Origin IGS: gattttataaacaatcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatctcaactttctatttccattttatcataaatcggtgatttttatgagtaatagttgagaggaagcgtttttattttaagcaaaagaaaagaggaactttcattcctctcttctttgattgtttataaaatc Mask Tandem Repeat Region ================================================ gattttataaacaatcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt Find is-nt database================================================ Query_seq: SMT_332:SMT_333|SMT_332:SMT_333:phosphoglycerate kinase:hypothetical protein:->->:272762..272895 134 gattttataaacaatcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_332:SMT_333|SMT_332:SMT_333:phosphoglycerate kinase:hypothetical protein:->->:272762..272895 134 gattttataaacaatcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_332:SMT_333|SMT_332:SMT_333:phosphoglycerate kinase:hypothetical protein:->->:272762..272895 134 gattttataaacaatcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattttataaacaatcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt Predict ORF larger than 30AA ================================================ gattttataaacaatcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt 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================================================ gattttataaacaatcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -7.1 Tail_Score: -4.18044 Start: 20 End: 47 Full_Region: ttattttaagcaaaa gaaaagaggaa ctttca ttcctctcttc tttgattgtttataa ...................gaaaagaggaactttcattcctctcttc....................................................................................... Find igs database================================================ Query_seq: SMT_332:SMT_333|SMT_332:SMT_333:phosphoglycerate kinase:hypothetical protein:->->:272762..272895 134 gattttataaacaatcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: smit_SMT_332_SMT_333|phosphoglycerate kinase:hypothetical protein|POSITIVE:POSITIVE|[272762,272895]|134 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 gattttataaacaatcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt gattttataaacaatcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt Inter-species Hit: Count: 3 Min: 1 Max: 134 Len: 134 Subject: NC_008533_SPD_0445_SPD_0446|phosphoglycerate kinase:hypothetical protein|POSITIVE:POSITIVE|[454909,455043]|135 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 gattttataaacaa-tcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt gattttataaacaaatcaaagaagagagggatgagagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt Subject: NC_003098_spr0441_spr0442|phosphoglycerate kinase:hypothetical protein|POSITIVE:POSITIVE|[447379,447513]|135 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 gattttataaacaa-tcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt gattttataaacaaatcaaagaagagagggatgagagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt Subject: NC_003028_SP_0499_SP_0500|phosphoglycerate kinase:hypothetical protein|POSITIVE:POSITIVE|[482795,482929]|135 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 gattttataaacaa-tcaaagaagagaggaatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt gattttataaataaatcaaagaagagagggatgaaagttcctcttttcttttgcttaaaataaaaacgcttcctctcaactattactcataaaaatcaccgatttatgataaaatggaaatagaaagttgagatt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUUAUAAACAAUCAAAGAAGAGAGGAAUGAAAGUUCCUCUUUUCUUUUGCUUAAAAUAAAAACGCUUCCUCUCAACUAUUACUCAUAAAAAUCACCGAUUUAUGAUAAAAUGGAAAUAGAAAGUUGAGAUU ..((((((........(((((((((((((((....)))))))))))))))........))))))........((((((((.....(((((((.........)))))))....((....))....)))))))).. (-34.19) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUCAACUUUCUAUUUCCAUUUUAUCAUAAAUCGGUGAUUUUUAUGAGUAAUAGUUGAGAGGAAGCGUUUUUAUUUUAAGCAAAAGAAAAGAGGAACUUUCAUUCCUCUCUUCUUUGAUUGUUUAUAAAAUC ..((((((((...(((((.......(((((......)))))......)))))..))))))))................((((((((((((.(((((((......))))))).)))))...)))))))....... (-31.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 237 52 14 197 162 smit:SMT_1042|5end_hypothetical_cytosolic_protein_984972..985202_NEGATIVE 236 120 71 123 74 smit:SMT_1341|5end_putative_cell_division_protein_1319115..1319345_NEGATIVE 228 55 14 123 66 smit:SMT_1531|5end_hypothetical_protein_1515997..1516227_NEGATIVE 220 87 41 221 173 smit:SMT_2046|5end_choline_binding_protein_C_1957519..1957749_NEGATIVE 219 51 19 178 138 smit:SMT_1494|5end_nucleoside_diphosphate_kinase_1479500..1479730_POSITIVE 219 56 17 171 128 smit:SMT_1074|5end_catabolite_control_protein_A_1013285..1013515_NEGATIVE 215 45 16 206 182 smit:SMT_102|5end_competence-specific_global_transcription_modulator_34108..34338_POSITIVE 212 90 47 166 131 smit:SMT_2049|5end_3-oxoacyl-_1959539..1959769_NEGATIVE 212 58 19 111 72 smit:SMT_403|5end_two-component_sensor_kinase_YesM_331580..331810_POSITIVE 209 89 52 91 55 smit:SMT_1276|5end_rod_shape-determining_protein_MreD_1239412..1239642_POSITIVE 203 46 11 147 120 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 200 53 19 156 113 smit:SMT_1806|5end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781229..1781459_POSITIVE 200 53 19 156 113 smit:SMT_1635|5end_putative_N-acetyldiaminopimelate_deacetylase_1621426..1621656_POSITIVE 200 57 12 60 19 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 198 45 5 114 81 smit:SMT_942|5end_hypothetical_protein_894067..894297_NEGATIVE 198 52 11 218 176 smit:SMT_431|5end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate_synthetase_372199..372429_POSITIVE 197 70 21 163 109 smit:SMT_1305|5end_glycerol_kinase_1268217..1268447_POSITIVE 195 76 36 216 166 smit:SMT_1016|5end_alcohol_dehydrogenase,_zinc-containing_954094..954324_NEGATIVE 195 100 66 106 57 smit:SMT_931|5end_cobyric_acid_synthase_884491..884721_POSITIVE 194 56 20 160 123 smit:SMT_1367|5end_K02237_competence_protein_ComEA_1347522..1347752_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 50 17 74 41 smit:SMT_332|3end_phosphoglycerate_kinase_272701..272851_POSITIVE 264 53 12 52 2 smit:SMT_594|3end_lysyl-tRNA_synthetase_510348..510498_NEGATIVE 240 80 40 151 119 smit:SMT_2056|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1966735..1966885_POSITIVE 240 55 24 61 32 smit:SMT_1753|3end_tryptophan_synthase_beta_chain_1731652..1731802_POSITIVE 237 52 14 59 24 smit:SMT_1043|3end_chaperonin_GroEL_985110..985260_NEGATIVE 234 56 25 90 63 smit:SMT_1983|3end_glycerophosphoryl_diester_phosphodiesterase_1913455..1913605_NEGATIVE 228 55 14 126 69 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE 228 80 38 68 17 smit:SMT_1007|3end_radical_SAM_domain_protein_947549..947699_POSITIVE 225 51 19 92 54 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 220 87 41 143 95 smit:SMT_2047|3end_choline_binding_protein_F_1957597..1957747_NEGATIVE 219 51 19 92 52 smit:SMT_1493|3end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1479494..1479644_POSITIVE 219 87 48 65 23 smit:SMT_151|3end_K02073_D-methionine_transport_system_substrate-binding_protein_100393..100543_POSITIVE 215 45 16 85 61 smit:SMT_101|3end_cell_division_protein_34067..34217_POSITIVE 212 58 19 114 75 smit:SMT_402|3end_two-component_response_regulator_YesN_331663..331813_POSITIVE 210 78 35 128 85 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 209 89 52 91 55 smit:SMT_1275|3end_rod_shape-determining_protein_MreC_1239492..1239642_POSITIVE 203 46 11 91 64 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 202 46 14 91 66 smit:SMT_2045|3end_K+_transport_system,_NAD-binding_component_1956758..1956908_POSITIVE 202 57 17 94 52 smit:SMT_412|3end_hypothetical_protein_predicted_by_Glimmer/Critica_356436..356586_NEGATIVE 200 53 19 88 45 smit:SMT_1805|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1781241..1781391_POSITIVE