Origin IGS: tatgtcggtgcaccgatatatcagtgatagccaccgatataacggtgtgaattttacctagactaccttagttttatcgaaattctaaatattttaatacaaattcccgtatttttattaaaaatacgtcttattttgattttactatctttggcatgaaatttgcttatatataaccgaaagacactaaaaaacctttaaaaagcactaaaagtttatttaaaaaagtttgctttaaaataattttttaaggagaaaatt .........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 aattttctccttaaaaaattattttaaagcaaacttttttaaataaacttttagtgctttttaaaggttttttagtgtctttcggttatatataagcaaatttcatgccaaagatagtaaaatcaaaataagacgtatttttaataaaaatacgggaatttgtattaaaatatttagaatttcgataaaactaaggtagtctaggtaaaattcacaccgttatatcggtggctatcactgatatatcggtgcaccgacata Mask Tandem Repeat Region ================================================ tatgtcggtgcaccgatatatcagtgatagccaccgatataacggtgtgaattttacctagactaccttagttttatcgaaattctaaatattttaatacaaattcccgtatttttattaaaaatacgtcttattttgattttactatctttggcatgaaatttgcttatatataaccgaaagacactaaaaaacctttaaaaagcactaaaagtttatttaaaaaagtttgctttaaaataattttttaaggagaaaatt Find is-nt database================================================ Query_seq: TDE0010:TDE0011|TDE0010:TDE0011:MutT/nudix family protein:alkyl hydroperoxide reductase/peroxiredoxin:->->:15287..15547 261 tatgtcggtgcaccgatatatcagtgatagccaccgatataacggtgtgaattttacctagactaccttagttttatcgaaattctaaatattttaatacaaattcccgtatttttattaaaaatacgtcttattttgattttactatctttggcatgaaatttgcttatatataaccgaaagacactaaaaaacctttaaaaagcactaaaagtttatttaaaaaagtttgctttaaaataattttttaaggagaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0010:TDE0011|TDE0010:TDE0011:MutT/nudix family protein:alkyl hydroperoxide reductase/peroxiredoxin:->->:15287..15547 261 tatgtcggtgcaccgatatatcagtgatagccaccgatataacggtgtgaattttacctagactaccttagttttatcgaaattctaaatattttaatacaaattcccgtatttttattaaaaatacgtcttattttgattttactatctttggcatgaaatttgcttatatataaccgaaagacactaaaaaacctttaaaaagcactaaaagtttatttaaaaaagtttgctttaaaataattttttaaggagaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0010:TDE0011|TDE0010:TDE0011:MutT/nudix family protein:alkyl hydroperoxide reductase/peroxiredoxin:->->:15287..15547 261 tatgtcggtgcaccgatatatcagtgatagccaccgatataacggtgtgaattttacctagactaccttagttttatcgaaattctaaatattttaatacaaattcccgtatttttattaaaaatacgtcttattttgattttactatctttggcatgaaatttgcttatatataaccgaaagacactaaaaaacctttaaaaagcactaaaagtttatttaaaaaagtttgctttaaaataattttttaaggagaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatgtcggtgcaccgatatatcagtgatagccaccgatataacggtgtgaattttacctagactaccttagttttatcgaaattctaaatattttaatacaaattcccgtatttttattaaaaatacgtcttattttgattttactatctttggcatgaaatttgcttatatataaccgaaagacactaaaaaacctttaaaaagcactaaaagtttatttaaaaaagtttgctttaaaataattttttaaggagaaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 66 End: 170 ................................................................. R L K I S I R F I K I C I G T N K N F I R R I K I K S D K A H F K S M ........................................................................................... tatgtcggtgcaccgatatatcagtgatagccaccgatataacggtgtgaattttacctagactaccttagttttatcgaaattctaaatattttaatacaaattcccgtatttttattaaaaatacgtcttattttgattttactatctttggcatgaaatttgcttatatataaccgaaagacactaaaaaacctttaaaaagcactaaaagtttatttaaaaaagtttgctttaaaataattttttaaggagaaaatt 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================================================ PromScan Matrix: RpoN Strand: + Score: 90 Start: 151 End: 167 ......................................................................................................................................................TTGGCATGAAATTTGCT.............................................................................................. tatgtcggtgcaccgatatatcagtgatagccaccgatataacggtgtgaattttacctagactaccttagttttatcgaaattctaaatattttaatacaaattcccgtatttttattaaaaatacgtcttattttgattttactatctttggcatgaaatttgcttatatataaccgaaagacactaaaaaacctttaaaaagcactaaaagtttatttaaaaaagtttgctttaaaataattttttaaggagaaaatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 49 HP_score: -3.3 Tail_Score: -3.43919 Start: 92 End: 123 Full_Region: caaaataagacgtat ttttaataaaaat acggga atttgtattaaaa tatttagaatttcga ...........................................................................................ttttaataaaaatacgggaatttgtattaaaa.......................................................................................................................................... TransTerm Strand: + Conf: 89 HP_score: -9.9 Tail_Score: -3.79527 Start: 108 End: 128 Full_Region: TTTAATACAAATTCC CGTATTTTT ATT AAAAATACG TCTTATTTTGATTTT ...........................................................................................................CGTATTTTTATTAAAAATACG..................................................................................................................................... Find igs database================================================ Query_seq: TDE0010:TDE0011|TDE0010:TDE0011:MutT/nudix family protein:alkyl hydroperoxide reductase/peroxiredoxin:->->:15287..15547 261 tatgtcggtgcaccgatatatcagtgatagccaccgatataacggtgtgaattttacctagactaccttagttttatcgaaattctaaatattttaatacaaattcccgtatttttattaaaaatacgtcttattttgattttactatctttggcatgaaatttgcttatatataaccgaaagacactaaaaaacctttaaaaagcactaaaagtttatttaaaaaagtttgctttaaaataattttttaaggagaaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: NC_002967_TDE0010_TDE0011|MutT/nudix family protein:alkyl hydroperoxide reductase/peroxiredoxin|POSITIVE:POSITIVE|[15287, 15547]|261 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 tatgtcggtgcaccgatatatcagtgatagccaccgatataacggtgtgaattttacctagactaccttagttttatcgaaattctaaatattttaatacaaattcccgtatttttattaaaaatacgtcttattttgattttactatctttggcatgaaatttgcttatatataaccgaaagacac.......................................................................... tatgtcggtgcaccgatatatcagtgatagccaccgatataacggtgtgaattttacctagactaccttagttttatcgaaattctaaatattttaatacaaattcccgtatttttattaaaaatacgtcttattttgattttactatctttggcatgaaatttgcttatatataaccgaaagacac.......................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGUCGGUGCACCGAUAUAUCAGUGAUAGCCACCGAUAUAACGGUGUGAAUUUUACCUAGACUACCUUAGUUUUAUCGAAAUUCUAAAUAUUUUAAUACAAAUUCCCGUAUUUUUAUUAAAAAUACGUCUUAUUUUGAUUUUACUAUCUUUGGCAUGAAAUUUGCUUAUAUAUAACCGAAAGACAC ....(((((..((((.((((((.(((.....))).)))))).))))(..(((((((((.(((......((((...((((((((........((((((((.((((......)))).)))))))).........))))))))...)))))))..))..)))))))..).........)))))....... (-40.93) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUCUUUCGGUUAUAUAUAAGCAAAUUUCAUGCCAAAGAUAGUAAAAUCAAAAUAAGACGUAUUUUUAAUAAAAAUACGGGAAUUUGUAUUAAAAUAUUUAGAAUUUCGAUAAAACUAAGGUAGUCUAGGUAAAAUUCACACCGUUAUAUCGGUGGCUAUCACUGAUAUAUCGGUGCACCGACAUA .......(((((.........(((((((((........(((......))).........((((((((.....))))))))))))))))).......((((((((...((...........))...)))))))).......(((((.((((((((((.....)))))))))).))))).))))).... (-45.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 47 2 59 15 NC_002967:TDE2007|5end_ABC_transporter,_ATP-binding/permease_protein_2026819..2027049_POSITIVE 324 47 6 55 4 NC_002967:TDE1515|5end_permease_domain_protein_1561978..1562208_POSITIVE 264 47 4 203 150 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 261 50 4 202 151 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 260 47 2 201 154 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 258 48 3 170 130 NC_002967:TDE0988|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1015082..1015312_POSITIVE 255 50 3 219 176 NC_002967:TDE2057|5end_hypothetical_protein_2085343..2085573_NEGATIVE 254 36 6 173 139 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 253 47 7 123 74 NC_002967:TDE1512|5end_hypothetical_protein_1559203..1559433_POSITIVE 252 59 11 181 130 NC_002967:TDE1603|5end_ABC_transporter,_ATP-binding_protein_1654856..1655086_NEGATIVE 251 37 1 159 133 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 250 47 4 59 15 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 249 48 2 221 164 NC_002967:TDE0848|5end_hypothetical_protein_871269..871499_POSITIVE 241 60 21 180 136 NC_002967:TDE1734|5end_exodeoxyribonuclease_III_1788613..1788843_POSITIVE 239 50 3 105 50 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 239 60 13 90 37 NC_002967:TDE0955|5end_LemA_family_protein_978842..979072_POSITIVE 237 50 5 70 7 NC_002967:TDE1093|5end_hypothetical_protein_1127374..1127604_POSITIVE 233 48 4 54 3 NC_002967:TDE0650|5end_hypothetical_protein_684697..684927_POSITIVE 232 50 12 140 108 NC_002967:TDE1909|5end_conserved_hypothetical_protein_TIGR00159_1926872..1927102_NEGATIVE 230 47 1 230 188 NC_002967:TDE0691|5end_ABC_transporter,_ATP-binding/permease_protein_728062..728292_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 481 31 1 103 71 NC_002967:TDE0010|3end_MutT/nudix_family_protein_15226..15376_POSITIVE 294 47 3 133 88 NC_002967:TDE0735|3end_hypothetical_protein_774746..774896_NEGATIVE 265 47 3 38 2 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 263 48 1 142 102 NC_002967:TDE0156|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_180344..180494_NEGATIVE 260 49 1 79 29 NC_002967:TDE1664|3end_hypothetical_protein_1718982..1719132_POSITIVE 258 48 3 85 45 NC_002967:TDE0987|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1015077..1015227_POSITIVE 250 47 13 30 1 NC_002967:TDE2006|3end_hypothetical_protein_2026870..2027020_POSITIVE 250 47 4 62 18 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 245 156 115 74 24 NC_002967:TDE1514|3end_permease_domain_protein_1562009..1562159_POSITIVE 232 50 12 136 104 NC_002967:TDE1910|3end_1-deoxy-D-xylulose-5-phosphate_synthase_1926876..1927026_NEGATIVE 229 75 32 45 9 NC_002967:TDE1966|3end_trypsin_domain/PDZ_domain_protein_1981630..1981780_POSITIVE 228 45 9 33 3 NC_002967:TDE2536|3end_hypothetical_protein_2563341..2563491_POSITIVE 224 38 2 64 33 NC_002967:TDE2050|3end_hypothetical_protein_2079707..2079857_NEGATIVE 224 49 3 124 81 NC_002967:TDE2036|3end_ATPase,_AAA_family_2064140..2064290_NEGATIVE 222 64 27 71 32 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 220 180 132 69 10 NC_002967:TDE2511|3end_ABC_transporter,_ATP-binding/permease_protein_2537664..2537814_POSITIVE 219 49 5 150 110 NC_002967:TDE1733|3end_methionine_aminopeptidase,_type_I_1788679..1788829_POSITIVE 218 35 2 62 27 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 217 55 12 75 31 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 214 178 146 132 96 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE