Origin IGS: ctgaatcttatatgagacataaaaaataaaggatttaacccttttgacttgggtaaatccttttttcttgtttaaaaatcgtttgagcagagcgtttccaagcgagacttcacttgtctcgcttgggaacactgcacagaataaatcttatgagaaagttacattcctcaaatcaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattgatttgaggaatgtaactttctcataagatttattctgtgcagtgttcccaagcgagacaagtgaagtctcgcttggaaacgctctgctcaaacgatttttaaacaagaaaaaaggatttacccaagtcaaaagggttaaatcctttattttttatgtctcatataagattcag Mask Tandem Repeat Region ================================================ ctgaatcttatatgagacataaaaaataaaggatttaacccttttgacttgggtaaatccttttttcttgtttaaaaatcgtttgagcagagcgtttccaagcgagacttcacttgtctcgcttgggaacactgcacagaataaatcttatgagaaagttacattcctcaaatcaatc Find is-nt database================================================ Query_seq: SMT_1252:SMT_1253|SMT_1252:SMT_1253:hypothetical protein:beta-galactosidase:-><-:1212824..1213001 178 ctgaatcttatatgagacataaaaaataaaggatttaacccttttgacttgggtaaatccttttttcttgtttaaaaatcgtttgagcagagcgtttccaagcgagacttcacttgtctcgcttgggaacactgcacagaataaatcttatgagaaagttacattcctcaaatcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1252:SMT_1253|SMT_1252:SMT_1253:hypothetical protein:beta-galactosidase:-><-:1212824..1213001 178 ctgaatcttatatgagacataaaaaataaaggatttaacccttttgacttgggtaaatccttttttcttgtttaaaaatcgtttgagcagagcgtttccaagcgagacttcacttgtctcgcttgggaacactgcacagaataaatcttatgagaaagttacattcctcaaatcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1252:SMT_1253|SMT_1252:SMT_1253:hypothetical protein:beta-galactosidase:-><-:1212824..1213001 178 ctgaatcttatatgagacataaaaaataaaggatttaacccttttgacttgggtaaatccttttttcttgtttaaaaatcgtttgagcagagcgtttccaagcgagacttcacttgtctcgcttgggaacactgcacagaataaatcttatgagaaagttacattcctcaaatcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgaatcttatatgagacataaaaaataaaggatttaacccttttgacttgggtaaatccttttttcttgtttaaaaatcgtttgagcagagcgtttccaagcgagacttcacttgtctcgcttgggaacactgcacagaataaatcttatgagaaagttacattcctcaaatcaatc Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 26 End: 178 ......................... M K D L T L L T W V N P F F L F K N R L S R A F P S E T S L V S L G N T A Q N K S Y E K V T F L K S I Protein_Len: 44 Strand: - Start: 1 End: 132 Q I K Y S V Y F I F S K V R K V Q T F G K K K N L F R K L L A N G L S V E S T E S P F M .............................................. ctgaatcttatatgagacataaaaaataaaggatttaacccttttgacttgggtaaatccttttttcttgtttaaaaatcgtttgagcagagcgtttccaagcgagacttcacttgtctcgcttgggaacactgcacagaataaatcttatgagaaagttacattcctcaaatcaatc 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================================================ ctgaatcttatatgagacataaaaaataaaggatttaacccttttgacttgggtaaatccttttttcttgtttaaaaatcgtttgagcagagcgtttccaagcgagacttcacttgtctcgcttgggaacactgcacagaataaatcttatgagaaagttacattcctcaaatcaatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -2.6 Tail_Score: -5.43414 Start: 27 End: 37 Full_Region: ccaagtcaaaagggt taaa tcc ttta ttttttatgtctcat ..........................taaatccttta............................................................................................................................................. TransTerm Strand: + Conf: 81 HP_score: -3.0 Tail_Score: -5.72254 Start: 31 End: 60 Full_Region: GACATAAAAAATAAA GGATTTAACCC TTTTGACTT GGGTAAATCC TTTTTTCTTGTTTAA ..............................GGATTTAACCCTTTTGACTTGGGTAAATCC...................................................................................................................... TransTerm Strand: - Conf: 73 HP_score: -3.2 Tail_Score: -5.16969 Start: 31 End: 41 Full_Region: ttacccaagtcaaaa gggt taa atcc tttattttttatgtc ..............................gggttaaatcc......................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -16.3 Tail_Score: -2.78715 Start: 92 End: 132 Full_Region: gatttattctgtgca gtgttcccaagcgagac aagtgaa gtctcgcttggaaacgc tctgctcaaacgatt ...........................................................................................gtgttcccaagcgagacaagtgaagtctcgcttggaaacgc.............................................. Find igs database================================================ Query_seq: SMT_1252:SMT_1253|SMT_1252:SMT_1253:hypothetical protein:beta-galactosidase:-><-:1212824..1213001 178 ctgaatcttatatgagacataaaaaataaaggatttaacccttttgacttgggtaaatccttttttcttgtttaaaaatcgtttgagcagagcgtttccaagcgagacttcacttgtctcgcttgggaacactgcacagaataaatcttatgagaaagttacattcctcaaatcaatc Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: smit_SMT_1252_SMT_1253|hypothetical protein:beta-galactosidase|POSITIVE:NEGATIVE|[1212824, 1213001]|178 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 ctgaatcttatatgagacataaaaaataaaggatttaacccttttgacttgggtaaatccttttttcttgtttaaaaatcgtttgagcagagcgtttccaagcgagacttcacttgtctcgcttgggaacactgcacagaataaatcttatgagaaagttacattcctcaaatcaatc ctgaatcttatatgagacataaaaaataaaggatttaacccttttgacttgggtaaatccttttttcttgtttaaaaatcgtttgagcagagcgtttccaagcgagacttcacttgtctcgcttgggaacactgcacagaataaatcttatgagaaagttacattcctcaaatcaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAAUCUUAUAUGAGACAUAAAAAAUAAAGGAUUUAACCCUUUUGACUUGGGUAAAUCCUUUUUUCUUGUUUAAAAAUCGUUUGAGCAGAGCGUUUCCAAGCGAGACUUCACUUGUCUCGCUUGGGAACACUGCACAGAAUAAAUCUUAUGAGAAAGUUACAUUCCUCAAAUCAAUC ............((((...........((((((((((.(((.........)))))))))))))(((((..(..........((((.((((...(((((((((((((((.......))))))))))))))).)))).)))).........)..))))).........))))........ (-57.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUGAUUUGAGGAAUGUAACUUUCUCAUAAGAUUUAUUCUGUGCAGUGUUCCCAAGCGAGACAAGUGAAGUCUCGCUUGGAAACGCUCUGCUCAAACGAUUUUUAAACAAGAAAAAAGGAUUUACCCAAGUCAAAAGGGUUAAAUCCUUUAUUUUUUAUGUCUCAUAUAAGAUUCAG (((((...(((((((......)))))))............((.((((((((.(((((((((((.......))))))))))).)))))..))).))..))))).......(((((((((((((((((((.........))).)))))))))).))))))..((((......)))).... (-53.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 124 84 63 13 smit:SMT_1115|5end_K02245_competence_protein_ComGC_1052796..1053026_NEGATIVE 326 129 88 226 182 smit:SMT_558|5end_K09014_Fe-S_cluster_assembly_protein_SufB_475255..475485_POSITIVE 308 125 81 60 9 smit:SMT_310|5end_3-oxoacyl-_251370..251600_POSITIVE 306 135 98 182 140 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 303 124 87 202 163 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 296 127 81 209 153 smit:SMT_166|5end_hypothetical_protein_112987..113217_POSITIVE 294 128 87 218 169 smit:SMT_1945|5end_putative_dihydrolipoamide_S-acetyltransferase_1879961..1880191_POSITIVE 292 128 81 77 19 smit:SMT_580|5end_K04094_glucose_inhibited_division_protein_Gid_497421..497651_POSITIVE 291 130 81 180 130 smit:SMT_1007|5end_radical_SAM_domain_protein_947035..947265_POSITIVE 282 117 79 71 27 smit:SMT_765|5end_hypothetical_protein_672620..672850_NEGATIVE 280 127 83 186 144 smit:SMT_723|5end_hypothetical_protein_629475..629705_NEGATIVE 278 134 91 210 163 smit:SMT_845|5end_hypothetical_protein_791868..792098_NEGATIVE 275 126 81 113 65 smit:SMT_1259|5end_hypothetical_protein_1225139..1225369_POSITIVE 274 135 93 173 130 smit:SMT_2005|5end_pullulanase,_type_I_1926289..1926519_NEGATIVE 272 135 93 137 97 smit:SMT_983|5end_GTP_pyrophosphokinase_930304..930534_NEGATIVE 268 124 88 48 1 smit:SMT_1077|5end_GTP_cyclohydrolase_I_1015410..1015640_NEGATIVE 268 136 91 98 41 smit:SMT_104|5end_DNA_repair_protein_49623..49853_POSITIVE 267 116 71 227 183 smit:SMT_1748|5end_anthranilate_synthase_component_I_1726685..1726915_POSITIVE 267 136 92 108 56 smit:SMT_931|5end_cobyric_acid_synthase_884491..884721_POSITIVE 265 110 68 99 56 smit:SMT_323|5end_amino_acid_transport_ATP-binding_protein_261872..262102_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 124 84 61 11 smit:SMT_1116|3end_K02244_competence_protein_ComGB_1052798..1052948_NEGATIVE 313 113 80 43 16 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 291 139 91 51 2 smit:SMT_1324|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1294036..1294186_POSITIVE 278 120 80 62 23 smit:SMT_801|3end_glycyl-tRNA_synthetase_alpha_chain_709892..710042_NEGATIVE 276 75 36 81 39 smit:SMT_1624|3end_formate_acetyltransferase_1611421..1611571_NEGATIVE 274 135 93 45 2 smit:SMT_780|3end_peptidase_family_U32_688752..688902_NEGATIVE 268 136 92 70 20 smit:SMT_2031|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1945633..1945783_NEGATIVE 265 110 68 59 16 smit:SMT_324|3end_K02029_polar_amino_acid_transport_system_permease_protein_261912..262062_NEGATIVE 262 120 79 128 74 smit:SMT_1153|3end_alpha-mannosidase_1097383..1097533_NEGATIVE 260 122 87 111 63 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 259 130 85 87 32 smit:SMT_1933|3end_K02006_cobalt_transport_system_ATP-binding_protein_1871986..1872136_NEGATIVE 259 129 91 61 19 smit:SMT_1329|3end_GTP-binding_protein_CgtA_1304478..1304628_NEGATIVE 258 127 81 69 12 smit:SMT_1499|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483425..1483575_POSITIVE 253 96 59 134 98 smit:SMT_1451|3end_K02057_simple_sugar_transport_system_permease_protein_1433625..1433775_NEGATIVE 248 138 91 108 64 smit:SMT_1186|3end_hypothetical_protein_1144886..1145036_POSITIVE 248 120 72 72 15 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 247 141 103 145 102 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE 245 86 41 68 17 smit:SMT_629|3end_glycogen_synthase_535480..535630_POSITIVE 242 138 94 143 103 smit:SMT_1025|3end_hypothetical_protein_959550..959700_NEGATIVE 240 134 93 148 102 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE