Origin IGS: aaaggaggggaaaccctcttttttgtgggggaaaaggcaataaaacatgctggcggaatatttccagagttatattaaaaagctttataaaattcaacttgtatgatattataggaaataaaaagagtgagagagaacgatttttcagaaataggcaacaaggctggtatcgatatcattttgaaagtgtagttaaacgaggaaagataat .........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 attatctttcctcgtttaactacactttcaaaatgatatcgataccagccttgttgcctatttctgaaaaatcgttctctctcactctttttatttcctataatatcatacaagttgaattttataaagctttttaatataactctggaaatattccgccagcatgttttattgccttttcccccacaaaaaagagggtttcccctccttt Mask Tandem Repeat Region ================================================ aaaggaggggaaaccctcttttttgtgggggaaaaggcaataaaacatgctggcggaatatttccagagttatattaaaaagctttataaaattcaacttgtatgatattataggaaataaaaagagtgagagagaacgatttttcagaaataggcaacaaggctggtatcgatatcattttgaaagtgtagttaaacgaggaaagataat Find is-nt database================================================ Query_seq: SMT_364:SMT_365|SMT_364:SMT_365:ribosome-binding factor A:hypothetical protein:->->:301414..301624 211 aaaggaggggaaaccctcttttttgtgggggaaaaggcaataaaacatgctggcggaatatttccagagttatattaaaaagctttataaaattcaacttgtatgatattataggaaataaaaagagtgagagagaacgatttttcagaaataggcaacaaggctggtatcgatatcattttgaaagtgtagttaaacgaggaaagataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_364:SMT_365|SMT_364:SMT_365:ribosome-binding factor A:hypothetical protein:->->:301414..301624 211 aaaggaggggaaaccctcttttttgtgggggaaaaggcaataaaacatgctggcggaatatttccagagttatattaaaaagctttataaaattcaacttgtatgatattataggaaataaaaagagtgagagagaacgatttttcagaaataggcaacaaggctggtatcgatatcattttgaaagtgtagttaaacgaggaaagataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_364:SMT_365|SMT_364:SMT_365:ribosome-binding factor A:hypothetical protein:->->:301414..301624 211 aaaggaggggaaaccctcttttttgtgggggaaaaggcaataaaacatgctggcggaatatttccagagttatattaaaaagctttataaaattcaacttgtatgatattataggaaataaaaagagtgagagagaacgatttttcagaaataggcaacaaggctggtatcgatatcattttgaaagtgtagttaaacgaggaaagataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaggaggggaaaccctcttttttgtgggggaaaaggcaataaaacatgctggcggaatatttccagagttatattaaaaagctttataaaattcaacttgtatgatattataggaaataaaaagagtgagagagaacgatttttcagaaataggcaacaaggctggtatcgatatcattttgaaagtgtagttaaacgaggaaagataat Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 60 End: 209 ........................................................... M S R V I L K S F I K F N L Y D I I G N K K S E R E R F F R N R Q Q G W Y R Y H F E S V V K R G K I .. Protein_Len: 34 Strand: - Start: 78 End: 179 ............................................................................. F A K Y F E V Q I I N Y S I F L T L S F S K E S I P L L A P I S I M ................................ Protein_Len: 49 Strand: - Start: 2 End: 148 . L L P F G R K Q P P F P L L V H Q R F I E L T I N F L K I F N L K Y S I I P F L F L S L S R N K M ............................................................... aaaggaggggaaaccctcttttttgtgggggaaaaggcaataaaacatgctggcggaatatttccagagttatattaaaaagctttataaaattcaacttgtatgatattataggaaataaaaagagtgagagagaacgatttttcagaaataggcaacaaggctggtatcgatatcattttgaaagtgtagttaaacgaggaaagataat 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: 82 Start: 83 End: 112 ..................................................................................CTTTATAAAATTCAACTTGTATGATATTAT................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaggaggggaaaccctcttttttgtgggggaaaaggcaataaaacatgctggcggaatatttccagagttatattaaaaagctttataaaattcaacttgtatgatattataggaaataaaaagagtgagagagaacgatttttcagaaataggcaacaaggctggtatcgatatcattttgaaagtgtagttaaacgaggaaagataat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_364:SMT_365|SMT_364:SMT_365:ribosome-binding factor A:hypothetical protein:->->:301414..301624 211 aaaggaggggaaaccctcttttttgtgggggaaaaggcaataaaacatgctggcggaatatttccagagttatattaaaaagctttataaaattcaacttgtatgatattataggaaataaaaagagtgagagagaacgatttttcagaaataggcaacaaggctggtatcgatatcattttgaaagtgtagttaaacgaggaaagataat Intra-Species Hit: Count: 1 Min: 1 Max: 211 Len: 211 Subject: smit_SMT_364_SMT_365|ribosome-binding factor A:hypothetical protein|POSITIVE:POSITIVE|[301414,301624]|211 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 211 Query Start:1 Query End:211 Subject Strand: POSITIVE Subject Start: 1 Subject End: 211 aaaggaggggaaaccctcttttttgtgggggaaaaggcaataaaacatgctggcggaatatttccagagttatattaaaaagctttataaaattcaacttgtatgatattataggaaataaaaagagtgagagagaacgatttttcagaaataggcaacaaggctggtatcgatatcattttgaaagtgtagttaaacgaggaaagataat aaaggaggggaaaccctcttttttgtgggggaaaaggcaataaaacatgctggcggaatatttccagagttatattaaaaagctttataaaattcaacttgtatgatattataggaaataaaaagagtgagagagaacgatttttcagaaataggcaacaaggctggtatcgatatcattttgaaagtgtagttaaacgaggaaagataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGGAGGGGAAACCCUCUUUUUUGUGGGGGAAAAGGCAAUAAAACAUGCUGGCGGAAUAUUUCCAGAGUUAUAUUAAAAAGCUUUAUAAAAUUCAACUUGUAUGAUAUUAUAGGAAAUAAAAAGAGUGAGAGAGAACGAUUUUUCAGAAAUAGGCAACAAGGCUGGUAUCGAUAUCAUUUUGAAAGUGUAGUUAAACGAGGAAAGAUAAU (((((((((....))))))))).............((((........)))).........(((((...(((..((((....(((((...........((((((......))))))........(((((((.......((((...((((.....(....)....)))).))))...))))))).))))).))))..)))..)))))...... (-42.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUCUUUCCUCGUUUAACUACACUUUCAAAAUGAUAUCGAUACCAGCCUUGUUGCCUAUUUCUGAAAAAUCGUUCUCUCUCACUCUUUUUAUUUCCUAUAAUAUCAUACAAGUUGAAUUUUAUAAAGCUUUUUAAUAUAACUCUGGAAAUAUUCCGCCAGCAUGUUUUAUUGCCUUUUCCCCCACAAAAAAGAGGGUUUCCCCUCCUUU .....((((....((((((((....((((((((((....(((((.......)))))..))))).)))))......................((((......)))).......)))))))).....)))).....(((((.(((.((((..........))))...))).)))))...................(((((....))))).... (-22.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 69 29 59 28 smit:SMT_111|5end_alpha-1,2-mannosidase,_putative_61304..61534_NEGATIVE 303 55 14 138 96 smit:SMT_1006|5end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_946599..946829_POSITIVE 302 48 4 228 171 smit:SMT_346|5end_K01992_ABC-2_type_transport_system_permease_protein_284720..284950_POSITIVE 274 50 3 200 137 smit:SMT_911|5end_hypothetical_protein_862023..862253_POSITIVE 271 59 13 76 21 smit:SMT_2026|5end_K03466_DNA_segregation_ATPase_FtsK/SpoIIIE,_S-DNA-T_family_1942432..1942662_NEGATIVE 268 68 25 223 185 smit:SMT_1037|5end_alpha-galactosidase_979609..979839_NEGATIVE 268 68 25 223 185 smit:SMT_1030|5end_alpha-galactosidase_967829..968059_NEGATIVE 259 203 161 174 131 smit:SMT_2002|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1924405..1924635_NEGATIVE 259 203 161 213 170 smit:SMT_1966|5end_DNA_polymerase_III_alpha_subunit_1897934..1898164_POSITIVE 259 203 161 174 131 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 259 203 161 214 171 smit:SMT_1926|5end_mevalonate_kinase_1867692..1867922_POSITIVE 259 203 161 195 152 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 255 24 1 137 112 smit:SMT_1045|5end_cochaperonin_GroES_987582..987812_NEGATIVE 254 163 128 65 20 smit:SMT_876|5end_hypothetical_protein_predicted_by_Glimmer/Critica_823502..823732_NEGATIVE 254 163 128 183 138 smit:SMT_875|5end_nitroreductase_family_protein_823384..823614_NEGATIVE 250 27 1 151 127 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 249 71 32 172 132 smit:SMT_2053|5end_hypothetical_membrane_associated_protein_1964422..1964652_NEGATIVE 249 26 1 182 152 smit:SMT_803|5end_peptidoglycan_N-acetylglucosamine_deacetylase_713796..714026_NEGATIVE 248 165 122 191 154 smit:SMT_1714|5end_hypothetical_membrane_spanning_protein_1701356..1701586_POSITIVE 246 169 126 44 5 smit:SMT_997|5end_integral_membrane_protein_938243..938473_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 55 14 138 96 smit:SMT_1005|3end_possible_aluminum_resistance_protein_946679..946829_POSITIVE 269 167 122 57 3 smit:SMT_974|3end_DNA-binding_response_regulator_922170..922320_NEGATIVE 261 56 14 51 19 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 255 24 1 81 56 smit:SMT_1046|3end_chaperonin_GroEL_987638..987788_NEGATIVE 250 27 1 95 71 smit:SMT_2045|3end_K+_transport_system,_NAD-binding_component_1956758..1956908_POSITIVE 250 27 1 95 71 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 249 26 1 94 64 smit:SMT_804|3end_S-adenosylmethionine_synthetase_713884..714034_NEGATIVE 240 40 15 50 19 smit:SMT_624|3end_K07584_hypothetical_protein_530090..530240_POSITIVE 238 196 154 41 4 smit:SMT_1813|3end_amino_acid_transporter_1788232..1788382_POSITIVE 237 58 15 80 39 smit:SMT_1931|3end_23S_rRNA_methyltransferase_1870796..1870946_NEGATIVE 236 178 131 61 6 smit:SMT_1488|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468982..1469132_POSITIVE 236 175 136 76 39 smit:SMT_97|3end_hypothetical_protein_29011..29161_POSITIVE 233 43 2 101 53 smit:SMT_91|3end_hypothetical_protein_22852..23002_POSITIVE 232 175 135 65 23 smit:SMT_1322|3end_K02075_zinc/manganese_transport_system_permease_protein_1292257..1292407_POSITIVE 232 165 124 90 48 smit:SMT_460|3end_6-phospho-beta-glucosidase_399338..399488_POSITIVE 231 156 121 50 18 smit:SMT_881|3end_peptidoglycan_branched_peptide_synthesis_protein,_alanine_adding_enzyme_828305..828455_NEGATIVE 229 55 13 59 19 smit:SMT_1250|3end_hypothetical_protein_1210788..1210938_NEGATIVE 229 28 1 87 57 smit:SMT_1081|3end_K06901_putative_MFS_transporter,_AGZA_family,_xanthine/uracil_permease_1018595..1018745_NEGATIVE 228 57 15 66 31 smit:SMT_123|3end_hypothetical_protein_75623..75773_POSITIVE 222 38 12 73 45 smit:SMT_1958|3end_tryptophan_synthase,_beta_subunit_1892052..1892202_POSITIVE