Origin IGS: nnnnngcacgaatttaactggctgggaaaaaatggacaagtgttatcgttgcaaaagatgacaacaatggagaaagtgcaccttttaacggaagaattaatgcaactactaatcctgcagaacgtcaaaaaattgaaggttatgttgaatttgttgtaaaaaatcaaactactaaatatgatattaagactccagaaggaacagttagtgtagtagatccagcgaatgttacggctgacgaatttgaaaaaattaaagaaaaagtaaaaatcgaatactctcaaactaacgatgatgctaattttactagcaagagaggacaagctgtagacaatcaggcgacaagaatttctacgattacaaaagatgctaatggaaatcttgtt .........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 aacaagatttccattagcatcttttgtaatcgtagaaattcttgtcgcctgattgtctacagcttgtcctctcttgctagtaaaattagcatcatcgttagtttgagagtattcgatttttactttttctttaattttttcaaattcgtcagccgtaacattcgctggatctactacactaactgttccttctggagtcttaatatcatatttagtagtttgattttttacaacaaattcaacataaccttcaattttttgacgttctgcaggattagtagttgcattaattcttccgttaaaaggtgcactttctccattgttgtcatcttttgcaacgataacacttgtccattttttcccagccagttaaattcgtgcnnnnn Mask Tandem Repeat Region ================================================ nnnnngcacgaatttaactggctgggaaaaaatggacaagtgttatcgttgcaaaagatgacaacaatggagaaagtgcaccttttaacggaagaattaatgcaactactaatcctgcagaacgtcaaaaaattgaaggttatgttgaatttgttgtaaaaaatcaaactactaaatatgatattaagactccagaaggaacagttagtgtagtagatccagcgaatgttacggctgacgaatttgaaaaaattaaagaaaaagtaaaaatcgaatactctcaaactaacgatgatgctaattttactagcaagagaggacaagctgtagacaatcaggcgacaagaatttctacgattacaaaagatgctaatggaaatcttgtt Find is-nt database================================================ Query_seq: SMT_2104:SMT_2105|SMT_2104:SMT_2105:UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diaminopimelate ligase:hypothetical protein predicted by Glimmer/Critica:->->:1996212..1996597 386 nnnnngcacgaatttaactggctgggaaaaaatggacaagtgttatcgttgcaaaagatgacaacaatggagaaagtgcaccttttaacggaagaattaatgcaactactaatcctgcagaacgtcaaaaaattgaaggttatgttgaatttgttgtaaaaaatcaaactactaaatatgatattaagactccagaaggaacagttagtgtagtagatccagcgaatgttacggctgacgaatttgaaaaaattaaagaaaaagtaaaaatcgaatactctcaaactaacgatgatgctaattttactagcaagagaggacaagctgtagacaatcaggcgacaagaatttctacgattacaaaagatgctaatggaaatcttgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2104:SMT_2105|SMT_2104:SMT_2105:UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diaminopimelate ligase:hypothetical protein predicted by Glimmer/Critica:->->:1996212..1996597 386 nnnnngcacgaatttaactggctgggaaaaaatggacaagtgttatcgttgcaaaagatgacaacaatggagaaagtgcaccttttaacggaagaattaatgcaactactaatcctgcagaacgtcaaaaaattgaaggttatgttgaatttgttgtaaaaaatcaaactactaaatatgatattaagactccagaaggaacagttagtgtagtagatccagcgaatgttacggctgacgaatttgaaaaaattaaagaaaaagtaaaaatcgaatactctcaaactaacgatgatgctaattttactagcaagagaggacaagctgtagacaatcaggcgacaagaatttctacgattacaaaagatgctaatggaaatcttgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2104:SMT_2105|SMT_2104:SMT_2105:UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diaminopimelate ligase:hypothetical protein predicted by Glimmer/Critica:->->:1996212..1996597 386 nnnnngcacgaatttaactggctgggaaaaaatggacaagtgttatcgttgcaaaagatgacaacaatggagaaagtgcaccttttaacggaagaattaatgcaactactaatcctgcagaacgtcaaaaaattgaaggttatgttgaatttgttgtaaaaaatcaaactactaaatatgatattaagactccagaaggaacagttagtgtagtagatccagcgaatgttacggctgacgaatttgaaaaaattaaagaaaaagtaaaaatcgaatactctcaaactaacgatgatgctaattttactagcaagagaggacaagctgtagacaatcaggcgacaagaatttctacgattacaaaagatgctaatggaaatcttgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 nnnnngcacgaatttaactggctgggaaaaaatggacaagtgttatcgttgcaaaagatgacaacaatggagaaagtgcaccttttaacggaagaattaatgcaactactaatcctgcagaacgtcaaaaaattgaaggttatgttgaatttgttgtaaaaaatcaaactactaaatatgatattaagactccagaaggaacagttagtgtagtagatccagcgaatgttacggctgacgaatttgaaaaaattaaagaaaaagtaaaaatcgaatactctcaaactaacgatgatgctaattttactagcaagagaggacaagctgtagacaatcaggcgacaagaatttctacgattacaaaagatgctaatggaaatcttgtt Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 22 End: 156 ..................... M G K N G Q V L S L Q K M T T M E K V H L L T E E L M Q L L I L Q N V K K L K V M L N L L ...................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 18 End: 386 ................. M A G K K W T S V I V A K D D N N G E S A P F N G R I N A T T N P A E R Q K I E G Y V E F V V K N Q T T K Y D I K T P E Protein_Len: 35 Strand: - Start: 167 End: 271 ...................................................................................................................................................................... V V L Y S I L V G S P V T L T T S G A F T V A S S N S F I L S F T F M ................................................................................................................... Protein_Len: 60 Strand: - Start: 3 End: 380 .. C N T Y Y I W R I N R S V F K F F N F F F Y F D F V R L S V I I S I K S A L S S L S Y V I L R C S N R R N C F I S I S M ...... nnnnngcacgaatttaactggctgggaaaaaatggacaagtgttatcgttgcaaaagatgacaacaatggagaaagtgcaccttttaacggaagaattaatgcaactactaatcctgcagaacgtcaaaaaattgaaggttatgttgaatttgttgtaaaaaatcaaactactaaatatgatattaagactccagaaggaacagttagtgtagtagatccagcgaatgttacggctgacgaatttgaaaaaattaaagaaaaagtaaaaatcgaatactctcaaactaacgatgatgctaattttactagcaagagaggacaagctgtagacaatcaggcgacaagaatttctacgattacaaaagatgctaatggaaatcttgtt 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: 82 Start: 153 End: 182 ........................................................................................................................................................GTTGTAAAAAATCAAACTACTAAATATGAT............................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ nnnnngcacgaatttaactggctgggaaaaaatggacaagtgttatcgttgcaaaagatgacaacaatggagaaagtgcaccttttaacggaagaattaatgcaactactaatcctgcagaacgtcaaaaaattgaaggttatgttgaatttgttgtaaaaaatcaaactactaaatatgatattaagactccagaaggaacagttagtgtagtagatccagcgaatgttacggctgacgaatttgaaaaaattaaagaaaaagtaaaaatcgaatactctcaaactaacgatgatgctaattttactagcaagagaggacaagctgtagacaatcaggcgacaagaatttctacgattacaaaagatgctaatggaaatcttgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2104:SMT_2105|SMT_2104:SMT_2105:UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diaminopimelate ligase:hypothetical protein predicted by Glimmer/Critica:->->:1996212..1996597 386 nnnnngcacgaatttaactggctgggaaaaaatggacaagtgttatcgttgcaaaagatgacaacaatggagaaagtgcaccttttaacggaagaattaatgcaactactaatcctgcagaacgtcaaaaaattgaaggttatgttgaatttgttgtaaaaaatcaaactactaaatatgatattaagactccagaaggaacagttagtgtagtagatccagcgaatgttacggctgacgaatttgaaaaaattaaagaaaaagtaaaaatcgaatactctcaaactaacgatgatgctaattttactagcaagagaggacaagctgtagacaatcaggcgacaagaatttctacgattacaaaagatgctaatggaaatcttgtt Intra-Species Hit: Count: 1 Min: 6 Max: 386 Len: 381 Subject: smit_SMT_2104_SMT_2105|UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diaminopimelate ligase:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[1996212,1996597]|386 HSP 1 e-value: 1.0E-134 bit: 478.0 Len: 241 Query Start:6 Query End:246 Subject Strand: POSITIVE Subject Start: 6 Subject End: 246 .....gcacgaatttaactggctgggaaaaaatggacaagtgttatcgttgcaaaagatgacaacaatggagaaagtgcaccttttaacggaagaattaatgcaactactaatcctgcagaacgtcaaaaaattgaaggttatgttgaatttgttgtaaaaaatcaaactactaaatatgatattaagactccagaaggaacagttagtgtagtagatccagcgaatgttacggctgacgaatttg............................................................................................................................................ .....gcacgaatttaactggctgggaaaaaatggacaagtgttatcgttgcaaaagatgacaacaatggagaaagtgcaccttttaacggaagaattaatgcaactactaatcctgcagaacgtcaaaaaattgaaggttatgttgaatttgttgtaaaaaatcaaactactaaatatgatattaagactccagaaggaacagttagtgtagtagatccagcgaatgttacggctgacgaatttg............................................................................................................................................ HSP 2 e-value: 3.0E-59 bit: 230.0 Len: 116 Query Start:271 Query End:386 Subject Strand: POSITIVE Subject Start: 271 Subject End: 386 ..............................................................................................................................................................................................................................................................................tcgaatactctcaaactaacgatgatgctaattttactagcaagagaggacaagctgtagacaatcaggcgacaagaatttctacgattacaaaagatgctaatggaaatcttgtt ..............................................................................................................................................................................................................................................................................tcgaatactctcaaactaacgatgatgctaattttactagcaagagaggacaagctgtagacaatcaggcgacaagaatttctacgattacaaaagatgctaatggaaatcttgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCACGAAUUUAACUGGCUGGGAAAAAAUGGACAAGUGUUAUCGUUGCAAAAGAUGACAACAAUGGAGAAAGUGCACCUUUUAACGGAAGAAUUAAUGCAACUACUAAUCCUGCAGAACGUCAAAAAAUUGAAGGUUAUGUUGAAUUUGUUGUAAAAAAUCAAACUACUAAAUAUGAUAUUAAGACUCCAGAAGGAACAGUUAGUGUAGUAGAUCCAGCGAAUGUUACGGCUGACGAAUUUGAAAAAAUUAAAGAAAAAGUAAAAAUCGAAUACUCUCAAACUAACGAUGAUGCUAAUUUUACUAGCAAGAGAGGACAAGCUGUAGACAAUCAGGCGACAAGAAUUUCUACGAUUACAAAAGAUGCUAAUGGAAAUCUUGUU ((((((((((((((((((...........(((...(((((((.........))))))).....(((...((((((........(....)......))).))).....)))........)))...........))))).)))))))))).)))...........(((((.......(((((((...(((....)))....)))))))))))).......((.((((((((((....(((((....))))).......................(((((...(....)....(((((.......))))).)))))....)))))).)))).))....(((((((.(((((...((((((.....)).)))))))))))))))) (-73.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAGAUUUCCAUUAGCAUCUUUUGUAAUCGUAGAAAUUCUUGUCGCCUGAUUGUCUACAGCUUGUCCUCUCUUGCUAGUAAAAUUAGCAUCAUCGUUAGUUUGAGAGUAUUCGAUUUUUACUUUUUCUUUAAUUUUUUCAAAUUCGUCAGCCGUAACAUUCGCUGGAUCUACUACACUAACUGUUCCUUCUGGAGUCUUAAUAUCAUAUUUAGUAGUUUGAUUUUUUACAACAAAUUCAACAUAACCUUCAAUUUUUUGACGUUCUGCAGGAUUAGUAGUUGCAUUAAUUCUUCCGUUAAAAGGUGCACUUUCUCCAUUGUUGUCAUCUUUUGCAACGAUAACACUUGUCCAUUUUUUCCCAGCCAGUUAAAUUCGUGC .(((((..........((((((((((.....((((((.....(((((...(((((.((((..............(((((((...))))))).....((((((..(((((((.........))))))).....................(((((.(......).))))).........))))))..((((....)))).................)))).((((.(((.......))).)))).........)))))...))))))))))).((((((((......))))))))......)))))))))).........(((((((.((.....)))))))))....))))).............................. (-63.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 366 329 159 128 smit:SMT_1919|5end_aspartate_kinase_1862018..1862248_POSITIVE 322 376 334 89 54 smit:SMT_2164|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2037861..2038091_POSITIVE 294 337 299 58 12 smit:SMT_593|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_509398..509628_POSITIVE 284 224 187 42 1 smit:SMT_932|5end_tellurite_resistance_protein_885065..885295_POSITIVE 267 355 311 60 17 smit:SMT_243|5end_PTS_system,_mannose-specific_IIC_component_180901..181131_NEGATIVE 263 148 109 51 4 smit:SMT_1166|5end_DNA-binding_response_regulator_CiaR_1112484..1112714_NEGATIVE 259 230 186 50 6 smit:SMT_2145|5end_K05832_putative_ABC_transport_system_permease_protein_2022019..2022249_NEGATIVE 259 230 186 50 6 smit:SMT_1603|5end_K05832_putative_ABC_transport_system_permease_protein_1593374..1593604_POSITIVE 258 352 311 56 20 smit:SMT_346|5end_K01992_ABC-2_type_transport_system_permease_protein_284720..284950_POSITIVE 256 349 305 87 36 smit:SMT_1792|5end_K03307_solute:Na+_symporter,_SSS_family_1767774..1768004_NEGATIVE 256 349 305 87 36 smit:SMT_1175|5end_K03307_solute:Na+_symporter,_SSS_family_1127660..1127890_NEGATIVE 255 237 208 162 136 smit:SMT_362|5end_K02519_translation_initiation_factor_IF-2_296230..296460_POSITIVE 253 350 301 79 21 smit:SMT_582|5end_ATP_synthase_F0,_B_subunit_499003..499233_POSITIVE 252 350 301 62 2 smit:SMT_1534|5end_signal_peptidase_I_1517218..1517448_POSITIVE 250 328 281 170 128 smit:SMT_769|5end_spermidine/putrescine-binding_periplasmic_protein_680589..680819_NEGATIVE 248 357 314 226 172 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 247 77 36 40 8 smit:SMT_1265|5end_hypothetical_protein_1231261..1231491_NEGATIVE 247 348 312 183 142 smit:SMT_448|5end_K03707_transcriptional_activator_TenA_386789..387019_POSITIVE 246 330 281 67 16 smit:SMT_1460|5end_K02038_phosphate_transport_system_permease_protein_1441429..1441659_POSITIVE 245 340 292 49 1 smit:SMT_2036|5end_spermidine_synthase_1947879..1948109_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 376 334 65 30 smit:SMT_2163|3end_cell_division_protein_FtsA_2037917..2038067_POSITIVE 294 337 299 48 2 smit:SMT_592|3end_amino_acid_ABC_transporter,_ATP-binding_protein_509468..509618_POSITIVE 263 318 285 146 99 smit:SMT_422|3end_K02004_365876..366026_POSITIVE 258 352 311 59 23 smit:SMT_345|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_284803..284953_POSITIVE 256 349 305 85 34 smit:SMT_1176|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1127662..1127812_NEGATIVE 255 315 276 151 102 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 255 338 301 52 8 smit:SMT_1536|3end_trigger_factor_1520636..1520786_NEGATIVE 255 237 208 145 119 smit:SMT_361|3end_hypothetical_protein_296293..296443_POSITIVE 254 317 273 67 24 smit:SMT_1442|3end_hypothetical_protein_1425762..1425912_NEGATIVE 253 350 301 65 7 smit:SMT_581|3end_ATP_synthase_A_chain_499069..499219_POSITIVE 247 338 292 150 107 smit:SMT_128|3end_K03449_MFS_transporter,_CP_family,_cyanate_transporter_78702..78852_NEGATIVE 246 330 281 77 26 smit:SMT_1459|3end_K02037_phosphate_transport_system_permease_protein_1441519..1441669_POSITIVE 243 350 306 58 2 smit:SMT_1533|3end_ribonuclease_HIII_1517294..1517444_POSITIVE 243 341 313 59 30 smit:SMT_869|3end_hypothetical_protein_817228..817378_NEGATIVE 240 340 297 48 9 smit:SMT_2037|3end_lysine_decarboxylase_1947880..1948030_NEGATIVE 240 340 297 48 9 smit:SMT_1418|3end_lysine_decarboxylase_1401687..1401837_NEGATIVE 240 349 302 110 64 smit:SMT_702|3end_hypothetical_protein_611946..612096_NEGATIVE 239 78 32 55 6 smit:SMT_1083|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1021001..1021151_POSITIVE 237 235 195 57 18 smit:SMT_1954|3end_6-phospho-beta-glucosidase_1888831..1888981_POSITIVE 237 338 301 49 5 smit:SMT_1766|3end_sucrose-6-phosphate_hydrolase_1743101..1743251_POSITIVE