Origin IGS: tgacaaattccctgctagccgtcagtagtcataaatatattggacgacttttttcttgactgtcaacaagtttttctgttgctttgcaacaaagtctaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttagactttgttgcaaagcaacagaaaaacttgttgacagtcaagaaaaaagtcgtccaatatatttatgactactgacggctagcagggaatttgtca Mask Tandem Repeat Region ================================================ tgacaaattccctgctagccgtcagtagtcataaatatattggacgacttttttcttgactgtcaacaagtttttctgttgctttgcaacaaagtctaaaa Find is-nt database================================================ Query_seq: SSA_1651:SSA_1652|SSA_1651:SSA_1652:hypothetical protein:Acetyltransferases, putative:<-<-:1649944..1650044 101 tgacaaattccctgctagccgtcagtagtcataaatatattggacgacttttttcttgactgtcaacaagtttttctgttgctttgcaacaaagtctaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1651:SSA_1652|SSA_1651:SSA_1652:hypothetical protein:Acetyltransferases, putative:<-<-:1649944..1650044 101 tgacaaattccctgctagccgtcagtagtcataaatatattggacgacttttttcttgactgtcaacaagtttttctgttgctttgcaacaaagtctaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1651:SSA_1652|SSA_1651:SSA_1652:hypothetical protein:Acetyltransferases, putative:<-<-:1649944..1650044 101 tgacaaattccctgctagccgtcagtagtcataaatatattggacgacttttttcttgactgtcaacaagtttttctgttgctttgcaacaaagtctaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgacaaattccctgctagccgtcagtagtcataaatatattggacgacttttttcttgactgtcaacaagtttttctgttgctttgcaacaaagtctaaaa Predict ORF larger than 30AA ================================================ tgacaaattccctgctagccgtcagtagtcataaatatattggacgacttttttcttgactgtcaacaagtttttctgttgctttgcaacaaagtctaaaa 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================================================ tgacaaattccctgctagccgtcagtagtcataaatatattggacgacttttttcttgactgtcaacaagtttttctgttgctttgcaacaaagtctaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1651:SSA_1652|SSA_1651:SSA_1652:hypothetical protein:Acetyltransferases, putative:<-<-:1649944..1650044 101 tgacaaattccctgctagccgtcagtagtcataaatatattggacgacttttttcttgactgtcaacaagtttttctgttgctttgcaacaaagtctaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_009009_SSA_1651_SSA_1652|hypothetical protein:Acetyltransferases, putative|NEGATIVE:NEGATIVE|[1649944,1650044]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 tgacaaattccctgctagccgtcagtagtcataaatatattggacgacttttttcttgactgtcaacaagtttttctgttgctttgcaacaaagtctaaaa tgacaaattccctgctagccgtcagtagtcataaatatattggacgacttttttcttgactgtcaacaagtttttctgttgctttgcaacaaagtctaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACAAAUUCCCUGCUAGCCGUCAGUAGUCAUAAAUAUAUUGGACGACUUUUUUCUUGACUGUCAACAAGUUUUUCUGUUGCUUUGCAACAAAGUCUAAAA ...........(((((.......)))))...........((((((.........((((........))))......((((((...))))))..)))))).. (-16.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAGACUUUGUUGCAAAGCAACAGAAAAACUUGUUGACAGUCAAGAAAAAAGUCGUCCAAUAUAUUUAUGACUACUGACGGCUAGCAGGGAAUUUGUCA .....(((((((((((...))))))))....(((((((.(.((((.......((((((...........))))))..)))).).)))))))......))). (-21.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 887 50 1 141 92 NC_009009:SSA_1651|5end_hypothetical_protein_1649853..1650083_NEGATIVE 313 58 12 197 152 NC_009009:SSA_1217|5end_Conserved_uncharacterized_protein_1238964..1239194_POSITIVE 285 49 2 54 9 NC_009009:SSA_1602|5end_Exoribonuclease,_VacB/Rnb_family,_putative_1609370..1609600_NEGATIVE 283 32 6 34 8 NC_009009:SSA_1529|5end_Lysyl-tRNA_synthetase,_putative_1535871..1536101_POSITIVE 282 59 13 53 1 NC_009009:SSA_1893|5end_N-acetylglucosamine-6-phosphate_deacetylase,_putative_1890572..1890802_NEGATIVE 279 87 46 224 186 NC_009009:SSA_1871|5end_Penicillin-binding_protein_2X,_putative_1868873..1869103_NEGATIVE 275 47 9 180 142 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 269 57 13 110 61 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 263 50 12 44 1 NC_009009:SSA_1708|5end_hypothetical_protein_1698319..1698549_NEGATIVE 255 85 55 188 152 NC_009009:SSA_0184|5end_Competence_protein_ComYA,_putative_188156..188386_POSITIVE 251 89 48 186 144 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 251 97 54 220 170 NC_009009:SSA_1249|5end_hypothetical_protein_1273985..1274215_NEGATIVE 247 59 12 77 40 NC_009009:SSA_0144|5end_Transcriptional_regulator,_TetR_family,_putative_138565..138795_NEGATIVE 245 84 43 196 140 NC_009009:SSA_0786|5end_Proton-translocating_ATPase,_F1_sector,_alpha_subunit,_putative_768737..768967_POSITIVE 244 26 11 231 214 NC_009009:SSA_1744|5end_Iron_compound_ABC_transporter,_permease_protein,_putative_1730915..1731145_POSITIVE 244 86 47 135 100 NC_009009:SSA_1531|5end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_1539476..1539706_NEGATIVE 244 43 8 63 20 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 242 88 48 136 99 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 242 57 11 101 60 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 241 87 42 47 3 NC_009009:SSA_0536|5end_B12-dependent_diol_dehydratase_small_subunit,_putative_531342..531572_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 60 12 147 83 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 269 57 13 89 40 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 264 31 1 143 114 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 263 50 12 50 7 NC_009009:SSA_1709|3end_hypothetical_protein_1698313..1698463_NEGATIVE 255 85 55 58 22 NC_009009:SSA_0183|3end_hypothetical_protein_188106..188256_POSITIVE 248 50 3 143 95 NC_009009:SSA_0378|3end_TRZ/ATZ_family_hydrolase,_putative_368627..368777_POSITIVE 244 86 47 151 116 NC_009009:SSA_1532|3end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1539460..1539610_NEGATIVE 244 43 8 63 20 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 242 88 48 133 96 NC_009009:SSA_1880|3end_Glycyl-tRNA_synthetase_alpha_chain,_putative_1874265..1874415_NEGATIVE 242 57 11 82 41 NC_009009:SSA_0473|3end_Precorrin-6x_reductase,_putative_476331..476481_POSITIVE 242 86 41 133 92 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 237 29 12 69 53 NC_009009:SSA_1926|3end_hypothetical_protein_1915034..1915184_POSITIVE 230 98 53 69 25 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 229 89 48 134 87 NC_009009:SSA_1107|3end_Lipid/multidrug/protein-type_ABC_exporter,_ATP_binding/membrane-spanning_protein,_putative_1133784..1133934_POSITIVE 226 86 41 72 18 NC_009009:SSA_2042|3end_hypothetical_protein_2046669..2046819_NEGATIVE 225 87 41 151 106 NC_009009:SSA_0981|3end_3-isopropylmalate_dehydratase_small_subunit,_putative_986066..986216_POSITIVE 225 97 57 136 99 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 224 55 11 145 90 NC_009009:SSA_0193|3end_CAAX_amino_terminal_protease_family_protein,_putative_195075..195225_POSITIVE 223 89 41 128 73 NC_009009:SSA_1149|3end_Glycosyl_hydrolase,_family_1,_putative_1179876..1180026_POSITIVE 223 98 52 54 13 NC_009009:SSA_1081|3end_1-phosphofructokinase,_putative_1099269..1099419_POSITIVE