Origin IGS: tctccttcgcaatttatattgtattattatacaatatttttttataaaaacaaatgctttatgtagaaaaataataattttctatttttcagcttgtatatctgtattatttcaaatatttttctattttgtgagtttttccgaaagatgcttttataaaaaatctctttaaggggattaccctacttttctctacatttattttgtaaccttttattatccttgatttataaaagaaaagagaattttatgatacaatggttatatcttgttttaggggaaagaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttctttcccctaaaacaagatataaccattgtatcataaaattctcttttcttttataaatcaaggataataaaaggttacaaaataaatgtagagaaaagtagggtaatccccttaaagagattttttataaaagcatctttcggaaaaactcacaaaatagaaaaatatttgaaataatacagatatacaagctgaaaaatagaaaattattatttttctacataaagcatttgtttttataaaaaaatattgtataataatacaatataaattgcgaaggaga Mask Tandem Repeat Region ================================================ tctccttcgcaatttatattgtattattatacaatatttttttataaaaacaaatgctttatgtagaaaaataataattttctatttttcagcttgtatatctgtattatttcaaatatttttctattttgtgagtttttccgaaagatgcttttataaaaaatctctttaaggggattaccctacttttctctacatttattttgtaaccttttattatccttgatttataaaagaaaagagaattttatgatacaatggttatatcttgttttaggggaaagaa Find is-nt database================================================ Query_seq: SSA_1950:SSA_1951|SSA_1950:SSA_1951:ABC-type oligopeptide transport system, periplasmic component, putative:Penicillin-binding protein 3, putative:<-->:1946618..1946903 286 tctccttcgcaatttatattgtattattatacaatatttttttataaaaacaaatgctttatgtagaaaaataataattttctatttttcagcttgtatatctgtattatttcaaatatttttctattttgtgagtttttccgaaagatgcttttataaaaaatctctttaaggggattaccctacttttctctacatttattttgtaaccttttattatccttgatttataaaagaaaagagaattttatgatacaatggttatatcttgttttaggggaaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1950:SSA_1951|SSA_1950:SSA_1951:ABC-type oligopeptide transport system, periplasmic component, putative:Penicillin-binding protein 3, putative:<-->:1946618..1946903 286 tctccttcgcaatttatattgtattattatacaatatttttttataaaaacaaatgctttatgtagaaaaataataattttctatttttcagcttgtatatctgtattatttcaaatatttttctattttgtgagtttttccgaaagatgcttttataaaaaatctctttaaggggattaccctacttttctctacatttattttgtaaccttttattatccttgatttataaaagaaaagagaattttatgatacaatggttatatcttgttttaggggaaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1950:SSA_1951|SSA_1950:SSA_1951:ABC-type oligopeptide transport system, periplasmic component, putative:Penicillin-binding protein 3, putative:<-->:1946618..1946903 286 tctccttcgcaatttatattgtattattatacaatatttttttataaaaacaaatgctttatgtagaaaaataataattttctatttttcagcttgtatatctgtattatttcaaatatttttctattttgtgagtttttccgaaagatgcttttataaaaaatctctttaaggggattaccctacttttctctacatttattttgtaaccttttattatccttgatttataaaagaaaagagaattttatgatacaatggttatatcttgttttaggggaaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctccttcgcaatttatattgtattattatacaatatttttttataaaaacaaatgctttatgtagaaaaataataattttctatttttcagcttgtatatctgtattatttcaaatatttttctattttgtgagtttttccgaaagatgcttttataaaaaatctctttaaggggattaccctacttttctctacatttattttgtaaccttttattatccttgatttataaaagaaaagagaattttatgatacaatggttatatcttgttttaggggaaagaa Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 23 End: 169 ...................... M I I Q Y F F I K T N A L C R K I I I F Y F S A C I S V L F Q I F F Y F V S F S E R C F Y K K S L ..................................................................................................................... Protein_Len: 41 Strand: + Start: 163 End: 285 .................................................................................................................................................................. M S L R G L P Y F S L H L F C N L L L S L I Y K R K E N F M I Q W L Y L V L G E R . Protein_Len: 37 Strand: - Start: 110 End: 220 ............................................................................................................. K L Y K E I K H T K G F S A K I F F R K L P I V R S K E V N I K Y G K I M .................................................................. Protein_Len: 40 Strand: - Start: 45 End: 164 ............................................ L F L H K I Y F F L L K R N K L K Y I Q I I E F I K R N Q S N K R F I S K Y F M .......................................................................................................................... tctccttcgcaatttatattgtattattatacaatatttttttataaaaacaaatgctttatgtagaaaaataataattttctatttttcagcttgtatatctgtattatttcaaatatttttctattttgtgagtttttccgaaagatgcttttataaaaaatctctttaaggggattaccctacttttctctacatttattttgtaaccttttattatccttgatttataaaagaaaagagaattttatgatacaatggttatatcttgttttaggggaaagaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctccttcgcaatttatattgtattattatacaatatttttttataaaaacaaatgctttatgtagaaaaataataattttctatttttcagcttgtatatctgtattatttcaaatatttttctattttgtgagtttttccgaaagatgcttttataaaaaatctctttaaggggattaccctacttttctctacatttattttgtaaccttttattatccttgatttataaaagaaaagagaattttatgatacaatggttatatcttgttttaggggaaagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1950:SSA_1951|SSA_1950:SSA_1951:ABC-type oligopeptide transport system, periplasmic component, putative:Penicillin-binding protein 3, putative:<-->:1946618..1946903 286 tctccttcgcaatttatattgtattattatacaatatttttttataaaaacaaatgctttatgtagaaaaataataattttctatttttcagcttgtatatctgtattatttcaaatatttttctattttgtgagtttttccgaaagatgcttttataaaaaatctctttaaggggattaccctacttttctctacatttattttgtaaccttttattatccttgatttataaaagaaaagagaattttatgatacaatggttatatcttgttttaggggaaagaa Intra-Species Hit: Count: 1 Min: 1 Max: 286 Len: 286 Subject: NC_009009_SSA_1950_SSA_1951|ABC-type oligopeptide transport system, periplasmic component, putative:Penicillin-binding protein 3, putative|NEGATIVE:POSITIVE|[1946618,1946903]|286 HSP 1 e-value: 1.0E-76 bit: 287.0 Len: 145 Query Start:142 Query End:286 Subject Strand: POSITIVE Subject Start: 142 Subject End: 286 .............................................................................................................................................cgaaagatgcttttataaaaaatctctttaaggggattaccctacttttctctacatttattttgtaaccttttattatccttgatttataaaagaaaagagaattttatgatacaatggttatatcttgttttaggggaaagaa .............................................................................................................................................cgaaagatgcttttataaaaaatctctttaaggggattaccctacttttctctacatttattttgtaaccttttattatccttgatttataaaagaaaagagaattttatgatacaatggttatatcttgttttaggggaaagaa HSP 2 e-value: 5.0E-23 bit: 109.0 Len: 76 Query Start:1 Query End:76 Subject Strand: POSITIVE Subject Start: 1 Subject End: 76 tctccttcgcaatttatattgtattattatacaatannnnnnnataaaaacaaatgctttatgtagaaaaataata.................................................................................................................................................................................................................. tctccttcgcaatttatattgtattattatacaatatttttttataaaaacaaatgctttatgtagaaaaataata.................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCCUUCGCAAUUUAUAUUGUAUUAUUAUACAAUAUUUUUUUAUAAAAACAAAUGCUUUAUGUAGAAAAAUAAUAAUUUUCUAUUUUUCAGCUUGUAUAUCUGUAUUAUUUCAAAUAUUUUUCUAUUUUGUGAGUUUUUCCGAAAGAUGCUUUUAUAAAAAAUCUCUUUAAGGGGAUUACCCUACUUUUCUCUACAUUUAUUUUGUAACCUUUUAUUAUCCUUGAUUUAUAAAAGAAAAGAGAAUUUUAUGAUACAAUGGUUAUAUCUUGUUUUAGGGGAAAGAA ((((((..((((...(((((((((....))))))))).....(((((..((((..(((....((((((((.......)))))))).....))))))).....((((((((................(((((((((......(....).....)))))))))..(((((((.((((.....)))).........((((.......))))..(((((((.(((...)))..))))))).))))))).....))))))))....)))))..))))...))))))..... (-53.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUCCCCUAAAACAAGAUAUAACCAUUGUAUCAUAAAAUUCUCUUUUCUUUUAUAAAUCAAGGAUAAUAAAAGGUUACAAAAUAAAUGUAGAGAAAAGUAGGGUAAUCCCCUUAAAGAGAUUUUUUAUAAAAGCAUCUUUCGGAAAAACUCACAAAAUAGAAAAAUAUUUGAAAUAAUACAGAUAUACAAGCUGAAAAAUAGAAAAUUAUUAUUUUUCUACAUAAAGCAUUUGUUUUUAUAAAAAAAUAUUGUAUAAUAAUACAAUAUAAAUUGCGAAGGAGA .......(((((......((((((.....))))))......(((((...((((((((..(((...))).)))))))).((((.......)))))))))...)))))...((.((((...((..(((((((((((((((.............................(((((((........)))))))....(((......(((((((.......))))))).....)))...)))))))))))))))(((((((((....)))))))))...))...)))).)) (-51.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 650 140 91 231 182 NC_009009:SSA_1950|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component,_putative_1946527..1946757_NEGATIVE 260 217 172 91 54 NC_009009:SSA_0624|5end_hypothetical_protein_615079..615309_POSITIVE 251 130 81 149 98 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 243 243 205 48 10 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 243 243 205 183 145 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 240 170 127 83 39 NC_009009:SSA_2290|5end_hypothetical_protein_2291448..2291678_POSITIVE 240 170 127 83 39 NC_009009:SSA_2388|5end_hypothetical_protein_2031822..2032052_NEGATIVE 235 115 76 171 127 NC_009009:SSA_1936|5end_3-oxoacyl-[acyl-carrier_protein]_reductase,_putative_1923838..1924068_NEGATIVE 226 200 154 181 131 NC_009009:SSA_1756|5end_Conserved_uncharacterized_protein_1745291..1745521_NEGATIVE 224 207 164 140 95 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 221 45 1 144 98 NC_009009:SSA_2074|5end_Preprotein_translocase_subunit_YajC,_putative_2076935..2077165_NEGATIVE 219 210 164 128 79 NC_009009:SSA_2142|5end_Argininosuccinate_synthase,_putative_2143415..2143645_NEGATIVE 219 144 101 157 108 NC_009009:SSA_1288|5end_hypothetical_protein_1307578..1307808_NEGATIVE 215 136 91 208 165 NC_009009:SSA_2047|5end_hypothetical_protein_2049953..2050183_NEGATIVE 211 136 91 164 127 NC_009009:SSA_2307|5end_hypothetical_protein_2309909..2310139_NEGATIVE 207 214 182 134 98 NC_009009:SSA_0205|5end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_202722..202952_POSITIVE 205 206 164 95 47 NC_009009:SSA_2055|5end_hypothetical_protein_2058160..2058390_NEGATIVE 202 207 171 198 163 NC_009009:SSA_0128|5end_Adenylate_kinase,_putative_119201..119431_POSITIVE 201 176 132 108 61 NC_009009:SSA_2345|5end_hypothetical_protein_2346919..2347149_POSITIVE 201 223 181 109 70 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 142 102 70 25 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 245 227 182 125 78 NC_009009:SSA_1597|3end_hypothetical_protein_1603267..1603417_NEGATIVE 243 243 205 48 10 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 243 243 205 149 111 NC_009009:SSA_1412|3end_hypothetical_protein_1423994..1424144_NEGATIVE 240 170 127 60 16 NC_009009:SSA_2289|3end_Cadmium_efflux_system_transcriptional_regulator_(ArsR-like),_putative_2291505..2291655_POSITIVE 240 170 127 60 16 NC_009009:SSA_2389|3end_Arsenical_resistance_operon_transcription_repressor,_putative_2031845..2031995_NEGATIVE 240 170 127 60 16 NC_009009:SSA_2387|3end_Arsenical_resistance_operon_transcription_repressor,_putative_2031845..2031995_NEGATIVE 234 106 76 148 114 NC_009009:SSA_1937|3end_Malonyl-CoA:ACP_transacylase,_putative_1923851..1924001_NEGATIVE 219 115 75 133 92 NC_009009:SSA_1528|3end_Phosphoglycerate_mutase,_putative_1535850..1536000_POSITIVE 218 190 141 56 2 NC_009009:SSA_0852|3end_ATP-dependent_DNA_helicase,_putative_841418..841568_POSITIVE 218 207 165 94 49 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 215 104 75 124 92 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 200 142 109 115 88 NC_009009:SSA_1113|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_domain_and_a_winged-helix_DNA-binding_domains),_putative_1140520..1140670_POSITIVE 199 134 91 104 51 NC_009009:SSA_0950|3end_hypothetical_protein_957788..957938_POSITIVE 198 195 172 144 116 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 195 136 92 83 37 NC_009009:SSA_0665|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes_(MutT/NUDIX_family)_649154..649304_NEGATIVE 194 196 173 39 19 NC_009009:SSA_1745|3end_General_stress_response_protein_CsbD,_putative_1731997..1732147_NEGATIVE 194 190 143 113 60 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 193 191 172 21 2 NC_009009:SSA_2254|3end_Holliday_junction_DNA_helicase_ruvA,_putative_2249434..2249584_NEGATIVE 193 176 131 135 88 NC_009009:SSA_0367|3end_hypothetical_protein_359291..359441_POSITIVE