Origin IGS: gtatattttcacctctgctaagcattataacaaaattttcttcaaattggaaagttgaaagaggaagtattagacaaaagagatagcagcccgaatgaagaacgggctgccttttgaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttcaaaaggcagcccgttcttcattcgggctgctatctcttttgtctaatacttcctctttcaactttccaatttgaagaaaattttgttataatgcttagcagaggtgaaaatatac Mask Tandem Repeat Region ================================================ gtatattttcacctctgctaagcattataacaaaattttcttcaaattggaaagttgaaagaggaagtattagacaaaagagatagcagcccgaatgaagaacgggctgccttttgaaa Find is-nt database================================================ Query_seq: SSA_0208:SSA_0209|SSA_0208:SSA_0209:Conserved uncharacterized protein:Glutamyl aminopeptidase, putative:<-<-:206543..206661 119 gtatattttcacctctgctaagcattataacaaaattttcttcaaattggaaagttgaaagaggaagtattagacaaaagagatagcagcccgaatgaagaacgggctgccttttgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0208:SSA_0209|SSA_0208:SSA_0209:Conserved uncharacterized protein:Glutamyl aminopeptidase, putative:<-<-:206543..206661 119 gtatattttcacctctgctaagcattataacaaaattttcttcaaattggaaagttgaaagaggaagtattagacaaaagagatagcagcccgaatgaagaacgggctgccttttgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0208:SSA_0209|SSA_0208:SSA_0209:Conserved uncharacterized protein:Glutamyl aminopeptidase, putative:<-<-:206543..206661 119 gtatattttcacctctgctaagcattataacaaaattttcttcaaattggaaagttgaaagaggaagtattagacaaaagagatagcagcccgaatgaagaacgggctgccttttgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtatattttcacctctgctaagcattataacaaaattttcttcaaattggaaagttgaaagaggaagtattagacaaaagagatagcagcccgaatgaagaacgggctgccttttgaaa Predict ORF larger than 30AA ================================================ gtatattttcacctctgctaagcattataacaaaattttcttcaaattggaaagttgaaagaggaagtattagacaaaagagatagcagcccgaatgaagaacgggctgccttttgaaa 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: 24 End: 53 .......................TTTCCAATTTGAAGAAAATTTTGTTATAAT.................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtatattttcacctctgctaagcattataacaaaattttcttcaaattggaaagttgaaagaggaagtattagacaaaagagatagcagcccgaatgaagaacgggctgccttttgaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0208:SSA_0209|SSA_0208:SSA_0209:Conserved uncharacterized protein:Glutamyl aminopeptidase, putative:<-<-:206543..206661 119 gtatattttcacctctgctaagcattataacaaaattttcttcaaattggaaagttgaaagaggaagtattagacaaaagagatagcagcccgaatgaagaacgggctgccttttgaaa Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_009009_SSA_0208_SSA_0209|Conserved uncharacterized protein:Glutamyl aminopeptidase, putative|NEGATIVE:NEGATIVE|[206543,206661]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 gtatattttcacctctgctaagcattataacaaaattttcttcaaattggaaagttgaaagaggaagtattagacaaaagagatagcagcccgaatgaagaacgggctgccttttgaaa gtatattttcacctctgctaagcattataacaaaattttcttcaaattggaaagttgaaagaggaagtattagacaaaagagatagcagcccgaatgaagaacgggctgccttttgaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUAUUUUCACCUCUGCUAAGCAUUAUAACAAAAUUUUCUUCAAAUUGGAAAGUUGAAAGAGGAAGUAUUAGACAAAAGAGAUAGCAGCCCGAAUGAAGAACGGGCUGCCUUUUGAAA ...........(((((((...))..........((((((((.......))))))))...)))))..........((((((.....((((((((.........))))))))))))))... (-29.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCAAAAGGCAGCCCGUUCUUCAUUCGGGCUGCUAUCUCUUUUGUCUAAUACUUCCUCUUUCAACUUUCCAAUUUGAAGAAAAUUUUGUUAUAAUGCUUAGCAGAGGUGAAAAUAUAC ........(((((((((.........))))))))).((.((((((.(((........((((.(((.........))))))).......((......)).))))))))).))........ (-26.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 966 110 61 201 152 NC_009009:SSA_0208|5end_Conserved_uncharacterized_protein_206452..206682_NEGATIVE 301 110 72 70 19 NC_009009:SSA_1493|5end_hypothetical_protein_1499480..1499710_NEGATIVE 293 95 53 52 22 NC_009009:SSA_0424|5end_Exopolysaccharide_biosynthesis_protein,_putative_422233..422463_NEGATIVE 282 107 72 32 2 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 280 89 51 227 193 NC_009009:SSA_0936|5end_FAD_synthase,_putative_945139..945369_POSITIVE 258 107 63 71 22 NC_009009:SSA_0067|5end_Acyltransferase_(yrhL-like_subfamily_of_SGNH-hydrolases),_putative_68005..68235_POSITIVE 258 106 61 174 116 NC_009009:SSA_0017|5end_Cell_shape_determining_protein_MreC,_putative_22811..23041_POSITIVE 253 92 53 219 179 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 250 110 63 181 130 NC_009009:SSA_0770|5end_Ribonucleoside-diphosphate_reductase,_putative_751411..751641_NEGATIVE 250 110 61 173 129 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 243 110 77 186 146 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 243 94 52 172 130 NC_009009:SSA_0201|5end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_199825..200055_POSITIVE 242 110 73 161 115 NC_009009:SSA_1527|5end_hypothetical_protein_1534587..1534817_POSITIVE 241 109 79 217 190 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 238 110 83 24 3 NC_009009:SSA_1519|5end_Polysaccharide/teichoic_acid_transporter,_putative_1526069..1526299_NEGATIVE 236 88 47 66 29 NC_009009:SSA_1591|5end_Dipeptidase,_putative_1595451..1595681_NEGATIVE 235 110 61 189 115 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 230 108 81 150 127 NC_009009:SSA_0944|5end_Phosphate_import_ATP-binding_protein_pstB_2,_putative_951741..951971_POSITIVE 230 110 81 79 50 NC_009009:SSA_0798|5end_ABC_transporter_membrane-spanning_permease-macrolide_efflux,_putative_780463..780693_POSITIVE 228 110 72 208 173 NC_009009:SSA_2299|5end_hypothetical_protein_2301545..2301775_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 109 63 99 45 NC_009009:SSA_2256|3end_hypothetical_protein_2251235..2251385_POSITIVE 293 95 53 55 25 NC_009009:SSA_0425|3end_Glycosyltransferase,_putative_422230..422380_NEGATIVE 288 110 61 147 104 NC_009009:SSA_1065|3end_Beta-hexosamidase_A,_putative_1084130..1084280_POSITIVE 286 110 85 36 4 NC_009009:SSA_1494|3end_Conserved_uncharacterized_protein_1499514..1499664_NEGATIVE 280 110 61 62 8 NC_009009:SSA_1014|3end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1018798..1018948_POSITIVE 259 108 78 57 28 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE 258 107 63 81 32 NC_009009:SSA_0066|3end_hypothetical_protein_68095..68245_POSITIVE 255 109 67 82 45 NC_009009:SSA_1745|3end_General_stress_response_protein_CsbD,_putative_1731997..1732147_NEGATIVE 250 110 61 63 19 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 246 107 71 49 6 NC_009009:SSA_2255|3end_Transcriptional_regulator,_XRE_family,_putative_2250730..2250880_POSITIVE 243 94 52 77 35 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE 243 108 62 72 28 NC_009009:SSA_0144|3end_Transcriptional_regulator,_TetR_family,_putative_137993..138143_NEGATIVE 235 110 61 89 15 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 233 109 62 87 45 NC_009009:SSA_1951|3end_Penicillin-binding_protein_3,_putative_1948103..1948253_POSITIVE 231 110 75 120 85 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 230 108 81 139 116 NC_009009:SSA_0943|3end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_951810..951960_POSITIVE 226 110 61 73 24 NC_009009:SSA_2109|3end_Elongation_factor_G,_putative_2112787..2112937_NEGATIVE 226 91 55 129 91 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE 225 108 74 87 40 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 222 110 67 148 102 NC_009009:SSA_0306|3end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_303035..303185_POSITIVE