Origin IGS: ttcaatacataagtcccgaataccataaaatataagaaaaaagagctaaaaaggcaataggttttgctcatttttggtgccggatgttgaattttataagtctatatcgaatataaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttatattcgatatagacttataaaattcaacatccggcaccaaaaatgagcaaaacctattgcctttttagctcttttttcttatattttatggtattcgggacttatgtattgaa Mask Tandem Repeat Region ================================================ ttcaatacataagtcccgaataccataaaatataagaaaaaagagctaaaaaggcaataggttttgctcatttttggtgccggatgttgaattttataagtctatatcgaatataaac Find is-nt database================================================ Query_seq: TDE0935:TDE0936|TDE0935:TDE0936:hypothetical protein:hypothetical protein:<-<-:959844..959961 118 ttcaatacataagtcccgaataccataaaatataagaaaaaagagctaaaaaggcaataggttttgctcatttttggtgccggatgttgaattttataagtctatatcgaatataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0935:TDE0936|TDE0935:TDE0936:hypothetical protein:hypothetical protein:<-<-:959844..959961 118 ttcaatacataagtcccgaataccataaaatataagaaaaaagagctaaaaaggcaataggttttgctcatttttggtgccggatgttgaattttataagtctatatcgaatataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0935:TDE0936|TDE0935:TDE0936:hypothetical protein:hypothetical protein:<-<-:959844..959961 118 ttcaatacataagtcccgaataccataaaatataagaaaaaagagctaaaaaggcaataggttttgctcatttttggtgccggatgttgaattttataagtctatatcgaatataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcaatacataagtcccgaataccataaaatataagaaaaaagagctaaaaaggcaataggttttgctcatttttggtgccggatgttgaattttataagtctatatcgaatataaac Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 3 End: 92 .. L V Y T G F V M F Y L F F S S F L C Y T K S M K P A P H Q M .......................... ttcaatacataagtcccgaataccataaaatataagaaaaaagagctaaaaaggcaataggttttgctcatttttggtgccggatgttgaattttataagtctatatcgaatataaac 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: 87 Start: 29 End: 58 ............................ATTGCCTTTTTAGCTCTTTTTTCTTATATT............................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcaatacataagtcccgaataccataaaatataagaaaaaagagctaaaaaggcaataggttttgctcatttttggtgccggatgttgaattttataagtctatatcgaatataaac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -2.4 Tail_Score: -3.46611 Start: 54 End: 67 Full_Region: cggcaccaaaaatga gcaa aaccta ttgc ctttttagctctttt .....................................................gcaaaacctattgc................................................... Find igs database================================================ Query_seq: TDE0935:TDE0936|TDE0935:TDE0936:hypothetical protein:hypothetical protein:<-<-:959844..959961 118 ttcaatacataagtcccgaataccataaaatataagaaaaaagagctaaaaaggcaataggttttgctcatttttggtgccggatgttgaattttataagtctatatcgaatataaac Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_002967_TDE0935_TDE0936|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[959844,959961]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 ttcaatacataagtcccgaataccataaaatataagaaaaaagagctaaaaaggcaataggttttgctcatttttggtgccggatgttgaattttataagtctatatcgaatataaac ttcaatacataagtcccgaataccataaaatataagaaaaaagagctaaaaaggcaataggttttgctcatttttggtgccggatgttgaattttataagtctatatcgaatataaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAUACAUAAGUCCCGAAUACCAUAAAAUAUAAGAAAAAAGAGCUAAAAAGGCAAUAGGUUUUGCUCAUUUUUGGUGCCGGAUGUUGAAUUUUAUAAGUCUAUAUCGAAUAUAAAC ((((((......((((.(..(((((............((((.((((....(((((.....))))))))).)))))))))).)))))))))).((((((..((......)).)))))). (-14.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUAUAUUCGAUAUAGACUUAUAAAAUUCAACAUCCGGCACCAAAAAUGAGCAAAACCUAUUGCCUUUUUAGCUCUUUUUUCUUAUAUUUUAUGGUAUUCGGGACUUAUGUAUUGAA ((((((((...))))))))........((((((((((((.((((((((.((((((((..........)))).)))).))))............))))..)))).....))))..)))) (-15.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 875 90 41 181 132 NC_002967:TDE0935|5end_hypothetical_protein_959753..959983_NEGATIVE 701 48 1 231 184 NC_002967:TDE0934|5end_chaperonin,_10_kDa_959661..959891_NEGATIVE 291 88 43 125 65 NC_002967:TDE1372|5end_hypothetical_protein_1416897..1417127_NEGATIVE 265 100 53 94 41 NC_002967:TDE2382|5end_cobinamide_kinase/cobinamide_phosphate_guanyltransferase_2412278..2412508_POSITIVE 264 89 45 66 24 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 262 90 45 219 172 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 262 94 52 54 6 NC_002967:TDE1726|5end_polyA_polymerase_family_protein_1779546..1779776_POSITIVE 261 97 51 60 16 NC_002967:TDE2478|5end_excinuclease_ABC,_C_subunit_2500873..2501103_POSITIVE 260 97 53 207 157 NC_002967:TDE2507|5end_hypothetical_protein_2531735..2531965_NEGATIVE 258 97 54 51 6 NC_002967:TDE0463|5end_purine_nucleoside_phosphorylase_517183..517413_POSITIVE 253 82 50 99 65 NC_002967:TDE2490|5end_primosomal_protein_N'_2514685..2514915_NEGATIVE 252 84 52 32 2 NC_002967:TDE2144|5end_hypothetical_protein_2181746..2181976_NEGATIVE 249 91 60 61 21 NC_002967:TDE2564|5end_PemK_family_protein_2589975..2590205_POSITIVE 249 85 54 54 21 NC_002967:TDE1034|5end_magnesium_and_cobalt_transporter,_putative_1062454..1062684_POSITIVE 248 90 43 124 72 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 248 89 45 62 12 NC_002967:TDE1360|5end_xanthine/uracil_permease_family_protein_1399297..1399527_POSITIVE 242 107 66 93 44 NC_002967:TDE0378|5end_hypothetical_protein_432164..432394_POSITIVE 242 100 51 94 45 NC_002967:TDE0122|5end_dihydrouridine_synthase,_putative_141539..141769_NEGATIVE 239 84 44 107 63 NC_002967:TDE1414|5end_phosphonopyruvate_decarboxylase,_putative_1456812..1457042_POSITIVE 238 96 52 190 123 NC_002967:TDE2322|5end_flagellar_protein_FliL-related_protein_2357810..2358040_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 83 44 143 89 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 261 97 51 56 12 NC_002967:TDE2477|3end_selenocysteine_synthase_2500949..2501099_POSITIVE 259 100 53 118 74 NC_002967:TDE1669|3end_hemolysin_1723878..1724028_POSITIVE 257 91 54 70 32 NC_002967:TDE0603|3end_hypothetical_protein_641885..642035_POSITIVE 253 82 50 79 45 NC_002967:TDE2491|3end_DNA_polymerase_domain_protein_2514705..2514855_NEGATIVE 249 91 60 74 34 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 247 90 42 131 73 NC_002967:TDE2407|3end_amidophosphoribosyltransferase_2433644..2433794_NEGATIVE 246 88 42 74 37 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 246 84 43 151 111 NC_002967:TDE1727|3end_hypothetical_protein_1780774..1780924_NEGATIVE 244 92 52 58 11 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 242 82 42 110 72 NC_002967:TDE2326|3end_cobyric_acid_synthase_CobQ,_putative_2362027..2362177_POSITIVE 242 100 51 90 41 NC_002967:TDE0123|3end_hypothetical_protein_141543..141693_NEGATIVE 242 109 61 149 96 NC_002967:TDE0007|3end_hypothetical_protein_10808..10958_POSITIVE 241 84 41 69 33 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE 239 84 44 106 62 NC_002967:TDE1413|3end_cytidylyltransferase/phosphoenolpyruvate_phosphomutase,_putative_1456891..1457041_POSITIVE 238 96 52 136 69 NC_002967:TDE2323|3end_mechanosensitive_ion_channel_family_protein_2357864..2358014_NEGATIVE 235 86 44 143 101 NC_002967:TDE1245|3end_hypothetical_protein_1277905..1278055_NEGATIVE 232 89 43 151 100 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 231 80 40 51 12 NC_002967:TDE0922|3end_ABC_transporter,_ATP-binding/permease_protein_941847..941997_NEGATIVE 230 84 45 45 8 NC_002967:TDE1377|3end_hypothetical_protein_1419083..1419233_NEGATIVE