Origin IGS: gtgaagattctccattcttaaatttagctattatgcttctctttattgtatcttatttttacaaaaatttctaagaaaaactgaactttttatggaaaaaataaaaagcagaagaaatctcctgcttttttattgagctaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctagctcaataaaaaagcaggagatttcttctgctttttattttttccataaaaagttcagtttttcttagaaatttttgtaaaaataagatacaataaagagaagcataatagctaaatttaagaatggagaatcttcac Mask Tandem Repeat Region ================================================ gtgaagattctccattcttaaatttagctattatgcttctctttattgtatcttatttttacaaaaatttctaagaaaaactgaactttttatggaaaaaataaaaagcagaagaaatctcctgcttttttattgagctaga Find is-nt database================================================ Query_seq: SMT_1222:SMT_1223|SMT_1222:SMT_1223:pneumococcal surface protein A:pneumococcal surface protein A:<-<-:1187099..1187240 142 gtgaagattctccattcttaaatttagctattatgcttctctttattgtatcttatttttacaaaaatttctaagaaaaactgaactttttatggaaaaaataaaaagcagaagaaatctcctgcttttttattgagctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1222:SMT_1223|SMT_1222:SMT_1223:pneumococcal surface protein A:pneumococcal surface protein A:<-<-:1187099..1187240 142 gtgaagattctccattcttaaatttagctattatgcttctctttattgtatcttatttttacaaaaatttctaagaaaaactgaactttttatggaaaaaataaaaagcagaagaaatctcctgcttttttattgagctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1222:SMT_1223|SMT_1222:SMT_1223:pneumococcal surface protein A:pneumococcal surface protein A:<-<-:1187099..1187240 142 gtgaagattctccattcttaaatttagctattatgcttctctttattgtatcttatttttacaaaaatttctaagaaaaactgaactttttatggaaaaaataaaaagcagaagaaatctcctgcttttttattgagctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgaagattctccattcttaaatttagctattatgcttctctttattgtatcttatttttacaaaaatttctaagaaaaactgaactttttatggaaaaaataaaaagcagaagaaatctcctgcttttttattgagctaga Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 14 End: 133 ............. M L K F S Y Y A S L Y C I L F L Q K F L R K T E L F M E K I K S R R N L L L F Y ......... gtgaagattctccattcttaaatttagctattatgcttctctttattgtatcttatttttacaaaaatttctaagaaaaactgaactttttatggaaaaaataaaaagcagaagaaatctcctgcttttttattgagctaga 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================================================ gtgaagattctccattcttaaatttagctattatgcttctctttattgtatcttatttttacaaaaatttctaagaaaaactgaactttttatggaaaaaataaaaagcagaagaaatctcctgcttttttattgagctaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -5.5 Tail_Score: -5.46657 Start: 108 End: 125 Full_Region: TGGAAAAAATAAAAA GCAGAAG AAAT CTCCTGC TTTTTTATTGAGCTA ...........................................................................................................GCAGAAGAAATCTCCTGC................. Find igs database================================================ Query_seq: SMT_1222:SMT_1223|SMT_1222:SMT_1223:pneumococcal surface protein A:pneumococcal surface protein A:<-<-:1187099..1187240 142 gtgaagattctccattcttaaatttagctattatgcttctctttattgtatcttatttttacaaaaatttctaagaaaaactgaactttttatggaaaaaataaaaagcagaagaaatctcctgcttttttattgagctaga Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: smit_SMT_1222_SMT_1223|pneumococcal surface protein A:pneumococcal surface protein A|NEGATIVE:NEGATIVE|[1187099,1187240]|142 HSP 1 e-value: 9.0E-54 bit: 210.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 gtgaagattctccattcttaaatttagctattatgcttctctttattgtatcttatttttacaaaaatttctaagaaaaactgaactttttatggnnnnnnnnnnnngcagaagaaatctcctgcttttttattgagctaga gtgaagattctccattcttaaatttagctattatgcttctctttattgtatcttatttttacaaaaatttctaagaaaaactgaactttttatggaaaaaataaaaagcagaagaaatctcctgcttttttattgagctaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGAAGAUUCUCCAUUCUUAAAUUUAGCUAUUAUGCUUCUCUUUAUUGUAUCUUAUUUUUACAAAAAUUUCUAAGAAAAACUGAACUUUUUAUGGAAAAAAUAAAAAGCAGAAGAAAUCUCCUGCUUUUUUAUUGAGCUAGA ...((((........))))...(((((((................(((((.........)))))...((((((.(((((.......))))).))))))....(((((((((.((....)).))))))))).....))))))) (-24.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAGCUCAAUAAAAAAGCAGGAGAUUUCUUCUGCUUUUUAUUUUUUCCAUAAAAAGUUCAGUUUUUCUUAGAAAUUUUUGUAAAAAUAAGAUACAAUAAAGAGAAGCAUAAUAGCUAAAUUUAAGAAUGGAGAAUCUUCAC ..(((((.....((((((((((((....)))))))))))).....................(((((((((......((((((....)))))).......))))))))).....)))))..........(((((...))))). (-30.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 744 50 1 141 92 smit:SMT_1222|5end_pneumococcal_surface_protein_A_1187008..1187238_NEGATIVE 236 45 2 135 95 smit:SMT_134|5end_LysM_domain_protein_85427..85657_POSITIVE 233 58 11 182 143 smit:SMT_1636|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1622568..1622798_POSITIVE 231 130 81 158 109 smit:SMT_293|5end_dTDP-4-dehydrorhamnose_reductase_235919..236149_POSITIVE 230 76 31 137 93 smit:SMT_549|5end_hypothetical_cytosolic_protein_467057..467287_POSITIVE 218 139 94 218 170 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 217 39 8 134 97 smit:SMT_399|5end_cytochrome_c-type_biogenesis_protein_CcdA_328366..328596_POSITIVE 215 140 116 120 94 smit:SMT_1058|5end_primosomal_protein_DnaI_996486..996716_POSITIVE 215 42 9 227 190 smit:SMT_434|5end_orotidine_5'-phosphate_decarboxylase_376107..376337_POSITIVE 212 47 5 106 60 smit:SMT_1619|5end_K02006_cobalt_transport_system_ATP-binding_protein_1606526..1606756_NEGATIVE 207 63 22 124 80 smit:SMT_2027|5end_competence-specific_global_transcription_modulator_1943204..1943434_NEGATIVE 206 140 92 223 173 smit:SMT_1283|5end_K02240_competence_protein_ComFA_1245667..1245897_POSITIVE 202 139 106 58 16 smit:SMT_1333|5end_glycosyltransferase_1308635..1308865_NEGATIVE 199 130 89 226 192 smit:SMT_1362|5end_chaperone_protein_hscC_1343078..1343308_NEGATIVE 198 43 1 102 40 smit:SMT_1877|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1834039..1834269_POSITIVE 198 45 2 202 165 smit:SMT_1346|5end_tellurite_resistance_protein_TehB_1324703..1324933_NEGATIVE 198 44 7 203 161 smit:SMT_1098|5end_hypothetical_protein_1041992..1042222_NEGATIVE 197 131 99 194 163 smit:SMT_1530|5end_K07456_DNA_mismatch_repair_protein_MutS2_1515346..1515576_NEGATIVE 197 50 2 59 5 smit:SMT_725|5end_hypothetical_protein_630415..630645_NEGATIVE 195 48 1 157 109 smit:SMT_1506|5end_Cl-channel,_voltage-gated_family_protein_1489986..1490216_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 130 81 92 43 smit:SMT_292|3end_dTDP-glucose_4,6-dehydratase_235933..236083_POSITIVE 227 58 11 91 43 smit:SMT_120|3end_hypothetical_protein_72943..73093_POSITIVE 215 140 116 119 93 smit:SMT_1057|3end_replicative_DNA_helicase_996565..996715_POSITIVE 213 40 2 151 106 smit:SMT_739|3end_50S_ribosomal_protein_L7/L12_643274..643424_NEGATIVE 203 137 99 60 21 smit:SMT_405|3end_zinc_metalloprotease_ZmpB,_truncated_339938..340088_POSITIVE 200 54 11 134 97 smit:SMT_1255|3end_cell_division_protein_FtsH_1220987..1221137_NEGATIVE 199 130 89 50 16 smit:SMT_1363|3end_50S_ribosomal_protein_L20_1343254..1343404_NEGATIVE 198 43 1 118 56 smit:SMT_1876|3end_transcriptional_regulator,_MarR_family_1834135..1834285_POSITIVE 198 44 7 151 109 smit:SMT_1099|3end_protein_tyrosine_phosphatase_1042044..1042194_NEGATIVE 197 131 99 91 60 smit:SMT_1531|3end_hypothetical_protein_1515449..1515599_NEGATIVE 197 50 2 62 8 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 195 44 4 80 38 smit:SMT_181|3end_50S_ribosomal_protein_L24_120510..120660_POSITIVE 192 54 22 137 103 smit:SMT_1154|3end_tryptophanyl-tRNA_synthetase_1098154..1098304_NEGATIVE 191 49 2 74 23 smit:SMT_2039|3end_malolactic_enzyme_1949681..1949831_NEGATIVE 191 127 81 76 30 smit:SMT_1412|3end_hypothetical_protein_1396411..1396561_POSITIVE 190 54 13 146 96 smit:SMT_660|3end_two-component_sensor_histidine_kinase_570538..570688_NEGATIVE 189 139 95 65 12 smit:SMT_932|3end_tellurite_resistance_protein_885402..885552_POSITIVE 189 138 108 135 107 smit:SMT_760|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_665693..665843_NEGATIVE 188 76 36 55 15 smit:SMT_1375|3end_putative_glucose-inhibited_division_protein_1353104..1353254_NEGATIVE 187 133 107 46 18 smit:SMT_1030|3end_alpha-galactosidase_965667..965817_NEGATIVE