Origin IGS: aacaacctccatcaatgataatctacaattttttatacctgattaacaggtataagtcaagagtataaataatattttttatattaatactttaacattcatactttgtcatttttattatattgatattttgcagtttttagagtattgtctttatatggttagccaaataattaaactgtccttataaaactttccacaatttataggggcaatcgcaaaaagtggaaaaattatattttaaggaaaatttt .........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 aaaattttccttaaaatataatttttccactttttgcgattgcccctataaattgtggaaagttttataaggacagtttaattatttggctaaccatataaagacaatactctaaaaactgcaaaatatcaatataataaaaatgacaaagtatgaatgttaaagtattaatataaaaaatattatttatactcttgacttatacctgttaatcaggtataaaaaattgtagattatcattgatggaggttgtt Mask Tandem Repeat Region ================================================ aacaacctccatcaatgataatctacaattttttatacctgattaacaggtataagtcaagagtataaataatattttttatattaatactttaacattcatactttgtcatttttattatattgatattttgcagtttttagagtattgtctttatatggttagccaaataattaaactgtccttataaaactttccacaatttataggggcaatcgcaaaaagtggaaaaattatattttaaggaaaatttt Find is-nt database================================================ Query_seq: TDE1610:TDE1611|TDE1610:TDE1611:DNA-binding protein:hypothetical protein:<-->:1659587..1659840 254 aacaacctccatcaatgataatctacaattttttatacctgattaacaggtataagtcaagagtataaataatattttttatattaatactttaacattcatactttgtcatttttattatattgatattttgcagtttttagagtattgtctttatatggttagccaaataattaaactgtccttataaaactttccacaatttataggggcaatcgcaaaaagtggaaaaattatattttaaggaaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1610:TDE1611|TDE1610:TDE1611:DNA-binding protein:hypothetical protein:<-->:1659587..1659840 254 aacaacctccatcaatgataatctacaattttttatacctgattaacaggtataagtcaagagtataaataatattttttatattaatactttaacattcatactttgtcatttttattatattgatattttgcagtttttagagtattgtctttatatggttagccaaataattaaactgtccttataaaactttccacaatttataggggcaatcgcaaaaagtggaaaaattatattttaaggaaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1610:TDE1611|TDE1610:TDE1611:DNA-binding protein:hypothetical protein:<-->:1659587..1659840 254 aacaacctccatcaatgataatctacaattttttatacctgattaacaggtataagtcaagagtataaataatattttttatattaatactttaacattcatactttgtcatttttattatattgatattttgcagtttttagagtattgtctttatatggttagccaaataattaaactgtccttataaaactttccacaatttataggggcaatcgcaaaaagtggaaaaattatattttaaggaaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaacctccatcaatgataatctacaattttttatacctgattaacaggtataagtcaagagtataaataatattttttatattaatactttaacattcatactttgtcatttttattatattgatattttgcagtttttagagtattgtctttatatggttagccaaataattaaactgtccttataaaactttccacaatttataggggcaatcgcaaaaagtggaaaaattatattttaaggaaaatttt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 65 End: 187 ................................................................ M N N I F Y I N T L T F I L C H F Y Y I D I L Q F L E Y C L Y M V S Q I I K L S L ................................................................... aacaacctccatcaatgataatctacaattttttatacctgattaacaggtataagtcaagagtataaataatattttttatattaatactttaacattcatactttgtcatttttattatattgatattttgcagtttttagagtattgtctttatatggttagccaaataattaaactgtccttataaaactttccacaatttataggggcaatcgcaaaaagtggaaaaattatattttaaggaaaatttt 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: 32 End: 61 ...............................CTTGACTTATACCTGTTAATCAGGTATAAA................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 122 End: 151 .........................................................................................................................ATTGATATTTTGCAGTTTTTAGAGTATTGT....................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 203 End: 232 ..........................................................................................................................................................................................................TTTTCCACTTTTTGCGATTGCCCCTATAAA...................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacaacctccatcaatgataatctacaattttttatacctgattaacaggtataagtcaagagtataaataatattttttatattaatactttaacattcatactttgtcatttttattatattgatattttgcagtttttagagtattgtctttatatggttagccaaataattaaactgtccttataaaactttccacaatttataggggcaatcgcaaaaagtggaaaaattatattttaaggaaaatttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 50 HP_score: -2.4 Tail_Score: -4.06786 Start: 70 End: 86 Full_Region: tgaatgttaaagtat taatat aaaaa atatta tttatactcttgact .....................................................................taatataaaaaatatta........................................................................................................................................................................ Find igs database================================================ Query_seq: TDE1610:TDE1611|TDE1610:TDE1611:DNA-binding protein:hypothetical protein:<-->:1659587..1659840 254 aacaacctccatcaatgataatctacaattttttatacctgattaacaggtataagtcaagagtataaataatattttttatattaatactttaacattcatactttgtcatttttattatattgatattttgcagtttttagagtattgtctttatatggttagccaaataattaaactgtccttataaaactttccacaatttataggggcaatcgcaaaaagtggaaaaattatattttaaggaaaatttt Intra-Species Hit: Count: 1 Min: 1 Max: 254 Len: 254 Subject: NC_002967_TDE1610_TDE1611|DNA-binding protein:hypothetical protein|NEGATIVE:POSITIVE|[1659587,1659840]|254 HSP 1 e-value: 5.0E-63 bit: 242.0 Len: 122 Query Start:133 Query End:254 Subject Strand: POSITIVE Subject Start: 133 Subject End: 254 ....................................................................................................................................gcagtttttagagtattgtctttatatggttagccaaataattaaactgtccttataaaactttccacaatttataggggcaatcgcaaaaagtggaaaaattatattttaaggaaaatttt ....................................................................................................................................gcagtttttagagtattgtctttatatggttagccaaataattaaactgtccttataaaactttccacaatttataggggcaatcgcaaaaagtggaaaaattatattttaaggaaaatttt HSP 2 e-value: 8.0E-28 bit: 125.0 Len: 63 Query Start:1 Query End:63 Subject Strand: POSITIVE Subject Start: 1 Subject End: 63 aacaacctccatcaatgataatctacaattttttatacctgattaacaggtataagtcaagag............................................................................................................................................................................................... aacaacctccatcaatgataatctacaattttttatacctgattaacaggtataagtcaagag............................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAACCUCCAUCAAUGAUAAUCUACAAUUUUUUAUACCUGAUUAACAGGUAUAAGUCAAGAGUAUAAAUAAUAUUUUUUAUAUUAAUACUUUAACAUUCAUACUUUGUCAUUUUUAUUAUAUUGAUAUUUUGCAGUUUUUAGAGUAUUGUCUUUAUAUGGUUAGCCAAAUAAUUAAACUGUCCUUAUAAAACUUUCCACAAUUUAUAGGGGCAAUCGCAAAAAGUGGAAAAAUUAUAUUUUAAGGAAAAUUUU .......(((...((((((((..........((((((((((.....))))))))))...(((((((...((((((.....)))))))))))))............)))))))).........((.((.((((((......(((((......)))))..(((....)))...........((((((((((((...........))))))))))))...)))))).)).))...............)))....... (-48.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUUUCCUUAAAAUAUAAUUUUUCCACUUUUUGCGAUUGCCCCUAUAAAUUGUGGAAAGUUUUAUAAGGACAGUUUAAUUAUUUGGCUAACCAUAUAAAGACAAUACUCUAAAAACUGCAAAAUAUCAAUAUAAUAAAAAUGACAAAGUAUGAAUGUUAAAGUAUUAAUAUAAAAAAUAUUAUUUAUACUCUUGACUUAUACCUGUUAAUCAGGUAUAAAAAAUUGUAGAUUAUCAUUGAUGGAGGUUGUU .(((((.(((((((((............((((((..(((((.........)))))..))))))))).)))))).)))))..((((.(((....))).)))).((((((.(((((....((((((......................(((((((((((((......(((....)))........)))))))))).)))..(((((((((.....)))))))))....)))))).(((....)))))))))))))) (-50.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 759 50 1 141 92 NC_002967:TDE1610|5end_DNA-binding_protein_1659496..1659726_NEGATIVE 275 247 209 66 27 NC_002967:TDE1480|5end_hypothetical_protein_1525581..1525811_NEGATIVE 267 229 182 64 11 NC_002967:TDE2739|5end_hypothetical_protein_2794673..2794903_POSITIVE 265 230 184 51 10 NC_002967:TDE1651|5end_BioY_family_protein_1698732..1698962_NEGATIVE 239 186 143 227 185 NC_002967:TDE0325|5end_hypothetical_protein_358051..358281_POSITIVE 235 168 127 142 99 NC_002967:TDE2577|5end_hypothetical_protein_2602903..2603133_NEGATIVE 234 220 176 145 104 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 229 230 181 138 99 NC_002967:TDE1021|5end_lipoprotein,_putative_1053564..1053794_NEGATIVE 224 139 95 154 109 NC_002967:TDE2424|5end_50S_ribosomal_protein_L1_2454717..2454947_NEGATIVE 223 247 208 57 10 NC_002967:TDE0834|5end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854863..855093_NEGATIVE 222 150 104 210 156 NC_002967:TDE2140|5end_protease_II_2175140..2175370_NEGATIVE 222 80 35 85 39 NC_002967:TDE1020|5end_dicarboxylate_transporter,_periplasmic_dicarboxylate-binding_protein,_putative_1052593..1052823_NEGATIVE 220 49 3 121 78 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 217 165 123 215 174 NC_002967:TDE0822|5end_hypothetical_protein_844467..844697_POSITIVE 217 165 123 126 85 NC_002967:TDE0821|5end_hypothetical_protein_844378..844608_POSITIVE 217 229 183 52 1 NC_002967:TDE0334|5end_hypothetical_protein_374048..374278_NEGATIVE 215 198 159 113 65 NC_002967:TDE2267|5end_HRDC_domain_protein_2304464..2304694_NEGATIVE 212 48 6 211 162 NC_002967:TDE1217|5end_flagellar_assembly_protein_1249511..1249741_POSITIVE 209 219 179 201 152 NC_002967:TDE2165|5end_hydrogenase_accessory_protein_HypB_2197715..2197945_NEGATIVE 207 167 122 52 6 NC_002967:TDE1695|5end_CoA-substrate-specific_enzyme_activase_domain_protein_1754000..1754230_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 235 168 127 145 102 NC_002967:TDE2578|3end_hypothetical_protein_2602900..2603050_NEGATIVE 223 220 179 39 1 NC_002967:TDE1909|3end_conserved_hypothetical_protein_TIGR00159_1926048..1926198_NEGATIVE 223 247 208 53 6 NC_002967:TDE0835|3end_NADH-ubiquinone_oxidoreductase_854867..855017_NEGATIVE 222 80 35 88 42 NC_002967:TDE1021|3end_lipoprotein,_putative_1052590..1052740_NEGATIVE 220 49 3 109 66 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 215 138 95 151 107 NC_002967:TDE2425|3end_50S_ribosomal_protein_L11_2454719..2454869_NEGATIVE 214 228 199 80 52 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 210 219 174 50 4 NC_002967:TDE2673|3end_hypothetical_protein_2711670..2711820_NEGATIVE 204 110 62 45 9 NC_002967:TDE1482|3end_peptidase,_M24_family_protein_1528733..1528883_POSITIVE 204 167 125 139 80 NC_002967:TDE0117|3end_lipoprotein,_putative_136607..136757_POSITIVE 201 199 156 55 8 NC_002967:TDE2008|3end_ABC_transporter,_ATP-binding/permease_protein_2030415..2030565_POSITIVE 200 118 71 138 93 NC_002967:TDE0418|3end_lipoprotein,_putative_470893..471043_POSITIVE 198 167 127 124 92 NC_002967:TDE0575|3end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_606252..606402_NEGATIVE 196 228 198 35 8 NC_002967:TDE2629|3end_peptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_2670962..2671112_POSITIVE 196 186 157 79 51 NC_002967:TDE0968|3end_translation_elongation_factor_P_992563..992713_NEGATIVE 195 214 191 151 125 NC_002967:TDE2228|3end_aminoacyl-histidine_dipeptidase,_putative_2267287..2267437_NEGATIVE 195 232 193 78 34 NC_002967:TDE1881|3end_methyltransferase,_putative_1903631..1903781_POSITIVE 194 168 129 49 4 NC_002967:TDE2302|3end_HD_domain_protein_2343135..2343285_POSITIVE 194 85 50 75 42 NC_002967:TDE0363|3end_hypothetical_protein_409536..409686_NEGATIVE 193 220 174 144 91 NC_002967:TDE2387|3end_4-alpha-glucanotransferase_2417742..2417892_POSITIVE