Origin IGS: ataaataatacgaatttgtctgcagaagaagctgctaagcagatttcagataaaatggaatacatagagaaaggacacccacnnnnnttaattaattaannnnngtgcaagaaatcagcgatcagtaattttaacagacgtaattgatttttcaaatcagtaccagctg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagctggtactgatttgaaaaatcaattacgtctgttaaaattactgatcgctgatttcttgcacnnnnnttaattaattaannnnngtgggtgtcctttctctatgtattccattttatctgaaatctgcttagcagcttcttctgcagacaaattcgtattatttat Mask Tandem Repeat Region ================================================ ataaataatacgaatttgtctgcagaagaagctgctaagcagatttcagataaaatggaatacatagagaaaggacacccacnnnnnttaattaattaannnnngtgcaagaaatcagcgatcagtaattttaacagacgtaattgatttttcaaatcagtaccagctg Find is-nt database================================================ Query_seq: SMT_380:SMT_381|SMT_380:SMT_381:hypothetical protein:hypothetical protein:->->:317005..317173 169 ataaataatacgaatttgtctgcagaagaagctgctaagcagatttcagataaaatggaatacatagagaaaggacacccacnnnnnttaattaattaannnnngtgcaagaaatcagcgatcagtaattttaacagacgtaattgatttttcaaatcagtaccagctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_380:SMT_381|SMT_380:SMT_381:hypothetical protein:hypothetical protein:->->:317005..317173 169 ataaataatacgaatttgtctgcagaagaagctgctaagcagatttcagataaaatggaatacatagagaaaggacacccacnnnnnttaattaattaannnnngtgcaagaaatcagcgatcagtaattttaacagacgtaattgatttttcaaatcagtaccagctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_380:SMT_381|SMT_380:SMT_381:hypothetical protein:hypothetical protein:->->:317005..317173 169 ataaataatacgaatttgtctgcagaagaagctgctaagcagatttcagataaaatggaatacatagagaaaggacacccacnnnnnttaattaattaannnnngtgcaagaaatcagcgatcagtaattttaacagacgtaattgatttttcaaatcagtaccagctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaataatacgaatttgtctgcagaagaagctgctaagcagatttcagataaaatggaatacatagagaaaggacacccacnnnnnttaattaattaannnnngtgcaagaaatcagcgatcagtaattttaacagacgtaattgatttttcaaatcagtaccagctg Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 1 End: 96 M N N T N L S A E E A A K Q I S D K M E Y I E K G H P X X L I N ......................................................................... Protein_Len: 30 Strand: - Start: 3 End: 92 .. F L V F K D A S S A A L C I E S L I S Y M S F P C G X X X M ............................................................................. ataaataatacgaatttgtctgcagaagaagctgctaagcagatttcagataaaatggaatacatagagaaaggacacccacnnnnnttaattaattaannnnngtgcaagaaatcagcgatcagtaattttaacagacgtaattgatttttcaaatcagtaccagctg 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: 81 Start: 128 End: 157 ...............................................................................................................................ATTTGAAAAATCAATTACGTCTGTTAAAAT............ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataaataatacgaatttgtctgcagaagaagctgctaagcagatttcagataaaatggaatacatagagaaaggacacccacnnnnnttaattaattaannnnngtgcaagaaatcagcgatcagtaattttaacagacgtaattgatttttcaaatcagtaccagctg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_380:SMT_381|SMT_380:SMT_381:hypothetical protein:hypothetical protein:->->:317005..317173 169 ataaataatacgaatttgtctgcagaagaagctgctaagcagatttcagataaaatggaatacatagagaaaggacacccacnnnnnttaattaattaannnnngtgcaagaaatcagcgatcagtaattttaacagacgtaattgatttttcaaatcagtaccagctg Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: smit_SMT_380_SMT_381|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[317005,317173]|169 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 ataaataatacgaatttgtctgcagaagaagctgctaagcagatttcagataaaatggaatacatagagaaaggacacccacnnnnnttaattaattaannnnngtgcaagaaatcagcgatcagtaattttaacagacgtaattgatttttcaaatcagtaccagctg ataaataatacgaatttgtctgcagaagaagctgctaagcagatttcagataaaatggaatacatagagaaaggacacccacnnnnnttaattaattaannnnngtgcaagaaatcagcgatcagtaattttaacagacgtaattgatttttcaaatcagtaccagctg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAUAAUACGAAUUUGUCUGCAGAAGAAGCUGCUAAGCAGAUUUCAGAUAAAAUGGAAUACAUAGAGAAAGGACACCCACNNNNNUUAAUUAAUUAANNNNNGUGCAAGAAAUCAGCGAUCAGUAAUUUUAACAGACGUAAUUGAUUUUUCAAAUCAGUACCAGCUG .................(((((..((((..((((....((.((((((.......(((.....))).......((....))..............................)))))).))...))))..))))..)))))...(((((((.....)))))))........ (-26.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCUGGUACUGAUUUGAAAAAUCAAUUACGUCUGUUAAAAUUACUGAUCGCUGAUUUCUUGCACNNNNNUUAAUUAAUUAANNNNNGUGGGUGUCCUUUCUCUAUGUAUUCCAUUUUAUCUGAAAUCUGCUUAGCAGCUUCUUCUGCAGACAAAUUCGUAUUAUUUAU ....((((((.((((.....))))......((((((........(((...((.((((((...(((.....((((....)))).....)))((.((.(.........).)).)).........)))))).))....)))........))))))......))))))..... (-24.09) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 68 22 184 144 smit:SMT_1082|5end_Cof_family_protein_1020153..1020383_POSITIVE 246 50 9 180 131 smit:SMT_1647|5end_3-isopropylmalate_dehydratase_small_subunit_1633403..1633633_POSITIVE 244 51 22 52 27 smit:SMT_400|5end_hypothetical_protein_329090..329320_POSITIVE 242 59 15 106 64 smit:SMT_1390|5end_hypothetical_protein_1367321..1367551_NEGATIVE 237 53 12 178 124 smit:SMT_1767|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_1744121..1744351_NEGATIVE 234 58 15 170 124 smit:SMT_1752|5end_N-(5'-phosphoribosyl)-anthranilate_isomerase_1729772..1730002_POSITIVE 233 42 12 152 110 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 231 50 12 68 36 smit:SMT_1907|5end_phosphate-binding_protein_1854105..1854335_POSITIVE 230 47 8 148 115 smit:SMT_1350|5end_multidrug_resistance_efflux_pump_1329225..1329455_NEGATIVE 230 55 12 53 6 smit:SMT_1275|5end_rod_shape-determining_protein_MreC_1238594..1238824_POSITIVE 230 52 13 189 141 smit:SMT_178|5end_50S_ribosomal_protein_L29_119161..119391_POSITIVE 226 129 105 185 159 smit:SMT_1475|5end_K02004_1455873..1456103_POSITIVE 226 50 16 52 17 smit:SMT_274|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_215221..215451_POSITIVE 225 59 14 220 183 smit:SMT_485|5end_hypothetical_protein_421401..421631_NEGATIVE 222 68 22 182 129 smit:SMT_234|5end_aminopeptidase_PepS_172830..173060_POSITIVE 221 48 11 60 20 smit:SMT_1380|5end_pyrroline-5-carboxylate_reductase_1358464..1358694_NEGATIVE 221 151 118 55 18 smit:SMT_1112|5end_K02248_competence_protein_ComGF_1051848..1052078_NEGATIVE 219 69 22 82 24 smit:SMT_847|5end_thioredoxin_reductase_792800..793030_POSITIVE 218 51 15 199 158 smit:SMT_975|5end_hypothetical_protein_922953..923183_POSITIVE 217 54 16 216 172 smit:SMT_991|5end_hypothetical_protein_934425..934655_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 51 22 38 13 smit:SMT_399|3end_cytochrome_c-type_biogenesis_protein_CcdA_329156..329306_POSITIVE 233 42 12 137 95 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 221 48 11 56 16 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 221 151 118 92 55 smit:SMT_1113|3end_hypothetical_protein_1051811..1051961_NEGATIVE 217 54 16 112 68 smit:SMT_992|3end_hypothetical_protein_934529..934679_NEGATIVE 214 52 12 54 14 smit:SMT_1114|3end_competence_protein_1052076..1052226_NEGATIVE 210 44 9 56 15 smit:SMT_2010|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1929770..1929920_POSITIVE 209 54 15 76 37 smit:SMT_380|3end_hypothetical_protein_316944..317094_POSITIVE 204 57 22 149 107 smit:SMT_233|3end_hypothetical_protein_172888..173038_POSITIVE 203 57 20 69 34 smit:SMT_2138|3end_cell_division_protein_FtsA_2017145..2017295_POSITIVE 203 57 20 69 34 smit:SMT_2136|3end_cell_division_protein_FtsA_2015859..2016009_POSITIVE 203 57 20 69 34 smit:SMT_2128|3end_cell_division_protein_FtsA_2010152..2010302_POSITIVE 203 57 20 69 34 smit:SMT_1547|3end_cell_division_protein_FtsA_1532446..1532596_POSITIVE 200 52 12 57 14 smit:SMT_2129|3end_cell_division_protein_FtsZ_2010694..2010844_POSITIVE 199 49 13 60 9 smit:SMT_853|3end_ATP-dependent_endopeptidase_clp_ATP-binding_subunit_ClpX_798053..798203_NEGATIVE 199 69 24 108 63 smit:SMT_598|3end_K07273_lysozyme_514012..514162_NEGATIVE 197 52 22 102 70 smit:SMT_1936|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1874189..1874339_POSITIVE 197 80 32 68 4 smit:SMT_771|3end_spermidine/putrescine_transport_system_permease_protein_PotB_681356..681506_NEGATIVE 195 64 27 68 29 smit:SMT_944|3end_PhnA_protein_894768..894918_NEGATIVE 194 51 18 57 17 smit:SMT_1867|3end_peptide_chain_release_factor_1_1827910..1828060_NEGATIVE