Origin IGS: ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaagggtctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggtgtgatt .........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 aatcacacctccaaaatctacatttgtcaattacaattatcagtatactcttaaaatctacatttgtcaactatgaaattaatcttttctttgaaaaattgaattttaaccctatgataaaggatttgcagtcaaatcttactatataaactatgaaaatatgctatactaaagaaaaaagaaaacaaccactaggggtgcgtaaagctgagattaacgactgttagaccctttgactcaatctaggtaatgctagctgatggaagtggaaatgataatggggactagcagtcttctattgcctttctaaaacagactagcttgttcttaagaatacaaacttcagttggttgggaggttttag Mask Tandem Repeat Region ================================================ ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaagggtctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggtgtgatt Find is-nt database================================================ Query_seq: SMT_452:SMT_453|SMT_452:SMT_453:phosphomethylpyrimidine kinase:CopAB ATPase metal-fist type repressor:<-->:390659..391022 364 ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaagggtctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggtgtgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_452:SMT_453|SMT_452:SMT_453:phosphomethylpyrimidine kinase:CopAB ATPase metal-fist type repressor:<-->:390659..391022 364 ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaagggtctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggtgtgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_452:SMT_453|SMT_452:SMT_453:phosphomethylpyrimidine kinase:CopAB ATPase metal-fist type repressor:<-->:390659..391022 364 ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaagggtctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggtgtgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaagggtctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggtgtgatt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 219 End: 341 .......................................................................................................................................................................................................................... I T L N S Q L D K I M P N F N L K E F F L N I E Y N V F T S K L L I S I I T I S M ....................... ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaagggtctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggtgtgatt 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: 89 Start: 294 End: 323 .....................................................................................................................................................................................................................................................................................................GTTGACAAATGTAGATTTTAAGAGTATACT......................................... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 334 End: 363 .............................................................................................................................................................................................................................................................................................................................................ATTGACAAATGTAGATTTTGGAGGTGTGAT. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaagggtctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggtgtgatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_452:SMT_453|SMT_452:SMT_453:phosphomethylpyrimidine kinase:CopAB ATPase metal-fist type repressor:<-->:390659..391022 364 ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaagggtctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggtgtgatt Intra-Species Hit: Count: 1 Min: 1 Max: 364 Len: 364 Subject: smit_SMT_452_SMT_453|phosphomethylpyrimidine kinase:CopAB ATPase metal-fist type repressor|NEGATIVE:POSITIVE|[390659,391022]|364 HSP 1 e-value: 0.0 bit: 722.0 Len: 364 Query Start:1 Query End:364 Subject Strand: POSITIVE Subject Start: 1 Subject End: 364 ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaagggtctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggtgtgatt ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaagggtctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggtgtgatt Inter-species Hit: Count: 3 Min: 1 Max: 358 Len: 358 Subject: NC_008533_SPD_0632_SPD_0633|phosphomethylpyrimidine kinase:transcriptional regulator, putative|NEGATIVE:POSITIVE|[653374,653738]|365 HSP 1 e-value: 1.0E-156 bit: 553.0 Len: 358 Query Start:1 Query End:358 Subject Strand: POSITIVE Subject Start: 1 Subject End: 359 ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaaggg-tctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggt...... ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcagagggatctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatatttttattgtttatatagtaatatttgactgcaaatcgtttttcaaatgattaaaattctatttttcgaagaaaatattatttctataattgacaaatgtagattttaagagtatactgatgagtgtaattgacaaatgtagattttggaggt...... Subject: NC_003028_SP_0726_SP_0727|phosphomethylpyrimidine kinase:transcriptional repressor, putative|NEGATIVE:POSITIVE|[691260,691618]|359 HSP 1 e-value: 1.0E-156 bit: 553.0 Len: 358 Query Start:1 Query End:358 Subject Strand: POSITIVE Subject Start: 1 Subject End: 359 ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaaggg-tctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgataattgtaattgacaaatgtagattttggaggt...... ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcagagggatctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatatttttattgtttatatagtaatatttgactgcaaatcgtttttcaaatgattaaaattctatttttcgaagaaaatattatttctataattgacaaatgtagattttaagagtatactgatgagtgtaattgacaaatgtagattttggaggt...... Subject: NC_003098_spr0638_spr0639|phosphomethylpyrimidine kinase:COPAB ATPase metal-fist type repressor|NEGATIVE:POSITIVE|[645843,646177]|335 HSP 1 e-value: 1.0E-142 bit: 505.0 Len: 326 Query Start:1 Query End:326 Subject Strand: POSITIVE Subject Start: 1 Subject End: 327 ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcaaaggg-tctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatattttcatagtttatatagtaagatttgactgcaaatcctttatcatagggttaaaattcaatttttcaaagaaaagattaatttcatagttgacaaatgtagattttaagagtatactgat...................................... ctaaaacctcccaaccaactgaagtttgtattcttaagaacaagctagtctgttttagaaaggcaatagaagactgctagtccccattatcatttccacttccatcagctagcattacctagattgagtcagagggatctaacagtcgttaatctcagctttacgcacccctagtggttgttttcttttttctttagtatagcatatttttattgtttatatagtaatatttgactgcaaatcgtttttcaaatgattaaaattctatttttcgaagaaaatattatttctataattgacaaatgtagattttaagagtatactgat...................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAAAACCUCCCAACCAACUGAAGUUUGUAUUCUUAAGAACAAGCUAGUCUGUUUUAGAAAGGCAAUAGAAGACUGCUAGUCCCCAUUAUCAUUUCCACUUCCAUCAGCUAGCAUUACCUAGAUUGAGUCAAAGGGUCUAACAGUCGUUAAUCUCAGCUUUACGCACCCCUAGUGGUUGUUUUCUUUUUUCUUUAGUAUAGCAUAUUUUCAUAGUUUAUAUAGUAAGAUUUGACUGCAAAUCCUUUAUCAUAGGGUUAAAAUUCAAUUUUUCAAAGAAAAGAUUAAUUUCAUAGUUGACAAAUGUAGAUUUUAAGAGUAUACUGAUAAUUGUAAUUGACAAAUGUAGAUUUUGGAGGU .....((((((...............(((((((((((((.(..(((..((((...))))..))).......(((((.(((.(((....................((((((((......)))).))))......))).))).))))).......((((((....(((.((.....)).)))....((((((((((.((((((..(((....)))..))))))...((((.((((.....((((((.......)))))).....)))).)))).))))))))))..........))))))........).)))))))))))))...(((.((((.....)))).))).......)))))) (-67.37) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUCCAAAAUCUACAUUUGUCAAUUACAAUUAUCAGUAUACUCUUAAAAUCUACAUUUGUCAACUAUGAAAUUAAUCUUUUCUUUGAAAAAUUGAAUUUUAACCCUAUGAUAAAGGAUUUGCAGUCAAAUCUUACUAUAUAAACUAUGAAAAUAUGCUAUACUAAAGAAAAAAGAAAACAACCACUAGGGGUGCGUAAAGCUGAGAUUAACGACUGUUAGACCCUUUGACUCAAUCUAGGUAAUGCUAGCUGAUGGAAGUGGAAAUGAUAAUGGGGACUAGCAGUCUUCUAUUGCCUUUCUAAAACAGACUAGCUUGUUCUUAAGAAUACAAACUUCAGUUGGUUGGGAGGUUUUAG ((((((..((((.((..((((((..(((........)))...........(((((.((..(((.((((((((((....(((((...)))))....)))))))..(((((((((((((.(((((((((.(((((((((.(((....(((....)))..........................(((......)))..))).)).)))))))...))))).)))).))))))..)))...))))......))).)))..)).)))))..))))))(((((((.((((((((...................))))).))).)))))))...............)).)))).))))))..... (-71.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 942 120 71 211 162 smit:SMT_452|5end_phosphomethylpyrimidine_kinase_390568..390798_NEGATIVE 344 109 61 55 1 smit:SMT_1510|5end_ribose_5-phosphate_isomerase_1493488..1493718_NEGATIVE 314 166 127 134 86 smit:SMT_1793|5end_inosine-5'-monophosphate_dehydrogenase_1767985..1768215_POSITIVE 312 100 51 69 29 smit:SMT_1870|5end_K07566_putative_translation_factor_1829819..1830049_NEGATIVE 306 111 71 106 69 smit:SMT_1514|5end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1496640..1496870_NEGATIVE 302 156 111 183 133 smit:SMT_501|5end_ABC_transporter,_ATP-binding_protein_433227..433457_POSITIVE 294 146 103 59 16 smit:SMT_1307|5end_glycerol_uptake_facilitator_protein_1271664..1271894_POSITIVE 292 109 61 227 179 smit:SMT_1541|5end_isopentenyl-diphosphate_delta-isomerase_1526093..1526323_NEGATIVE 285 81 44 93 49 smit:SMT_2135|5end_dipeptidase_2015053..2015283_NEGATIVE 282 138 95 203 141 smit:SMT_1897|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1848858..1849088_NEGATIVE 282 120 72 207 155 smit:SMT_929|5end_hypothetical_protein_883342..883572_NEGATIVE 282 156 111 229 187 smit:SMT_152|5end_sensor_histidine_kinase,_putative_100759..100989_POSITIVE 281 175 141 42 6 smit:SMT_1657|5end_glutamine-binding_protein_/_glutamine_transport_system_permease_protein_GlnP_1648077..1648307_NEGATIVE 280 90 44 91 40 smit:SMT_1800|5end_exonuclease_RexA_1773788..1774018_NEGATIVE 272 187 143 107 64 smit:SMT_1096|5end_glyceraldehyde-3-phosphate_dehydrogenase_1038376..1038606_NEGATIVE 272 114 72 219 173 smit:SMT_1078|5end_folylpolyglutamate_synthase_1016713..1016943_NEGATIVE 272 115 81 46 8 smit:SMT_351|5end_hypothetical_protein_290289..290519_POSITIVE 271 182 143 223 175 smit:SMT_1060|5end_K03977_GTP-binding_protein_998106..998336_POSITIVE 269 120 71 57 6 smit:SMT_1852|5end_1,4-alpha-glucan_branching_enzyme_1817690..1817920_NEGATIVE 269 137 96 55 22 smit:SMT_1395|5end_K07025_putative_hydrolase_of_the_HAD_superfamily_1371310..1371540_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 110 61 142 99 smit:SMT_124|3end_hypothetical_protein_75590..75740_NEGATIVE 312 100 51 85 45 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 301 120 72 142 96 smit:SMT_1717|3end_DNA-3-methyladenine_glycosylase_I_1703711..1703861_NEGATIVE 278 83 42 65 18 smit:SMT_1583|3end_polysaccharide_transporter,_PST_family_1574609..1574759_POSITIVE 275 114 72 151 106 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 269 120 71 60 9 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 267 150 101 93 43 smit:SMT_425|3end_hypothetical_cytosolic_protein_368424..368574_POSITIVE 266 148 101 149 100 smit:SMT_807|3end_hypothetical_protein_predicted_by_Glimmer/Critica_716708..716858_NEGATIVE 265 175 135 84 43 smit:SMT_1496|3end_conserved_hypothetical_protein_TIGR00150_1481522..1481672_POSITIVE 265 124 92 44 6 smit:SMT_580|3end_K04094_glucose_inhibited_division_protein_Gid_498034..498184_POSITIVE 263 183 143 92 45 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 263 87 43 67 18 smit:SMT_414|3end_K03665_GTP-binding_protein_HflX_358872..359022_POSITIVE 261 96 56 90 53 smit:SMT_1349|3end_K03075_preprotein_translocase_SecG_subunit_1327604..1327754_NEGATIVE 256 173 132 132 97 smit:SMT_1551|3end_K02221_YggT_family_protein_1535202..1535352_POSITIVE 254 160 113 52 14 smit:SMT_1733|3end_DNA_repair_protein_RecN_1718636..1718786_POSITIVE 254 209 170 41 2 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 254 150 104 140 103 smit:SMT_128|3end_K03449_MFS_transporter,_CP_family,_cyanate_transporter_78702..78852_NEGATIVE 249 130 83 151 109 smit:SMT_1189|3end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1146663..1146813_NEGATIVE 248 83 41 65 22 smit:SMT_615|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_525617..525767_POSITIVE 247 114 81 144 112 smit:SMT_991|3end_hypothetical_protein_934033..934183_NEGATIVE