Origin IGS: tatttaaaaataaattttccgaataaccaaagagcagacccaattctactctttggttatacttttcttccattagttattggattaaatcaaaaattagtgtataatatcctagggtcgattatacaagtaagatcggctttatattgatttgttatgctttgccttcccactggaataggcttttgatgtaacattttgcaattaatgctgtttaagatttattaatgcttactatttttatagtcgtacaataagaaatttaaatatttatataagtatatttaaagggaagaata .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tattcttccctttaaatatacttatataaatatttaaatttcttattgtacgactataaaaatagtaagcattaataaatcttaaacagcattaattgcaaaatgttacatcaaaagcctattccagtgggaaggcaaagcataacaaatcaatataaagccgatcttacttgtataatcgaccctaggatattatacactaatttttgatttaatccaataactaatggaagaaaagtataaccaaagagtagaattgggtctgctctttggttattcggaaaatttatttttaaata Mask Tandem Repeat Region ================================================ tatttaaaaataaattttccgaataaccaaagagcagacccaattctactctttggttatacttttcttccattagttattggattaaatcaaaaattagtgtataatatcctagggtcgattatacaagtaagatcggctttatattgatttgttatgctttgccttcccactggaataggcttttgatgtaacattttgcaattaatgctgtttaagatttattaatgcttactatttttatagtcgtacaataagaaatttaaatatttatataagtatatttaaagggaagaata Find is-nt database================================================ Query_seq: TDE2071:TDE2072|TDE2071:TDE2072:hypothetical protein:hypothetical protein:->->:2098654..2098952 299 tatttaaaaataaattttccgaataaccaaagagcagacccaattctactctttggttatacttttcttccattagttattggattaaatcaaaaattagtgtataatatcctagggtcgattatacaagtaagatcggctttatattgatttgttatgctttgccttcccactggaataggcttttgatgtaacattttgcaattaatgctgtttaagatttattaatgcttactatttttatagtcgtacaataagaaatttaaatatttatataagtatatttaaagggaagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2071:TDE2072|TDE2071:TDE2072:hypothetical protein:hypothetical protein:->->:2098654..2098952 299 tatttaaaaataaattttccgaataaccaaagagcagacccaattctactctttggttatacttttcttccattagttattggattaaatcaaaaattagtgtataatatcctagggtcgattatacaagtaagatcggctttatattgatttgttatgctttgccttcccactggaataggcttttgatgtaacattttgcaattaatgctgtttaagatttattaatgcttactatttttatagtcgtacaataagaaatttaaatatttatataagtatatttaaagggaagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2071:TDE2072|TDE2071:TDE2072:hypothetical protein:hypothetical protein:->->:2098654..2098952 299 tatttaaaaataaattttccgaataaccaaagagcagacccaattctactctttggttatacttttcttccattagttattggattaaatcaaaaattagtgtataatatcctagggtcgattatacaagtaagatcggctttatattgatttgttatgctttgccttcccactggaataggcttttgatgtaacattttgcaattaatgctgtttaagatttattaatgcttactatttttatagtcgtacaataagaaatttaaatatttatataagtatatttaaagggaagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatttaaaaataaattttccgaataaccaaagagcagacccaattctactctttggttatacttttcttccattagttattggattaaatcaaaaattagtgtataatatcctagggtcgattatacaagtaagatcggctttatattgatttgttatgctttgccttcccactggaataggcttttgatgtaacattttgcaattaatgctgtttaagatttattaatgcttactatttttatagtcgtacaataagaaatttaaatatttatataagtatatttaaagggaagaata Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 10 End: 147 ......... M N F P N N Q R A D P I L L F G Y T F L P L V I G L N Q K L V Y N I L G S I I Q V R S A L Y ........................................................................................................................................................ Protein_Len: 43 Strand: - Start: 93 End: 221 ............................................................................................ F N T Y L I R P D I I C T L D A K Y Q N T I S Q R G V P I P K Q H L M K C N I S N L M .............................................................................. tatttaaaaataaattttccgaataaccaaagagcagacccaattctactctttggttatacttttcttccattagttattggattaaatcaaaaattagtgtataatatcctagggtcgattatacaagtaagatcggctttatattgatttgttatgctttgccttcccactggaataggcttttgatgtaacattttgcaattaatgctgtttaagatttattaatgcttactatttttatagtcgtacaataagaaatttaaatatttatataagtatatttaaagggaagaata 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: 84 Start: 79 End: 108 ..............................................................................ATTGGATTAAATCAAAAATTAGTGTATAAT............................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatttaaaaataaattttccgaataaccaaagagcagacccaattctactctttggttatacttttcttccattagttattggattaaatcaaaaattagtgtataatatcctagggtcgattatacaagtaagatcggctttatattgatttgttatgctttgccttcccactggaataggcttttgatgtaacattttgcaattaatgctgtttaagatttattaatgcttactatttttatagtcgtacaataagaaatttaaatatttatataagtatatttaaagggaagaata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.8 Tail_Score: -4.72631 Start: 21 End: 62 Full_Region: AAAAATAAATTTTCC GAATAACCAAAGAGCAGA CCCAAT TCTACTCTTTGGTTATAC TTTTCTTCCATTAGT ....................GAATAACCAAAGAGCAGACCCAATTCTACTCTTTGGTTATAC............................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 93 HP_score: -11.6 Tail_Score: -3.6279 Start: 27 End: 56 Full_Region: ggaagaaaagtataa ccaaagagtaga attggg tctgctctttgg ttattcggaaaattt ..........................ccaaagagtagaattgggtctgctctttgg................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 61 HP_score: -4.3 Tail_Score: -4.07618 Start: 32 End: 51 Full_Region: aaaagtataaccaaa gagtaga attggg tctgctc tttggttattcggaa ...............................gagtagaattgggtctgctc........................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: TDE2071:TDE2072|TDE2071:TDE2072:hypothetical protein:hypothetical protein:->->:2098654..2098952 299 tatttaaaaataaattttccgaataaccaaagagcagacccaattctactctttggttatacttttcttccattagttattggattaaatcaaaaattagtgtataatatcctagggtcgattatacaagtaagatcggctttatattgatttgttatgctttgccttcccactggaataggcttttgatgtaacattttgcaattaatgctgtttaagatttattaatgcttactatttttatagtcgtacaataagaaatttaaatatttatataagtatatttaaagggaagaata Intra-Species Hit: Count: 1 Min: 1 Max: 299 Len: 299 Subject: NC_002967_TDE2071_TDE2072|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2098654,2098952]|299 HSP 1 e-value: 1.0E-168 bit: 593.0 Len: 299 Query Start:1 Query End:299 Subject Strand: POSITIVE Subject Start: 1 Subject End: 299 tatttaaaaataaattttccgaataaccaaagagcagacccaattctactctttggttatacttttcttccattagttattggattaaatcaaaaattagtgtataatatcctagggtcgattatacaagtaagatcggctttatattgatttgttatgctttgccttcccactggaataggcttttgatgtaacattttgcaattaatgctgtttaagatttattaatgcttactatttttatagtcgtacaataagaaatttaaatatttatataagtatatttaaagggaagaata tatttaaaaataaattttccgaataaccaaagagcagacccaattctactctttggttatacttttcttccattagttattggattaaatcaaaaattagtgtataatatcctagggtcgattatacaagtaagatcggctttatattgatttgttatgctttgccttcccactggaataggcttttgatgtaacattttgcaattaatgctgtttaagatttattaatgcttactatttttatagtcgtacaataagaaatttaaatatttatataagtatatttaaagggaagaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUAAAAAUAAAUUUUCCGAAUAACCAAAGAGCAGACCCAAUUCUACUCUUUGGUUAUACUUUUCUUCCAUUAGUUAUUGGAUUAAAUCAAAAAUUAGUGUAUAAUAUCCUAGGGUCGAUUAUACAAGUAAGAUCGGCUUUAUAUUGAUUUGUUAUGCUUUGCCUUCCCACUGGAAUAGGCUUUUGAUGUAACAUUUUGCAAUUAAUGCUGUUUAAGAUUUAUUAAUGCUUACUAUUUUUAUAGUCGUACAAUAAGAAAUUUAAAUAUUUAUAUAAGUAUAUUUAAAGGGAAGAAUA ......................((((((((((((.(((......))).))))))))))))....(((((((.....((((((...((((((..((((.(((((.((((....(((((((((((.((....)).)))))))))))....((..((((((((...(((((((....)))..))))....).)))))))..))...)))))))))))))..))))))....(((..(((((....))))).)))))))))....(((((((((..........))))))))).))))))).. (-67.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUCUUCCCUUUAAAUAUACUUAUAUAAAUAUUUAAAUUUCUUAUUGUACGACUAUAAAAAUAGUAAGCAUUAAUAAAUCUUAAACAGCAUUAAUUGCAAAAUGUUACAUCAAAAGCCUAUUCCAGUGGGAAGGCAAAGCAUAACAAAUCAAUAUAAAGCCGAUCUUACUUGUAUAAUCGACCCUAGGAUAUUAUACACUAAUUUUUGAUUUAAUCCAAUAACUAAUGGAAGAAAAGUAUAACCAAAGAGUAGAAUUGGGUCUGCUCUUUGGUUAUUCGGAAAAUUUAUUUUUAAAUA ..(((((((.(((((((((..........)))))))))....((((((....(((((....)))))......................(((.....))).....((((.((((((((........(((((((.(((.......................)))..)))))))((((((((...((...))..))))))))....)))))))).)))).)))))).....)))))))..(.((((((((((((((((......)))))))))))))))).).....(((((....))))). (-61.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 177 131 217 158 NC_002967:TDE0885|5end_50S_ribosomal_protein_L19_902945..903175_POSITIVE 275 149 101 151 87 NC_002967:TDE2195|5end_RNA_pseudouridylate_synthase_family_protein_2231121..2231351_POSITIVE 274 70 27 174 129 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 273 186 159 231 198 NC_002967:TDE2142|5end_methyl-accepting_chemotaxis_protein_2175769..2175999_POSITIVE 273 188 151 218 183 NC_002967:TDE1011|5end_hypothetical_protein_1038101..1038331_POSITIVE 271 56 12 186 134 NC_002967:TDE2229|5end_hypothetical_protein_2269077..2269307_NEGATIVE 261 222 181 225 184 NC_002967:TDE2379|5end_hypothetical_protein_2408669..2408899_POSITIVE 256 200 154 63 26 NC_002967:TDE0349|5end_phosphoenolpyruvate_synthase,_putative_391093..391323_POSITIVE 255 156 112 82 34 NC_002967:TDE2257|5end_5'-nucleotidase_family_protein_2295104..2295334_NEGATIVE 255 176 136 121 78 NC_002967:TDE2138|5end_ankyrin_repeat_protein_2171631..2171861_POSITIVE 251 199 152 218 174 NC_002967:TDE2640|5end_hypothetical_protein_2680034..2680264_POSITIVE 248 186 141 103 54 NC_002967:TDE0179|5end_hypothetical_protein_212881..213111_NEGATIVE 247 199 155 140 94 NC_002967:TDE2746|5end_type_I_restriction-modification_system,_M_subunit_2802135..2802365_NEGATIVE 245 72 31 90 51 NC_002967:TDE0574|5end_surface_protein,_putative_604925..605155_POSITIVE 244 179 131 206 164 NC_002967:TDE1291|5end_HD_domain_protein_1329213..1329443_NEGATIVE 243 170 126 100 43 NC_002967:TDE1938|5end_hypothetical_protein_1953640..1953870_POSITIVE 243 170 121 103 57 NC_002967:TDE1698|5end_serine/threonine_protein_phosphatase_family_protein_1757184..1757414_NEGATIVE 242 191 161 53 21 NC_002967:TDE2069|5end_endoribonuclease_L-PSP,_putative_2096632..2096862_POSITIVE 242 70 29 100 51 NC_002967:TDE1673|5end_ATP-dependent_protease_ATP-binding_subunit_1726878..1727108_POSITIVE 241 172 133 75 33 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 175 135 124 82 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 294 60 23 68 31 NC_002967:TDE2071|3end_hypothetical_protein_2098593..2098743_POSITIVE 257 149 102 89 36 NC_002967:TDE0073|3end_riboflavin_biosynthesis_protein_RibF,_putative_83159..83309_NEGATIVE 255 176 136 119 76 NC_002967:TDE2137|3end_hypothetical_protein_2171709..2171859_POSITIVE 254 70 23 144 93 NC_002967:TDE0731|3end_hypothetical_protein_770691..770841_NEGATIVE 253 139 91 64 28 NC_002967:TDE2230|3end_hypothetical_protein_2269453..2269603_POSITIVE 248 186 141 130 81 NC_002967:TDE0180|3end_hypothetical_protein_212854..213004_NEGATIVE 247 199 155 137 91 NC_002967:TDE2747|3end_type_I_restriction-modification_system,_R_subunit_2802138..2802288_NEGATIVE 245 191 164 61 30 NC_002967:TDE0814|3end_transcriptional_regulator,_putative_835709..835859_NEGATIVE 244 179 131 105 63 NC_002967:TDE1292|3end_TldD/PmbA_family_protein_1329314..1329464_NEGATIVE 243 202 164 94 58 NC_002967:TDE2437|3end_cyclic_nucleotide_binding_domain_protein_2467418..2467568_NEGATIVE 243 170 121 101 55 NC_002967:TDE1699|3end_hypothetical_protein_1757186..1757336_NEGATIVE 242 171 138 114 88 NC_002967:TDE1725|3end_hypothetical_protein_1778393..1778543_NEGATIVE 242 70 29 107 58 NC_002967:TDE1672|3end_ATP-dependent_Clp_protease,_proteolytic_subunit_ClpP_1726965..1727115_POSITIVE 241 191 158 142 108 NC_002967:TDE2504|3end_O-sialoglycoprotein_endopeptidase_2530097..2530247_POSITIVE 239 170 135 129 80 NC_002967:TDE0696|3end_hypothetical_protein_734210..734360_POSITIVE 239 140 92 72 23 NC_002967:TDE0139|3end_hypothetical_protein_160121..160271_NEGATIVE 238 175 136 123 86 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE 237 204 164 55 11 NC_002967:TDE2663|3end_isoleucyl-tRNA_synthetase_2698616..2698766_NEGATIVE 234 168 130 85 48 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE