Origin IGS: atcttacttattatatcacattcaaaagcaaaaaaaaatttaaaagaaaaagtaagcggatgaaatcctttttaaatttttttgtcagatatacttgacactttttccaaaaagtattatactagcataaaataaaagtcaaatataactgacaaacttgttgaaagttatcagttatagtattagaaaggaagggtgta .........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 tacacccttcctttctaatactataactgataactttcaacaagtttgtcagttatatttgacttttattttatgctagtataatactttttggaaaaagtgtcaagtatatctgacaaaaaaatttaaaaaggatttcatccgcttactttttcttttaaatttttttttgcttttgaatgtgatataataagtaagat Mask Tandem Repeat Region ================================================ atcttacttattatatcacattcaaaagcaaaaaaaaatttaaaagaaaaagtaagcggatgaaatcctttttaaatttttttgtcagatatacttgacactttttccaaaaagtattatactagcataaaataaaagtcaaatataactgacaaacttgttgaaagttatcagttatagtattagaaaggaagggtgta Find is-nt database================================================ Query_seq: SSA_1873:SSA_1874|SSA_1873:SSA_1874:S-adenosyl-methyltransferase mraW, putative:YorfE protein, putative:<-->:1870235..1870434 200 atcttacttattatatcacattcaaaagcaaaaaaaaatttaaaagaaaaagtaagcggatgaaatcctttttaaatttttttgtcagatatacttgacactttttccaaaaagtattatactagcataaaataaaagtcaaatataactgacaaacttgttgaaagttatcagttatagtattagaaaggaagggtgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1873:SSA_1874|SSA_1873:SSA_1874:S-adenosyl-methyltransferase mraW, putative:YorfE protein, putative:<-->:1870235..1870434 200 atcttacttattatatcacattcaaaagcaaaaaaaaatttaaaagaaaaagtaagcggatgaaatcctttttaaatttttttgtcagatatacttgacactttttccaaaaagtattatactagcataaaataaaagtcaaatataactgacaaacttgttgaaagttatcagttatagtattagaaaggaagggtgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1873:SSA_1874|SSA_1873:SSA_1874:S-adenosyl-methyltransferase mraW, putative:YorfE protein, putative:<-->:1870235..1870434 200 atcttacttattatatcacattcaaaagcaaaaaaaaatttaaaagaaaaagtaagcggatgaaatcctttttaaatttttttgtcagatatacttgacactttttccaaaaagtattatactagcataaaataaaagtcaaatataactgacaaacttgttgaaagttatcagttatagtattagaaaggaagggtgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcttacttattatatcacattcaaaagcaaaaaaaaatttaaaagaaaaagtaagcggatgaaatcctttttaaatttttttgtcagatatacttgacactttttccaaaaagtattatactagcataaaataaaagtcaaatataactgacaaacttgttgaaagttatcagttatagtattagaaaggaagggtgta Predict ORF larger than 30AA ================================================ atcttacttattatatcacattcaaaagcaaaaaaaaatttaaaagaaaaagtaagcggatgaaatcctttttaaatttttttgtcagatatacttgacactttttccaaaaagtattatactagcataaaataaaagtcaaatataactgacaaacttgttgaaagttatcagttatagtattagaaaggaagggtgta 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: 90 Start: 94 End: 123 .............................................................................................CTTGACACTTTTTCCAAAAAGTATTATACT............................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 10 End: 39 .........ATTTTTTTTTGCTTTTGAATGTGATATAAT................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcttacttattatatcacattcaaaagcaaaaaaaaatttaaaagaaaaagtaagcggatgaaatcctttttaaatttttttgtcagatatacttgacactttttccaaaaagtattatactagcataaaataaaagtcaaatataactgacaaacttgttgaaagttatcagttatagtattagaaaggaagggtgta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -5.4 Tail_Score: -4.97888 Start: 58 End: 68 Full_Region: AAAGAAAAAGTAAGC GGAT GAA ATCC TTTTTAAATTTTTTT .........................................................GGATGAAATCC.................................................................................................................................... TransTerm Strand: + Conf: 39 HP_score: -2.5 Tail_Score: -2.73875 Start: 146 End: 177 Full_Region: AATAAAAGTCAAATA TAACTGACAAACTT GTTGA AAGTTATCAGTTA TAGTATTAGAAAGGA .................................................................................................................................................TAACTGACAAACTTGTTGAAAGTTATCAGTTA....................... Find igs database================================================ Query_seq: SSA_1873:SSA_1874|SSA_1873:SSA_1874:S-adenosyl-methyltransferase mraW, putative:YorfE protein, putative:<-->:1870235..1870434 200 atcttacttattatatcacattcaaaagcaaaaaaaaatttaaaagaaaaagtaagcggatgaaatcctttttaaatttttttgtcagatatacttgacactttttccaaaaagtattatactagcataaaataaaagtcaaatataactgacaaacttgttgaaagttatcagttatagtattagaaaggaagggtgta Intra-Species Hit: Count: 1 Min: 52 Max: 200 Len: 149 Subject: NC_009009_SSA_1873_SSA_1874|S-adenosyl-methyltransferase mraW, putative:YorfE protein, putative|NEGATIVE:POSITIVE|[1870235,1870434]|200 HSP 1 e-value: 1.0E-66 bit: 254.0 Len: 149 Query Start:52 Query End:200 Subject Strand: POSITIVE Subject Start: 52 Subject End: 200 ...................................................gtaagcggatgaaatcctttttaaannnnnnngtcagatatacttgacactttttccaaaaagtattatactagcataaaataaaagtcaaatataactgacaaacttgttgaaagttatcagttatagtattagaaaggaagggtgta ...................................................gtaagcggatgaaatcctttttaaatttttttgtcagatatacttgacactttttccaaaaagtattatactagcataaaataaaagtcaaatataactgacaaacttgttgaaagttatcagttatagtattagaaaggaagggtgta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAGCGGAUGAAAUCCUUUUUAAAUUUUUUUGUCAGAUAUACUUGACACUUUUUCCAAAAAGUAUUAUACUAGCAUAAAAUAAAAGUCAAAUAUAACUGACAAACUUGUUGAAAGUUAUCAGUUAUAGUAUUAGAAAGGAAGGGUGUA ..............((((((((((..((((.((..((((((((((...............))))).))).))..)).))))...........(((((((((..(((((.....))))).)))))))))...))))))))))........ (-28.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACACCCUUCCUUUCUAAUACUAUAACUGAUAACUUUCAACAAGUUUGUCAGUUAUAUUUGACUUUUAUUUUAUGCUAGUAUAAUACUUUUUGGAAAAAGUGUCAAGUAUAUCUGACAAAAAAAUUUAAAAAGGAUUUCAUCCGCUUAC ........((((((.(((.........(((......))).....((((((((.((((((((((.(((.(((((....((((...))))...))))).))).)))))))))).)))))))).....))).)))))).............. (-31.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 742 50 1 192 143 NC_009009:SSA_1873|5end_S-adenosyl-methyltransferase_mraW,_putative_1870144..1870374_NEGATIVE 242 70 26 183 141 NC_009009:SSA_2231|5end_Heme/copper-type_cytochrome/quinol_oxidases,_subunit_1,_putative_2232928..2233158_NEGATIVE 227 76 31 140 85 NC_009009:SSA_0172|5end_Transcriptional_regulator,_XRE_family,_putative_169140..169370_POSITIVE 214 47 4 41 4 NC_009009:SSA_2247|5end_hypothetical_protein_2242645..2242875_POSITIVE 214 82 44 153 103 NC_009009:SSA_0575|5end_Hydrolase,_HAD_superfamily,_putative_569527..569757_POSITIVE 213 30 3 31 3 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 213 30 3 166 138 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 207 49 3 68 23 NC_009009:SSA_1229|5end_hypothetical_protein_1252421..1252651_NEGATIVE 207 49 3 192 147 NC_009009:SSA_1227|5end_Aminoglycoside_adenylyltransferase,_putative_1252297..1252527_NEGATIVE 207 56 15 132 99 NC_009009:SSA_1109|5end_ABC_transporter_ATP_binding/permease_protein,_putative_1133718..1133948_POSITIVE 206 47 10 212 176 NC_009009:SSA_1717|5end_Modification_methylase_DpnIIB,_putative_1704958..1705188_NEGATIVE 197 140 106 32 2 NC_009009:SSA_0638|5end_Tryptophan_synthase_alpha_chain,_putative_626935..627165_POSITIVE 192 140 106 194 159 NC_009009:SSA_0264|5end_PEP_phosphonomutase-like_protein,_putative_258400..258630_POSITIVE 191 65 28 63 13 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 191 36 4 56 24 NC_009009:SSA_1579|5end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1582851..1583081_POSITIVE 191 45 4 218 172 NC_009009:SSA_1484|5end_DNA_ligase,_putative_1492188..1492418_NEGATIVE 190 36 1 90 49 NC_009009:SSA_0704|5end_Isocitrate_dehydrogenase_[NADP],_putative_689274..689504_POSITIVE 189 59 11 104 40 NC_009009:SSA_1857|5end_Conserved_DivIVA-like_protein,_putative_1853087..1853317_NEGATIVE 189 56 16 106 73 NC_009009:SSA_1727|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713420..1713650_NEGATIVE 187 36 6 50 19 NC_009009:SSA_1975|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1971132..1971362_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 70 26 144 102 NC_009009:SSA_2233|3end_hypothetical_protein_2232967..2233117_NEGATIVE 232 127 98 108 79 NC_009009:SSA_0252|3end_hypothetical_protein_245042..245192_NEGATIVE 213 30 3 31 3 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 213 30 3 132 104 NC_009009:SSA_1412|3end_hypothetical_protein_1423994..1424144_NEGATIVE 207 56 15 118 85 NC_009009:SSA_1107|3end_Lipid/multidrug/protein-type_ABC_exporter,_ATP_binding/membrane-spanning_protein,_putative_1133784..1133934_POSITIVE 202 46 4 143 104 NC_009009:SSA_1646|3end_hypothetical_protein_1646322..1646472_NEGATIVE 198 139 94 53 11 NC_009009:SSA_0613|3end_Glucosyltransferase,_putative_606633..606783_POSITIVE 197 140 106 39 9 NC_009009:SSA_0637|3end_Tryptophan_synthase_beta_chain,_putative_627022..627172_POSITIVE 195 58 13 120 77 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE 194 58 14 111 75 NC_009009:SSA_1907|3end_hypothetical_protein_1900813..1900963_POSITIVE 193 35 5 130 102 NC_009009:SSA_1382|3end_hypothetical_protein_1399797..1399947_NEGATIVE 191 65 28 70 20 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 191 36 4 54 22 NC_009009:SSA_1578|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1582929..1583079_POSITIVE 191 45 4 112 66 NC_009009:SSA_1485|3end_Citrulline_cluster-linked_gene,_putative_1492294..1492444_NEGATIVE 190 36 1 88 47 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 189 56 16 102 69 NC_009009:SSA_1728|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713424..1713574_NEGATIVE 186 49 1 65 15 NC_009009:SSA_0193|3end_CAAX_amino_terminal_protease_family_protein,_putative_195075..195225_POSITIVE 182 129 102 140 118 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 181 60 15 133 80 NC_009009:SSA_2303|3end_hypothetical_protein_2304113..2304263_NEGATIVE 181 64 26 109 75 NC_009009:SSA_2269|3end_hypothetical_protein_2269392..2269542_NEGATIVE