Origin IGS: gtttttgtcctcctgatatttaagataaaaatattttataactaattagtgatatatacaaaaatgatgctcatcctatttgtccatctgtatgaaataggatgactgtcgtcagcatggctttgccatggtcgaaagagacttccaaagagcatcgtcaccaaaataccataccaaaagccccagaaaaatctgaggcttagtattattatcaagattcgttagaaagc .........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 gctttctaacgaatcttgataataatactaagcctcagatttttctggggcttttggtatggtattttggtgacgatgctctttggaagtctctttcgaccatggcaaagccatgctgacgacagtcatcctatttcatacagatggacaaataggatgagcatcatttttgtatatatcactaattagttataaaatatttttatcttaaatatcaggaggacaaaaac Mask Tandem Repeat Region ================================================ gtttttgtcctcctgatatttaagataaaaatattttataactaattagtgatatatacaaaaatgatgctcatcctatttgtccatctgtatgaaataggatgactgtcgtcagcatggctttgccatggtcgaaagagacttccaaagagcatcgtcaccaaaataccataccaaaagccccagaaaaatctgaggcttagtattattatcaagattcgttagaaagc Find is-nt database================================================ Query_seq: SSA_2106:SSA_2107|SSA_2106:SSA_2107:Flavin monoxygenase, putative:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing], putative:<-<-:2109155..2109384 230 gtttttgtcctcctgatatttaagataaaaatattttataactaattagtgatatatacaaaaatgatgctcatcctatttgtccatctgtatgaaataggatgactgtcgtcagcatggctttgccatggtcgaaagagacttccaaagagcatcgtcaccaaaataccataccaaaagccccagaaaaatctgaggcttagtattattatcaagattcgttagaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2106:SSA_2107|SSA_2106:SSA_2107:Flavin monoxygenase, putative:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing], putative:<-<-:2109155..2109384 230 gtttttgtcctcctgatatttaagataaaaatattttataactaattagtgatatatacaaaaatgatgctcatcctatttgtccatctgtatgaaataggatgactgtcgtcagcatggctttgccatggtcgaaagagacttccaaagagcatcgtcaccaaaataccataccaaaagccccagaaaaatctgaggcttagtattattatcaagattcgttagaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2106:SSA_2107|SSA_2106:SSA_2107:Flavin monoxygenase, putative:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing], putative:<-<-:2109155..2109384 230 gtttttgtcctcctgatatttaagataaaaatattttataactaattagtgatatatacaaaaatgatgctcatcctatttgtccatctgtatgaaataggatgactgtcgtcagcatggctttgccatggtcgaaagagacttccaaagagcatcgtcaccaaaataccataccaaaagccccagaaaaatctgaggcttagtattattatcaagattcgttagaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttttgtcctcctgatatttaagataaaaatattttataactaattagtgatatatacaaaaatgatgctcatcctatttgtccatctgtatgaaataggatgactgtcgtcagcatggctttgccatggtcgaaagagacttccaaagagcatcgtcaccaaaataccataccaaaagccccagaaaaatctgaggcttagtattattatcaagattcgttagaaagc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 102 End: 200 ..................................................................................................... M T V V S M A L P W S K E T S K E H R H Q N T I P K A P E K S E A .............................. Protein_Len: 39 Strand: + Start: 106 End: 222 ......................................................................................................... M S S A W L C H G R K R L P K S I V T K I P Y Q K P Q K N L R L S I I I K I R ........ Protein_Len: 58 Strand: - Start: 45 End: 218 ............................................ N T I Y V F I I S M R N T W R Y S I P H S D D A H S Q W P R F L S G F L M T V L I G Y W F G W F F R L S L I I I L M ............ gtttttgtcctcctgatatttaagataaaaatattttataactaattagtgatatatacaaaaatgatgctcatcctatttgtccatctgtatgaaataggatgactgtcgtcagcatggctttgccatggtcgaaagagacttccaaagagcatcgtcaccaaaataccataccaaaagccccagaaaaatctgaggcttagtattattatcaagattcgttagaaagc 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: 33 End: 62 ................................TTTGTATATATCACTAATTAGTTATAAAAT........................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttttgtcctcctgatatttaagataaaaatattttataactaattagtgatatatacaaaaatgatgctcatcctatttgtccatctgtatgaaataggatgactgtcgtcagcatggctttgccatggtcgaaagagacttccaaagagcatcgtcaccaaaataccataccaaaagccccagaaaaatctgaggcttagtattattatcaagattcgttagaaagc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2106:SSA_2107|SSA_2106:SSA_2107:Flavin monoxygenase, putative:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing], putative:<-<-:2109155..2109384 230 gtttttgtcctcctgatatttaagataaaaatattttataactaattagtgatatatacaaaaatgatgctcatcctatttgtccatctgtatgaaataggatgactgtcgtcagcatggctttgccatggtcgaaagagacttccaaagagcatcgtcaccaaaataccataccaaaagccccagaaaaatctgaggcttagtattattatcaagattcgttagaaagc Intra-Species Hit: Count: 1 Min: 1 Max: 230 Len: 230 Subject: NC_009009_SSA_2106_SSA_2107|Flavin monoxygenase, putative:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing], putative|NEGATIVE:NEGATIVE|[2109155,2109384]|230 HSP 1 e-value: 1.0E-127 bit: 456.0 Len: 230 Query Start:1 Query End:230 Subject Strand: POSITIVE Subject Start: 1 Subject End: 230 gtttttgtcctcctgatatttaagataaaaatattttataactaattagtgatatatacaaaaatgatgctcatcctatttgtccatctgtatgaaataggatgactgtcgtcagcatggctttgccatggtcgaaagagacttccaaagagcatcgtcaccaaaataccataccaaaagccccagaaaaatctgaggcttagtattattatcaagattcgttagaaagc gtttttgtcctcctgatatttaagataaaaatattttataactaattagtgatatatacaaaaatgatgctcatcctatttgtccatctgtatgaaataggatgactgtcgtcagcatggctttgccatggtcgaaagagacttccaaagagcatcgtcaccaaaataccataccaaaagccccagaaaaatctgaggcttagtattattatcaagattcgttagaaagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUGUCCUCCUGAUAUUUAAGAUAAAAAUAUUUUAUAACUAAUUAGUGAUAUAUACAAAAAUGAUGCUCAUCCUAUUUGUCCAUCUGUAUGAAAUAGGAUGACUGUCGUCAGCAUGGCUUUGCCAUGGUCGAAAGAGACUUCCAAAGAGCAUCGUCACCAAAAUACCAUACCAAAAGCCCCAGAAAAAUCUGAGGCUUAGUAUUAUUAUCAAGAUUCGUUAGAAAGC (((((((((..............))))))))).((((.((((.((((..(((((.((((....(((((((((.((((((((.............))))))))........(((..((((((...)))))).((....))))).......)))))))))...................(((((.((((....)))).))))).))))...))))).)))).)))).)))). (-57.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUUCUAACGAAUCUUGAUAAUAAUACUAAGCCUCAGAUUUUUCUGGGGCUUUUGGUAUGGUAUUUUGGUGACGAUGCUCUUUGGAAGUCUCUUUCGACCAUGGCAAAGCCAUGCUGACGACAGUCAUCCUAUUUCAUACAGAUGGACAAAUAGGAUGAGCAUCAUUUUUGUAUAUAUCACUAAUUAGUUAUAAAAUAUUUUUAUCUUAAAUAUCAGGAGGACAAAAAC ...(((....)))((((((((...(((((((((((((((....)))))))))..))))))........(((((.(((((((.(((((((...))))))).((((((...))))))..(((....))).(((((((((((....)))))...)))))).)))))))..(((((((..((........))..))))))).....))))).....)))))))).......... (-61.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 953 130 81 221 172 NC_009009:SSA_2106|5end_Flavin_monoxygenase,_putative_2109064..2109294_NEGATIVE 342 170 125 56 8 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 334 147 104 108 64 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 327 138 106 231 198 NC_009009:SSA_0356|5end_Dipeptidase,_putative_349259..349489_POSITIVE 320 147 103 62 15 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 318 150 101 217 169 NC_009009:SSA_0047|5end_NAD(P)H_dehydrogenase_(Quinone),_putative_52850..53080_NEGATIVE 314 159 114 210 161 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 307 128 84 194 148 NC_009009:SSA_1499|5end_50S_ribosomal_protein_L35,_putative_1504357..1504587_NEGATIVE 305 198 151 58 9 NC_009009:SSA_1574|5end_Glycosyl_transferase,_family_1,_putative_1577930..1578160_NEGATIVE 305 147 106 157 114 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 302 131 98 224 187 NC_009009:SSA_0759|5end_Acetylglutamate_kinase,_putative_741841..742071_POSITIVE 302 159 111 203 142 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 301 153 111 182 142 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 299 145 101 192 151 NC_009009:SSA_2301|5end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2303268..2303498_NEGATIVE 298 150 103 174 139 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 297 159 111 201 156 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 296 157 111 59 12 NC_009009:SSA_0036|5end_Secreted_protein,_possible_function_in_cell-wall_metabolism_(amidase),_putative_43999..44229_NEGATIVE 295 159 112 157 108 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 294 158 112 61 15 NC_009009:SSA_1371|5end_FmtA-like_protein,_putative_1388832..1389062_NEGATIVE 294 164 123 219 183 NC_009009:SSA_0920|5end_hypothetical_protein_930896..931126_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 142 108 50 11 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 335 198 155 59 5 NC_009009:SSA_0422|3end_Phosphoglycerate_mutase_family_protein,_putative_420839..420989_POSITIVE 335 219 179 102 61 NC_009009:SSA_0377|3end_ABC-type_methionine_transporter,_permease_component,_putative_367218..367368_POSITIVE 334 147 104 82 38 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 320 147 101 142 86 NC_009009:SSA_1854|3end_Conserved_uncharacterized_protein_1849433..1849583_NEGATIVE 320 147 103 72 25 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 306 203 167 123 92 NC_009009:SSA_0149|3end_hypothetical_protein_143833..143983_POSITIVE 305 198 151 56 7 NC_009009:SSA_1575|3end_Glycosyl_transferase,_putative_1577932..1578082_NEGATIVE 298 137 106 151 119 NC_009009:SSA_0355|3end_DNA_mismatch_repair_protein,_putative_349260..349410_POSITIVE 297 159 111 146 101 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 293 138 94 149 106 NC_009009:SSA_2302|3end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2303304..2303454_NEGATIVE 293 127 83 150 97 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE 289 127 81 96 34 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 287 159 112 90 35 NC_009009:SSA_1324|3end_Ceramide_glucosyltransferase,_putative_1340428..1340578_NEGATIVE 284 128 88 149 102 NC_009009:SSA_0049|3end_Dihydroxyacetone_kinase_(Dak1),_putative_54681..54831_POSITIVE 282 130 86 112 59 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 281 165 121 139 89 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 277 188 147 76 30 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 276 147 102 128 87 NC_009009:SSA_1783|3end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1768102..1768252_NEGATIVE 276 134 108 151 109 NC_009009:SSA_0768|3end_Ribonucleoside-diphosphate_reductase_2,_beta_subunit,_putative_748136..748286_NEGATIVE