Origin IGS: aatagatacctcaaagatagtataatacaaatagacattattttcaaatatttagaaataaattggaatttattttattatttctaaacatttaaaaataatctttttctataatcaaaaaatagtccattttggtatggcatgatagtaaatcttgtgaggttttgtagcaagtattcaaataaaaagcgcatactatcaggaataaaaaacttgatagtatacgttttatcctagaaatatttgctggctgtttttctcaaactgactttttaagaagttaccttatcagcaatttcaaataagtttatggagctatctttggaaaaactgtagaatttcaaaaattactacagaccttgaattttacttatcatttcaatgatttagattgc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcaatctaaatcattgaaatgataagtaaaattcaaggtctgtagtaatttttgaaattctacagtttttccaaagatagctccataaacttatttgaaattgctgataaggtaacttcttaaaaagtcagtttgagaaaaacagccagcaaatatttctaggataaaacgtatactatcaagttttttattcctgatagtatgcgctttttatttgaatacttgctacaaaacctcacaagatttactatcatgccataccaaaatggactattttttgattatagaaaaagattatttttaaatgtttagaaataataaaataaattccaatttatttctaaatatttgaaaataatgtctatttgtattatactatctttgaggtatctatt Mask Tandem Repeat Region ================================================ aatagatacctcaaagatagtataatacaaatagacattattttcaaatatttagaaataaattggaatttattttattatttctaaacatttaaaaataatctttttctataatcaaaaaatagtccattttggtatggcatgatagtaaatcttgtgaggttttgtagcaagtattcaaataaaaagcgcatactatcaggaataaaaaacttgatagtatacgttttatcctagaaatatttgctggctgtttttctcaaactgactttttaagaagttaccttatcagcaatttcaaataagtttatggagctatctttggaaaaactgtagaatttcaaaaattactacagaccttgaattttacttatcatttcaatgatttagattgc Find is-nt database================================================ Query_seq: SMT_251:SMT_252|SMT_251:SMT_252:hypothetical protein:K07720 two-component system, response regulator YesN:<-<-:187149..187543 395 aatagatacctcaaagatagtataatacaaatagacattattttcaaatatttagaaataaattggaatttattttattatttctaaacatttaaaaataatctttttctataatcaaaaaatagtccattttggtatggcatgatagtaaatcttgtgaggttttgtagcaagtattcaaataaaaagcgcatactatcaggaataaaaaacttgatagtatacgttttatcctagaaatatttgctggctgtttttctcaaactgactttttaagaagttaccttatcagcaatttcaaataagtttatggagctatctttggaaaaactgtagaatttcaaaaattactacagaccttgaattttacttatcatttcaatgatttagattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_251:SMT_252|SMT_251:SMT_252:hypothetical protein:K07720 two-component system, response regulator YesN:<-<-:187149..187543 395 aatagatacctcaaagatagtataatacaaatagacattattttcaaatatttagaaataaattggaatttattttattatttctaaacatttaaaaataatctttttctataatcaaaaaatagtccattttggtatggcatgatagtaaatcttgtgaggttttgtagcaagtattcaaataaaaagcgcatactatcaggaataaaaaacttgatagtatacgttttatcctagaaatatttgctggctgtttttctcaaactgactttttaagaagttaccttatcagcaatttcaaataagtttatggagctatctttggaaaaactgtagaatttcaaaaattactacagaccttgaattttacttatcatttcaatgatttagattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_251:SMT_252|SMT_251:SMT_252:hypothetical protein:K07720 two-component system, response regulator YesN:<-<-:187149..187543 395 aatagatacctcaaagatagtataatacaaatagacattattttcaaatatttagaaataaattggaatttattttattatttctaaacatttaaaaataatctttttctataatcaaaaaatagtccattttggtatggcatgatagtaaatcttgtgaggttttgtagcaagtattcaaataaaaagcgcatactatcaggaataaaaaacttgatagtatacgttttatcctagaaatatttgctggctgtttttctcaaactgactttttaagaagttaccttatcagcaatttcaaataagtttatggagctatctttggaaaaactgtagaatttcaaaaattactacagaccttgaattttacttatcatttcaatgatttagattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatagatacctcaaagatagtataatacaaatagacattattttcaaatatttagaaataaattggaatttattttattatttctaaacatttaaaaataatctttttctataatcaaaaaatagtccattttggtatggcatgatagtaaatcttgtgaggttttgtagcaagtattcaaataaaaagcgcatactatcaggaataaaaaacttgatagtatacgttttatcctagaaatatttgctggctgtttttctcaaactgactttttaagaagttaccttatcagcaatttcaaataagtttatggagctatctttggaaaaactgtagaatttcaaaaattactacagaccttgaattttacttatcatttcaatgatttagattgc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 142 End: 234 ............................................................................................................................................. M I V N L V R F C S K Y S N K K R I L S G I K N L I V Y V L S ................................................................................................................................................................. Protein_Len: 35 Strand: + Start: 198 End: 302 ..................................................................................................................................................................................................... M R N K K L D S I R F I L E I F A G C F S Q T D F L R S Y L I S N F K ............................................................................................. Protein_Len: 49 Strand: - Start: 95 End: 241 .............................................................................................. F Y D K E I I L F Y D M K T H C S L L D Q S T K Y C T N L Y F A C V I L F L F S S L I R K I R S M .......................................................................................................................................................... Protein_Len: 44 Strand: - Start: 87 End: 218 ...................................................................................... V N L F L R K R Y D F F L G N Q Y P M I T F R T L N Q L L Y E F L F R M S D P I F F K M ................................................................................................................................................................................. aatagatacctcaaagatagtataatacaaatagacattattttcaaatatttagaaataaattggaatttattttattatttctaaacatttaaaaataatctttttctataatcaaaaaatagtccattttggtatggcatgatagtaaatcttgtgaggttttgtagcaagtattcaaataaaaagcgcatactatcaggaataaaaaacttgatagtatacgttttatcctagaaatatttgctggctgtttttctcaaactgactttttaagaagttaccttatcagcaatttcaaataagtttatggagctatctttggaaaaactgtagaatttcaaaaattactacagaccttgaattttacttatcatttcaatgatttagattgc 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: 88 Start: 19 End: 48 ..................TTTGAAAATAATGTCTATTTGTATTATACT........................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 52 End: 81 ...................................................TTAGAAATAAATTGGAATTTATTTTATTAT.......................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 145 End: 174 ................................................................................................................................................CTTGCTACAAAACCTCACAAGATTTACTAT............................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatagatacctcaaagatagtataatacaaatagacattattttcaaatatttagaaataaattggaatttattttattatttctaaacatttaaaaataatctttttctataatcaaaaaatagtccattttggtatggcatgatagtaaatcttgtgaggttttgtagcaagtattcaaataaaaagcgcatactatcaggaataaaaaacttgatagtatacgttttatcctagaaatatttgctggctgtttttctcaaactgactttttaagaagttaccttatcagcaatttcaaataagtttatggagctatctttggaaaaactgtagaatttcaaaaattactacagaccttgaattttacttatcatttcaatgatttagattgc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 67 HP_score: -2.5 Tail_Score: -5.30616 Start: 189 End: 227 Full_Region: tatttctaggataaa acgtatactatcaag ttttttatt cctgatagtatgcgc tttttatttgaatac ............................................................................................................................................................................................acgtatactatcaagttttttattcctgatagtatgcgc........................................................................................................................................................................ TransTerm Strand: + Conf: 72 HP_score: -6.0 Tail_Score: -4.4648 Start: 190 End: 226 Full_Region: TATTCAAATAAAAAG CGCATACTATCAGG AATAAAAAA CTTGATAGTATACG TTTTATCCTAGAAAT .............................................................................................................................................................................................CGCATACTATCAGGAATAAAAAACTTGATAGTATACG......................................................................................................................................................................... TransTerm Strand: - Conf: 65 HP_score: -6.0 Tail_Score: -3.77285 Start: 190 End: 226 Full_Region: atttctaggataaaa cgtatactatcaag ttttttatt cctgatagtatgcg ctttttatttgaata .............................................................................................................................................................................................cgtatactatcaagttttttattcctgatagtatgcg......................................................................................................................................................................... TransTerm Strand: - Conf: 79 HP_score: -7.1 Tail_Score: -4.57569 Start: 331 End: 356 Full_Region: agtaaaattcaaggt ctgtagtaattt ttg aaattctacag tttttccaaagatag ..........................................................................................................................................................................................................................................................................................................................................ctgtagtaatttttgaaattctacag....................................... Find igs database================================================ Query_seq: SMT_251:SMT_252|SMT_251:SMT_252:hypothetical protein:K07720 two-component system, response regulator YesN:<-<-:187149..187543 395 aatagatacctcaaagatagtataatacaaatagacattattttcaaatatttagaaataaattggaatttattttattatttctaaacatttaaaaataatctttttctataatcaaaaaatagtccattttggtatggcatgatagtaaatcttgtgaggttttgtagcaagtattcaaataaaaagcgcatactatcaggaataaaaaacttgatagtatacgttttatcctagaaatatttgctggctgtttttctcaaactgactttttaagaagttaccttatcagcaatttcaaataagtttatggagctatctttggaaaaactgtagaatttcaaaaattactacagaccttgaattttacttatcatttcaatgatttagattgc Intra-Species Hit: Count: 1 Min: 1 Max: 395 Len: 395 Subject: smit_SMT_251_SMT_252|hypothetical protein:K07720 two-component system, response regulator YesN|NEGATIVE:NEGATIVE|[187149,187543]|395 HSP 1 e-value: 1.0E-165 bit: 581.0 Len: 293 Query Start:103 Query End:395 Subject Strand: POSITIVE Subject Start: 103 Subject End: 395 ......................................................................................................ctttttctataatcaaaaaatagtccattttggtatggcatgatagtaaatcttgtgaggttttgtagcaagtattcaaataaaaagcgcatactatcaggaataaaaaacttgatagtatacgttttatcctagaaatatttgctggctgtttttctcaaactgactttttaagaagttaccttatcagcaatttcaaataagtttatggagctatctttggaaaaactgtagaatttcaaaaattactacagaccttgaattttacttatcatttcaatgatttagattgc ......................................................................................................ctttttctataatcaaaaaatagtccattttggtatggcatgatagtaaatcttgtgaggttttgtagcaagtattcaaataaaaagcgcatactatcaggaataaaaaacttgatagtatacgttttatcctagaaatatttgctggctgtttttctcaaactgactttttaagaagttaccttatcagcaatttcaaataagtttatggagctatctttggaaaaactgtagaatttcaaaaattactacagaccttgaattttacttatcatttcaatgatttagattgc HSP 2 e-value: 2.0E-11 bit: 71.9 Len: 36 Query Start:1 Query End:36 Subject Strand: POSITIVE Subject Start: 1 Subject End: 36 aatagatacctcaaagatagtataatacaaatagac....................................................................................................................................................................................................................................................................................................................................................................... aatagatacctcaaagatagtataatacaaatagac....................................................................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAGAUACCUCAAAGAUAGUAUAAUACAAAUAGACAUUAUUUUCAAAUAUUUAGAAAUAAAUUGGAAUUUAUUUUAUUAUUUCUAAACAUUUAAAAAUAAUCUUUUUCUAUAAUCAAAAAAUAGUCCAUUUUGGUAUGGCAUGAUAGUAAAUCUUGUGAGGUUUUGUAGCAAGUAUUCAAAUAAAAAGCGCAUACUAUCAGGAAUAAAAAACUUGAUAGUAUACGUUUUAUCCUAGAAAUAUUUGCUGGCUGUUUUUCUCAAACUGACUUUUUAAGAAGUUACCUUAUCAGCAAUUUCAAAUAAGUUUAUGGAGCUAUCUUUGGAAAAACUGUAGAAUUUCAAAAAUUACUACAGACCUUGAAUUUUACUUAUCAUUUCAAUGAUUUAGAUUGC ..........(((((((((((.........(((((.((((((((.((((.(((((((((((..(((((....)))))))))))))))).)))).)))))))).....))))).............((((((((((....((.(((((((((.(((((.((((((...((((((((((((......((((((.(((((((((((.........))))))))))).))))))......).)))))))))))...((((.....)))).)))))).)))))..))))..)))))))....))))).......)))))))))))))))).....((((((((((.....)))).)))))).............((.(((((....)))))..))..... (-87.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAUCUAAAUCAUUGAAAUGAUAAGUAAAAUUCAAGGUCUGUAGUAAUUUUUGAAAUUCUACAGUUUUUCCAAAGAUAGCUCCAUAAACUUAUUUGAAAUUGCUGAUAAGGUAACUUCUUAAAAAGUCAGUUUGAGAAAAACAGCCAGCAAAUAUUUCUAGGAUAAAACGUAUACUAUCAAGUUUUUUAUUCCUGAUAGUAUGCGCUUUUUAUUUGAAUACUUGCUACAAAACCUCACAAGAUUUACUAUCAUGCCAUACCAAAAUGGACUAUUUUUUGAUUAUAGAAAAAGAUUAUUUUUAAAUGUUUAGAAAUAAUAAAAUAAAUUCCAAUUUAUUUCUAAAUAUUUGAAAAUAAUGUCUAUUUGUAUUAUACUAUCUUUGAGGUAUCUAUU ((.((((..(((((....))))).............((.((((((.((((.....)))))))))).....))..)))).))............(((.((((((((..(((((.....)))))...)).)))))).))).........(((((.(((((...((((((((((((((((((((.(.........).))))))))))))..))))))))))))).))))).....((((((.(((((....(((.((((.......((((((((..(((((((....)))))))..(((((((((((((((((((((((((................))))))))))))))))))))))))))))))))))))).)))..)))))))))))....... (-91.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 662 50 1 141 92 smit:SMT_251|5end_hypothetical_protein_187058..187288_NEGATIVE 292 170 127 51 12 smit:SMT_544|5end_aminoglycoside_6-adenylyltransferase_460292..460522_POSITIVE 281 238 193 107 55 smit:SMT_1010|5end_hypothetical_protein_948292..948522_POSITIVE 279 164 127 58 13 smit:SMT_1042|5end_hypothetical_cytosolic_protein_984972..985202_NEGATIVE 278 169 123 131 69 smit:SMT_2046|5end_choline_binding_protein_C_1957519..1957749_NEGATIVE 276 274 243 103 75 smit:SMT_2065|5end_transcriptional_regulator,_MarR_family_1972665..1972895_POSITIVE 276 274 243 103 75 smit:SMT_1320|5end_transcriptional_regulator,_MarR_family_1290234..1290464_POSITIVE 261 160 123 88 49 smit:SMT_1305|5end_glycerol_kinase_1268217..1268447_POSITIVE 253 170 125 70 38 smit:SMT_2085|5end_K01207_beta-N-acetylhexosaminidase_1983039..1983269_POSITIVE 253 275 236 215 177 smit:SMT_1971|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1903282..1903512_POSITIVE 249 167 126 186 129 smit:SMT_664|5end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_575930..576160_NEGATIVE 249 325 283 151 107 smit:SMT_233|5end_hypothetical_protein_172656..172886_POSITIVE 248 299 252 220 167 smit:SMT_737|5end_hypothetical_protein_642746..642976_NEGATIVE 245 266 221 165 120 smit:SMT_2150|5end_threonyl-tRNA_synthetase_2024673..2024903_POSITIVE 235 149 101 176 134 smit:SMT_859|5end_K02086_DNA_replication_protein_804058..804288_NEGATIVE 228 169 124 201 161 smit:SMT_468|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_404710..404940_POSITIVE 228 169 124 201 161 smit:SMT_433|5end_cell_division_protein_DivIB_374621..374851_POSITIVE 225 300 252 214 155 smit:SMT_1592|5end_putative_hemolysin_1579655..1579885_POSITIVE 223 163 124 231 190 smit:SMT_769|5end_spermidine/putrescine-binding_periplasmic_protein_680589..680819_NEGATIVE 221 167 130 203 166 smit:SMT_203|5end_putative_ABC_transporter_BitD_134912..135142_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 230 184 71 23 smit:SMT_779|3end_ribonuclease_BN,_putative_687883..688033_NEGATIVE 336 230 186 78 32 smit:SMT_778|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_687834..687984_POSITIVE 290 219 172 54 4 smit:SMT_937|3end_dipeptidase_890741..890891_POSITIVE 282 230 186 59 14 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE 281 238 193 95 43 smit:SMT_1009|3end_hypothetical_protein_predicted_by_Glimmer/Critica_948360..948510_POSITIVE 249 325 283 132 88 smit:SMT_232|3end_DNA_polymerase_III,_alpha_subunit,_Gram-positive_type_172717..172867_POSITIVE 248 299 252 67 14 smit:SMT_738|3end_hypothetical_protein_predicted_by_Glimmer/Critica_642899..643049_NEGATIVE 245 266 221 146 101 smit:SMT_2149|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2024734..2024884_POSITIVE 245 230 182 73 22 smit:SMT_130|3end_capsular_polysaccharide_biosynthesis_protein_82925..83075_POSITIVE 239 260 221 146 107 smit:SMT_2132|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2013732..2013882_POSITIVE 230 150 102 144 83 smit:SMT_693|3end_hypothetical_protein_604078..604228_POSITIVE 226 230 185 56 10 smit:SMT_1615|3end_K02016_iron_complex_transport_system_substrate-binding_protein_1601734..1601884_NEGATIVE 224 162 125 52 10 smit:SMT_2025|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1940995..1941145_NEGATIVE 216 193 153 54 9 smit:SMT_911|3end_hypothetical_protein_862720..862870_POSITIVE 214 260 215 90 44 smit:SMT_1460|3end_K02038_phosphate_transport_system_permease_protein_1442393..1442543_POSITIVE 211 256 227 47 17 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 210 316 280 144 109 smit:SMT_1014|3end_galactokinase_950645..950795_NEGATIVE 210 164 125 143 105 smit:SMT_908|3end_hypothetical_protein_856073..856223_NEGATIVE 210 180 154 132 105 smit:SMT_856|3end_peroxide_resistance_protein,non-heme_iron-containing_ferritin_800130..800280_NEGATIVE 210 300 253 148 96 smit:SMT_180|3end_50S_ribosomal_protein_L14_120126..120276_POSITIVE