Origin IGS: ttctagcttccaattccgttatgattccgcgttatcggcttttgcctaactttagttatgcctgcaagccgatgcctagactcacttaggaattgaaacctagaaacatattctgagcatagctcaatcattaactagcaagtgcagcttgcaaactactagtaagaggagaaatataaa .........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 tttatatttctcctcttactagtagtttgcaagctgcacttgctagttaatgattgagctatgctcagaatatgtttctaggtttcaattcctaagtgagtctaggcatcggcttgcaggcataactaaagttaggcaaaagccgataacgcggaatcataacggaattggaagctagaa Mask Tandem Repeat Region ================================================ ttctagcttccaattccgttatgattccgcgttatcggcttttgcctaactttagttatgcctgcaagccgatgcctagactcacttaggaattgaaacctagaaacatattctgagcatagctcaatcattaactagcaagtgcagcttgcaaactactagtaagaggagaaatataaa Find is-nt database================================================ Query_seq: SSA_2391:SSA_0120|SSA_2391:SSA_0120:30S ribosomal protein S14, putative:30S ribosomal protein S8, putative:->->:114578..114757 180 ttctagcttccaattccgttatgattccgcgttatcggcttttgcctaactttagttatgcctgcaagccgatgcctagactcacttaggaattgaaacctagaaacatattctgagcatagctcaatcattaactagcaagtgcagcttgcaaactactagtaagaggagaaatataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2391:SSA_0120|SSA_2391:SSA_0120:30S ribosomal protein S14, putative:30S ribosomal protein S8, putative:->->:114578..114757 180 ttctagcttccaattccgttatgattccgcgttatcggcttttgcctaactttagttatgcctgcaagccgatgcctagactcacttaggaattgaaacctagaaacatattctgagcatagctcaatcattaactagcaagtgcagcttgcaaactactagtaagaggagaaatataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2391:SSA_0120|SSA_2391:SSA_0120:30S ribosomal protein S14, putative:30S ribosomal protein S8, putative:->->:114578..114757 180 ttctagcttccaattccgttatgattccgcgttatcggcttttgcctaactttagttatgcctgcaagccgatgcctagactcacttaggaattgaaacctagaaacatattctgagcatagctcaatcattaactagcaagtgcagcttgcaaactactagtaagaggagaaatataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctagcttccaattccgttatgattccgcgttatcggcttttgcctaactttagttatgcctgcaagccgatgcctagactcacttaggaattgaaacctagaaacatattctgagcatagctcaatcattaactagcaagtgcagcttgcaaactactagtaagaggagaaatataaa Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: - Start: 6 End: 131 ..... * S G I G N H N R T I P K Q R V K T I G A L R H R S E S L F Q F R S V Y E S C L E I M ................................................. ttctagcttccaattccgttatgattccgcgttatcggcttttgcctaactttagttatgcctgcaagccgatgcctagactcacttaggaattgaaacctagaaacatattctgagcatagctcaatcattaactagcaagtgcagcttgcaaactactagtaagaggagaaatataaa 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================================================ ttctagcttccaattccgttatgattccgcgttatcggcttttgcctaactttagttatgcctgcaagccgatgcctagactcacttaggaattgaaacctagaaacatattctgagcatagctcaatcattaactagcaagtgcagcttgcaaactactagtaagaggagaaatataaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2391:SSA_0120|SSA_2391:SSA_0120:30S ribosomal protein S14, putative:30S ribosomal protein S8, putative:->->:114578..114757 180 ttctagcttccaattccgttatgattccgcgttatcggcttttgcctaactttagttatgcctgcaagccgatgcctagactcacttaggaattgaaacctagaaacatattctgagcatagctcaatcattaactagcaagtgcagcttgcaaactactagtaagaggagaaatataaa Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: NC_009009_SSA_2391_SSA_0120|30S ribosomal protein S14, putative:30S ribosomal protein S8, putative|POSITIVE:POSITIVE|[114578,114757]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 ttctagcttccaattccgttatgattccgcgttatcggcttttgcctaactttagttatgcctgcaagccgatgcctagactcacttaggaattgaaacctagaaacatattctgagcatagctcaatcattaactagcaagtgcagcttgcaaactactagtaagaggagaaatataaa ttctagcttccaattccgttatgattccgcgttatcggcttttgcctaactttagttatgcctgcaagccgatgcctagactcacttaggaattgaaacctagaaacatattctgagcatagctcaatcattaactagcaagtgcagcttgcaaactactagtaagaggagaaatataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUAGCUUCCAAUUCCGUUAUGAUUCCGCGUUAUCGGCUUUUGCCUAACUUUAGUUAUGCCUGCAAGCCGAUGCCUAGACUCACUUAGGAAUUGAAACCUAGAAACAUAUUCUGAGCAUAGCUCAAUCAUUAACUAGCAAGUGCAGCUUGCAAACUACUAGUAAGAGGAGAAAUAUAAA ((((((.((.(((((((....(((.((...((.((((((((..((.((((....)))).))....))))))))))...)).)))....))))))).)).)))))).....((((((((...))))........(((((....(((.....))).....)))))......))))....... (-46.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUAUUUCUCCUCUUACUAGUAGUUUGCAAGCUGCACUUGCUAGUUAAUGAUUGAGCUAUGCUCAGAAUAUGUUUCUAGGUUUCAAUUCCUAAGUGAGUCUAGGCAUCGGCUUGCAGGCAUAACUAAAGUUAGGCAAAAGCCGAUAACGCGGAAUCAUAACGGAAUUGGAAGCUAGAA ..(((((((....((..((((((((..(((.....))).))))))))....))..((((...)))).)))))))..(((((.((((((((((...((((.(((.(..((((((((....((.((((....)))).))..))))))))..)..))).))))...)))))))))).))))). (-61.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 90 41 56 6 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 339 89 41 219 170 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 336 70 23 58 11 NC_009009:SSA_1182|5end_Gid-like_protein,_putative_1210866..1211096_NEGATIVE 328 76 34 58 13 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 320 80 31 181 125 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 317 80 34 217 159 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 307 78 31 81 35 NC_009009:SSA_0941|5end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_949157..949387_POSITIVE 306 169 127 207 166 NC_009009:SSA_1921|5end_hypothetical_protein_1910875..1911105_POSITIVE 303 80 35 212 159 NC_009009:SSA_0860|5end_N-acetylmuramidase/lysin,_putative_847615..847845_POSITIVE 302 80 32 66 9 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 302 79 34 204 149 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 298 42 4 54 10 NC_009009:SSA_0434|5end_Glutamate_formiminotransferase,_putative_436568..436798_NEGATIVE 296 45 5 223 184 NC_009009:SSA_1540|5end_hypothetical_protein_1545268..1545498_NEGATIVE 296 80 38 38 7 NC_009009:SSA_0584|5end_hypothetical_protein_575806..576036_POSITIVE 293 76 35 52 8 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 292 69 21 65 24 NC_009009:SSA_0822|5end_Large_conductance_mechano-sensitive_ion_channel,_putative_801972..802202_NEGATIVE 291 77 31 53 2 NC_009009:SSA_0525|5end_Microcompartment_protein,_putative_523487..523717_POSITIVE 291 76 37 52 11 NC_009009:SSA_0386|5end_Glycine-betaine_ABC_transporter,_ATPase_component,_putative_381455..381685_NEGATIVE 290 108 61 226 169 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 290 101 61 54 10 NC_009009:SSA_2252|5end_hypothetical_protein_2248649..2248879_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 102 62 147 103 NC_009009:SSA_1368|3end_hypothetical_protein_1383748..1383898_NEGATIVE 353 90 41 63 13 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 328 76 34 46 1 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 306 169 127 136 95 NC_009009:SSA_1920|3end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1910884..1911034_POSITIVE 304 78 32 42 4 NC_009009:SSA_1889|3end_Conserved_uncharacterized_protein_1886283..1886433_NEGATIVE 302 80 32 60 3 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 299 45 1 142 98 NC_009009:SSA_0698|3end_Peptide_chain_release_factor_3,_putative_682007..682157_POSITIVE 298 80 36 82 40 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 295 78 35 71 7 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 293 76 35 59 15 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 290 75 33 112 57 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 289 46 15 62 27 NC_009009:SSA_1770|3end_hypothetical_protein_1757484..1757634_NEGATIVE 287 50 8 40 2 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 287 164 121 146 109 NC_009009:SSA_0780|3end_Acid_phosphatase_(PAP2_family),_putative_765328..765478_POSITIVE 282 71 36 128 86 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 282 96 59 59 18 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 282 46 12 39 6 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 282 85 44 57 24 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 281 80 35 118 76 NC_009009:SSA_0509|3end_Propanediol_utilization_protein,_putative_508538..508688_POSITIVE 280 70 21 130 78 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE