Origin IGS: gtttttcaatttttttataagagcttaaaaaattatcaataaaaaaatgagattttccataaaaagactgagcttatcggtcttcaaaacacaaaaaatgccgataatcaaaagcggagaagaaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattttcttctccgcttttgattatcggcattttttgtgttttgaagaccgataagctcagtctttttatggaaaatctcatttttttattgataattttttaagctcttataaaaaaattgaaaaac Mask Tandem Repeat Region ================================================ gtttttcaatttttttataagagcttaaaaaattatcaataaaaaaatgagattttccataaaaagactgagcttatcggtcttcaaaacacaaaaaatgccgataatcaaaagcggagaagaaaatt Find is-nt database================================================ Query_seq: TDE2273:TDE2274|TDE2273:TDE2274:hypothetical protein:hypothetical protein:->->:2310213..2310340 128 gtttttcaatttttttataagagcttaaaaaattatcaataaaaaaatgagattttccataaaaagactgagcttatcggtcttcaaaacacaaaaaatgccgataatcaaaagcggagaagaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2273:TDE2274|TDE2273:TDE2274:hypothetical protein:hypothetical protein:->->:2310213..2310340 128 gtttttcaatttttttataagagcttaaaaaattatcaataaaaaaatgagattttccataaaaagactgagcttatcggtcttcaaaacacaaaaaatgccgataatcaaaagcggagaagaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2273:TDE2274|TDE2273:TDE2274:hypothetical protein:hypothetical protein:->->:2310213..2310340 128 gtttttcaatttttttataagagcttaaaaaattatcaataaaaaaatgagattttccataaaaagactgagcttatcggtcttcaaaacacaaaaaatgccgataatcaaaagcggagaagaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttttcaatttttttataagagcttaaaaaattatcaataaaaaaatgagattttccataaaaagactgagcttatcggtcttcaaaacacaaaaaatgccgataatcaaaagcggagaagaaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 32 End: 127 ............................... M I N K K M R F S I K R L S L S V F K T Q K M P I I K S G E E N . gtttttcaatttttttataagagcttaaaaaattatcaataaaaaaatgagattttccataaaaagactgagcttatcggtcttcaaaacacaaaaaatgccgataatcaaaagcggagaagaaaatt 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================================================ gtttttcaatttttttataagagcttaaaaaattatcaataaaaaaatgagattttccataaaaagactgagcttatcggtcttcaaaacacaaaaaatgccgataatcaaaagcggagaagaaaatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 60 HP_score: -2.2 Tail_Score: -4.83615 Start: 66 End: 82 Full_Region: tttttgtgttttgaa gaccga taagc tcagtc tttttatggaaaatc .................................................................gaccgataagctcagtc.............................................. Find igs database================================================ Query_seq: TDE2273:TDE2274|TDE2273:TDE2274:hypothetical protein:hypothetical protein:->->:2310213..2310340 128 gtttttcaatttttttataagagcttaaaaaattatcaataaaaaaatgagattttccataaaaagactgagcttatcggtcttcaaaacacaaaaaatgccgataatcaaaagcggagaagaaaatt Intra-Species Hit: Count: 1 Min: 17 Max: 128 Len: 112 Subject: NC_002967_TDE2273_TDE2274|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2310213,2310340]|128 HSP 1 e-value: 7.0E-45 bit: 180.0 Len: 112 Query Start:17 Query End:128 Subject Strand: POSITIVE Subject Start: 17 Subject End: 128 ................ataagagcttaaaaaattatcaatnnnnnnntgagattttccataaaaagactgagcttatcggtcttcaaaacacaaaaaatgccgataatcaaaagcggagaagaaaatt ................ataagagcttaaaaaattatcaataaaaaaatgagattttccataaaaagactgagcttatcggtcttcaaaacacaaaaaatgccgataatcaaaagcggagaagaaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAGAGCUUAAAAAAUUAUCAAUAAAAAAAUGAGAUUUUCCAUAAAAAGACUGAGCUUAUCGGUCUUCAAAACACAAAAAAUGCCGAUAAUCAAAAGCGGAGAAGAAAAUU ......((((.....((((((.........(((.(.....))))...((((((((.....))))))))..................))))))...))))............. (-16.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUCUUCUCCGCUUUUGAUUAUCGGCAUUUUUUGUGUUUUGAAGACCGAUAAGCUCAGUCUUUUUAUGGAAAAUCUCAUUUUUUUAUUGAUAAUUUUUUAAGCUCUUAU .............((((..(((((((((.((((((..((....((((((.((.....)).)))))).))..))))))))............)))))))....))))...... (-19.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 90 48 99 60 NC_002967:TDE2000|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_2017859..2018089_POSITIVE 252 105 61 72 26 NC_002967:TDE0752|5end_hypothetical_protein_791353..791583_POSITIVE 252 68 32 70 27 NC_002967:TDE0434|5end_rubrerythrin_488909..489139_POSITIVE 241 110 71 41 2 NC_002967:TDE2630|5end_peptide_ABC_transporter,_permease_protein,_putative_2670879..2671109_POSITIVE 238 65 30 148 108 NC_002967:TDE2082|5end_hypothetical_protein_2112587..2112817_NEGATIVE 237 87 41 183 142 NC_002967:TDE0940|5end_hypothetical_protein_963136..963366_POSITIVE 232 87 63 51 31 NC_002967:TDE1225|5end_zinc_ABC_transporter,_ATP-binding_protein_1259518..1259748_NEGATIVE 232 106 81 42 18 NC_002967:TDE0652|5end_hypothetical_protein_688177..688407_POSITIVE 229 69 32 181 141 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 226 99 52 159 107 NC_002967:TDE1409|5end_flagellar_filament_outer_layer_protein_FlaA,_putative_1451561..1451791_POSITIVE 226 100 53 59 13 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 225 108 61 144 98 NC_002967:TDE1936|5end_hypothetical_protein_1953086..1953316_POSITIVE 225 108 61 52 6 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 222 67 30 219 184 NC_002967:TDE0512|5end_hypothetical_protein_561442..561672_NEGATIVE 222 87 49 152 111 NC_002967:TDE0400|5end_transcriptional_regulator,_LysR_family_451803..452033_NEGATIVE 220 109 83 187 161 NC_002967:TDE1783|5end_hypothetical_protein_1823605..1823835_NEGATIVE 220 87 46 176 140 NC_002967:TDE0654|5end_peptidase,_M20/M25/M40_family_689606..689836_POSITIVE 220 109 83 187 161 NC_002967:TDE0059|5end_hypothetical_protein_67294..67524_POSITIVE 215 110 61 82 26 NC_002967:TDE2448|5end_hypothetical_protein_2477417..2477647_NEGATIVE 214 99 51 68 18 NC_002967:TDE2564|5end_PemK_family_protein_2589975..2590205_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 110 71 44 5 NC_002967:TDE2629|3end_peptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_2670962..2671112_POSITIVE 238 65 30 123 83 NC_002967:TDE2083|3end_anti-anti-sigma_factor_2112612..2112762_NEGATIVE 232 87 63 24 4 NC_002967:TDE1226|3end_zinc_ABC_transporter,_periplasmic_zinc-binding_protein_1259545..1259695_NEGATIVE 226 99 52 137 85 NC_002967:TDE1408|3end_flagellar_filament_outer_layer_protein_FlaA,_putative_1451619..1451769_POSITIVE 226 67 36 86 54 NC_002967:TDE0361|3end_transporter,_putative_407442..407592_POSITIVE 225 108 61 144 98 NC_002967:TDE1935|3end_hypothetical_protein_1953166..1953316_POSITIVE 222 67 30 142 107 NC_002967:TDE0513|3end_hypothetical_protein_561519..561669_NEGATIVE 222 87 49 118 77 NC_002967:TDE0401|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_451837..451987_NEGATIVE 219 68 24 88 52 NC_002967:TDE2565|3end_hypothetical_protein_2590392..2590542_NEGATIVE 219 88 54 119 86 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 214 99 51 81 31 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 212 100 51 56 18 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 211 107 75 140 110 NC_002967:TDE0565|3end_hypothetical_protein_597230..597380_POSITIVE 210 71 35 146 114 NC_002967:TDE1458|3end_hypothetical_protein_1506259..1506409_NEGATIVE 209 89 47 61 8 NC_002967:TDE2234|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2272310..2272460_NEGATIVE 207 69 29 56 12 NC_002967:TDE2462|3end_hypothetical_protein_2488305..2488455_NEGATIVE 206 75 31 51 1 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 205 74 31 97 53 NC_002967:TDE1569|3end_hypothetical_protein_1619975..1620125_POSITIVE 204 70 29 145 105 NC_002967:TDE1785|3end_hypothetical_protein_1825194..1825344_POSITIVE 203 80 36 74 31 NC_002967:TDE2226|3end_ABC_transporter,_substrate-binding_protein,_putative_2266412..2266562_POSITIVE