Origin IGS: cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaagcaaaacaaggggaaagtt .........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 aactttccccttgttttgctttccaaactttatagttgcccatagtatatcatactttcataagaagactcaaaaaatcctccagattctactctgaaggattcctatcttatttcacaacaatattaaccaatttggttggcttcaatagtccagtggactattgaaggtggcagatagagctaataaactcg Mask Tandem Repeat Region ================================================ cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaagcaaaacaaggggaaagtt Find is-nt database================================================ Query_seq: SMT_208:SMT_209|SMT_208:SMT_209:leucyl-tRNA synthetase:acetyltransferase, GNAT family:->->:142619..142812 194 cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaagcaaaacaaggggaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_208:SMT_209|SMT_208:SMT_209:leucyl-tRNA synthetase:acetyltransferase, GNAT family:->->:142619..142812 194 cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaagcaaaacaaggggaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_208:SMT_209|SMT_208:SMT_209:leucyl-tRNA synthetase:acetyltransferase, GNAT family:->->:142619..142812 194 cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaagcaaaacaaggggaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaagcaaaacaaggggaaagtt Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: - Start: 31 End: 159 .............................. Y D V P S N F G V L N T L I T T F Y S L F G E S Y F R S S K K L R R I F T H Y V I P M ................................... cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaagcaaaacaaggggaaagtt 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: 147 End: 176 ..................................................................................................................................................CTTTCCAAACTTTATAGTTGCCCATAGTAT.................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaagcaaaacaaggggaaagtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -3.4 Tail_Score: -3.48696 Start: 53 End: 65 Full_Region: ACTGGACTATTGAAG CCAA CCAAA TTGG TTAATATTGTTGTGA ....................................................CCAACCAAATTGG................................................................................................................................. TransTerm Strand: + Conf: 88 HP_score: -7.5 Tail_Score: -5.17054 Start: 94 End: 117 Full_Region: GAAATAAGATAGGAA TCCTTCAGA GTAGAA TCTGGAGGA TTTTTTGAGTCTTCT .............................................................................................TCCTTCAGAGTAGAATCTGGAGGA............................................................................. TransTerm Strand: - Conf: 57 HP_score: -5.3 Tail_Score: -3.43985 Start: 94 End: 117 Full_Region: agaagactcaaaaaa tcctccaga ttctac tctgaagga ttcctatcttatttc .............................................................................................tcctccagattctactctgaagga............................................................................. Find igs database================================================ Query_seq: SMT_208:SMT_209|SMT_208:SMT_209:leucyl-tRNA synthetase:acetyltransferase, GNAT family:->->:142619..142812 194 cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaagcaaaacaaggggaaagtt Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: smit_SMT_208_SMT_209|leucyl-tRNA synthetase:acetyltransferase, GNAT family|POSITIVE:POSITIVE|[142619,142812]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaagcaaaacaaggggaaagtt cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaagcaaaacaaggggaaagtt Inter-species Hit: Count: 3 Min: 1 Max: 176 Len: 176 Subject: NC_003028_SP_0254_SP_0255|leucyl-tRNA synthetase:acetyltransferase, GNAT family|POSITIVE:POSITIVE|[227254,227447]|194 HSP 1 e-value: 5.0E-81 bit: 301.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaag.................. cgagtttattagctctatctgccaccttcaatagtccactggactattgaagccaactaaattagttaacattgttgtgaaataagataggagtccttcagagtagaatctggaggattttttgaatcttcttatgaaagtatgatatactatgggcaactataaagtttgaaaag.................. Subject: NC_008533_SPD_0238_SPD_0239|leucyl-tRNA synthetase:acetyltransferase, GNAT family protein|POSITIVE:POSITIVE|[229772,229964]|193 HSP 1 e-value: 2.0E-46 bit: 186.0 Len: 126 Query Start:51 Query End:176 Subject Strand: POSITIVE Subject Start: 50 Subject End: 175 ..................................................agccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaag.................. ..................................................agccaactaaactcgttaatatcgttgtgaaataaggtaggaatccttcagagtagaatctggaggattttttgaatcttcttatgaaagtatggtatactatgggcaactataaagtttgaaaag.................. Subject: NC_003098_spr0235_spr0236|leucyl-tRNA synthetase:hypothetical protein|POSITIVE:POSITIVE|[229771,229963]|193 HSP 1 e-value: 2.0E-46 bit: 186.0 Len: 126 Query Start:51 Query End:176 Subject Strand: POSITIVE Subject Start: 50 Subject End: 175 ..................................................agccaaccaaattggttaatattgttgtgaaataagataggaatccttcagagtagaatctggaggattttttgagtcttcttatgaaagtatgatatactatgggcaactataaagtttggaaag.................. ..................................................agccaactaaactcgttaatatcgttgtgaaataaggtaggaatccttcagagtagaatctggaggattttttgaatcttcttatgaaagtatggtatactatgggcaactataaagtttgaaaag.................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAGUUUAUUAGCUCUAUCUGCCACCUUCAAUAGUCCACUGGACUAUUGAAGCCAACCAAAUUGGUUAAUAUUGUUGUGAAAUAAGAUAGGAAUCCUUCAGAGUAGAAUCUGGAGGAUUUUUUGAGUCUUCUUAUGAAAGUAUGAUAUACUAUGGGCAACUAUAAAGUUUGGAAAG .(((((....)))))..........((((((((((((...))))))))))))....(((((((.....((((..(......((((((.((((((((((((((......)))))))))))))).......))))))......)..))))..(((((....))))).))))))).... (-55.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUCCAAACUUUAUAGUUGCCCAUAGUAUAUCAUACUUUCAUAAGAAGACUCAAAAAAUCCUCCAGAUUCUACUCUGAAGGAUUCCUAUCUUAUUUCACAACAAUAUUAACCAAUUUGGUUGGCUUCAAUAGUCCAGUGGACUAUUGAAGGUGGCAGAUAGAGCUAAUAAACUCG .......((((....)))).....((((........((((.....))))........((((((.((((......)))).)))))).((((((....((((........(((((.....))))).((((((((((((...)))))))))))))))).)))))).))))......... (-40.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 50 1 115 64 smit:SMT_1670|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1658613..1658843_POSITIVE 301 58 13 206 164 smit:SMT_929|5end_hypothetical_protein_883342..883572_NEGATIVE 297 48 12 207 174 smit:SMT_1500|5end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483384..1483614_POSITIVE 293 50 3 69 20 smit:SMT_239|5end_hypothetical_protein_177103..177333_POSITIVE 291 58 11 70 18 smit:SMT_1562|5end_hypothetical_protein_1554992..1555222_NEGATIVE 286 55 12 118 79 smit:SMT_367|5end_hypothetical_protein_302318..302548_POSITIVE 283 60 11 212 151 smit:SMT_1386|5end_phosphoenolpyruvate-protein_phosphotransferase_1362806..1363036_POSITIVE 279 43 1 141 103 smit:SMT_226|5end_putative_L-glutamine-D-fructose-6-phosphate_amidotransferase_163630..163860_POSITIVE 274 60 14 57 6 smit:SMT_1621|5end_K09134_hypothetical_protein_1608104..1608334_NEGATIVE 271 130 84 61 5 smit:SMT_1284|5end_predicted_amidophosphoribosyltransferase_1246962..1247192_POSITIVE 263 56 11 162 119 smit:SMT_1506|5end_Cl-channel,_voltage-gated_family_protein_1489986..1490216_NEGATIVE 258 58 19 199 168 smit:SMT_1626|5end_undecaprenyl-diphosphatase_1616028..1616258_NEGATIVE 258 58 11 226 188 smit:SMT_1026|5end_sucrose_phosphorylase_962324..962554_NEGATIVE 258 35 9 224 197 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 254 38 11 194 163 smit:SMT_629|5end_glycogen_synthase_533967..534197_POSITIVE 253 58 11 211 155 smit:SMT_1201|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1163920..1164150_NEGATIVE 252 59 12 57 5 smit:SMT_2058|5end_hypoxanthine-guanine_phosphoribosyltransferase_1967697..1967927_NEGATIVE 252 41 11 226 186 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 251 54 13 124 94 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 249 53 18 175 140 smit:SMT_1631|5end_phosphopantothenoylcysteine_synthase/decarboxylase_1618359..1618589_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 52 26 65 39 smit:SMT_208|3end_leucyl-tRNA_synthetase_142558..142708_POSITIVE 286 55 12 118 79 smit:SMT_366|3end_hypothetical_protein_302398..302548_POSITIVE 283 55 11 116 74 smit:SMT_1123|3end_hypothetical_protein_1060229..1060379_POSITIVE 278 120 72 99 51 smit:SMT_1356|3end_fibronectin-binding_protein-like_protein_A_1334269..1334419_POSITIVE 275 54 11 48 10 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE 271 130 84 64 8 smit:SMT_1283|3end_K02240_competence_protein_ComFA_1247045..1247195_POSITIVE 258 58 19 138 107 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE 258 58 11 44 6 smit:SMT_451|3end_thiamine-phosphate_pyrophosphorylase_389647..389797_POSITIVE 252 130 83 117 72 smit:SMT_1504|3end_topology_modulation_protein_1487808..1487958_POSITIVE 249 59 12 101 60 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 248 66 21 117 60 smit:SMT_1913|3end_RBL02035_1858765..1858915_POSITIVE 245 53 11 76 30 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 244 145 101 69 15 smit:SMT_1198|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1158837..1158987_NEGATIVE 243 60 11 111 53 smit:SMT_2081|3end_glycosyltransferase_1981336..1981486_POSITIVE 242 58 11 148 106 smit:SMT_1013|3end_galactose-1-phosphate_uridylyltransferase_949601..949751_NEGATIVE 242 58 13 99 56 smit:SMT_493|3end_K01996_branched-chain_amino_acid_transport_system_ATP-binding_protein_427927..428077_POSITIVE 241 60 12 135 89 smit:SMT_808|3end_hypothetical_protein_predicted_by_Glimmer/Critica_717897..718047_NEGATIVE 239 46 1 70 27 smit:SMT_1612|3end_K06024_segregation_and_condensation_protein_B_1600701..1600851_POSITIVE 239 113 75 44 1 smit:SMT_1041|3end_K07586_hypothetical_protein_984164..984314_POSITIVE 238 57 12 46 4 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE