Origin IGS: tccatttcctttctatatcatacctcacgagactctaaaaaagagacggtatgaaaatttcgttttcatgattctacttattccattttatcactatttgtaaacactttcaagctttttttgaagattatttgaaaaaatttcataggaagctatgtttatgaagaaaaaatcaccttttcttgatttttaatcctatttgctgtatgataagggaaaagaaaggggggcagaaat .........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 atttctgcccccctttcttttcccttatcatacagcaaataggattaaaaatcaagaaaaggtgattttttcttcataaacatagcttcctatgaaattttttcaaataatcttcaaaaaaagcttgaaagtgtttacaaatagtgataaaatggaataagtagaatcatgaaaacgaaattttcataccgtctcttttttagagtctcgtgaggtatgatatagaaaggaaatgga Mask Tandem Repeat Region ================================================ tccatttcctttctatatcatacctcacgagactctaaaaaagagacggtatgaaaatttcgttttcatgattctacttattccattttatcactatttgtaaacactttcaagctttttttgaagattatttgaaaaaatttcataggaagctatgtttatgaagaaaaaatcaccttttcttgatttttaatcctatttgctgtatgataagggaaaagaaaggggggcagaaat Find is-nt database================================================ Query_seq: SMT_1074:SMT_1075|SMT_1074:SMT_1075:catabolite control protein A:hypothetical protein:<-->:1013376..1013612 237 tccatttcctttctatatcatacctcacgagactctaaaaaagagacggtatgaaaatttcgttttcatgattctacttattccattttatcactatttgtaaacactttcaagctttttttgaagattatttgaaaaaatttcataggaagctatgtttatgaagaaaaaatcaccttttcttgatttttaatcctatttgctgtatgataagggaaaagaaaggggggcagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1074:SMT_1075|SMT_1074:SMT_1075:catabolite control protein A:hypothetical protein:<-->:1013376..1013612 237 tccatttcctttctatatcatacctcacgagactctaaaaaagagacggtatgaaaatttcgttttcatgattctacttattccattttatcactatttgtaaacactttcaagctttttttgaagattatttgaaaaaatttcataggaagctatgtttatgaagaaaaaatcaccttttcttgatttttaatcctatttgctgtatgataagggaaaagaaaggggggcagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1074:SMT_1075|SMT_1074:SMT_1075:catabolite control protein A:hypothetical protein:<-->:1013376..1013612 237 tccatttcctttctatatcatacctcacgagactctaaaaaagagacggtatgaaaatttcgttttcatgattctacttattccattttatcactatttgtaaacactttcaagctttttttgaagattatttgaaaaaatttcataggaagctatgtttatgaagaaaaaatcaccttttcttgatttttaatcctatttgctgtatgataagggaaaagaaaggggggcagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccatttcctttctatatcatacctcacgagactctaaaaaagagacggtatgaaaatttcgttttcatgattctacttattccattttatcactatttgtaaacactttcaagctttttttgaagattatttgaaaaaatttcataggaagctatgtttatgaagaaaaaatcaccttttcttgatttttaatcctatttgctgtatgataagggaaaagaaaggggggcagaaat Predict ORF larger than 30AA ================================================ tccatttcctttctatatcatacctcacgagactctaaaaaagagacggtatgaaaatttcgttttcatgattctacttattccattttatcactatttgtaaacactttcaagctttttttgaagattatttgaaaaaatttcataggaagctatgtttatgaagaaaaaatcaccttttcttgatttttaatcctatttgctgtatgataagggaaaagaaaggggggcagaaat 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: 182 End: 211 .....................................................................................................................................................................................CTTGATTTTTAATCCTATTTGCTGTATGAT.......................... PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 85 End: 114 ....................................................................................CTTGAAAGTGTTTACAAATAGTGATAAAAT........................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tccatttcctttctatatcatacctcacgagactctaaaaaagagacggtatgaaaatttcgttttcatgattctacttattccattttatcactatttgtaaacactttcaagctttttttgaagattatttgaaaaaatttcataggaagctatgtttatgaagaaaaaatcaccttttcttgatttttaatcctatttgctgtatgataagggaaaagaaaggggggcagaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1074:SMT_1075|SMT_1074:SMT_1075:catabolite control protein A:hypothetical protein:<-->:1013376..1013612 237 tccatttcctttctatatcatacctcacgagactctaaaaaagagacggtatgaaaatttcgttttcatgattctacttattccattttatcactatttgtaaacactttcaagctttttttgaagattatttgaaaaaatttcataggaagctatgtttatgaagaaaaaatcaccttttcttgatttttaatcctatttgctgtatgataagggaaaagaaaggggggcagaaat Intra-Species Hit: Count: 1 Min: 1 Max: 237 Len: 237 Subject: smit_SMT_1074_SMT_1075|catabolite control protein A:hypothetical protein|NEGATIVE:POSITIVE|[1013376,1013612]|237 HSP 1 e-value: 1.0E-119 bit: 428.0 Len: 237 Query Start:1 Query End:237 Subject Strand: POSITIVE Subject Start: 1 Subject End: 237 tccatttcctttctatatcatacctcacgagactctaaaaaagagacggtatgaaaatttcgttttcatgattctacttattccattttatcactatttgtaaacactttcaagcnnnnnnngaagattatttgaaaaaatttcataggaagctatgtttatgaagaaaaaatcaccttttcttgatttttaatcctatttgctgtatgataagggaaaagaaaggggggcagaaat tccatttcctttctatatcatacctcacgagactctaaaaaagagacggtatgaaaatttcgttttcatgattctacttattccattttatcactatttgtaaacactttcaagctttttttgaagattatttgaaaaaatttcataggaagctatgtttatgaagaaaaaatcaccttttcttgatttttaatcctatttgctgtatgataagggaaaagaaaggggggcagaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCAUUUCCUUUCUAUAUCAUACCUCACGAGACUCUAAAAAAGAGACGGUAUGAAAAUUUCGUUUUCAUGAUUCUACUUAUUCCAUUUUAUCACUAUUUGUAAACACUUUCAAGCUUUUUUUGAAGAUUAUUUGAAAAAAUUUCAUAGGAAGCUAUGUUUAUGAAGAAAAAAUCACCUUUUCUUGAUUUUUAAUCCUAUUUGCUGUAUGAUAAGGGAAAAGAAAGGGGGGCAGAAAU ((..(..(((((((...(((((((.(....).((((.....))))..)))))))..........................((((...((((((...((..((((((......((((((((.((((....((((....)))))))).)))))))).))))))..))..((((((((........))))))))................)))))).)))).)))))))..)...))... (-49.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCUGCCCCCCUUUCUUUUCCCUUAUCAUACAGCAAAUAGGAUUAAAAAUCAAGAAAAGGUGAUUUUUUCUUCAUAAACAUAGCUUCCUAUGAAAUUUUUUCAAAUAAUCUUCAAAAAAAGCUUGAAAGUGUUUACAAAUAGUGAUAAAAUGGAAUAAGUAGAAUCAUGAAAACGAAAUUUUCAUACCGUCUCUUUUUUAGAGUCUCGUGAGGUAUGAUAUAGAAAGGAAAUGGA ..........((.(((((((((...((((((((..((....(((..((((((((........))))))))..))).((((((((((((....((((..((........))..))))....))))).....)))))))......(.(((....(((((.(((.(((...(((((((.....)))))))....)))))))))))..))).).))..))))))))..))))))))).)). (-47.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 858 50 1 141 92 smit:SMT_1074|5end_catabolite_control_protein_A_1013285..1013515_NEGATIVE 289 100 57 139 97 smit:SMT_875|5end_nitroreductase_family_protein_823384..823614_NEGATIVE 272 207 167 135 93 smit:SMT_606|5end_cytochrome_c-type_biogenesis_protein_CcdA_519390..519620_POSITIVE 267 217 172 198 152 smit:SMT_706|5end_hypothetical_protein_616222..616452_NEGATIVE 244 218 175 142 98 smit:SMT_1655|5end_glucose-6-phosphate_1-dehydrogenase_1645021..1645251_NEGATIVE 244 50 1 166 99 smit:SMT_1540|5end_hypothetical_protein_1525005..1525235_NEGATIVE 242 100 58 113 74 smit:SMT_1039|5end_tRNA_(uracil-5-)_-methyltransferase_982698..982928_NEGATIVE 237 215 175 157 111 smit:SMT_2085|5end_K01207_beta-N-acetylhexosaminidase_1983039..1983269_POSITIVE 235 135 94 49 1 smit:SMT_901|5end_hypothetical_protein_851434..851664_NEGATIVE 234 230 193 136 100 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 229 120 75 139 96 smit:SMT_560|5end_predicted_permease_478095..478325_POSITIVE 226 50 1 194 149 smit:SMT_1091|5end_competence-specific_global_transcription_modulator_1033040..1033270_NEGATIVE 224 229 181 180 125 smit:SMT_1411|5end_ATP-dependent_nuclease_subunit_B_1395478..1395708_NEGATIVE 224 213 174 144 98 smit:SMT_491|5end_K01998_branched-chain_amino_acid_transport_system_permease_protein_425417..425647_POSITIVE 223 85 41 80 33 smit:SMT_798|5end_hypothetical_protein_705788..706018_POSITIVE 222 230 192 199 155 smit:SMT_1728|5end_exodeoxyribonuclease_VII_large_subunit_1713248..1713478_POSITIVE 221 217 175 156 97 smit:SMT_669|5end_ribose-phosphate_pyrophosphokinase_578160..578390_POSITIVE 220 95 57 199 163 smit:SMT_1469|5end_GTP_pyrophosphokinase_1450582..1450812_POSITIVE 216 190 145 111 66 smit:SMT_1169|5end_phosphorylase,_Pnp/UDP_family_1117350..1117580_NEGATIVE 216 36 3 131 96 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 93 57 145 110 smit:SMT_876|3end_hypothetical_protein_predicted_by_Glimmer/Critica_823371..823521_NEGATIVE 262 69 25 137 88 smit:SMT_1676|3end_S4_domain_protein_1661396..1661546_NEGATIVE 244 50 1 88 21 smit:SMT_1541|3end_isopentenyl-diphosphate_delta-isomerase_1525083..1525233_NEGATIVE 235 135 94 59 11 smit:SMT_902|3end_hypothetical_protein_851424..851574_NEGATIVE 234 230 193 80 44 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 231 127 81 72 31 smit:SMT_380|3end_hypothetical_protein_316944..317094_POSITIVE 226 129 84 50 2 smit:SMT_1340|3end_phosphoenolpyruvate_carboxylase_1315171..1315321_NEGATIVE 226 50 1 74 29 smit:SMT_1092|3end_transcription_antitermination_factor_1033160..1033310_NEGATIVE 224 213 174 140 94 smit:SMT_490|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_425493..425643_POSITIVE 223 85 41 61 14 smit:SMT_797|3end_hypothetical_protein_705849..705999_POSITIVE 222 230 192 72 28 smit:SMT_1727|3end_uridine_kinase_1713201..1713351_POSITIVE 216 230 202 37 6 smit:SMT_1933|3end_K02006_cobalt_transport_system_ATP-binding_protein_1871986..1872136_NEGATIVE 216 36 3 134 99 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 214 65 21 69 19 smit:SMT_1931|3end_23S_rRNA_methyltransferase_1870796..1870946_NEGATIVE 211 49 1 68 18 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 210 50 2 120 78 smit:SMT_1392|3end_dihydroxyacetone_kinase_1369186..1369336_POSITIVE 209 54 18 113 75 smit:SMT_220|3end_Hypothetical_zinc_metalloprotease_153086..153236_POSITIVE 209 229 194 90 62 smit:SMT_161|3end_putative_folyl-polyglutamate_synthetase_106586..106736_POSITIVE 203 230 182 74 20 smit:SMT_1847|3end_hypothetical_protein_1812697..1812847_POSITIVE 202 67 23 80 41 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE