Origin IGS: aactgaggattgataaaaaataaaatgcgtcatatcaagaaaataagaatcttgatatgacgcatttttggatgaagatttttacaaggagtttcctagattat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataatctaggaaactccttgtaaaaatcttcatccaaaaatgcgtcatatcaagattcttattttcttgatatgacgcattttattttttatcaatcctcagtt Mask Tandem Repeat Region ================================================ aactgaggattgataaaaaataaaatgcgtcatatcaagaaaataagaatcttgatatgacgcatttttggatgaagatttttacaaggagtttcctagattat Find is-nt database================================================ Query_seq: SMT_637:SMT_638|SMT_637:SMT_638:lactose phosphotransferase system repressor:hypothetical protein:-><-:543166..543269 104 aactgaggattgataaaaaataaaatgcgtcatatcaagaaaataagaatcttgatatgacgcatttttggatgaagatttttacaaggagtttcctagattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_637:SMT_638|SMT_637:SMT_638:lactose phosphotransferase system repressor:hypothetical protein:-><-:543166..543269 104 aactgaggattgataaaaaataaaatgcgtcatatcaagaaaataagaatcttgatatgacgcatttttggatgaagatttttacaaggagtttcctagattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_637:SMT_638|SMT_637:SMT_638:lactose phosphotransferase system repressor:hypothetical protein:-><-:543166..543269 104 aactgaggattgataaaaaataaaatgcgtcatatcaagaaaataagaatcttgatatgacgcatttttggatgaagatttttacaaggagtttcctagattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aactgaggattgataaaaaataaaatgcgtcatatcaagaaaataagaatcttgatatgacgcatttttggatgaagatttttacaaggagtttcctagattat Predict ORF larger than 30AA ================================================ aactgaggattgataaaaaataaaatgcgtcatatcaagaaaataagaatcttgatatgacgcatttttggatgaagatttttacaaggagtttcctagattat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aactgaggattgataaaaaataaaatgcgtcatatcaagaaaataagaatcttgatatgacgcatttttggatgaagatttttacaaggagtttcctagattat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -15.0 Tail_Score: -5.28778 Start: 21 End: 69 Full_Region: taaaaatcttcatcc aaaaatgcgtcatatcaaga ttcttattt tcttgatatgacgcatttta ttttttatcaatcct ....................aaaaatgcgtcatatcaagattcttattttcttgatatgacgcatttta................................... TransTerm Strand: - Conf: 100 HP_score: -14.9 Tail_Score: -5.49579 Start: 26 End: 64 Full_Region: atcttcatccaaaaa tgcgtcatatcaaga ttcttattt tcttgatatgacgca ttttattttttatca .........................tgcgtcatatcaagattcttattttcttgatatgacgca........................................ Find igs database================================================ Query_seq: SMT_637:SMT_638|SMT_637:SMT_638:lactose phosphotransferase system repressor:hypothetical protein:-><-:543166..543269 104 aactgaggattgataaaaaataaaatgcgtcatatcaagaaaataagaatcttgatatgacgcatttttggatgaagatttttacaaggagtttcctagattat Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: smit_SMT_637_SMT_638|lactose phosphotransferase system repressor:hypothetical protein|POSITIVE:NEGATIVE|[543166,543269]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 aactgaggattgataaaaaataaaatgcgtcatatcaagaaaataagaatcttgatatgacgcatttttggatgaagatttttacaaggagtttcctagattat aactgaggattgataaaaaataaaatgcgtcatatcaagaaaataagaatcttgatatgacgcatttttggatgaagatttttacaaggagtttcctagattat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUGAGGAUUGAUAAAAAAUAAAAUGCGUCAUAUCAAGAAAAUAAGAAUCUUGAUAUGACGCAUUUUUGGAUGAAGAUUUUUACAAGGAGUUUCCUAGAUUAU ...((((((((..........(((((((((((((((((((.........)))))))))))))))))))........))))))))..(((.....)))....... (-31.57) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUCUAGGAAACUCCUUGUAAAAAUCUUCAUCCAAAAAUGCGUCAUAUCAAGAUUCUUAUUUUCUUGAUAUGACGCAUUUUAUUUUUUAUCAAUCCUCAGUU .....((((((.((.....))...............(((((((((((((((((((.........)))))))))))))))))))............)))).)).. (-29.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 100 62 178 137 smit:SMT_742|5end_hypothetical_protein_646818..647048_NEGATIVE 242 97 53 129 86 smit:SMT_1305|5end_glycerol_kinase_1268217..1268447_POSITIVE 239 99 51 146 100 smit:SMT_578|5end_lipoprotein_signal_peptidase_496061..496291_POSITIVE 238 65 26 82 53 smit:SMT_2164|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2037861..2038091_POSITIVE 235 94 51 57 11 smit:SMT_321|5end_hypothetical_protein_259930..260160_POSITIVE 227 85 50 120 82 smit:SMT_1225|5end_50S_ribosomal_protein_L13_1188575..1188805_POSITIVE 218 97 51 231 186 smit:SMT_1542|5end_phosphomevalonate_kinase_1527084..1527314_NEGATIVE 215 86 43 132 77 smit:SMT_1375|5end_putative_glucose-inhibited_division_protein_1354438..1354668_NEGATIVE 210 94 58 171 140 smit:SMT_230|5end_hypothetical_protein_predicted_by_Glimmer/Critica_165830..166060_NEGATIVE 206 96 56 214 167 smit:SMT_396|5end_putative_nicotinate_phosphoribosyltransferase_325062..325292_POSITIVE 200 100 51 74 23 smit:SMT_1362|5end_chaperone_protein_hscC_1343078..1343308_NEGATIVE 200 100 62 172 132 smit:SMT_200|5end_hypothetical_protein_129747..129977_POSITIVE 196 98 57 147 108 smit:SMT_168|5end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_113670..113900_POSITIVE 194 70 27 87 33 smit:SMT_367|5end_hypothetical_protein_302318..302548_POSITIVE 192 97 52 158 116 smit:SMT_493|5end_K01996_branched-chain_amino_acid_transport_system_ATP-binding_protein_427137..427367_POSITIVE 191 69 29 167 116 smit:SMT_832|5end_hypothetical_protein_775104..775334_NEGATIVE 188 90 50 225 176 smit:SMT_1446|5end_pneumococcal_vaccine_antigen_A_1429610..1429840_NEGATIVE 186 99 61 104 59 smit:SMT_1328|5end_hypothetical_protein_1304468..1304698_NEGATIVE 186 78 32 182 141 smit:SMT_1134|5end_glutamyl-tRNA_synthetase_1076464..1076694_NEGATIVE 184 100 51 171 116 smit:SMT_1296|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1257290..1257520_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 477 68 22 69 23 smit:SMT_637|3end_lactose_phosphotransferase_system_repressor_543105..543255_POSITIVE 239 99 51 149 103 smit:SMT_577|3end_transcriptional_regulator,_LysR_family_496144..496294_POSITIVE 238 65 26 58 29 smit:SMT_2163|3end_cell_division_protein_FtsA_2037917..2038067_POSITIVE 216 100 61 130 92 smit:SMT_1902|3end_proton-translocating_NADH-quinone_oxidoreductase,_chain_L_1852028..1852178_NEGATIVE 206 96 56 99 52 smit:SMT_395|3end_hypothetical_protein_325027..325177_POSITIVE 204 99 60 74 33 smit:SMT_1899|3end_hypothetical_protein_1850337..1850487_POSITIVE 197 92 51 89 59 smit:SMT_1489|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1470714..1470864_POSITIVE 194 97 62 91 48 smit:SMT_668|3end_hypothetical_protein_predicted_by_Glimmer/Critica_578057..578207_NEGATIVE 194 70 27 87 33 smit:SMT_366|3end_hypothetical_protein_302398..302548_POSITIVE 191 69 29 88 37 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 186 99 61 94 49 smit:SMT_1329|3end_GTP-binding_protein_CgtA_1304478..1304628_NEGATIVE 186 78 32 54 13 smit:SMT_1135|3end_glucose-6-phosphate_isomerase_1076592..1076742_NEGATIVE 183 98 58 62 25 smit:SMT_1380|3end_pyrroline-5-carboxylate_reductase_1357667..1357817_NEGATIVE 182 97 69 149 116 smit:SMT_1165|3end_sensor_protein_CiaH_1110486..1110636_NEGATIVE 182 70 22 72 25 smit:SMT_779|3end_ribonuclease_BN,_putative_687883..688033_NEGATIVE 180 100 52 116 69 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 178 98 82 24 8 smit:SMT_1475|3end_K02004_1458661..1458811_POSITIVE 178 78 49 44 12 smit:SMT_871|3end_K03311_branched-chain_amino_acid:cation_transporter,_LIVCS_family_818835..818985_NEGATIVE 177 100 61 53 9 smit:SMT_1630|3end_hypothetical_protein_1618141..1618291_POSITIVE 175 92 58 71 41 smit:SMT_1487|3end_hypothetical_protein_1467076..1467226_POSITIVE