Origin IGS: actattctcgctttctatttgctggctttattataccataaatccataggagacacaaaaagcactggagcaaacgtccaatgcttgagtcttatttagctgag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcagctaaataagactcaagcattggacgtttgctccagtgctttttgtgtctcctatggatttatggtataataaagccagcaaatagaaagcgagaatagt Mask Tandem Repeat Region ================================================ actattctcgctttctatttgctggctttattataccataaatccataggagacacaaaaagcactggagcaaacgtccaatgcttgagtcttatttagctgag Find is-nt database================================================ Query_seq: SSA_1787:SSA_1788|SSA_1787:SSA_1788:Diaminopimelate decarboxylase, putative:Integral membrane protein, possible receptor, putative:<-<-:1771642..1771745 104 actattctcgctttctatttgctggctttattataccataaatccataggagacacaaaaagcactggagcaaacgtccaatgcttgagtcttatttagctgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1787:SSA_1788|SSA_1787:SSA_1788:Diaminopimelate decarboxylase, putative:Integral membrane protein, possible receptor, putative:<-<-:1771642..1771745 104 actattctcgctttctatttgctggctttattataccataaatccataggagacacaaaaagcactggagcaaacgtccaatgcttgagtcttatttagctgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1787:SSA_1788|SSA_1787:SSA_1788:Diaminopimelate decarboxylase, putative:Integral membrane protein, possible receptor, putative:<-<-:1771642..1771745 104 actattctcgctttctatttgctggctttattataccataaatccataggagacacaaaaagcactggagcaaacgtccaatgcttgagtcttatttagctgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actattctcgctttctatttgctggctttattataccataaatccataggagacacaaaaagcactggagcaaacgtccaatgcttgagtcttatttagctgag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 4 End: 96 ... M L A F Y L L A L L Y H K S I G D T K S T G A N V Q C L S L I ........ actattctcgctttctatttgctggctttattataccataaatccataggagacacaaaaagcactggagcaaacgtccaatgcttgagtcttatttagctgag 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: 84 Start: 30 End: 59 .............................TTTGTGTCTCCTATGGATTTATGGTATAAT............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actattctcgctttctatttgctggctttattataccataaatccataggagacacaaaaagcactggagcaaacgtccaatgcttgagtcttatttagctgag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -3.4 Tail_Score: -3.2661 Start: 62 End: 84 Full_Region: TAGGAGACACAAAAA GCACTGGA GCAAACG TCCAATGC TTGAGTCTTATTTAG .............................................................GCACTGGAGCAAACGTCCAATGC.................... Find igs database================================================ Query_seq: SSA_1787:SSA_1788|SSA_1787:SSA_1788:Diaminopimelate decarboxylase, putative:Integral membrane protein, possible receptor, putative:<-<-:1771642..1771745 104 actattctcgctttctatttgctggctttattataccataaatccataggagacacaaaaagcactggagcaaacgtccaatgcttgagtcttatttagctgag Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_009009_SSA_1787_SSA_1788|Diaminopimelate decarboxylase, putative:Integral membrane protein, possible receptor, putative|NEGATIVE:NEGATIVE|[1771642,1771745]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 actattctcgctttctatttgctggctttattataccataaatccataggagacacaaaaagcactggagcaaacgtccaatgcttgagtcttatttagctgag actattctcgctttctatttgctggctttattataccataaatccataggagacacaaaaagcactggagcaaacgtccaatgcttgagtcttatttagctgag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAUUCUCGCUUUCUAUUUGCUGGCUUUAUUAUACCAUAAAUCCAUAGGAGACACAAAAAGCACUGGAGCAAACGUCCAAUGCUUGAGUCUUAUUUAGCUGAG ......((((((..........(((.(((((......))))).)))...(((((.....(((((.((((.......)))).)))))..)))))....))).))) (-21.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAGCUAAAUAAGACUCAAGCAUUGGACGUUUGCUCCAGUGCUUUUUGUGUCUCCUAUGGAUUUAUGGUAUAAUAAAGCCAGCAAAUAGAAAGCGAGAAUAGU (((.(((.....((((.(((((((((((.(....))))))))))...)).)))).((((.......((((........))))....))))..))))))...... (-28.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 925 90 41 181 132 NC_009009:SSA_1787|5end_Diaminopimelate_decarboxylase,_putative_1771551..1771781_NEGATIVE 305 45 5 164 128 NC_009009:SSA_2205|5end_Transcription_antitermination_factor_NusG,_putative_2206100..2206330_NEGATIVE 286 73 31 154 99 NC_009009:SSA_0864|5end_hypothetical_protein_856318..856548_NEGATIVE 278 100 66 44 6 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 277 41 2 132 88 NC_009009:SSA_1296|5end_hypothetical_protein_1313013..1313243_NEGATIVE 272 79 31 147 91 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 270 100 51 200 146 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 262 60 12 152 102 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 260 56 11 140 102 NC_009009:SSA_0767|5end_Diacylglycerol_kinase_catalytic_domain_protein,_putative_747087..747317_POSITIVE 255 92 51 85 40 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 253 93 61 59 15 NC_009009:SSA_0727|5end_Metal-dependent_membrane_protease,_putative_712735..712965_POSITIVE 252 42 2 127 88 NC_009009:SSA_0888|5end_Magnesium/cobalt_transporter,_putative_881329..881559_POSITIVE 252 92 61 51 14 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 250 87 45 223 181 NC_009009:SSA_1657|5end_hypothetical_protein_1653231..1653461_NEGATIVE 250 89 45 59 22 NC_009009:SSA_0803|5end_hypothetical_protein_785145..785375_POSITIVE 250 92 64 216 186 NC_009009:SSA_0153|5end_hypothetical_protein_148677..148907_POSITIVE 248 88 41 176 127 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 248 89 41 59 5 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 246 55 11 146 100 NC_009009:SSA_1982|5end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975873..1976103_NEGATIVE 244 49 1 93 47 NC_009009:SSA_0903|5end_NAD(P)H_dehydrogenase_(quinone),_putative_893242..893472_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 79 31 57 1 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 262 60 12 67 17 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 261 50 2 140 91 NC_009009:SSA_2213|3end_Nucleotide_sugar_dehydratase,_putative_2214047..2214197_NEGATIVE 255 92 51 51 6 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 252 92 61 40 3 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 250 89 45 62 25 NC_009009:SSA_0802|3end_hypothetical_protein_785228..785378_POSITIVE 248 89 41 66 12 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 238 92 62 77 49 NC_009009:SSA_0537|3end_Propanediol_utilization:dioldehydratase_reactivation,_putative_533893..534043_POSITIVE 236 100 61 96 49 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 235 91 56 53 16 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 233 92 61 62 24 NC_009009:SSA_0937|3end_Arsenate_reductase,_glutaredoxin_family,_putative_946664..946814_POSITIVE 230 100 66 48 20 NC_009009:SSA_0838|3end_GtfB,_putative_826829..826979_POSITIVE 229 87 43 148 89 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 227 79 34 149 100 NC_009009:SSA_0490|3end_Cobalamin_5'-phosphate_synthase,_putative_491044..491194_POSITIVE 225 86 43 80 42 NC_009009:SSA_0820|3end_Ribosomal_protein_S21,_putative_801505..801655_POSITIVE 225 86 48 57 26 NC_009009:SSA_0111|3end_30S_ribosomal_protein_S19,_putative_111033..111183_POSITIVE 224 90 55 85 52 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 224 86 46 75 31 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 223 28 1 122 99 NC_009009:SSA_1439|3end_hypothetical_protein_1443624..1443774_NEGATIVE 222 97 62 96 55 NC_009009:SSA_1005|3end_Sugar_ABC_transporter,_permease_protein,_putative_1006941..1007091_POSITIVE