Origin IGS: atacgaatccagactatcgtttttatttaaagacttattttccttaataactttttcgatatgaataagtatataatttagagtgccaataggaaaatatttttcaaattcagctataaaaattttttttacaatttctatttcttcatctaaaaatatttttcttaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttaagaaaaatatttttagatgaagaaatagaaattgtaaaaaaaatttttatagctgaatttgaaaaatattttcctattggcactctaaattatatacttattcatatcgaaaaagttattaaggaaaataagtctttaaataaaaacgatagtctggattcgtat Mask Tandem Repeat Region ================================================ atacgaatccagactatcgtttttatttaaagacttattttccttaataactttttcgatatgaataagtatataatttagagtgccaataggaaaatatttttcaaattcagctataaaaattttttttacaatttctatttcttcatctaaaaatatttttcttaaa Find is-nt database================================================ Query_seq: TDE1780:TDE1781|TDE1780:TDE1781:hypothetical protein:hypothetical protein:<-<-:1822399..1822567 169 atacgaatccagactatcgtttttatttaaagacttattttccttaataactttttcgatatgaataagtatataatttagagtgccaataggaaaatatttttcaaattcagctataaaaattttttttacaatttctatttcttcatctaaaaatatttttcttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1780:TDE1781|TDE1780:TDE1781:hypothetical protein:hypothetical protein:<-<-:1822399..1822567 169 atacgaatccagactatcgtttttatttaaagacttattttccttaataactttttcgatatgaataagtatataatttagagtgccaataggaaaatatttttcaaattcagctataaaaattttttttacaatttctatttcttcatctaaaaatatttttcttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1780:TDE1781|TDE1780:TDE1781:hypothetical protein:hypothetical protein:<-<-:1822399..1822567 169 atacgaatccagactatcgtttttatttaaagacttattttccttaataactttttcgatatgaataagtatataatttagagtgccaataggaaaatatttttcaaattcagctataaaaattttttttacaatttctatttcttcatctaaaaatatttttcttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atacgaatccagactatcgtttttatttaaagacttattttccttaataactttttcgatatgaataagtatataatttagagtgccaataggaaaatatttttcaaattcagctataaaaattttttttacaatttctatttcttcatctaaaaatatttttcttaaa Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: - Start: 1 End: 159 Y S D L S D N K N L S K N E K I V K E I H I L I Y N L T G I P F Y K E F E A I F I K K V I E I E E D L F M .......... atacgaatccagactatcgtttttatttaaagacttattttccttaataactttttcgatatgaataagtatataatttagagtgccaataggaaaatatttttcaaattcagctataaaaattttttttacaatttctatttcttcatctaaaaatatttttcttaaa 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================================================ atacgaatccagactatcgtttttatttaaagacttattttccttaataactttttcgatatgaataagtatataatttagagtgccaataggaaaatatttttcaaattcagctataaaaattttttttacaatttctatttcttcatctaaaaatatttttcttaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1780:TDE1781|TDE1780:TDE1781:hypothetical protein:hypothetical protein:<-<-:1822399..1822567 169 atacgaatccagactatcgtttttatttaaagacttattttccttaataactttttcgatatgaataagtatataatttagagtgccaataggaaaatatttttcaaattcagctataaaaattttttttacaatttctatttcttcatctaaaaatatttttcttaaa Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: NC_002967_TDE1780_TDE1781|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1822399,1822567]|169 HSP 1 e-value: 6.0E-77 bit: 287.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 atacgaatccagactatcgtttttatttaaagacttattttccttaataactttttcgatatgaataagtatataatttagagtgccaataggaaaatatttttcaaattcagctataaaaannnnnnnnacaatttctatttcttcatctaaaaatatttttcttaaa atacgaatccagactatcgtttttatttaaagacttattttccttaataactttttcgatatgaataagtatataatttagagtgccaataggaaaatatttttcaaattcagctataaaaattttttttacaatttctatttcttcatctaaaaatatttttcttaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACGAAUCCAGACUAUCGUUUUUAUUUAAAGACUUAUUUUCCUUAAUAACUUUUUCGAUAUGAAUAAGUAUAUAAUUUAGAGUGCCAAUAGGAAAAUAUUUUUCAAAUUCAGCUAUAAAAAUUUUUUUUACAAUUUCUAUUUCUUCAUCUAAAAAUAUUUUUCUUAAA ..........(((..(..(((((((..(.((((..(((((((((.....(((((....(((((......))))).....)))))......))))))))).................(((((.....)))))...........)))).)..)))))))..)..))).... (-17.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAGAAAAAUAUUUUUAGAUGAAGAAAUAGAAAUUGUAAAAAAAAUUUUUAUAGCUGAAUUUGAAAAAUAUUUUCCUAUUGGCACUCUAAAUUAUAUACUUAUUCAUAUCGAAAAAGUUAUUAAGGAAAAUAAGUCUUUAAAUAAAAACGAUAGUCUGGAUUCGUAU ...((((......(((((((((..((..(((((((((........)))))))))..))..))))))))).(((((((((.((((....)))).......((((.(((.....))).)))).....)))))))))..)))).........((((..........)))).. (-27.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 705 90 41 181 132 NC_002967:TDE1780|5end_hypothetical_protein_1822308..1822538_NEGATIVE 240 70 21 127 73 NC_002967:TDE0042|5end_phosphate_acetyltransferase_48676..48906_POSITIVE 203 130 81 114 65 NC_002967:TDE0964|5end_hypothetical_protein_987079..987309_POSITIVE 196 56 17 118 88 NC_002967:TDE0772|5end_50S_ribosomal_protein_L22_809084..809314_POSITIVE 192 129 81 102 55 NC_002967:TDE2289|5end_phosphoribulokinase/uridine_kinase_family_protein_2325764..2325994_POSITIVE 190 43 5 229 187 NC_002967:TDE1919|5end_hypothetical_protein_1939890..1940120_NEGATIVE 188 74 33 130 95 NC_002967:TDE2240|5end_hypothetical_protein_2278422..2278652_NEGATIVE 186 46 3 108 59 NC_002967:TDE1088|5end_hypothetical_protein_1119955..1120185_NEGATIVE 184 63 21 123 86 NC_002967:TDE0310|5end_hypothetical_protein_341620..341850_POSITIVE 182 44 3 111 77 NC_002967:TDE2340|5end_FMN-binding_domain_protein_2377855..2378085_NEGATIVE 180 48 15 179 151 NC_002967:TDE0891|5end_transcriptional_regulator,_putative_907592..907822_POSITIVE 176 60 14 120 79 NC_002967:TDE2505|5end_hypothetical_protein_2530125..2530355_POSITIVE 175 88 42 134 87 NC_002967:TDE2444|5end_hypothetical_protein_2474212..2474442_NEGATIVE 174 58 11 196 151 NC_002967:TDE2197|5end_hypothetical_protein_2232848..2233078_NEGATIVE 174 46 1 90 27 NC_002967:TDE1387|5end_RNA_pseudouridylate_synthase_family_protein_1427732..1427962_NEGATIVE 174 42 8 152 117 NC_002967:TDE0550|5end_hypothetical_protein_587723..587953_NEGATIVE 173 51 20 113 85 NC_002967:TDE1588|5end_tryptophanyl-tRNA_synthetase_1635813..1636043_POSITIVE 173 150 102 168 121 NC_002967:TDE1534|5end_hypothetical_protein_1579128..1579358_NEGATIVE 172 49 4 200 166 NC_002967:TDE2096|5end_hypothetical_protein_2123200..2123430_POSITIVE 169 117 85 58 25 NC_002967:TDE2684|5end_hypothetical_protein_2724848..2725078_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 203 130 81 117 68 NC_002967:TDE0963|3end_DNA_polymerase_IV_987162..987312_POSITIVE 196 56 17 107 77 NC_002967:TDE0771|3end_ribosomal_protein_S19_809153..809303_POSITIVE 191 50 2 64 13 NC_002967:TDE2719|3end_hypothetical_protein_2777015..2777165_POSITIVE 188 74 33 46 11 NC_002967:TDE2241|3end_glycosyl_transferase,_group_2_family_protein_2278506..2278656_NEGATIVE 186 46 3 93 44 NC_002967:TDE1089|3end_hypothetical_protein_1119970..1120120_NEGATIVE 184 63 21 119 82 NC_002967:TDE0309|3end_lipoprotein,_putative_341696..341846_POSITIVE 182 44 3 100 66 NC_002967:TDE2341|3end_membrane-associated_zinc_metalloprotease,_putative_2377866..2378016_NEGATIVE 180 48 15 111 83 NC_002967:TDE0890|3end_hypothetical_protein_907604..907754_POSITIVE 174 58 11 142 97 NC_002967:TDE2198|3end_pyruvate-ferredoxin_oxidoreductase_2232902..2233052_NEGATIVE 174 42 8 132 97 NC_002967:TDE0551|3end_hypothetical_protein_587743..587893_NEGATIVE 173 51 20 105 77 NC_002967:TDE1587|3end_aspartyl-tRNA_synthetase_1635885..1636035_POSITIVE 169 57 15 123 84 NC_002967:TDE0054|3end_flagellar_biosynthesis_protein_63636..63786_POSITIVE 166 66 29 117 68 NC_002967:TDE0681|3end_protein_export_protein_SecD_718856..719006_NEGATIVE 164 47 6 108 62 NC_002967:TDE0196|3end_hypothetical_protein_232845..232995_POSITIVE 163 150 101 105 52 NC_002967:TDE1820|3end_hypothetical_protein_1854297..1854447_NEGATIVE 161 150 103 99 54 NC_002967:TDE1889|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_1909500..1909650_NEGATIVE 161 116 78 137 91 NC_002967:TDE1338|3end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_1375823..1375973_POSITIVE 159 44 5 60 27 NC_002967:TDE2683|3end_sigma_factor_WhiG_2723367..2723517_NEGATIVE 158 43 4 99 61 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 157 95 69 52 32 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE