Origin IGS: tcaaaatttatactattaaaatctactttagataaaacctgttaatgtttacacagcattagcaggtttttttgtaaatttgcagttaagctaaacttacaaaaaagactagacaagctgcatagaaaatattaaactcattttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaaatgagtttaatattttctatgcagcttgtctagtcttttttgtaagtttagcttaactgcaaatttacaaaaaaacctgctaatgctgtgtaaacattaacaggttttatctaaagtagattttaatagtataaattttga Mask Tandem Repeat Region ================================================ tcaaaatttatactattaaaatctactttagataaaacctgttaatgtttacacagcattagcaggtttttttgtaaatttgcagttaagctaaacttacaaaaaagactagacaagctgcatagaaaatattaaactcattttat Find is-nt database================================================ Query_seq: TDE2508:TDE2509|TDE2508:TDE2509:hypothetical protein:transcriptional regulator, AraC family:->->:2533182..2533327 146 tcaaaatttatactattaaaatctactttagataaaacctgttaatgtttacacagcattagcaggtttttttgtaaatttgcagttaagctaaacttacaaaaaagactagacaagctgcatagaaaatattaaactcattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2508:TDE2509|TDE2508:TDE2509:hypothetical protein:transcriptional regulator, AraC family:->->:2533182..2533327 146 tcaaaatttatactattaaaatctactttagataaaacctgttaatgtttacacagcattagcaggtttttttgtaaatttgcagttaagctaaacttacaaaaaagactagacaagctgcatagaaaatattaaactcattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2508:TDE2509|TDE2508:TDE2509:hypothetical protein:transcriptional regulator, AraC family:->->:2533182..2533327 146 tcaaaatttatactattaaaatctactttagataaaacctgttaatgtttacacagcattagcaggtttttttgtaaatttgcagttaagctaaacttacaaaaaagactagacaagctgcatagaaaatattaaactcattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaaatttatactattaaaatctactttagataaaacctgttaatgtttacacagcattagcaggtttttttgtaaatttgcagttaagctaaacttacaaaaaagactagacaagctgcatagaaaatattaaactcattttat Predict ORF larger than 30AA ================================================ tcaaaatttatactattaaaatctactttagataaaacctgttaatgtttacacagcattagcaggtttttttgtaaatttgcagttaagctaaacttacaaaaaagactagacaagctgcatagaaaatattaaactcattttat 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================================================ tcaaaatttatactattaaaatctactttagataaaacctgttaatgtttacacagcattagcaggtttttttgtaaatttgcagttaagctaaacttacaaaaaagactagacaagctgcatagaaaatattaaactcattttat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.0 Tail_Score: -5.68039 Start: 38 End: 66 Full_Region: CTACTTTAGATAAAA CCTGTTAATGTT TACAC AGCATTAGCAGG TTTTTTTGTAAATTT .....................................CCTGTTAATGTTTACACAGCATTAGCAGG................................................................................ TransTerm Strand: - Conf: 66 HP_score: -4.6 Tail_Score: -4.54047 Start: 38 End: 66 Full_Region: aaatttacaaaaaaa cctgctaatgct gtgta aacattaacagg ttttatctaaagtag .....................................cctgctaatgctgtgtaaacattaacagg................................................................................ Find igs database================================================ Query_seq: TDE2508:TDE2509|TDE2508:TDE2509:hypothetical protein:transcriptional regulator, AraC family:->->:2533182..2533327 146 tcaaaatttatactattaaaatctactttagataaaacctgttaatgtttacacagcattagcaggtttttttgtaaatttgcagttaagctaaacttacaaaaaagactagacaagctgcatagaaaatattaaactcattttat Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_002967_TDE2508_TDE2509|hypothetical protein:transcriptional regulator, AraC family|POSITIVE:POSITIVE|[2533182,2533327]|146 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 tcaaaatttatactattaaaatctactttagataaaacctgttaatgtttacacagcattagcaggnnnnnnngtaaatttgcagttaagctaaacttacaaaaaagactagacaagctgcatagaaaatattaaactcattttat tcaaaatttatactattaaaatctactttagataaaacctgttaatgtttacacagcattagcaggtttttttgtaaatttgcagttaagctaaacttacaaaaaagactagacaagctgcatagaaaatattaaactcattttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAAUUUAUACUAUUAAAAUCUACUUUAGAUAAAACCUGUUAAUGUUUACACAGCAUUAGCAGGUUUUUUUGUAAAUUUGCAGUUAAGCUAAACUUACAAAAAAGACUAGACAAGCUGCAUAGAAAAUAUUAAACUCAUUUUAU ...(((((((((........(((((...)))))((((((((((((((((.....))))))))))))))))..)))))))))((((((...(((..(((......)))..)))...))))))......................... (-32.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAUGAGUUUAAUAUUUUCUAUGCAGCUUGUCUAGUCUUUUUUGUAAGUUUAGCUUAACUGCAAAUUUACAAAAAAACCUGCUAAUGCUGUGUAAACAUUAACAGGUUUUAUCUAAAGUAGAUUUUAAUAGUAUAAAUUUUGA .......(((((((........((((((((.....(((..((((((((((((((.((......))))))))))))))))..))).....))))))))...........(((..(((((...)))))...)))....)))))))... (-29.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 234 76 39 208 178 NC_002967:TDE1623|5end_hypothetical_protein_1671980..1672210_NEGATIVE 220 96 54 189 142 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 219 120 72 74 19 NC_002967:TDE2628|5end_hypothetical_protein_2669068..2669298_POSITIVE 217 110 64 221 173 NC_002967:TDE1526|5end_hypothetical_protein_1570565..1570795_POSITIVE 215 92 62 185 152 NC_002967:TDE2115|5end_HAMP_domain_protein_2144760..2144990_NEGATIVE 207 75 37 144 103 NC_002967:TDE0112|5end_hypothetical_protein_132044..132274_POSITIVE 206 137 96 155 121 NC_002967:TDE1014|5end_hypothetical_protein_1045544..1045774_NEGATIVE 203 130 83 88 47 NC_002967:TDE2722|5end_carhohydrate_kinase,_FGGY_family_2780874..2781104_NEGATIVE 203 87 47 117 86 NC_002967:TDE0446|5end_fibronectin_type_III_domain_protein_501269..501499_POSITIVE 201 72 46 56 30 NC_002967:TDE1175|5end_chaperonin_GroEL_1205151..1205381_NEGATIVE 200 70 21 165 120 NC_002967:TDE0211|5end_ABC_transporter,_permease_protein,_cysTW_family_247286..247516_NEGATIVE 199 88 46 78 31 NC_002967:TDE0702|5end_ABC_transporter,_ATP-binding_protein_737969..738199_NEGATIVE 198 91 59 228 195 NC_002967:TDE0632|5end_anti-anti-sigma_factor_667431..667661_POSITIVE 198 116 71 65 13 NC_002967:TDE0117|5end_lipoprotein,_putative_135613..135843_POSITIVE 197 66 21 222 169 NC_002967:TDE0507|5end_hypothetical_protein_558992..559222_NEGATIVE 194 84 41 71 26 NC_002967:TDE1715|5end_phosphoglycerate_kinase_1770762..1770992_NEGATIVE 191 129 82 77 36 NC_002967:TDE2096|5end_hypothetical_protein_2123200..2123430_POSITIVE 191 84 46 62 22 NC_002967:TDE0731|5end_hypothetical_protein_771347..771577_NEGATIVE 191 91 54 231 188 NC_002967:TDE0584|5end_permease,_putative_623134..623364_NEGATIVE 190 92 52 172 126 NC_002967:TDE1998|5end_phosphohexose_mutase_family_protein_2015300..2015530_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 70 34 57 21 NC_002967:TDE2508|3end_hypothetical_protein_2533121..2533271_POSITIVE 234 76 39 117 87 NC_002967:TDE1624|3end_glycine_dehydrogenase_subunit_2_1672071..1672221_NEGATIVE 222 92 54 91 53 NC_002967:TDE1356|3end_lipoprotein,_putative_1395674..1395824_NEGATIVE 220 96 54 103 56 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 215 126 82 52 1 NC_002967:TDE0139|3end_hypothetical_protein_160121..160271_NEGATIVE 214 108 64 151 108 NC_002967:TDE2230|3end_hypothetical_protein_2269453..2269603_POSITIVE 207 75 37 134 93 NC_002967:TDE0111|3end_hypothetical_protein_132114..132264_POSITIVE 203 130 83 91 50 NC_002967:TDE2723|3end_phosphoribosylpyrophosphate_synthetase_2780871..2781021_NEGATIVE 202 85 56 137 104 NC_002967:TDE0793|3end_hypothetical_protein_819205..819355_POSITIVE 199 88 46 81 34 NC_002967:TDE0703|3end_transcriptional_regulator,_AbrB_family_737966..738116_NEGATIVE 191 129 82 80 39 NC_002967:TDE2095|3end_hypothetical_protein_2123283..2123433_POSITIVE 191 67 22 149 90 NC_002967:TDE1804|3end_hypothetical_protein_1839476..1839626_NEGATIVE 190 64 22 121 85 NC_002967:TDE2717|3end_phosphatidate_cytidylyltransferase,_putative_2773921..2774071_NEGATIVE 190 92 52 48 2 NC_002967:TDE1997|3end_hypothetical_protein_2015256..2015406_POSITIVE 190 73 36 105 68 NC_002967:TDE0865|3end_hypothetical_protein_887599..887749_POSITIVE 188 73 37 73 39 NC_002967:TDE1898|3end_translocase_1918122..1918272_NEGATIVE 183 86 48 135 101 NC_002967:TDE1860|3end_hypothetical_protein_1886762..1886912_POSITIVE 183 92 54 37 1 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 182 58 15 136 83 NC_002967:TDE2673|3end_hypothetical_protein_2711670..2711820_NEGATIVE 180 99 56 109 53 NC_002967:TDE2507|3end_hypothetical_protein_2531643..2531793_NEGATIVE