Origin IGS: cggagttacggtttacaggtgatcaggtgggtccgaatgctgtccgaaaacctatgggcggtggataaaaagcttttttctttaaataaagaaaatgcttaaatcttatctgattttaatcactgtcttatgtttctccggtttgtttctttgttaagcttgtttttcggttacgaaagaccggttaactttttaatctcgtcatttttaatgcgggaaatattagacttgcctacgtcttttaggaggatctc .........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 gagatcctcctaaaagacgtaggcaagtctaatatttcccgcattaaaaatgacgagattaaaaagttaaccggtctttcgtaaccgaaaaacaagcttaacaaagaaacaaaccggagaaacataagacagtgattaaaatcagataagatttaagcattttctttatttaaagaaaaaagctttttatccaccgcccataggttttcggacagcattcggacccacctgatcacctgtaaaccgtaactccg Mask Tandem Repeat Region ================================================ cggagttacggtttacaggtgatcaggtgggtccgaatgctgtccgaaaacctatgggcggtggataaaaagcttttttctttaaataaagaaaatgcttaaatcttatctgattttaatcactgtcttatgtttctccggtttgtttctttgttaagcttgtttttcggttacgaaagaccggttaactttttaatctcgtcatttttaatgcgggaaatattagacttgcctacgtcttttaggaggatctc Find is-nt database================================================ Query_seq: TDE0764:TDE0765|TDE0764:TDE0765:hypothetical protein:translation elongation factor Tu:<-->:804618..804871 254 cggagttacggtttacaggtgatcaggtgggtccgaatgctgtccgaaaacctatgggcggtggataaaaagcttttttctttaaataaagaaaatgcttaaatcttatctgattttaatcactgtcttatgtttctccggtttgtttctttgttaagcttgtttttcggttacgaaagaccggttaactttttaatctcgtcatttttaatgcgggaaatattagacttgcctacgtcttttaggaggatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0764:TDE0765|TDE0764:TDE0765:hypothetical protein:translation elongation factor Tu:<-->:804618..804871 254 cggagttacggtttacaggtgatcaggtgggtccgaatgctgtccgaaaacctatgggcggtggataaaaagcttttttctttaaataaagaaaatgcttaaatcttatctgattttaatcactgtcttatgtttctccggtttgtttctttgttaagcttgtttttcggttacgaaagaccggttaactttttaatctcgtcatttttaatgcgggaaatattagacttgcctacgtcttttaggaggatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0764:TDE0765|TDE0764:TDE0765:hypothetical protein:translation elongation factor Tu:<-->:804618..804871 254 cggagttacggtttacaggtgatcaggtgggtccgaatgctgtccgaaaacctatgggcggtggataaaaagcttttttctttaaataaagaaaatgcttaaatcttatctgattttaatcactgtcttatgtttctccggtttgtttctttgttaagcttgtttttcggttacgaaagaccggttaactttttaatctcgtcatttttaatgcgggaaatattagacttgcctacgtcttttaggaggatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cggagttacggtttacaggtgatcaggtgggtccgaatgctgtccgaaaacctatgggcggtggataaaaagcttttttctttaaataaagaaaatgcttaaatcttatctgattttaatcactgtcttatgtttctccggtttgtttctttgttaagcttgtttttcggttacgaaagaccggttaactttttaatctcgtcatttttaatgcgggaaatattagacttgcctacgtcttttaggaggatctc Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 103 End: 252 ...................................................................................................... M L S D F N H C L M F L R F V S L L S L F F G Y E R P V N F L I S S F L M R E I L D L P T S F R R I .. cggagttacggtttacaggtgatcaggtgggtccgaatgctgtccgaaaacctatgggcggtggataaaaagcttttttctttaaataaagaaaatgcttaaatcttatctgattttaatcactgtcttatgtttctccggtttgtttctttgttaagcttgtttttcggttacgaaagaccggttaactttttaatctcgtcatttttaatgcgggaaatattagacttgcctacgtcttttaggaggatctc 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================================================ cggagttacggtttacaggtgatcaggtgggtccgaatgctgtccgaaaacctatgggcggtggataaaaagcttttttctttaaataaagaaaatgcttaaatcttatctgattttaatcactgtcttatgtttctccggtttgtttctttgttaagcttgtttttcggttacgaaagaccggttaactttttaatctcgtcatttttaatgcgggaaatattagacttgcctacgtcttttaggaggatctc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -4.6 Tail_Score: -4.82667 Start: 153 End: 189 Full_Region: CCGGTTTGTTTCTTT GTTAAGCTTGTTTTTCG GTTA CGAAAGACCGGTTAAC TTTTTAATCTCGTCA ........................................................................................................................................................GTTAAGCTTGTTTTTCGGTTACGAAAGACCGGTTAAC................................................................. Find igs database================================================ Query_seq: TDE0764:TDE0765|TDE0764:TDE0765:hypothetical protein:translation elongation factor Tu:<-->:804618..804871 254 cggagttacggtttacaggtgatcaggtgggtccgaatgctgtccgaaaacctatgggcggtggataaaaagcttttttctttaaataaagaaaatgcttaaatcttatctgattttaatcactgtcttatgtttctccggtttgtttctttgttaagcttgtttttcggttacgaaagaccggttaactttttaatctcgtcatttttaatgcgggaaatattagacttgcctacgtcttttaggaggatctc Intra-Species Hit: Count: 1 Min: 1 Max: 254 Len: 254 Subject: NC_002967_TDE0764_TDE0765|hypothetical protein:translation elongation factor Tu|NEGATIVE:POSITIVE|[804618,804871]|254 HSP 1 e-value: 1.0E-142 bit: 504.0 Len: 254 Query Start:1 Query End:254 Subject Strand: POSITIVE Subject Start: 1 Subject End: 254 cggagttacggtttacaggtgatcaggtgggtccgaatgctgtccgaaaacctatgggcggtggataaaaagcttttttctttaaataaagaaaatgcttaaatcttatctgattttaatcactgtcttatgtttctccggtttgtttctttgttaagcttgtttttcggttacgaaagaccggttaactttttaatctcgtcatttttaatgcgggaaatattagacttgcctacgtcttttaggaggatctc cggagttacggtttacaggtgatcaggtgggtccgaatgctgtccgaaaacctatgggcggtggataaaaagcttttttctttaaataaagaaaatgcttaaatcttatctgattttaatcactgtcttatgtttctccggtttgtttctttgttaagcttgtttttcggttacgaaagaccggttaactttttaatctcgtcatttttaatgcgggaaatattagacttgcctacgtcttttaggaggatctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGAGUUACGGUUUACAGGUGAUCAGGUGGGUCCGAAUGCUGUCCGAAAACCUAUGGGCGGUGGAUAAAAAGCUUUUUUCUUUAAAUAAAGAAAAUGCUUAAAUCUUAUCUGAUUUUAAUCACUGUCUUAUGUUUCUCCGGUUUGUUUCUUUGUUAAGCUUGUUUUUCGGUUACGAAAGACCGGUUAACUUUUUAAUCUCGUCAUUUUUAAUGCGGGAAAUAUUAGACUUGCCUACGUCUUUUAGGAGGAUCUC (((((..(((....(((((.((((((((((((((....((((((((........)))))))))))....((((..((((((((....)))))))).))))....))))))))))).....).))))....)))..)))))............(((((.((.((((((((....)))))))).))))))).......(((((.(((.....))))))))......((((((.((((.......))))))).))). (-70.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAUCCUCCUAAAAGACGUAGGCAAGUCUAAUAUUUCCCGCAUUAAAAAUGACGAGAUUAAAAAGUUAACCGGUCUUUCGUAACCGAAAAACAAGCUUAACAAAGAAACAAACCGGAGAAACAUAAGACAGUGAUUAAAAUCAGAUAAGAUUUAAGCAUUUUCUUUAUUUAAAGAAAAAAGCUUUUUAUCCACCGCCCAUAGGUUUUCGGACAGCAUUCGGACCCACCUGAUCACCUGUAAACCGUAACUCCG (((..........(((((.(((((..((((.((.((((((((((.....))).............((((((..((.(((((....))))).))..).)))))............))).)))).)).))))..............(((((((....(((.((((((((....))))))))..))))))))))....)))..)).)))))(((((((...((((......))))....))))...)))...))).. (-47.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1023 60 11 151 102 NC_002967:TDE0764|5end_hypothetical_protein_804527..804757_NEGATIVE 357 46 2 210 159 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 343 63 23 170 130 NC_002967:TDE0151|5end_integral_membrane_protein,_YeeE/YedE_family_173101..173331_NEGATIVE 335 64 24 63 19 NC_002967:TDE0947|5end_translation_elongation_factor_G,_putative_970792..971022_NEGATIVE 322 43 1 67 28 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 317 59 11 193 132 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 314 74 33 33 3 NC_002967:TDE0104|5end_3-dehydroquinate_synthase_124714..124944_NEGATIVE 313 50 1 212 162 NC_002967:TDE2094|5end_hypothetical_protein_2121319..2121549_NEGATIVE 312 43 1 188 144 NC_002967:TDE2717|5end_phosphatidate_cytidylyltransferase,_putative_2774547..2774777_NEGATIVE 310 64 25 219 179 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 308 63 26 81 29 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 303 62 25 229 192 NC_002967:TDE2299|5end_apolipoprotein_N-acyltransferase_2338280..2338510_POSITIVE 303 47 1 178 118 NC_002967:TDE1233|5end_hypothetical_protein_1267203..1267433_POSITIVE 302 59 12 214 170 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 296 61 21 231 171 NC_002967:TDE1590|5end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1637516..1637746_POSITIVE 290 170 121 179 122 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 288 59 12 177 115 NC_002967:TDE1975|5end_hypothetical_protein_1988869..1989099_POSITIVE 288 159 119 68 29 NC_002967:TDE1914|5end_Holliday_junction_DNA_helicase_RuvB_1931920..1932150_NEGATIVE 285 70 25 148 100 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 285 66 24 47 1 NC_002967:TDE0354|5end_general_stress_protein_14_398367..398597_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 76 34 101 61 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 343 63 23 149 109 NC_002967:TDE0152|3end_amino_acid_permease_family_protein_173122..173272_NEGATIVE 341 170 123 140 80 NC_002967:TDE1063|3end_methionyl-tRNA_synthetase_1092968..1093118_POSITIVE 319 73 31 142 102 NC_002967:TDE0598|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_637358..637508_NEGATIVE 309 46 4 144 101 NC_002967:TDE2209|3end_CarB_family_protein_2249300..2249450_POSITIVE 308 63 26 59 7 NC_002967:TDE2767|3end_flagellar_protein-related_protein_2820896..2821046_NEGATIVE 299 197 151 138 82 NC_002967:TDE1991|3end_hypothetical_protein_2008634..2008784_NEGATIVE 297 169 122 84 46 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 296 187 141 128 80 NC_002967:TDE2691|3end_hypothetical_protein_2729346..2729496_POSITIVE 294 74 39 43 12 NC_002967:TDE2483|3end_hypothetical_protein_2505880..2506030_NEGATIVE 288 159 119 60 21 NC_002967:TDE1915|3end_alcohol_dehydrogenase,_iron-containing_1931928..1932078_NEGATIVE 287 65 27 52 14 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 284 45 1 47 1 NC_002967:TDE2062|3end_hypothetical_protein_2087802..2087952_NEGATIVE 283 64 25 151 110 NC_002967:TDE2325|3end_hypothetical_protein_2361177..2361327_POSITIVE 282 67 23 142 101 NC_002967:TDE1844|3end_DNA_integrase_1873197..1873347_NEGATIVE 278 169 122 106 44 NC_002967:TDE0555|3end_hypothetical_protein_590983..591133_NEGATIVE 277 80 37 78 45 NC_002967:TDE2219|3end_hypothetical_protein_2258961..2259111_NEGATIVE 277 61 22 74 39 NC_002967:TDE1028|3end_hypothetical_protein_1058661..1058811_POSITIVE 275 76 32 151 118 NC_002967:TDE1743|3end_chromate_transport_protein_1797940..1798090_NEGATIVE 275 75 34 146 95 NC_002967:TDE0175|3end_pyrrolidone-carboxylate_peptidase_208129..208279_NEGATIVE