Origin IGS: aaagaactccttttaaataatatatctccgacatcattctactaaaaaatagattgtttgacaactaaaacttttcaaaaatattacaaaaataaatatctgttcaataagtgcagggtttgactaggatgtgtatttttcctataatcataactagagaaaacgcttgtataaattacctaaggaggtgctt .........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 aagcacctccttaggtaatttatacaagcgttttctctagttatgattataggaaaaatacacatcctagtcaaaccctgcacttattgaacagatatttatttttgtaatatttttgaaaagttttagttgtcaaacaatctattttttagtagaatgatgtcggagatatattatttaaaaggagttcttt Mask Tandem Repeat Region ================================================ aaagaactccttttaaataatatatctccgacatcattctactaaaaaatagattgtttgacaactaaaacttttcaaaaatattacaaaaataaatatctgttcaataagtgcagggtttgactaggatgtgtatttttcctataatcataactagagaaaacgcttgtataaattacctaaggaggtgctt Find is-nt database================================================ Query_seq: SSA_0991:SSA_0992|SSA_0991:SSA_0992:Deoxyribonuclease, putative:hypothetical protein:<-->:993433..993625 193 aaagaactccttttaaataatatatctccgacatcattctactaaaaaatagattgtttgacaactaaaacttttcaaaaatattacaaaaataaatatctgttcaataagtgcagggtttgactaggatgtgtatttttcctataatcataactagagaaaacgcttgtataaattacctaaggaggtgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0991:SSA_0992|SSA_0991:SSA_0992:Deoxyribonuclease, putative:hypothetical protein:<-->:993433..993625 193 aaagaactccttttaaataatatatctccgacatcattctactaaaaaatagattgtttgacaactaaaacttttcaaaaatattacaaaaataaatatctgttcaataagtgcagggtttgactaggatgtgtatttttcctataatcataactagagaaaacgcttgtataaattacctaaggaggtgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0991:SSA_0992|SSA_0991:SSA_0992:Deoxyribonuclease, putative:hypothetical protein:<-->:993433..993625 193 aaagaactccttttaaataatatatctccgacatcattctactaaaaaatagattgtttgacaactaaaacttttcaaaaatattacaaaaataaatatctgttcaataagtgcagggtttgactaggatgtgtatttttcctataatcataactagagaaaacgcttgtataaattacctaaggaggtgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagaactccttttaaataatatatctccgacatcattctactaaaaaatagattgtttgacaactaaaacttttcaaaaatattacaaaaataaatatctgttcaataagtgcagggtttgactaggatgtgtatttttcctataatcataactagagaaaacgcttgtataaattacctaaggaggtgctt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 87 End: 176 ...................................................................................... L F L Y R N L L H L T Q S P H T N K R Y D Y S S F V S T Y M ................. aaagaactccttttaaataatatatctccgacatcattctactaaaaaatagattgtttgacaactaaaacttttcaaaaatattacaaaaataaatatctgttcaataagtgcagggtttgactaggatgtgtatttttcctataatcataactagagaaaacgcttgtataaattacctaaggaggtgctt 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: 119 End: 148 ......................................................................................................................TTTGACTAGGATGTGTATTTTTCCTATAAT............................................. PromScan Matrix: RpoD-17 Strand: - Score: 89 Start: 36 End: 65 ...................................GTTGTCAAACAATCTATTTTTTAGTAGAAT................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 147 End: 176 ..................................................................................................................................................ATTTATACAAGCGTTTTCTCTAGTTATGAT................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagaactccttttaaataatatatctccgacatcattctactaaaaaatagattgtttgacaactaaaacttttcaaaaatattacaaaaataaatatctgttcaataagtgcagggtttgactaggatgtgtatttttcctataatcataactagagaaaacgcttgtataaattacctaaggaggtgctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0991:SSA_0992|SSA_0991:SSA_0992:Deoxyribonuclease, putative:hypothetical protein:<-->:993433..993625 193 aaagaactccttttaaataatatatctccgacatcattctactaaaaaatagattgtttgacaactaaaacttttcaaaaatattacaaaaataaatatctgttcaataagtgcagggtttgactaggatgtgtatttttcctataatcataactagagaaaacgcttgtataaattacctaaggaggtgctt Intra-Species Hit: Count: 1 Min: 1 Max: 193 Len: 193 Subject: NC_009009_SSA_0991_SSA_0992|Deoxyribonuclease, putative:hypothetical protein|NEGATIVE:POSITIVE|[993433,993625]|193 HSP 1 e-value: 1.0E-105 bit: 383.0 Len: 193 Query Start:1 Query End:193 Subject Strand: POSITIVE Subject Start: 1 Subject End: 193 aaagaactccttttaaataatatatctccgacatcattctactaaaaaatagattgtttgacaactaaaacttttcaaaaatattacaaaaataaatatctgttcaataagtgcagggtttgactaggatgtgtatttttcctataatcataactagagaaaacgcttgtataaattacctaaggaggtgctt aaagaactccttttaaataatatatctccgacatcattctactaaaaaatagattgtttgacaactaaaacttttcaaaaatattacaaaaataaatatctgttcaataagtgcagggtttgactaggatgtgtatttttcctataatcataactagagaaaacgcttgtataaattacctaaggaggtgctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAACUCCUUUUAAAUAAUAUAUCUCCGACAUCAUUCUACUAAAAAAUAGAUUGUUUGACAACUAAAACUUUUCAAAAAUAUUACAAAAAUAAAUAUCUGUUCAAUAAGUGCAGGGUUUGACUAGGAUGUGUAUUUUUCCUAUAAUCAUAACUAGAGAAAACGCUUGUAUAAAUUACCUAAGGAGGUGCUU ......................(((((((..................(((((((.((((........))))..........((((.....))))...)))))))......(((((((((((..((((..((((.(((........))))))).))))...)))).)))))))...........)))))))... (-28.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCACCUCCUUAGGUAAUUUAUACAAGCGUUUUCUCUAGUUAUGAUUAUAGGAAAAAUACACAUCCUAGUCAAACCCUGCACUUAUUGAACAGAUAUUUAUUUUUGUAAUAUUUUUGAAAAGUUUUAGUUGUCAAACAAUCUAUUUUUUAGUAGAAUGAUGUCGGAGAUAUAUUAUUUAAAAGGAGUUCUUU ......(((((((((((((.(((....(..((((..(((..........)))..))))..)...(((..((((....((((.........(((((........)))))........((((((((....((((.....))))..))))))))))))..))))...))).))).))))))))..)))))...... (-30.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 766 140 91 231 182 NC_009009:SSA_0991|5end_Deoxyribonuclease,_putative_993342..993572_NEGATIVE 296 129 81 154 107 NC_009009:SSA_0018|5end_Cell-shape_determining_protein_MreD,_putative_23628..23858_POSITIVE 278 143 112 231 199 NC_009009:SSA_0072|5end_ABC_sugar_transporter,_MsmK-like_protein,_putative_75922..76152_POSITIVE 262 140 96 78 39 NC_009009:SSA_1350|5end_hypothetical_protein_1367412..1367642_NEGATIVE 246 169 122 206 165 NC_009009:SSA_1797|5end_Aminodeoxychorismate_lyase,_putative_1779947..1780177_NEGATIVE 236 131 97 153 110 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 236 137 96 184 135 NC_009009:SSA_0561|5end_RNA:NAD_2'-phosphotransferase,_putative_553630..553860_POSITIVE 235 169 121 183 134 NC_009009:SSA_2229|5end_hypothetical_protein_2228994..2229224_NEGATIVE 232 149 101 231 178 NC_009009:SSA_1987|5end_hypothetical_protein_1983368..1983598_NEGATIVE 227 166 121 150 95 NC_009009:SSA_0728|5end_Protease,_putative_713688..713918_POSITIVE 223 131 100 191 152 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 220 145 101 105 61 NC_009009:SSA_0149|5end_hypothetical_protein_143574..143804_POSITIVE 219 129 96 197 158 NC_009009:SSA_1381|5end_hypothetical_protein_1399565..1399795_NEGATIVE 218 134 102 82 46 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 218 68 21 60 11 NC_009009:SSA_0959|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_domain_and_a_winged-helix_DNA-binding_domains),_putative_967842..968072_POSITIVE 215 142 101 159 113 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 215 135 98 42 3 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 214 121 99 69 43 NC_009009:SSA_0855|5end_O-acetylhomoserine_sulfhydrylase,_putative_841832..842062_POSITIVE 213 128 92 52 6 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 213 140 99 69 37 NC_009009:SSA_1314|5end_Fe-S-cluster_oxidoreductase,_putative_1331240..1331470_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 128 81 151 105 NC_009009:SSA_0017|3end_Cell_shape_determining_protein_MreC,_putative_23706..23856_POSITIVE 242 120 94 147 122 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE 238 160 112 147 104 NC_009009:SSA_1798|3end_hypothetical_protein_1779998..1780148_NEGATIVE 236 131 97 131 88 NC_009009:SSA_0895|3end_ATP-binding_cassette_transporter-like_protein,_putative_887763..887913_POSITIVE 226 128 98 45 21 NC_009009:SSA_1323|3end_hypothetical_protein_1339788..1339938_NEGATIVE 222 134 95 67 26 NC_009009:SSA_0851|3end_Cation_efflux_family_protein,_putative_837644..837794_NEGATIVE 222 144 116 145 119 NC_009009:SSA_0843|3end_hypothetical_protein_828478..828628_POSITIVE 221 140 99 106 63 NC_009009:SSA_1265|3end_50S_ribosomal_protein_L19,_putative_1290184..1290334_NEGATIVE 218 134 102 79 43 NC_009009:SSA_2278|3end_Ukp_protein,_putative_2280410..2280560_NEGATIVE 218 133 105 43 13 NC_009009:SSA_0258|3end_hypothetical_protein_253022..253172_POSITIVE 216 150 109 67 27 NC_009009:SSA_2020|3end_hypothetical_protein_2022471..2022621_POSITIVE 215 135 98 49 10 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 210 131 98 75 37 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 208 154 111 69 18 NC_009009:SSA_0133|3end_50S_ribosomal_protein_L17,_putative_122562..122712_POSITIVE 205 133 97 77 35 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 201 143 109 141 110 NC_009009:SSA_1045|3end_hypothetical_protein_1061832..1061982_POSITIVE 199 128 81 138 88 NC_009009:SSA_1809|3end_PTS_system_glucose-specific_EIIC_BA_component_(EIICBA-Glc)_(EII-_Glc/EIII-Glc),_putative_1792227..1792377_NEGATIVE 196 134 101 146 110 NC_009009:SSA_0824|3end_DNA_primase_(bacterial_type),_putative_803941..804091_POSITIVE 193 156 111 69 13 NC_009009:SSA_0434|3end_Glutamate_formiminotransferase,_putative_435669..435819_NEGATIVE 192 145 101 140 92 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE