Origin IGS: ttagcacctcatattgtaataaattaccaccccgtattttaaaaaatgaagacgaaaatgtcaacatcaaagacaagctattgtcaagaaacaaataaaaggttacaatggaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttccattgtaaccttttatttgtttcttgacaatagcttgtctttgatgttgacattttcgtcttcattttttaaaatacggggtggtaatttattacaatatgaggtgctaa Mask Tandem Repeat Region ================================================ ttagcacctcatattgtaataaattaccaccccgtattttaaaaaatgaagacgaaaatgtcaacatcaaagacaagctattgtcaagaaacaaataaaaggttacaatggaaaa Find is-nt database================================================ Query_seq: TDE2243:TDE2244|TDE2243:TDE2244:CutC family protein:hypothetical protein:<-->:2283045..2283159 115 ttagcacctcatattgtaataaattaccaccccgtattttaaaaaatgaagacgaaaatgtcaacatcaaagacaagctattgtcaagaaacaaataaaaggttacaatggaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2243:TDE2244|TDE2243:TDE2244:CutC family protein:hypothetical protein:<-->:2283045..2283159 115 ttagcacctcatattgtaataaattaccaccccgtattttaaaaaatgaagacgaaaatgtcaacatcaaagacaagctattgtcaagaaacaaataaaaggttacaatggaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2243:TDE2244|TDE2243:TDE2244:CutC family protein:hypothetical protein:<-->:2283045..2283159 115 ttagcacctcatattgtaataaattaccaccccgtattttaaaaaatgaagacgaaaatgtcaacatcaaagacaagctattgtcaagaaacaaataaaaggttacaatggaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttagcacctcatattgtaataaattaccaccccgtattttaaaaaatgaagacgaaaatgtcaacatcaaagacaagctattgtcaagaaacaaataaaaggttacaatggaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 2 End: 109 . L V E Y Q L L N G G R I K F F S S S F T L M L S L S N D L F L Y F T V M ...... ttagcacctcatattgtaataaattaccaccccgtattttaaaaaatgaagacgaaaatgtcaacatcaaagacaagctattgtcaagaaacaaataaaaggttacaatggaaaa 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: 92 Start: 36 End: 65 ...................................GTTGACATTTTCGTCTTCATTTTTTAAAAT.................................................. PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 80 End: 109 ...............................................................................ATTGTCAAGAAACAAATAAAAGGTTACAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttagcacctcatattgtaataaattaccaccccgtattttaaaaaatgaagacgaaaatgtcaacatcaaagacaagctattgtcaagaaacaaataaaaggttacaatggaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2243:TDE2244|TDE2243:TDE2244:CutC family protein:hypothetical protein:<-->:2283045..2283159 115 ttagcacctcatattgtaataaattaccaccccgtattttaaaaaatgaagacgaaaatgtcaacatcaaagacaagctattgtcaagaaacaaataaaaggttacaatggaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002967_TDE2243_TDE2244|CutC family protein:hypothetical protein|NEGATIVE:POSITIVE|[2283045,2283159]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 ttagcacctcatattgtaataaattaccaccccgtattttaaaaaatgaagacgaaaatgtcaacatcaaagacaagctattgtcaagaaacaaataaaaggttacaatggaaaa ttagcacctcatattgtaataaattaccaccccgtattttaaaaaatgaagacgaaaatgtcaacatcaaagacaagctattgtcaagaaacaaataaaaggttacaatggaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGCACCUCAUAUUGUAAUAAAUUACCACCCCGUAUUUUAAAAAAUGAAGACGAAAAUGUCAACAUCAAAGACAAGCUAUUGUCAAGAAACAAAUAAAAGGUUACAAUGGAAAA ........((.(((((((((.........................(((..(((......)))..)))....(((((....)))))................)))))))))))... (-15.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCCAUUGUAACCUUUUAUUUGUUUCUUGACAAUAGCUUGUCUUUGAUGUUGACAUUUUCGUCUUCAUUUUUUAAAAUACGGGGUGGUAAUUUAUUACAAUAUGAGGUGCUAA ............((((..(((((.......(((((....)))))...((((..(((......)))..)))).....)))))..))))((((.(((((......))))).)))).. (-18.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 769 80 31 171 122 NC_002967:TDE2243|5end_CutC_family_protein_2282954..2283184_NEGATIVE 229 95 51 166 119 NC_002967:TDE1447|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_1492612..1492842_POSITIVE 229 49 6 84 42 NC_002967:TDE0530|5end_hypothetical_protein_574363..574593_POSITIVE 211 88 41 193 139 NC_002967:TDE1226|5end_zinc_ABC_transporter,_periplasmic_zinc-binding_protein_1260483..1260713_NEGATIVE 208 42 7 112 76 NC_002967:TDE1416|5end_ABC_transporter,_permease_protein_1459796..1460026_POSITIVE 204 79 31 189 129 NC_002967:TDE0765|5end_translation_elongation_factor_Tu_804732..804962_POSITIVE 196 44 2 140 91 NC_002967:TDE1938|5end_hypothetical_protein_1953640..1953870_POSITIVE 194 71 49 133 111 NC_002967:TDE0175|5end_pyrrolidone-carboxylate_peptidase_208782..209012_NEGATIVE 192 35 2 91 60 NC_002967:TDE2247|5end_PemK_family_protein_2286362..2286592_POSITIVE 192 20 2 111 93 NC_002967:TDE2036|5end_ATPase,_AAA_family_2066638..2066868_NEGATIVE 191 34 4 183 156 NC_002967:TDE1086|5end_conserved_hypothetical_protein_TIGR00255_1117786..1118016_POSITIVE 191 36 4 114 79 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 184 40 4 170 140 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 182 72 31 38 6 NC_002967:TDE2617|5end_cyclic_nucleotide-binding_protein_2659344..2659574_NEGATIVE 182 107 63 205 156 NC_002967:TDE0189|5end_hypothetical_protein_226460..226690_NEGATIVE 180 40 8 148 120 NC_002967:TDE2430|5end_bacteriocin_ABC_transporter,_bacteriocin-binding_protein,_putative_2459173..2459403_NEGATIVE 180 77 32 58 9 NC_002967:TDE2104|5end_hypothetical_protein_2131083..2131313_NEGATIVE 179 34 2 52 19 NC_002967:TDE1279|5end_phosphoribosylformylglycinamidine_synthase_II_1315115..1315345_NEGATIVE 177 62 27 135 97 NC_002967:TDE1643|5end_PASTA_domain_protein_1694551..1694781_NEGATIVE 176 105 73 199 169 NC_002967:TDE2655|5end_hypothetical_protein_2693070..2693300_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 211 93 51 151 106 NC_002967:TDE1446|3end_hypothetical_protein_1492679..1492829_POSITIVE 208 42 7 107 71 NC_002967:TDE1415|3end_nucleotidyl_transferase/aminotransferase,_class_V_1459871..1460021_POSITIVE 194 71 49 115 93 NC_002967:TDE0176|3end_hypothetical_protein_208800..208950_NEGATIVE 192 35 2 103 72 NC_002967:TDE2246|3end_hypothetical_protein_2286454..2286604_POSITIVE 192 20 2 102 84 NC_002967:TDE2037|3end_ATP:guanido_phosphotransferase_domain_protein_2066647..2066797_NEGATIVE 191 36 4 75 40 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 180 40 8 151 123 NC_002967:TDE2431|3end_bacteriocin_ABC_transporter,_ATP-binding/permease_protein,_putative_2459170..2459320_NEGATIVE 177 62 27 108 70 NC_002967:TDE1644|3end_methionyl-tRNA_formyltransferase_1694578..1694728_NEGATIVE 176 85 50 147 108 NC_002967:TDE0565|3end_hypothetical_protein_597230..597380_POSITIVE 175 36 3 69 24 NC_002967:TDE2653|3end_hypothetical_protein_2691744..2691894_POSITIVE 175 103 68 38 1 NC_002967:TDE2454|3end_hypothetical_protein_2482351..2482501_NEGATIVE 173 90 48 89 54 NC_002967:TDE2723|3end_phosphoribosylpyrophosphate_synthetase_2780871..2781021_NEGATIVE 170 43 4 141 101 NC_002967:TDE0396|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_446860..447010_POSITIVE 169 31 1 97 69 NC_002967:TDE2142|3end_methyl-accepting_chemotaxis_protein_2177987..2178137_POSITIVE 168 108 64 76 25 NC_002967:TDE1986|3end_adenylate_cyclase,_putative_2000283..2000433_NEGATIVE 166 49 3 73 30 NC_002967:TDE1537|3end_polyprenyl_synthetase_family_protein_1580472..1580622_NEGATIVE 166 89 48 73 29 NC_002967:TDE1027|3end_ribonuclease_III_1058382..1058532_POSITIVE 166 41 2 111 70 NC_002967:TDE0124|3end_rhomboid_family_protein_142244..142394_NEGATIVE 163 79 51 122 97 NC_002967:TDE0523|3end_hypothetical_protein_569238..569388_NEGATIVE 161 64 26 55 18 NC_002967:TDE1186|3end_hypothetical_protein_1212985..1213135_NEGATIVE