUAGGAUAUUGGACAAUCCUUUUUCACCUCCUUUUUAUAAUAUUUCUUACUUAAAAUUAUACAGGAAAUAUUACCUAUAGAGCUUUAUCAUAAAGAGAGAAAAAAGAAAAAGUCUGAAUACAAAUCAGACUUUUAAACUUAGAAGGUUAUGUUGAGAAAUCAC .........((((((...(((((..((((((........)))))..)..))))).((((((....(((((((...(((((((((((..............)))))))))))......((......))..)))).)))........((((((((((.......))))))))))......)))))).........)))))).. (-39.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 84 43 165 122 NC_009009:SSA_1436|5end_hypothetical_protein_1443125..1443355_NEGATIVE 257 169 132 80 43 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 256 70 21 168 115 NC_009009:SSA_0012|5end_Beta-lactamase_class_A,_putative_9916..10146_POSITIVE 250 49 1 137 93 NC_009009:SSA_1341|5end_Carbamoyl-phosphate_synthase_large_chain,_putative_1359827..1360057_NEGATIVE 249 84 51 98 69 NC_009009:SSA_1730|5end_hypothetical_protein_1716057..1716287_NEGATIVE 249 42 2 82 35 NC_009009:SSA_1611|5end_Era-like_GTP-binding_protein,_putative_1616032..1616262_NEGATIVE 248 70 25 230 181 NC_009009:SSA_2035|5end_Conserved_uncharacterized_protein_2040288..2040518_NEGATIVE 248 84 45 89 38 NC_009009:SSA_1381|5end_hypothetical_protein_1399565..1399795_NEGATIVE 239 110 62 74 19 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 237 70 21 208 153 NC_009009:SSA_0553|5end_hypothetical_protein_548911..549141_POSITIVE 235 90 52 138 92 NC_009009:SSA_0106|5end_30S_ribosomal_protein_S10,_putative_107772..108002_POSITIVE 233 60 18 219 174 NC_009009:SSA_0881|5end_Lipoprotein,_putative_876204..876434_POSITIVE 223 68 26 170 121 NC_009009:SSA_0614|5end_Transporter,_putative_607974..608204_NEGATIVE 222 89 45 132 82 NC_009009:SSA_1607|5end_Formamidopyrimidine-DNA_glycosylase,_putative_1613255..1613485_NEGATIVE 220 66 31 229 193 NC_009009:SSA_0851|5end_Cation_efflux_family_protein,_putative_838900..839130_NEGATIVE 218 74 35 116 74 NC_009009:SSA_0865|5end_hypothetical_protein_856378..856608_POSITIVE 218 165 129 146 107 NC_009009:SSA_0352|5end_Ribonuclease_HIII,_putative_345879..346109_NEGATIVE 218 100 53 124 84 NC_009009:SSA_0308|5end_hypothetical_protein_304385..304615_POSITIVE 217 50 1 221 178 NC_009009:SSA_1586|5end_hypothetical_protein_1588182..1588412_NEGATIVE 217 70 26 47 1 NC_009009:SSA_0011|5end_hypothetical_protein_9795..10025_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 68 32 121 82 NC_009009:SSA_0906|3end_CshA-like_fibrillar_surface_protein_C_917411..917561_POSITIVE 266 70 27 120 75 NC_009009:SSA_2345|3end_hypothetical_protein_2347502..2347652_POSITIVE 258 84 43 148 105 NC_009009:SSA_1438|3end_Acetyltransferase,_putative_1443142..1443292_NEGATIVE 257 169 132 83 46 NC_009009:SSA_0097|3end_Multi_antimicrobial_extrusion_(MATE)_family_transporter,_putative_99505..99655_POSITIVE 250 49 1 113 69 NC_009009:SSA_1342|3end_Carbamoyl-phosphate_synthase_small_chain,_putative_1359851..1360001_NEGATIVE 237 70 21 118 63 NC_009009:SSA_0552|3end_Cof_family_protein,_putative_548901..549051_POSITIVE 233 60 18 143 98 NC_009009:SSA_0880|3end_Lipoprotein,_putative_876208..876358_POSITIVE 222 89 45 104 54 NC_009009:SSA_1608|3end_hypothetical_protein_1613283..1613433_NEGATIVE 218 100 53 72 32 NC_009009:SSA_0307|3end_Glutamine_synthetase_type_1,_putative_304413..304563_POSITIVE 213 69 36 99 57 NC_009009:SSA_0060|3end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_62735..62885_POSITIVE 210 54 19 127 96 NC_009009:SSA_1494|3end_Conserved_uncharacterized_protein_1499514..1499664_NEGATIVE 210 68 24 127 80 NC_009009:SSA_0904|3end_CshA-like_fibrillar_surface_protein_A_902958..903108_POSITIVE 210 59 18 79 33 NC_009009:SSA_0513|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_512237..512387_POSITIVE 208 76 34 119 78 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 205 100 53 47 1 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 205 70 27 134 90 NC_009009:SSA_1391|3end_hypothetical_protein_1406158..1406308_NEGATIVE 205 161 124 58 26 NC_009009:SSA_1298|3end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1316627..1316777_POSITIVE 205 87 52 116 71 NC_009009:SSA_1006|3end_Dextransucrase,_putative_1008601..1008751_POSITIVE 205 105 67 116 64 NC_009009:SSA_0831|3end_Nucleotide_sugar_synthetase-like_protein,_putative_816755..816905_POSITIVE 205 139 100 147 107 NC_009009:SSA_0735|3end_Integral_membrane_protein,_putative_717680..717830_POSITIVE