Origin IGS: gatgaagattattgtacctgcaacccgtgccaatatcgggccaggttttgnnnnnttaattaattaannnnngctggaaagaatagaaataatattgaagaagctttgaaagatttttatgat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcataaaaatctttcaaagcttcttcaatattatttctattctttccagcnnnnnttaattaattaannnnncaaaacctggcccgatattggcacgggttgcaggtacaataatcttcatc Mask Tandem Repeat Region ================================================ gatgaagattattgtacctgcaacccgtgccaatatcgggccaggttttgnnnnnttaattaattaannnnngctggaaagaatagaaataatattgaagaagctttgaaagatttttatgat Find is-nt database================================================ Query_seq: SMT_1934:SMT_1935|SMT_1934:SMT_1935:homoserine dehydrogenase:hypothetical protein predicted by Glimmer/Critica:->->:1873211..1873333 123 gatgaagattattgtacctgcaacccgtgccaatatcgggccaggttttgnnnnnttaattaattaannnnngctggaaagaatagaaataatattgaagaagctttgaaagatttttatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1934:SMT_1935|SMT_1934:SMT_1935:homoserine dehydrogenase:hypothetical protein predicted by Glimmer/Critica:->->:1873211..1873333 123 gatgaagattattgtacctgcaacccgtgccaatatcgggccaggttttgnnnnnttaattaattaannnnngctggaaagaatagaaataatattgaagaagctttgaaagatttttatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1934:SMT_1935|SMT_1934:SMT_1935:homoserine dehydrogenase:hypothetical protein predicted by Glimmer/Critica:->->:1873211..1873333 123 gatgaagattattgtacctgcaacccgtgccaatatcgggccaggttttgnnnnnttaattaattaannnnngctggaaagaatagaaataatattgaagaagctttgaaagatttttatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgaagattattgtacctgcaacccgtgccaatatcgggccaggttttgnnnnnttaattaattaannnnngctggaaagaatagaaataatattgaagaagctttgaaagatttttatgat Predict ORF larger than 30AA ================================================ gatgaagattattgtacctgcaacccgtgccaatatcgggccaggttttgnnnnnttaattaattaannnnngctggaaagaatagaaataatattgaagaagctttgaaagatttttatgat 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: 83 Start: 94 End: 123 .............................................................................................ATTGAAGAAGCTTTGAAAGATTTTTATGAT Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: - Score: 82 Start: 28 End: 44 ...........................CTGGCCCGATATTGGCA............................................................................... gatgaagattattgtacctgcaacccgtgccaatatcgggccaggttttgnnnnnttaattaattaannnnngctggaaagaatagaaataatattgaagaagctttgaaagatttttatgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1934:SMT_1935|SMT_1934:SMT_1935:homoserine dehydrogenase:hypothetical protein predicted by Glimmer/Critica:->->:1873211..1873333 123 gatgaagattattgtacctgcaacccgtgccaatatcgggccaggttttgnnnnnttaattaattaannnnngctggaaagaatagaaataatattgaagaagctttgaaagatttttatgat Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: smit_SMT_1934_SMT_1935|homoserine dehydrogenase:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[1873211,1873333]|123 HSP 1 e-value: 4.0E-46 bit: 184.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 gatgaagattattgtacctgcaacccgtgccaatatcgggccaggttttgnnnnnttaattaattaannnnngctggaaagaatagaaataatattgaagaagctttgaaagatttttatgat gatgaagattattgtacctgcaacccgtgccaatatcgggccaggttttgnnnnnttaattaattaannnnngctggaaagaatagaaataatattgaagaagctttgaaagatttttatgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAAGAUUAUUGUACCUGCAACCCGUGCCAAUAUCGGGCCAGGUUUUGNNNNNUUAAUUAAUUAANNNNNGCUGGAAAGAAUAGAAAUAAUAUUGAAGAAGCUUUGAAAGAUUUUUAUGAU .(((((((((.....(((((...((((.........)))).)))))..........................(((......((((.......)))).....))).......)))))))))... (-17.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUAAAAAUCUUUCAAAGCUUCUUCAAUAUUAUUUCUAUUCUUUCCAGCNNNNNUUAAUUAAUUAANNNNNCAAAACCUGGCCCGAUAUUGGCACGGGUUGCAGGUACAAUAAUCUUCAUC .............................................................................((((((((((.........)))))..)))))............... (-13.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 50 17 191 150 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 273 44 2 61 23 smit:SMT_426|5end_hypothetical_protein_368344..368574_POSITIVE 270 45 12 41 3 smit:SMT_814|5end_UDP-N-acetyl_muramate-alanine_ligase_723666..723896_NEGATIVE 262 48 2 191 137 smit:SMT_946|5end_hypothetical_protein_896409..896639_NEGATIVE 260 44 6 215 174 smit:SMT_1788|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1765029..1765259_NEGATIVE 254 50 12 54 7 smit:SMT_1529|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1512880..1513110_NEGATIVE 254 48 6 43 1 smit:SMT_599|5end_glucosamine-1-phosphate_N-acetyltransferase_/_UDP-N-acetylglucosamine_pyrophosphorylase_514918..515148_POSITIVE 253 50 12 212 167 smit:SMT_1675|5end_adenylosuccinate_synthetase_1661147..1661377_NEGATIVE 253 46 6 197 158 smit:SMT_563|5end_thioredoxin_reductase_480988..481218_POSITIVE 253 43 17 213 174 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 252 47 5 52 9 smit:SMT_1749|5end_anthranilate_synthase_component_II_1727434..1727664_POSITIVE 251 49 18 154 124 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 248 46 13 69 20 smit:SMT_2010|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1929514..1929744_POSITIVE 247 48 1 175 114 smit:SMT_1897|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1848858..1849088_NEGATIVE 247 45 2 191 145 smit:SMT_1129|5end_hypothetical_protein_1063926..1064156_NEGATIVE 240 48 1 68 16 smit:SMT_761|5end_prephenate_dehydrogenase_667150..667380_NEGATIVE 240 48 1 68 16 smit:SMT_752|5end_prephenate_dehydrogenase_656791..657021_NEGATIVE 239 45 17 59 34 smit:SMT_414|5end_K03665_GTP-binding_protein_HflX_357554..357784_POSITIVE 237 46 1 226 181 smit:SMT_1646|5end_3-isopropylmalate_dehydratase_large_subunit_1632011..1632241_POSITIVE 236 49 26 194 167 smit:SMT_1190|5end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1148232..1148462_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 44 1 123 76 smit:SMT_890|3end_K02029_polar_amino_acid_transport_system_permease_protein_837692..837842_POSITIVE 273 44 2 61 23 smit:SMT_425|3end_hypothetical_cytosolic_protein_368424..368574_POSITIVE 268 50 3 79 29 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 255 46 14 68 25 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE 252 47 5 55 12 smit:SMT_1748|3end_anthranilate_synthase_component_I_1727517..1727667_POSITIVE 251 49 18 141 111 smit:SMT_795|3end_similar_to_O6-alkylguanine-DNA-alkyltransferase_703500..703650_NEGATIVE 245 50 11 82 38 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 240 48 1 58 6 smit:SMT_753|3end_chorismate_synthase_656801..656951_NEGATIVE 239 45 17 66 41 smit:SMT_413|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_357641..357791_POSITIVE 234 45 19 30 1 smit:SMT_815|3end_hypothetical_protein_723677..723827_NEGATIVE 233 44 1 149 95 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 231 89 56 51 17 smit:SMT_1740|3end_choline_binding_protein_PcpA_1721674..1721824_NEGATIVE 231 46 15 37 3 smit:SMT_1444|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1427887..1428037_NEGATIVE 230 50 6 61 13 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 230 49 16 63 29 smit:SMT_1862|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1825460..1825610_POSITIVE 225 45 1 133 82 smit:SMT_1303|3end_tRNA-dihydrouridine_synthase_1264676..1264826_NEGATIVE 221 43 12 45 13 smit:SMT_785|3end_hypothetical_protein_696307..696457_NEGATIVE 216 44 16 71 34 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 216 46 1 138 88 smit:SMT_485|3end_hypothetical_protein_420229..420379_NEGATIVE 214 50 18 35 5 smit:SMT_968|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_913299..913449_NEGATIVE