Origin IGS: ttttcacctcatttaaattgtgcgatattttagcatttttgatgtttttatgcaagagtccgcattgcctcaagttaaaatttttttgccgatttagagggtaatttaaccgcaatgcgaatacttgacttattataaaactatgatacaattatattaagcctgtttaattaggagcgcttt .........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 aaagcgctcctaattaaacaggcttaatataattgtatcatagttttataataagtcaagtattcgcattgcggttaaattaccctctaaatcggcaaaaaaattttaacttgaggcaatgcggactcttgcataaaaacatcaaaaatgctaaaatatcgcacaatttaaatgaggtgaaaa Mask Tandem Repeat Region ================================================ ttttcacctcatttaaattgtgcgatattttagcatttttgatgtttttatgcaagagtccgcattgcctcaagttaaaatttttttgccgatttagagggtaatttaaccgcaatgcgaatacttgacttattataaaactatgatacaattatattaagcctgtttaattaggagcgcttt Find is-nt database================================================ Query_seq: TDE0968:TDE0969|TDE0968:TDE0969:translation elongation factor P:hypothetical protein:<-->:993217..993399 183 ttttcacctcatttaaattgtgcgatattttagcatttttgatgtttttatgcaagagtccgcattgcctcaagttaaaatttttttgccgatttagagggtaatttaaccgcaatgcgaatacttgacttattataaaactatgatacaattatattaagcctgtttaattaggagcgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0968:TDE0969|TDE0968:TDE0969:translation elongation factor P:hypothetical protein:<-->:993217..993399 183 ttttcacctcatttaaattgtgcgatattttagcatttttgatgtttttatgcaagagtccgcattgcctcaagttaaaatttttttgccgatttagagggtaatttaaccgcaatgcgaatacttgacttattataaaactatgatacaattatattaagcctgtttaattaggagcgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0968:TDE0969|TDE0968:TDE0969:translation elongation factor P:hypothetical protein:<-->:993217..993399 183 ttttcacctcatttaaattgtgcgatattttagcatttttgatgtttttatgcaagagtccgcattgcctcaagttaaaatttttttgccgatttagagggtaatttaaccgcaatgcgaatacttgacttattataaaactatgatacaattatattaagcctgtttaattaggagcgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcacctcatttaaattgtgcgatattttagcatttttgatgtttttatgcaagagtccgcattgcctcaagttaaaatttttttgccgatttagagggtaatttaaccgcaatgcgaatacttgacttattataaaactatgatacaattatattaagcctgtttaattaggagcgcttt Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: - Start: 2 End: 151 . K V E N L N H S I K A N K I N K H L L G C Q R L N F N K Q R N L P Y N L R L A F V Q S I I F S H Y M ................................ ttttcacctcatttaaattgtgcgatattttagcatttttgatgtttttatgcaagagtccgcattgcctcaagttaaaatttttttgccgatttagagggtaatttaaccgcaatgcgaatacttgacttattataaaactatgatacaattatattaagcctgtttaattaggagcgcttt 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: 85 Start: 132 End: 161 ...................................................................................................................................CTTAATATAATTGTATCATAGTTTTATAAT...................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 27 End: 56 ..........................CTTGCATAAAAACATCAAAAATGCTAAAAT............................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcacctcatttaaattgtgcgatattttagcatttttgatgtttttatgcaagagtccgcattgcctcaagttaaaatttttttgccgatttagagggtaatttaaccgcaatgcgaatacttgacttattataaaactatgatacaattatattaagcctgtttaattaggagcgcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0968:TDE0969|TDE0968:TDE0969:translation elongation factor P:hypothetical protein:<-->:993217..993399 183 ttttcacctcatttaaattgtgcgatattttagcatttttgatgtttttatgcaagagtccgcattgcctcaagttaaaatttttttgccgatttagagggtaatttaaccgcaatgcgaatacttgacttattataaaactatgatacaattatattaagcctgtttaattaggagcgcttt Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: NC_002967_TDE0968_TDE0969|translation elongation factor P:hypothetical protein|NEGATIVE:POSITIVE|[993217,993399]|183 HSP 1 e-value: 5.0E-87 bit: 321.0 Len: 183 Query Start:1 Query End:183 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 ttttcacctcatttaaattgtgcgatattttagcatttttgatgtttttatgcaagagtccgcattgcctcaagttaaaannnnnnngccgatttagagggtaatttaaccgcaatgcgaatacttgacttattataaaactatgatacaattatattaagcctgtttaattaggagcgcttt ttttcacctcatttaaattgtgcgatattttagcatttttgatgtttttatgcaagagtccgcattgcctcaagttaaaatttttttgccgatttagagggtaatttaaccgcaatgcgaatacttgacttattataaaactatgatacaattatattaagcctgtttaattaggagcgcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCACCUCAUUUAAAUUGUGCGAUAUUUUAGCAUUUUUGAUGUUUUUAUGCAAGAGUCCGCAUUGCCUCAAGUUAAAAUUUUUUUGCCGAUUUAGAGGGUAAUUUAACCGCAAUGCGAAUACUUGACUUAUUAUAAAACUAUGAUACAAUUAUAUUAAGCCUGUUUAAUUAGGAGCGCUUU ...................((((..((.((.((((..((((((((..((...((((.((.((((((((.....((((((......(((((.........))))))))))).)))))))).)).))))...(((((((....))))))).))..))))))))..)))).)).))...))))... (-35.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCGCUCCUAAUUAAACAGGCUUAAUAUAAUUGUAUCAUAGUUUUAUAAUAAGUCAAGUAUUCGCAUUGCGGUUAAAUUACCCUCUAAAUCGGCAAAAAAAUUUUAACUUGAGGCAAUGCGGACUCUUGCAUAAAAACAUCAAAAAUGCUAAAAUAUCGCACAAUUUAAAUGAGGUGAAAA ..((((...............(((((.(((((.............))))).)))))((((..(((((((((((((((((....((........)).........)))))))....))))))))))..)))).................))))......((((.((.......))..))))... (-30.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 868 100 51 191 142 NC_002967:TDE0968|5end_translation_elongation_factor_P_993126..993356_NEGATIVE 378 100 54 203 161 NC_002967:TDE2323|5end_mechanosensitive_ion_channel_family_protein_2359084..2359314_NEGATIVE 305 90 43 185 134 NC_002967:TDE0166|5end_hypothetical_protein_195871..196101_NEGATIVE 300 94 51 194 154 NC_002967:TDE1651|5end_BioY_family_protein_1698732..1698962_NEGATIVE 290 71 32 131 91 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 281 57 17 112 72 NC_002967:TDE1307|5end_hypothetical_protein_1340954..1341184_POSITIVE 273 70 22 59 4 NC_002967:TDE0074|5end_amino_acid_permease_family_protein_85499..85729_NEGATIVE 260 121 94 219 185 NC_002967:TDE1061|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_1086646..1086876_POSITIVE 260 121 94 92 58 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 259 100 58 113 77 NC_002967:TDE0886|5end_hypothetical_protein_903341..903571_POSITIVE 257 98 55 96 47 NC_002967:TDE1441|5end_dTDP-glucose_4,6-dehydratase_1486247..1486477_POSITIVE 254 99 52 108 55 NC_002967:TDE1451|5end_hypothetical_protein_1498968..1499198_NEGATIVE 254 90 41 89 40 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 251 104 61 149 104 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 250 99 56 189 142 NC_002967:TDE0319|5end_hypothetical_protein_351460..351690_POSITIVE 249 130 83 46 4 NC_002967:TDE1048|5end_30S_ribosomal_protein_S7_1074482..1074712_POSITIVE 246 70 26 200 156 NC_002967:TDE0462|5end_metallo-beta-lactamase_family_protein_516987..517217_NEGATIVE 245 100 53 55 10 NC_002967:TDE2122|5end_DHH_superfamily_protein_2155910..2156140_NEGATIVE 243 109 61 223 180 NC_002967:TDE1084|5end_folylpolyglutamate_synthetase,_putative_1116286..1116516_NEGATIVE 242 120 90 85 50 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 94 51 69 29 NC_002967:TDE1652|3end_ABC_transporter,_ATP-binding/permease_protein_1698857..1699007_NEGATIVE 294 100 56 130 96 NC_002967:TDE2784|3end_hypothetical_protein_2838627..2838777_POSITIVE 269 70 21 149 103 NC_002967:TDE1983|3end_hypothetical_protein_1993376..1993526_NEGATIVE 260 130 89 130 86 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE 260 70 22 118 67 NC_002967:TDE0598|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_637358..637508_NEGATIVE 259 130 86 126 83 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 259 100 58 76 40 NC_002967:TDE0885|3end_50S_ribosomal_protein_L19_903384..903534_POSITIVE 257 98 55 77 28 NC_002967:TDE1440|3end_glucose-1-phosphate_thymidylyltransferase_1486308..1486458_POSITIVE 256 180 133 132 91 NC_002967:TDE2739|3end_hypothetical_protein_2795169..2795319_POSITIVE 254 90 41 77 28 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 251 104 61 100 55 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 250 99 56 125 78 NC_002967:TDE0318|3end_hypothetical_protein_351476..351626_POSITIVE 240 73 33 85 43 NC_002967:TDE1460|3end_hypothetical_protein_1508707..1508857_NEGATIVE 239 74 33 122 78 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 237 42 4 54 11 NC_002967:TDE2169|3end_hypothetical_protein_2201509..2201659_POSITIVE 233 91 51 137 96 NC_002967:TDE1621|3end_hypothetical_protein_1668953..1669103_NEGATIVE 231 71 34 64 32 NC_002967:TDE0135|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_156377..156527_POSITIVE 230 92 53 143 101 NC_002967:TDE2333|3end_sanA_protein,_putative_2367871..2368021_NEGATIVE 230 103 61 100 58 NC_002967:TDE1915|3end_alcohol_dehydrogenase,_iron-containing_1931928..1932078_NEGATIVE 228 49 6 130 84 NC_002967:TDE2519|3end_hypothetical_protein_2544839..2544989_NEGATIVE