Origin IGS: tccttcctaaatctaataaattttactaatactagtttaccatatttttagtacgaaaggaaagagatacattgtcacgtccgattaatgttccgtttatagga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcctataaacggaacattaatcggacgtgacaatgtatctctttcctttcgtactaaaaatatggtaaactagtattagtaaaatttattagatttaggaagga Mask Tandem Repeat Region ================================================ tccttcctaaatctaataaattttactaatactagtttaccatatttttagtacgaaaggaaagagatacattgtcacgtccgattaatgttccgtttatagga Find is-nt database================================================ Query_seq: SSA_1315:SSA_1316|SSA_1315:SSA_1316:hypothetical protein:Nicotinamide mononucleotide transporter, putative:<-<-:1332143..1332246 104 tccttcctaaatctaataaattttactaatactagtttaccatatttttagtacgaaaggaaagagatacattgtcacgtccgattaatgttccgtttatagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1315:SSA_1316|SSA_1315:SSA_1316:hypothetical protein:Nicotinamide mononucleotide transporter, putative:<-<-:1332143..1332246 104 tccttcctaaatctaataaattttactaatactagtttaccatatttttagtacgaaaggaaagagatacattgtcacgtccgattaatgttccgtttatagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1315:SSA_1316|SSA_1315:SSA_1316:hypothetical protein:Nicotinamide mononucleotide transporter, putative:<-<-:1332143..1332246 104 tccttcctaaatctaataaattttactaatactagtttaccatatttttagtacgaaaggaaagagatacattgtcacgtccgattaatgttccgtttatagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccttcctaaatctaataaattttactaatactagtttaccatatttttagtacgaaaggaaagagatacattgtcacgtccgattaatgttccgtttatagga Predict ORF larger than 30AA ================================================ tccttcctaaatctaataaattttactaatactagtttaccatatttttagtacgaaaggaaagagatacattgtcacgtccgattaatgttccgtttatagga 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================================================ tccttcctaaatctaataaattttactaatactagtttaccatatttttagtacgaaaggaaagagatacattgtcacgtccgattaatgttccgtttatagga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1315:SSA_1316|SSA_1315:SSA_1316:hypothetical protein:Nicotinamide mononucleotide transporter, putative:<-<-:1332143..1332246 104 tccttcctaaatctaataaattttactaatactagtttaccatatttttagtacgaaaggaaagagatacattgtcacgtccgattaatgttccgtttatagga Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_009009_SSA_1315_SSA_1316|hypothetical protein:Nicotinamide mononucleotide transporter, putative|NEGATIVE:NEGATIVE|[1332143,1332246]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 tccttcctaaatctaataaattttactaatactagtttaccatatttttagtacgaaaggaaagagatacattgtcacgtccgattaatgttccgtttatagga tccttcctaaatctaataaattttactaatactagtttaccatatttttagtacgaaaggaaagagatacattgtcacgtccgattaatgttccgtttatagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUUCCUAAAUCUAAUAAAUUUUACUAAUACUAGUUUACCAUAUUUUUAGUACGAAAGGAAAGAGAUACAUUGUCACGUCCGAUUAAUGUUCCGUUUAUAGGA ....(((((....................((((((............)))))).....(((.......((((((((......)).))))))))).....))))) (-12.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUAUAAACGGAACAUUAAUCGGACGUGACAAUGUAUCUCUUUCCUUUCGUACUAAAAAUAUGGUAAACUAGUAUUAGUAAAAUUUAUUAGAUUUAGGAAGGA (((.......)))...........((((....))))...((((((((....(((((......)))))..((((((...........))))))....)))))))) (-16.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 843 100 51 191 142 NC_009009:SSA_1315|5end_hypothetical_protein_1332052..1332282_NEGATIVE 265 98 58 190 155 NC_009009:SSA_0414|5end_hypothetical_protein_410118..410348_POSITIVE 253 79 31 141 95 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 231 84 41 185 134 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 231 99 63 201 165 NC_009009:SSA_0777|5end_Glycogen_biosynthesis_protein_GlgD,_putative_759430..759660_POSITIVE 228 94 70 25 1 NC_009009:SSA_1081|5end_1-phosphofructokinase,_putative_1098278..1098508_POSITIVE 223 98 52 201 147 NC_009009:SSA_0938|5end_hypothetical_protein_946587..946817_POSITIVE 222 84 49 231 184 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 214 96 63 29 1 NC_009009:SSA_2365|5end_Cobalt_transport_protein_cbiQ,_putative_2368037..2368267_NEGATIVE 210 98 58 44 12 NC_009009:SSA_1299|5end_Maltose/maltodextrin_ABC_transport_system,_putative_1316629..1316859_POSITIVE 208 77 31 229 174 NC_009009:SSA_1989|5end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1985182..1985412_NEGATIVE 205 95 63 200 171 NC_009009:SSA_1506|5end_Lipopolysaccharide_biosynthesis_protein,_putative_1511222..1511452_NEGATIVE 201 56 21 154 114 NC_009009:SSA_0685|5end_hypothetical_protein_669032..669262_POSITIVE 199 97 51 70 29 NC_009009:SSA_2108|5end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2112464..2112694_NEGATIVE 199 95 54 39 4 NC_009009:SSA_1892|5end_hypothetical_protein_1889262..1889492_NEGATIVE 197 64 21 206 163 NC_009009:SSA_2088|5end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2093476..2093706_NEGATIVE 197 97 70 177 145 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 196 76 31 64 20 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 195 95 70 199 165 NC_009009:SSA_1704|5end_Conserved_uncharacterized_protein_1696401..1696631_NEGATIVE 194 81 51 211 177 NC_009009:SSA_0610|5end_LemA-like_protein,_putative_598968..599198_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 79 31 141 95 NC_009009:SSA_1531|3end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_1538778..1538928_NEGATIVE 247 99 55 50 9 NC_009009:SSA_0406|3end_hypothetical_protein_402196..402346_NEGATIVE 240 96 58 36 1 NC_009009:SSA_2366|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368030..2368180_NEGATIVE 228 94 70 28 4 NC_009009:SSA_1080|3end_Transcriptional_repressor_of_the_fructose_operon,_DeoR_family,_putative_1098361..1098511_POSITIVE 224 95 54 85 48 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 204 95 53 145 110 NC_009009:SSA_1971|3end_hypothetical_protein_1967597..1967747_POSITIVE 203 83 41 147 109 NC_009009:SSA_1721|3end_DNA_polymerase_III,_delta'_subunit,_putative_1707138..1707288_NEGATIVE 193 89 45 64 23 NC_009009:SSA_0952|3end_hypothetical_protein_958095..958245_POSITIVE 193 97 58 56 6 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 191 94 53 145 99 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 190 86 47 81 42 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE 188 93 54 53 17 NC_009009:SSA_1320|3end_hypothetical_protein_1336829..1336979_NEGATIVE 187 96 58 101 64 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 183 83 49 106 71 NC_009009:SSA_1134|3end_Xanthine_phosphoribosyltransferase,_putative_1160316..1160466_POSITIVE 183 96 70 68 39 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 181 87 52 134 92 NC_009009:SSA_0731|3end_Integral_membrane_protein,_putative_715654..715804_POSITIVE 178 83 58 136 112 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 177 99 54 76 20 NC_009009:SSA_1540|3end_hypothetical_protein_1544915..1545065_NEGATIVE 175 95 54 116 72 NC_009009:SSA_1303|3end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322474..1322624_NEGATIVE 175 45 2 105 51 NC_009009:SSA_0978|3end_hypothetical_protein_984082..984232_POSITIVE