Origin IGS: tattgtcattcctcctttttgttttagttttcgtttaagaaaactttaagactttttaagtataaaccgttttcatctaaaaatcaactatttatcataaaataattaaaaagattacatctgaaaatattgatatattgagttttagagaagtttttttgaatccttattaaaaaatttaatataaaaaagttggaagcgtattccaacttttaaaataggtttttattaga .........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 tctaataaaaacctattttaaaagttggaatacgcttccaacttttttatattaaattttttaataaggattcaaaaaaacttctctaaaactcaatatatcaatattttcagatgtaatctttttaattattttatgataaatagttgatttttagatgaaaacggtttatacttaaaaagtcttaaagttttcttaaacgaaaactaaaacaaaaaggaggaatgacaata Mask Tandem Repeat Region ================================================ tattgtcattcctcctttttgttttagttttcgtttaagaaaactttaagactttttaagtataaaccgttttcatctaaaaatcaactatttatcataaaataattaaaaagattacatctgaaaatattgatatattgagttttagagaagtttttttgaatccttattaaaaaatttaatataaaaaagttggaagcgtattccaacttttaaaataggtttttattaga Find is-nt database================================================ Query_seq: SMT_245:SMT_246|SMT_245:SMT_246:hypothetical protein predicted by Glimmer/Critica:alcohol dehydrogenase:<-<-:182055..182287 233 tattgtcattcctcctttttgttttagttttcgtttaagaaaactttaagactttttaagtataaaccgttttcatctaaaaatcaactatttatcataaaataattaaaaagattacatctgaaaatattgatatattgagttttagagaagtttttttgaatccttattaaaaaatttaatataaaaaagttggaagcgtattccaacttttaaaataggtttttattaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_245:SMT_246|SMT_245:SMT_246:hypothetical protein predicted by Glimmer/Critica:alcohol dehydrogenase:<-<-:182055..182287 233 tattgtcattcctcctttttgttttagttttcgtttaagaaaactttaagactttttaagtataaaccgttttcatctaaaaatcaactatttatcataaaataattaaaaagattacatctgaaaatattgatatattgagttttagagaagtttttttgaatccttattaaaaaatttaatataaaaaagttggaagcgtattccaacttttaaaataggtttttattaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_245:SMT_246|SMT_245:SMT_246:hypothetical protein predicted by Glimmer/Critica:alcohol dehydrogenase:<-<-:182055..182287 233 tattgtcattcctcctttttgttttagttttcgtttaagaaaactttaagactttttaagtataaaccgttttcatctaaaaatcaactatttatcataaaataattaaaaagattacatctgaaaatattgatatattgagttttagagaagtttttttgaatccttattaaaaaatttaatataaaaaagttggaagcgtattccaacttttaaaataggtttttattaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattgtcattcctcctttttgttttagttttcgtttaagaaaactttaagactttttaagtataaaccgttttcatctaaaaatcaactatttatcataaaataattaaaaagattacatctgaaaatattgatatattgagttttagagaagtttttttgaatccttattaaaaaatttaatataaaaaagttggaagcgtattccaacttttaaaataggtttttattaga Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 87 End: 209 ...................................................................................... S N I M F Y N F L N C R F I N I Y Q T K S F N K Q I R I L F N L I F F N S A Y E M ........................ tattgtcattcctcctttttgttttagttttcgtttaagaaaactttaagactttttaagtataaaccgttttcatctaaaaatcaactatttatcataaaataattaaaaagattacatctgaaaatattgatatattgagttttagagaagtttttttgaatccttattaaaaaatttaatataaaaaagttggaagcgtattccaacttttaaaataggtttttattaga 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: 84 Start: 59 End: 88 ..........................................................GTTGATTTTTAGATGAAAACGGTTTATACT................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 181 End: 210 ....................................................................................................................................................................................GTTGGAATACGCTTCCAACTTTTTTATATT....................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattgtcattcctcctttttgttttagttttcgtttaagaaaactttaagactttttaagtataaaccgttttcatctaaaaatcaactatttatcataaaataattaaaaagattacatctgaaaatattgatatattgagttttagagaagtttttttgaatccttattaaaaaatttaatataaaaaagttggaagcgtattccaacttttaaaataggtttttattaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 78 HP_score: -7.5 Tail_Score: -4.15854 Start: 192 End: 210 Full_Region: ATTTAATATAAAAAA GTTGGAA GCGTA TTCCAAC TTTTAAAATAGGTTT ...............................................................................................................................................................................................GTTGGAAGCGTATTCCAAC....................... Find igs database================================================ Query_seq: SMT_245:SMT_246|SMT_245:SMT_246:hypothetical protein predicted by Glimmer/Critica:alcohol dehydrogenase:<-<-:182055..182287 233 tattgtcattcctcctttttgttttagttttcgtttaagaaaactttaagactttttaagtataaaccgttttcatctaaaaatcaactatttatcataaaataattaaaaagattacatctgaaaatattgatatattgagttttagagaagtttttttgaatccttattaaaaaatttaatataaaaaagttggaagcgtattccaacttttaaaataggtttttattaga Intra-Species Hit: Count: 1 Min: 74 Max: 233 Len: 160 Subject: smit_SMT_245_SMT_246|hypothetical protein predicted by Glimmer/Critica:alcohol dehydrogenase|NEGATIVE:NEGATIVE|[182055,182287]|233 HSP 1 e-value: 3.0E-73 bit: 276.0 Len: 160 Query Start:74 Query End:233 Subject Strand: POSITIVE Subject Start: 74 Subject End: 233 .........................................................................catctaaaaatcaactatttatcataaaataattaaaaagattacatctgaaaatattgatatattgagttttagagaagnnnnnnngaatccttattaaaaaatttaatataaaaaagttggaagcgtattccaacttttaaaataggtttttattaga .........................................................................catctaaaaatcaactatttatcataaaataattaaaaagattacatctgaaaatattgatatattgagttttagagaagtttttttgaatccttattaaaaaatttaatataaaaaagttggaagcgtattccaacttttaaaataggtttttattaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUCUAAAAAUCAACUAUUUAUCAUAAAAUAAUUAAAAAGAUUACAUCUGAAAAUAUUGAUAUAUUGAGUUUUAGAGAAGUUUUUUUGAAUCCUUAUUAAAAAAUUUAAUAUAAAAAAGUUGGAAGCGUAUUCCAACUUUUAAAAUAGGUUUUUAUUAGA ..(((((.((....((((((............(((((((((((...(((((((...(..(....)..).)))))))..))))))))))).....((((((.....))))))...(((((((((((.....))))))))))).))))))....)).))))) (-31.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAAUAAAAACCUAUUUUAAAAGUUGGAAUACGCUUCCAACUUUUUUAUAUUAAAUUUUUUAAUAAGGAUUCAAAAAAACUUCUCUAAAACUCAAUAUAUCAAUAUUUUCAGAUGUAAUCUUUUUAAUUAUUUUAUGAUAAAUAGUUGAUUUUUAGAUG ...........(((.....(((((((((((.....)))))))))))...((((((.....)))))))))...............(((((((.....((((((..........))))))......((((((((((......)))))))))).))))))).. (-25.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 618 50 1 214 165 smit:SMT_245|5end_hypothetical_protein_predicted_by_Glimmer/Critica_181964..182194_NEGATIVE 218 153 119 152 123 smit:SMT_1700|5end_diaminopimelate_decarboxylase_1682032..1682262_POSITIVE 198 90 41 225 183 smit:SMT_1180|5end_putative_tagatose-6-phosphate_aldose/ketose_isomerase_1139202..1139432_NEGATIVE 192 141 114 193 171 smit:SMT_636|5end_ribonucleoside-diphosphate_reductase_beta_chain_541153..541383_POSITIVE 187 98 57 209 167 smit:SMT_265|5end_DNA-binding_protein_204073..204303_NEGATIVE 186 160 118 97 48 smit:SMT_1472|5end_hypothetical_protein,_coenzyme_PQQ_synthesis_homologue_1454262..1454492_NEGATIVE 184 99 56 54 13 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 178 141 112 220 187 smit:SMT_1778|5end_ATP-dependent_RNA_helicase_1754954..1755184_NEGATIVE 176 156 118 40 5 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 172 138 117 98 72 smit:SMT_1116|5end_K02244_competence_protein_ComGB_1053841..1054071_NEGATIVE 172 158 121 163 128 smit:SMT_400|5end_hypothetical_protein_329090..329320_POSITIVE 169 60 14 183 130 smit:SMT_1041|5end_K07586_hypothetical_protein_983551..983781_POSITIVE 169 90 58 161 136 smit:SMT_559|5end_D-alanyl-D-alanine_carboxypeptidase_478042..478272_NEGATIVE 168 49 3 227 169 smit:SMT_822|5end_putative_mucus_binding_protein_740574..740804_NEGATIVE 165 138 117 173 153 smit:SMT_1013|5end_galactose-1-phosphate_uridylyltransferase_950626..950856_NEGATIVE 164 93 67 228 203 smit:SMT_991|5end_hypothetical_protein_934425..934655_NEGATIVE 163 151 121 37 4 smit:SMT_1085|5end_sensor_histidine_kinase_(homolog_to_HK11_Spn)_1022267..1022497_NEGATIVE 161 88 46 54 16 smit:SMT_673|5end_K01926_AT-rich_DNA-binding_protein_580902..581132_POSITIVE 161 157 124 105 68 smit:SMT_600|5end_ADP-ribose_pyrophosphatase_516307..516537_POSITIVE 160 140 118 226 203 smit:SMT_703|5end_hypothetical_protein_612345..612575_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 141 107 86 51 smit:SMT_1778|3end_ATP-dependent_RNA_helicase_1753611..1753761_NEGATIVE 218 153 119 85 56 smit:SMT_1699|3end_purine_operon_repressor_1682045..1682195_POSITIVE 181 100 55 133 92 smit:SMT_1133|3end_cytidine/deoxycytidylate_deaminase_family_protein,_putative_1074556..1074706_NEGATIVE 178 141 112 81 48 smit:SMT_1779|3end_hypothetical_protein_1755093..1755243_NEGATIVE 178 98 51 56 3 smit:SMT_782|3end_GMP_synthase_692957..693107_NEGATIVE 172 158 121 149 114 smit:SMT_399|3end_cytochrome_c-type_biogenesis_protein_CcdA_329156..329306_POSITIVE 169 60 14 94 41 smit:SMT_1040|3end_K03565_regulatory_protein_983542..983692_POSITIVE 165 134 93 69 21 smit:SMT_484|3end_hypothetical_protein_419659..419809_NEGATIVE 165 154 117 146 103 smit:SMT_316|3end_acetyl-CoA_carboxylase_carboxyl_transferase_subunit_alpha_257391..257541_POSITIVE 164 148 118 115 82 smit:SMT_1671|3end_hypothetical_protein_1659392..1659542_NEGATIVE 164 93 67 124 99 smit:SMT_992|3end_hypothetical_protein_934529..934679_NEGATIVE 161 144 112 43 7 smit:SMT_1096|3end_glyceraldehyde-3-phosphate_dehydrogenase_1037366..1037516_NEGATIVE 161 157 124 95 58 smit:SMT_599|3end_glucosamine-1-phosphate_N-acetyltransferase_/_UDP-N-acetylglucosamine_pyrophosphorylase_516377..516527_POSITIVE 160 156 115 68 26 smit:SMT_1640|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1625989..1626139_NEGATIVE 160 151 119 151 103 smit:SMT_559|3end_D-alanyl-D-alanine_carboxypeptidase_476801..476951_NEGATIVE 159 51 11 65 28 smit:SMT_679|3end_LicC_protein_588383..588533_NEGATIVE 158 150 119 25 4 smit:SMT_1876|3end_transcriptional_regulator,_MarR_family_1834135..1834285_POSITIVE 158 97 53 94 40 smit:SMT_1253|3end_beta-galactosidase_1212912..1213062_NEGATIVE 157 73 33 76 32 smit:SMT_1555|3end_hypothetical_protein_1540223..1540373_NEGATIVE 150 150 104 85 41 smit:SMT_1250|3end_hypothetical_protein_1210788..1210938_NEGATIVE