Origin IGS: tattaaggtctcttttctttatttttttcttttggtgaaatagcaaagctattaagcacatgttctattatagcagattaaaaatagctgtcaagtttttttcttgacagagttaaaaattttttagctatgtcttttcaccttaaaaacgcaatgcgtttttactagcttactcgatataaatatatttaagagaaaacaaggcaaggatttttttcatttgcagtctcc .........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 ggagactgcaaatgaaaaaaatccttgccttgttttctcttaaatatatttatatcgagtaagctagtaaaaacgcattgcgtttttaaggtgaaaagacatagctaaaaaatttttaactctgtcaagaaaaaaacttgacagctatttttaatctgctataatagaacatgtgcttaatagctttgctatttcaccaaaagaaaaaaataaagaaaagagaccttaata Mask Tandem Repeat Region ================================================ tattaaggtctcttttctttatttttttcttttggtgaaatagcaaagctattaagcacatgttctattatagcagattaaaaatagctgtcaagtttttttcttgacagagttaaaaattttttagctatgtcttttcaccttaaaaacgcaatgcgtttttactagcttactcgatataaatatatttaagagaaaacaaggcaaggatttttttcatttgcagtctcc Find is-nt database================================================ Query_seq: SSA_1310:SSA_1311|SSA_1310:SSA_1311:30S ribosomal protein S16, putative:Hydrolase, haloacid dehalogenase-like family, putative:<-<-:1327701..1327931 231 tattaaggtctcttttctttatttttttcttttggtgaaatagcaaagctattaagcacatgttctattatagcagattaaaaatagctgtcaagtttttttcttgacagagttaaaaattttttagctatgtcttttcaccttaaaaacgcaatgcgtttttactagcttactcgatataaatatatttaagagaaaacaaggcaaggatttttttcatttgcagtctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1310:SSA_1311|SSA_1310:SSA_1311:30S ribosomal protein S16, putative:Hydrolase, haloacid dehalogenase-like family, putative:<-<-:1327701..1327931 231 tattaaggtctcttttctttatttttttcttttggtgaaatagcaaagctattaagcacatgttctattatagcagattaaaaatagctgtcaagtttttttcttgacagagttaaaaattttttagctatgtcttttcaccttaaaaacgcaatgcgtttttactagcttactcgatataaatatatttaagagaaaacaaggcaaggatttttttcatttgcagtctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1310:SSA_1311|SSA_1310:SSA_1311:30S ribosomal protein S16, putative:Hydrolase, haloacid dehalogenase-like family, putative:<-<-:1327701..1327931 231 tattaaggtctcttttctttatttttttcttttggtgaaatagcaaagctattaagcacatgttctattatagcagattaaaaatagctgtcaagtttttttcttgacagagttaaaaattttttagctatgtcttttcaccttaaaaacgcaatgcgtttttactagcttactcgatataaatatatttaagagaaaacaaggcaaggatttttttcatttgcagtctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattaaggtctcttttctttatttttttcttttggtgaaatagcaaagctattaagcacatgttctattatagcagattaaaaatagctgtcaagtttttttcttgacagagttaaaaattttttagctatgtcttttcaccttaaaaacgcaatgcgtttttactagcttactcgatataaatatatttaagagaaaacaaggcaaggatttttttcatttgcagtctcc Predict ORF larger than 30AA ================================================ tattaaggtctcttttctttatttttttcttttggtgaaatagcaaagctattaagcacatgttctattatagcagattaaaaatagctgtcaagtttttttcttgacagagttaaaaattttttagctatgtcttttcaccttaaaaacgcaatgcgtttttactagcttactcgatataaatatatttaagagaaaacaaggcaaggatttttttcatttgcagtctcc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattaaggtctcttttctttatttttttcttttggtgaaatagcaaagctattaagcacatgttctattatagcagattaaaaatagctgtcaagtttttttcttgacagagttaaaaattttttagctatgtcttttcaccttaaaaacgcaatgcgtttttactagcttactcgatataaatatatttaagagaaaacaaggcaaggatttttttcatttgcagtctcc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 59 HP_score: -4.3 Tail_Score: -4.02905 Start: 87 End: 111 Full_Region: taaaaaatttttaac tctgtcaag aaaaaaa cttgacagc tatttttaatctgct ......................................................................................tctgtcaagaaaaaaacttgacagc........................................................................................................................ TransTerm Strand: - Conf: 67 HP_score: -7.8 Tail_Score: -3.00658 Start: 88 End: 110 Full_Region: aaaaaatttttaact ctgtcaag aaaaaaa cttgacag ctatttttaatctgc .......................................................................................ctgtcaagaaaaaaacttgacag......................................................................................................................... TransTerm Strand: + Conf: 80 HP_score: -8.3 Tail_Score: -4.19238 Start: 106 End: 134 Full_Region: TCAAGTTTTTTTCTT GACAGAGTTAAAA ATT TTTTAGCTATGTC TTTTCACCTTAAAAA .........................................................................................................GACAGAGTTAAAAATTTTTTAGCTATGTC................................................................................................. Find igs database================================================ Query_seq: SSA_1310:SSA_1311|SSA_1310:SSA_1311:30S ribosomal protein S16, putative:Hydrolase, haloacid dehalogenase-like family, putative:<-<-:1327701..1327931 231 tattaaggtctcttttctttatttttttcttttggtgaaatagcaaagctattaagcacatgttctattatagcagattaaaaatagctgtcaagtttttttcttgacagagttaaaaattttttagctatgtcttttcaccttaaaaacgcaatgcgtttttactagcttactcgatataaatatatttaagagaaaacaaggcaaggatttttttcatttgcagtctcc Intra-Species Hit: Count: 1 Min: 34 Max: 210 Len: 177 Subject: NC_009009_SSA_1310_SSA_1311|30S ribosomal protein S16, putative:Hydrolase, haloacid dehalogenase-like family, putative|NEGATIVE:NEGATIVE|[1327701,1327931]|231 HSP 1 e-value: 2.0E-83 bit: 309.0 Len: 177 Query Start:34 Query End:210 Subject Strand: POSITIVE Subject Start: 34 Subject End: 210 .................................ggtgaaatagcaaagctattaagcacatgttctattatagcagattaaaaatagctgtcaagnnnnnnncttgacagagttaaaaattttttagctatgtcttttcaccttaaaaacgcaatgcgtttttactagcttactcgatataaatatatttaagagaaaacaaggcaagga..................... .................................ggtgaaatagcaaagctattaagcacatgttctattatagcagattaaaaatagctgtcaagtttttttcttgacagagttaaaaattttttagctatgtcttttcaccttaaaaacgcaatgcgtttttactagcttactcgatataaatatatttaagagaaaacaaggcaagga..................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGAAAUAGCAAAGCUAUUAAGCACAUGUUCUAUUAUAGCAGAUUAAAAAUAGCUGUCAAGUUUUUUUCUUGACAGAGUUAAAAAUUUUUUAGCUAUGUCUUUUCACCUUAAAAACGCAAUGCGUUUUUACUAGCUUACUCGAUAUAAAUAUAUUUAAGAGAAAACAAGGCAAGGA (((((((..(((.(((((..(((....((((.......))))............((((((((.......)))))))).........)))..))))).)))..))))))).(((((((((...)))))))))...((((.((((((((....)))))...)))......))))..... (-41.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUUGCCUUGUUUUCUCUUAAAUAUAUUUAUAUCGAGUAAGCUAGUAAAAACGCAUUGCGUUUUUAAGGUGAAAAGACAUAGCUAAAAAAUUUUUAACUCUGUCAAGAAAAAAACUUGACAGCUAUUUUUAAUCUGCUAUAAUAGAACAUGUGCUUAAUAGCUUUGCUAUUUCACC ..........((((.(((.((((....))))....))).))))...(((((((((...))))))))).(((((((((.((.(((((..............((((((((.......))))))))..........((((......))))............))))).)))).))))))) (-37.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 775 60 11 184 135 NC_009009:SSA_1310|5end_30S_ribosomal_protein_S16,_putative_1327610..1327840_NEGATIVE 293 83 41 137 94 NC_009009:SSA_2246|5end_Competence-damage_protein,_putative_2242496..2242726_NEGATIVE 265 66 22 78 33 NC_009009:SSA_1267|5end_crcB-like_protein_2,_putative_1291347..1291577_NEGATIVE 251 121 85 118 77 NC_009009:SSA_0184|5end_Competence_protein_ComYA,_putative_188156..188386_POSITIVE 248 64 32 134 96 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 246 59 17 94 50 NC_009009:SSA_0174|5end_Tyrosyl-tRNA_synthetase_1,_putative_171888..172118_NEGATIVE 241 58 12 85 33 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 240 44 4 174 136 NC_009009:SSA_0023|5end_Aspartate_aminotransferase,_putative_28529..28759_POSITIVE 235 109 61 76 25 NC_009009:SSA_0510|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_508523..508753_POSITIVE 231 109 61 184 121 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 230 78 31 180 124 NC_009009:SSA_0665|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes_(MutT/NUDIX_family)_649603..649833_NEGATIVE 226 110 61 100 57 NC_009009:SSA_1537|5end_Conserved_uncharacterized_protein_1544441..1544671_NEGATIVE 225 110 79 104 70 NC_009009:SSA_2342|5end_SPX_domain-like_protein,_putative_2343513..2343743_NEGATIVE 222 98 54 91 42 NC_009009:SSA_0068|5end_Alcohol-acetaldehyde_dehydrogenase,_putative_70114..70344_POSITIVE 219 150 101 229 169 NC_009009:SSA_2123|5end_Dimethyladenosine_transferase,_putative_2128536..2128766_NEGATIVE 219 78 39 169 140 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 217 77 31 158 109 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 216 126 86 153 106 NC_009009:SSA_2266|5end_4-alpha-glucanotransferase,_putative_2265741..2265971_NEGATIVE 216 96 51 229 183 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 215 139 92 140 86 NC_009009:SSA_1235|5end_Dihydroorotase,_putative_1261227..1261457_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 66 22 78 33 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 259 137 91 131 91 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 239 111 73 87 51 NC_009009:SSA_0349|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_341828..341978_POSITIVE 234 70 22 113 65 NC_009009:SSA_2378|3end_Two-component_system_transcriptional_regulator,_LytR/AlgR_family,_putative_2383129..2383279_NEGATIVE 230 80 31 144 90 NC_009009:SSA_2179|3end_Conserved_uncharacterized_protein_2178104..2178254_NEGATIVE 230 78 31 102 46 NC_009009:SSA_0666|3end_hypothetical_protein_649681..649831_NEGATIVE 229 136 94 149 104 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 225 136 94 147 104 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 221 109 61 80 34 NC_009009:SSA_1890|3end_Acetyltransferase,_putative_1887693..1887843_NEGATIVE 221 109 64 102 43 NC_009009:SSA_0706|3end_RNA_helicase,_putative_692909..693059_POSITIVE 215 139 92 127 73 NC_009009:SSA_1236|3end_Mutator_protein,_putative_1261240..1261390_NEGATIVE 213 140 93 70 22 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 212 96 55 78 36 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 211 60 15 90 45 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 210 137 94 54 16 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 209 58 11 51 9 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 207 96 51 74 25 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 205 96 56 124 82 NC_009009:SSA_2264|3end_hypothetical_protein_2261239..2261389_NEGATIVE 204 138 91 127 72 NC_009009:SSA_2228|3end_Acetyltransferase_(GNAT)_family,_putative_2228271..2228421_NEGATIVE 198 82 54 136 103 NC_009009:SSA_0543|3end_SecA,_putative_539878..540028_POSITIVE