Origin IGS: agacaggataagttgtcctttattttctggtttttcgtttttcttgccaaatatgttatttagaattcccataatatcaacctccgttatttagtataattatacccattttttatgcaatatcaacgtactgccattacatgttcttgtgtttctgatttttaccgtattatagtca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgactataatacggtaaaaatcagaaacacaagaacatgtaatggcagtacgttgatattgcataaaaaatgggtataattatactaaataacggaggttgatattatgggaattctaaataacatatttggcaagaaaaacgaaaaaccagaaaataaaggacaacttatcctgtct Mask Tandem Repeat Region ================================================ agacaggataagttgtcctttattttctggtttttcgtttttcttgccaaatatgttatttagaattcccataatatcaacctccgttatttagtataattatacccattttttatgcaatatcaacgtactgccattacatgttcttgtgtttctgatttttaccgtattatagtca Find is-nt database================================================ Query_seq: TDE0513:TDE0514|TDE0513:TDE0514:hypothetical protein:hypothetical protein:<-<-:562332..562509 178 agacaggataagttgtcctttattttctggtttttcgtttttcttgccaaatatgttatttagaattcccataatatcaacctccgttatttagtataattatacccattttttatgcaatatcaacgtactgccattacatgttcttgtgtttctgatttttaccgtattatagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0513:TDE0514|TDE0513:TDE0514:hypothetical protein:hypothetical protein:<-<-:562332..562509 178 agacaggataagttgtcctttattttctggtttttcgtttttcttgccaaatatgttatttagaattcccataatatcaacctccgttatttagtataattatacccattttttatgcaatatcaacgtactgccattacatgttcttgtgtttctgatttttaccgtattatagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0513:TDE0514|TDE0513:TDE0514:hypothetical protein:hypothetical protein:<-<-:562332..562509 178 agacaggataagttgtcctttattttctggtttttcgtttttcttgccaaatatgttatttagaattcccataatatcaacctccgttatttagtataattatacccattttttatgcaatatcaacgtactgccattacatgttcttgtgtttctgatttttaccgtattatagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agacaggataagttgtcctttattttctggtttttcgtttttcttgccaaatatgttatttagaattcccataatatcaacctccgttatttagtataattatacccattttttatgcaatatcaacgtactgccattacatgttcttgtgtttctgatttttaccgtattatagtca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 1 End: 90 S L I L Q G K N E P K E N K K G F I N N L I G M I D V E T M ........................................................................................ agacaggataagttgtcctttattttctggtttttcgtttttcttgccaaatatgttatttagaattcccataatatcaacctccgttatttagtataattatacccattttttatgcaatatcaacgtactgccattacatgttcttgtgtttctgatttttaccgtattatagtca 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================================================ agacaggataagttgtcctttattttctggtttttcgtttttcttgccaaatatgttatttagaattcccataatatcaacctccgttatttagtataattatacccattttttatgcaatatcaacgtactgccattacatgttcttgtgtttctgatttttaccgtattatagtca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0513:TDE0514|TDE0513:TDE0514:hypothetical protein:hypothetical protein:<-<-:562332..562509 178 agacaggataagttgtcctttattttctggtttttcgtttttcttgccaaatatgttatttagaattcccataatatcaacctccgttatttagtataattatacccattttttatgcaatatcaacgtactgccattacatgttcttgtgtttctgatttttaccgtattatagtca Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: NC_002967_TDE0513_TDE0514|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[562332,562509]|178 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 agacaggataagttgtcctttattttctggtttttcgtttttcttgccaaatatgttatttagaattcccataatatcaacctccgttatttagtataattatacccattttttatgcaatatcaacgtactgccattacatgttcttgtgtttctgatttttaccgtattatagtca agacaggataagttgtcctttattttctggtttttcgtttttcttgccaaatatgttatttagaattcccataatatcaacctccgttatttagtataattatacccattttttatgcaatatcaacgtactgccattacatgttcttgtgtttctgatttttaccgtattatagtca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACAGGAUAAGUUGUCCUUUAUUUUCUGGUUUUUCGUUUUUCUUGCCAAAUAUGUUAUUUAGAAUUCCCAUAAUAUCAACCUCCGUUAUUUAGUAUAAUUAUACCCAUUUUUUAUGCAAUAUCAACGUACUGCCAUUACAUGUUCUUGUGUUUCUGAUUUUUACCGUAUUAUAGUCA .(((.((((.....))))..........(((..............))).((((((.((.((((((...................((((((...((((((..(.......)..))))))...)).)))).........((((......)))).))))))....)).))))))...))). (-19.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACUAUAAUACGGUAAAAAUCAGAAACACAAGAACAUGUAAUGGCAGUACGUUGAUAUUGCAUAAAAAAUGGGUAUAAUUAUACUAAAUAACGGAGGUUGAUAUUAUGGGAAUUCUAAAUAACAUAUUUGGCAAGAAAAACGAAAAACCAGAAAAUAAAGGACAACUUAUCCUGUCU ...((((((((...(((...((..............((((((((.(((....))).))))))))........(((((....)))))........))..))).)))))))).................(((((................))))).......(((((........))))) (-21.79) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 794 50 1 141 92 NC_002967:TDE0513|5end_hypothetical_protein_562241..562471_NEGATIVE 276 48 1 180 129 NC_002967:TDE2405|5end_hypothetical_protein_2432050..2432280_NEGATIVE 261 47 5 61 23 NC_002967:TDE1647|5end_DNA-binding_protein_1696502..1696732_NEGATIVE 251 164 127 192 150 NC_002967:TDE1556|5end_hypothetical_protein_1598787..1599017_POSITIVE 247 48 5 103 57 NC_002967:TDE0898|5end_hypothetical_protein_915878..916108_POSITIVE 246 48 1 53 4 NC_002967:TDE0997|5end_glutamate_dehydrogenase_1025283..1025513_NEGATIVE 245 139 95 93 32 NC_002967:TDE0452|5end_hypothetical_protein_510143..510373_NEGATIVE 238 48 4 134 93 NC_002967:TDE0610|5end_3-hydroxyacyl-CoA_dehydrogenase,_putative_647286..647516_NEGATIVE 234 148 109 84 40 NC_002967:TDE1722|5end_hypothetical_protein_1776085..1776315_POSITIVE 233 48 4 79 20 NC_002967:TDE2303|5end_hypothetical_protein_2343055..2343285_POSITIVE 232 46 1 211 158 NC_002967:TDE1469|5end_conserved_hypothetical_protein_TIGR00150_1517764..1517994_NEGATIVE 229 43 2 61 22 NC_002967:TDE1914|5end_Holliday_junction_DNA_helicase_RuvB_1931920..1932150_NEGATIVE 229 48 8 209 161 NC_002967:TDE1627|5end_glycine_cleavage_system_T_protein_1676411..1676641_NEGATIVE 229 48 1 60 2 NC_002967:TDE1114|5end_transcriptional_regulator,_TetR_family_1148905..1149135_NEGATIVE 227 70 26 151 93 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 227 48 11 130 92 NC_002967:TDE2038|5end_UVR_domain_protein_2068201..2068431_NEGATIVE 225 87 65 221 199 NC_002967:TDE2316|5end_hypothetical_protein_2353080..2353310_POSITIVE 221 170 122 133 71 NC_002967:TDE1598|5end_ABC_transporter,_ATP-binding_protein_1648910..1649140_NEGATIVE 220 166 127 46 3 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 219 48 1 106 42 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 53 11 63 23 NC_002967:TDE2719|3end_hypothetical_protein_2777015..2777165_POSITIVE 261 47 5 77 39 NC_002967:TDE1648|3end_hypothetical_protein_1696486..1696636_NEGATIVE 248 128 81 112 71 NC_002967:TDE1907|3end_holo-(acyl-carrier-protein)_synthase_1924726..1924876_NEGATIVE 247 48 5 83 37 NC_002967:TDE0897|3end_ABC_transporter,_ATP-binding/permease_protein_915938..916088_POSITIVE 245 139 95 93 32 NC_002967:TDE0453|3end_hypothetical_protein_510143..510293_NEGATIVE 244 169 129 118 84 NC_002967:TDE0156|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_180344..180494_NEGATIVE 242 169 128 61 14 NC_002967:TDE2139|3end_hypothetical_protein_2172897..2173047_POSITIVE 242 57 11 55 5 NC_002967:TDE1192|3end_hypothetical_protein_1219573..1219723_POSITIVE 238 48 4 53 12 NC_002967:TDE0612|3end_hypothetical_protein_647367..647517_NEGATIVE 238 48 4 141 100 NC_002967:TDE0611|3end_hypothetical_protein_647279..647429_NEGATIVE 234 148 109 47 3 NC_002967:TDE1721|3end_radical_SAM_domain_protein_1776128..1776278_POSITIVE 233 48 4 79 20 NC_002967:TDE2302|3end_HD_domain_protein_2343135..2343285_POSITIVE 229 43 2 53 14 NC_002967:TDE1915|3end_alcohol_dehydrogenase,_iron-containing_1931928..1932078_NEGATIVE 229 48 8 141 93 NC_002967:TDE1628|3end_hypothetical_protein_1676479..1676629_NEGATIVE 228 48 8 117 59 NC_002967:TDE0406|3end_hypothetical_protein_458929..459079_POSITIVE 227 48 11 133 95 NC_002967:TDE2039|3end_lipoprotein_releasing_system,_permease_protein,_putative_2068198..2068348_NEGATIVE 221 170 122 123 61 NC_002967:TDE1599|3end_ABC_transporter,_ATP-binding/permease_protein_1648920..1649070_NEGATIVE 220 166 127 82 39 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 219 88 41 86 41 NC_002967:TDE0226|3end_hypothetical_protein_256394..256544_NEGATIVE 218 53 13 132 96 NC_002967:TDE0722|3end_lipoprotein,_putative_759864..760014_POSITIVE