Origin IGS: atttacgtaaaaagaggtagttaataaatattgaactgcaaaataattttttgtatatccgaaggggaagattgattttgacaatagaaaatacactaaaactggaacttaaaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttttaagttccagttttagtgtattttctattgtcaaaatcaatcttccccttcggatatacaaaaaattattttgcagttcaatatttattaactacctctttttacgtaaat Mask Tandem Repeat Region ================================================ atttacgtaaaaagaggtagttaataaatattgaactgcaaaataattttttgtatatccgaaggggaagattgattttgacaatagaaaatacactaaaactggaacttaaaaat Find is-nt database================================================ Query_seq: SSA_1169:SSA_1170|SSA_1169:SSA_1170:Conserved hypothetical protein with an alpha/beta hydrolase fold, putative:hypothetical protein:-><-:1196907..1197022 116 atttacgtaaaaagaggtagttaataaatattgaactgcaaaataattttttgtatatccgaaggggaagattgattttgacaatagaaaatacactaaaactggaacttaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1169:SSA_1170|SSA_1169:SSA_1170:Conserved hypothetical protein with an alpha/beta hydrolase fold, putative:hypothetical protein:-><-:1196907..1197022 116 atttacgtaaaaagaggtagttaataaatattgaactgcaaaataattttttgtatatccgaaggggaagattgattttgacaatagaaaatacactaaaactggaacttaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1169:SSA_1170|SSA_1169:SSA_1170:Conserved hypothetical protein with an alpha/beta hydrolase fold, putative:hypothetical protein:-><-:1196907..1197022 116 atttacgtaaaaagaggtagttaataaatattgaactgcaaaataattttttgtatatccgaaggggaagattgattttgacaatagaaaatacactaaaactggaacttaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttacgtaaaaagaggtagttaataaatattgaactgcaaaataattttttgtatatccgaaggggaagattgattttgacaatagaaaatacactaaaactggaacttaaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 24 End: 116 ....................... M N I E L Q N N F L Y I R R G R L I L T I E N T L K L E L K N Protein_Len: 32 Strand: - Start: 1 End: 96 N V Y F S T T L L Y Q V A F Y N K T Y G F P F I S K S L L F Y M .................... atttacgtaaaaagaggtagttaataaatattgaactgcaaaataattttttgtatatccgaaggggaagattgattttgacaatagaaaatacactaaaactggaacttaaaaat 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================================================ atttacgtaaaaagaggtagttaataaatattgaactgcaaaataattttttgtatatccgaaggggaagattgattttgacaatagaaaatacactaaaactggaacttaaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1169:SSA_1170|SSA_1169:SSA_1170:Conserved hypothetical protein with an alpha/beta hydrolase fold, putative:hypothetical protein:-><-:1196907..1197022 116 atttacgtaaaaagaggtagttaataaatattgaactgcaaaataattttttgtatatccgaaggggaagattgattttgacaatagaaaatacactaaaactggaacttaaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: NC_009009_SSA_1169_SSA_1170|Conserved hypothetical protein with an alpha/beta hydrolase fold, putative:hypothetical protein|POSITIVE:NEGATIVE|[1196907,1197022]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 atttacgtaaaaagaggtagttaataaatattgaactgcaaaataattttttgtatatccgaaggggaagattgattttgacaatagaaaatacactaaaactggaacttaaaaat atttacgtaaaaagaggtagttaataaatattgaactgcaaaataattttttgtatatccgaaggggaagattgattttgacaatagaaaatacactaaaactggaacttaaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUACGUAAAAAGAGGUAGUUAAUAAAUAUUGAACUGCAAAAUAAUUUUUUGUAUAUCCGAAGGGGAAGAUUGAUUUUGACAAUAGAAAAUACACUAAAACUGGAACUUAAAAAU .((((.((....((...((((.......(((((...(((((((.....)))))))..(((....)))..............)))))........))))...))...)).))))... (-14.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUAAGUUCCAGUUUUAGUGUAUUUUCUAUUGUCAAAAUCAAUCUUCCCCUUCGGAUAUACAAAAAAUUAUUUUGCAGUUCAAUAUUUAUUAACUACCUCUUUUUACGUAAAU .............((((.....(((((....((((.((((((......(((.....))).............))))))))))..))))).....)))).................. ( -7.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 226 108 62 70 28 NC_009009:SSA_1121|5end_Cytochrome_C-type_biogenesis_protein,_putative_1147149..1147379_POSITIVE 203 73 31 54 13 NC_009009:SSA_0801|5end_Mur_ligase_family_protein,_putative_784117..784347_NEGATIVE 202 87 46 93 48 NC_009009:SSA_1239|5end_hypothetical_protein_1264689..1264919_NEGATIVE 202 83 50 90 51 NC_009009:SSA_1053|5end_Pyruvate_phosphate_dikinase,_putative_1070068..1070298_NEGATIVE 197 84 56 176 144 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 197 74 43 150 120 NC_009009:SSA_0755|5end_hypothetical_protein_736212..736442_POSITIVE 194 88 49 209 163 NC_009009:SSA_0193|5end_CAAX_amino_terminal_protease_family_protein,_putative_194318..194548_POSITIVE 193 86 47 74 24 NC_009009:SSA_1935|5end_Beta-ketoacyl-ACP_synthase_II_(3-oxoacyl-(Acyl-carrier-protein)_synthase_II),_putative_1923039..1923269_NEGATIVE 193 79 31 189 142 NC_009009:SSA_0989|5end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991071..991301_POSITIVE 192 83 57 167 139 NC_009009:SSA_0291|5end_Oxidoreductase,_putative_285362..285592_POSITIVE 191 83 60 223 198 NC_009009:SSA_2050|5end_Arabinose_efflux_permease,_putative_2053255..2053485_POSITIVE 187 89 47 161 118 NC_009009:SSA_1636|5end_ABC-type_antibiotic_exporter,_ATPase_component,_putative_1640905..1641135_NEGATIVE 186 97 54 171 127 NC_009009:SSA_0564|5end_Potential_aminotransferase,_putative_555694..555924_POSITIVE 185 89 41 188 117 NC_009009:SSA_0424|5end_Exopolysaccharide_biosynthesis_protein,_putative_422233..422463_NEGATIVE 183 81 47 174 132 NC_009009:SSA_2314|5end_hypothetical_protein_2316335..2316565_NEGATIVE 183 92 60 194 157 NC_009009:SSA_1476|5end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1480173..1480403_POSITIVE 182 88 45 179 135 NC_009009:SSA_1214|5end_Conserved_uncharacterized_Lactobacillales_protein_1237482..1237712_POSITIVE 179 96 62 104 62 NC_009009:SSA_2149|5end_hypothetical_protein_2150821..2151051_NEGATIVE 177 93 58 162 122 NC_009009:SSA_0711|5end_hypothetical_protein_696631..696861_NEGATIVE 177 74 59 60 45 NC_009009:SSA_0306|5end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_302590..302820_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 234 97 61 68 29 NC_009009:SSA_0822|3end_Large_conductance_mechano-sensitive_ion_channel,_putative_801589..801739_NEGATIVE 193 79 31 97 50 NC_009009:SSA_0988|3end_TfoX_N-terminal_domain_family_protein,_putative_991059..991209_POSITIVE 187 89 47 49 6 NC_009009:SSA_1638|3end_hypothetical_protein_1641017..1641167_NEGATIVE 182 98 59 44 5 NC_009009:SSA_0363|3end_D-alanine/glycine/Na_permease,_putative_355275..355425_POSITIVE 179 96 62 48 6 NC_009009:SSA_2150|3end_hypothetical_protein_2150877..2151027_NEGATIVE 174 88 51 78 24 NC_009009:SSA_1265|3end_50S_ribosomal_protein_L19,_putative_1290184..1290334_NEGATIVE 171 67 42 43 19 NC_009009:SSA_1484|3end_DNA_ligase,_putative_1490230..1490380_NEGATIVE 171 39 1 77 32 NC_009009:SSA_1150|3end_Tautomerase,_putative_1179894..1180044_NEGATIVE 170 79 35 150 106 NC_009009:SSA_0350|3end_Helicase,_putative_341852..342002_NEGATIVE 168 86 50 121 81 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 168 78 36 92 52 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 168 43 16 74 37 NC_009009:SSA_0710|3end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_694773..694923_NEGATIVE 165 102 71 61 30 NC_009009:SSA_2226|3end_Organic_radical_activating_chaperone,_putative_2227151..2227301_NEGATIVE 164 74 36 145 106 NC_009009:SSA_1020|3end_hypothetical_protein_1036104..1036254_POSITIVE 162 76 53 147 117 NC_009009:SSA_1920|3end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1910884..1911034_POSITIVE 162 75 37 89 50 NC_009009:SSA_1244|3end_hypothetical_protein_1268465..1268615_NEGATIVE 162 72 36 113 83 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 160 84 50 49 10 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE 160 70 23 54 8 NC_009009:SSA_0391|3end_Pyruvate_oxidase,_putative_387801..387951_POSITIVE 160 110 64 76 25 NC_009009:SSA_0332|3end_hypothetical_protein_326924..327074_POSITIVE