Origin IGS: aattacaccctctttctttagaatatccctattatagcataattataggcttatcacaaatttaattcacctgaatttccctaatttttcaataagctttagctaatatttatccgaagcctagctctgaaatccagcaaaaatccagctctcttcagagaactggatggaaacttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaagtttccatccagttctctgaagagagctggatttttgctggatttcagagctaggcttcggataaatattagctaaagcttattgaaaaattagggaaattcaggtgaattaaatttgtgataagcctataattatgctataatagggatattctaaagaaagagggtgtaatt Mask Tandem Repeat Region ================================================ aattacaccctctttctttagaatatccctattatagcataattataggcttatcacaaatttaattcacctgaatttccctaatttttcaataagctttagctaatatttatccgaagcctagctctgaaatccagcaaaaatccagctctcttcagagaactggatggaaacttc Find is-nt database================================================ Query_seq: SSA_2241:SSA_2242|SSA_2241:SSA_2242:Conserved uncharacterized protein:hypothetical protein:<-<-:2238034..2238210 177 aattacaccctctttctttagaatatccctattatagcataattataggcttatcacaaatttaattcacctgaatttccctaatttttcaataagctttagctaatatttatccgaagcctagctctgaaatccagcaaaaatccagctctcttcagagaactggatggaaacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2241:SSA_2242|SSA_2241:SSA_2242:Conserved uncharacterized protein:hypothetical protein:<-<-:2238034..2238210 177 aattacaccctctttctttagaatatccctattatagcataattataggcttatcacaaatttaattcacctgaatttccctaatttttcaataagctttagctaatatttatccgaagcctagctctgaaatccagcaaaaatccagctctcttcagagaactggatggaaacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2241:SSA_2242|SSA_2241:SSA_2242:Conserved uncharacterized protein:hypothetical protein:<-<-:2238034..2238210 177 aattacaccctctttctttagaatatccctattatagcataattataggcttatcacaaatttaattcacctgaatttccctaatttttcaataagctttagctaatatttatccgaagcctagctctgaaatccagcaaaaatccagctctcttcagagaactggatggaaacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattacaccctctttctttagaatatccctattatagcataattataggcttatcacaaatttaattcacctgaatttccctaatttttcaataagctttagctaatatttatccgaagcctagctctgaaatccagcaaaaatccagctctcttcagagaactggatggaaacttc Predict ORF larger than 30AA ================================================ aattacaccctctttctttagaatatccctattatagcataattataggcttatcacaaatttaattcacctgaatttccctaatttttcaataagctttagctaatatttatccgaagcctagctctgaaatccagcaaaaatccagctctcttcagagaactggatggaaacttc 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: 87 Start: 31 End: 60 ..............................TTTGTGATAAGCCTATAATTATGCTATAAT..................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 42 End: 71 .........................................GGTGAATTAAATTTGTGATAAGCCTATAAT.......................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattacaccctctttctttagaatatccctattatagcataattataggcttatcacaaatttaattcacctgaatttccctaatttttcaataagctttagctaatatttatccgaagcctagctctgaaatccagcaaaaatccagctctcttcagagaactggatggaaacttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2241:SSA_2242|SSA_2241:SSA_2242:Conserved uncharacterized protein:hypothetical protein:<-<-:2238034..2238210 177 aattacaccctctttctttagaatatccctattatagcataattataggcttatcacaaatttaattcacctgaatttccctaatttttcaataagctttagctaatatttatccgaagcctagctctgaaatccagcaaaaatccagctctcttcagagaactggatggaaacttc Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: NC_009009_SSA_2241_SSA_2242|Conserved uncharacterized protein:hypothetical protein|NEGATIVE:NEGATIVE|[2238034,2238210]|177 HSP 1 e-value: 5.0E-96 bit: 351.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 aattacaccctctttctttagaatatccctattatagcataattataggcttatcacaaatttaattcacctgaatttccctaatttttcaataagctttagctaatatttatccgaagcctagctctgaaatccagcaaaaatccagctctcttcagagaactggatggaaacttc aattacaccctctttctttagaatatccctattatagcataattataggcttatcacaaatttaattcacctgaatttccctaatttttcaataagctttagctaatatttatccgaagcctagctctgaaatccagcaaaaatccagctctcttcagagaactggatggaaacttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUACACCCUCUUUCUUUAGAAUAUCCCUAUUAUAGCAUAAUUAUAGGCUUAUCACAAAUUUAAUUCACCUGAAUUUCCCUAAUUUUUCAAUAAGCUUUAGCUAAUAUUUAUCCGAAGCCUAGCUCUGAAAUCCAGCAAAAAUCCAGCUCUCUUCAGAGAACUGGAUGGAAACUUC ..........(((......)))...(((........((........((((((((...(((((.(((((....))))).....)))))....)))))))).(((((...(((....)))...)))))..........))....((((((.((((....)))).)))))))))...... (-29.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGUUUCCAUCCAGUUCUCUGAAGAGAGCUGGAUUUUUGCUGGAUUUCAGAGCUAGGCUUCGGAUAAAUAUUAGCUAAAGCUUAUUGAAAAAUUAGGGAAAUUCAGGUGAAUUAAAUUUGUGAUAAGCCUAUAAUUAUGCUAUAAUAGGGAUAUUCUAAAGAAAGAGGGUGUAAUU .((((((..(((((((((((....))))))))))).....(((((((((..((((((.(....).......))))))....((.(((....))).)).))))))))).......))))))........(((((.((......)).))))).(((((((........))))))).... (-42.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 852 140 91 231 182 NC_009009:SSA_2241|5end_Conserved_uncharacterized_protein_2237943..2238173_NEGATIVE 357 158 121 62 30 NC_009009:SSA_0835|5end_Accessory_secretory_protein_Asp3,_putative_821036..821266_POSITIVE 318 155 113 172 128 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 314 170 121 154 102 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 307 159 113 197 147 NC_009009:SSA_1483|5end_Sphingosine_kinase_(diacylglycerol_kinase),_putative_1490220..1490450_NEGATIVE 301 155 114 69 27 NC_009009:SSA_0312|5end_Hydrolase,_metallo-beta-lactamase_superfamily,_putative_308385..308615_NEGATIVE 298 158 113 209 152 NC_009009:SSA_0925|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_934749..934979_POSITIVE 297 156 114 200 152 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 296 166 121 206 157 NC_009009:SSA_2103|5end_hypothetical_protein_2106700..2106930_NEGATIVE 296 129 90 54 3 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 295 138 95 64 20 NC_009009:SSA_1325|5end_Ketoacyl_reductase_hetN,_putative_1342343..1342573_NEGATIVE 294 159 114 213 167 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 292 139 95 65 26 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 292 149 102 73 28 NC_009009:SSA_0858|5end_DTDP-L-rhamnose_synthase,_putative_845512..845742_POSITIVE 282 160 114 47 1 NC_009009:SSA_0677|5end_rRNA_methylase,_putative_659466..659696_POSITIVE 281 170 123 204 144 NC_009009:SSA_1801|5end_hypothetical_protein_1783314..1783544_NEGATIVE 279 165 121 56 5 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 277 170 121 66 22 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 277 157 113 65 2 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 276 160 118 178 130 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 158 121 65 33 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 324 151 115 75 41 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 302 169 122 83 38 NC_009009:SSA_1041|3end_Sugar_ABC_transporter,_permease_protein,_putative_1057434..1057584_POSITIVE 301 155 114 65 23 NC_009009:SSA_0313|3end_Conserved_uncharacterized_protein_308389..308539_NEGATIVE 299 170 123 125 79 NC_009009:SSA_1972|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1967811..1967961_NEGATIVE 297 156 114 64 16 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 296 166 121 150 101 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 293 89 43 140 91 NC_009009:SSA_1484|3end_DNA_ligase,_putative_1490230..1490380_NEGATIVE 289 169 123 60 11 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 282 160 114 54 8 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 282 160 117 146 98 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 281 170 123 149 89 NC_009009:SSA_1802|3end_Snf2_family_protein,_putative_1783369..1783519_NEGATIVE 275 168 122 85 38 NC_009009:SSA_1840|3end_RNA_binding_protein,_putative_1834060..1834210_NEGATIVE 275 158 112 66 30 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 267 166 121 77 40 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE 264 153 113 111 69 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 259 169 123 112 56 NC_009009:SSA_2166|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2163873..2164023_NEGATIVE 257 157 120 142 96 NC_009009:SSA_0865|3end_hypothetical_protein_856850..857000_POSITIVE 255 149 101 72 25 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 254 150 103 145 96 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE