Origin IGS: agattaaatatattatataattctgatctctgtatgttcatttttgaacgcacaaaaatagaaaattcaggttggtatattaaagttttgccgttaaataatactaatcacacaacgggctgtcacgctctaatttgtttatttttaaaaagatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatctttttaaaaataaacaaattagagcgtgacagcccgttgtgtgattagtattatttaacggcaaaactttaatataccaacctgaattttctatttttgtgcgttcaaaaatgaacatacagagatcagaattatataatatatttaatct Mask Tandem Repeat Region ================================================ agattaaatatattatataattctgatctctgtatgttcatttttgaacgcacaaaaatagaaaattcaggttggtatattaaagttttgccgttaaataatactaatcacacaacgggctgtcacgctctaatttgtttatttttaaaaagatta Find is-nt database================================================ Query_seq: TF0559:TF0560|TF0559:TF0560:methanol dehydrogenase regulator, MoxR-like; magnesium chelatase, subunit I:DNA-binding protein:->->:592148..592303 156 agattaaatatattatataattctgatctctgtatgttcatttttgaacgcacaaaaatagaaaattcaggttggtatattaaagttttgccgttaaataatactaatcacacaacgggctgtcacgctctaatttgtttatttttaaaaagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0559:TF0560|TF0559:TF0560:methanol dehydrogenase regulator, MoxR-like; magnesium chelatase, subunit I:DNA-binding protein:->->:592148..592303 156 agattaaatatattatataattctgatctctgtatgttcatttttgaacgcacaaaaatagaaaattcaggttggtatattaaagttttgccgttaaataatactaatcacacaacgggctgtcacgctctaatttgtttatttttaaaaagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0559:TF0560|TF0559:TF0560:methanol dehydrogenase regulator, MoxR-like; magnesium chelatase, subunit I:DNA-binding protein:->->:592148..592303 156 agattaaatatattatataattctgatctctgtatgttcatttttgaacgcacaaaaatagaaaattcaggttggtatattaaagttttgccgttaaataatactaatcacacaacgggctgtcacgctctaatttgtttatttttaaaaagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agattaaatatattatataattctgatctctgtatgttcatttttgaacgcacaaaaatagaaaattcaggttggtatattaaagttttgccgttaaataatactaatcacacaacgggctgtcacgctctaatttgtttatttttaaaaagatta Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 10 End: 156 ......... M L Y N S D L C M F I F E R T K I E N S G W Y I K V L P L N N T N H T T G C H A L I C L F L K R L agattaaatatattatataattctgatctctgtatgttcatttttgaacgcacaaaaatagaaaattcaggttggtatattaaagttttgccgttaaataatactaatcacacaacgggctgtcacgctctaatttgtttatttttaaaaagatta 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: 82 Start: 98 End: 127 .................................................................................................CGTGACAGCCCGTTGTGTGATTAGTATTAT............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agattaaatatattatataattctgatctctgtatgttcatttttgaacgcacaaaaatagaaaattcaggttggtatattaaagttttgccgttaaataatactaatcacacaacgggctgtcacgctctaatttgtttatttttaaaaagatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 39 HP_score: -2.1 Tail_Score: -2.62175 Start: 30 End: 70 Full_Region: ATATAATTCTGATCT CTGTATGTTCATTTTTG AACGCA CAAAAATAGAAAATTCAG GTTGGTATATTAAAG .............................CTGTATGTTCATTTTTGAACGCACAAAAATAGAAAATTCAG...................................................................................... Find igs database================================================ Query_seq: TF0559:TF0560|TF0559:TF0560:methanol dehydrogenase regulator, MoxR-like; magnesium chelatase, subunit I:DNA-binding protein:->->:592148..592303 156 agattaaatatattatataattctgatctctgtatgttcatttttgaacgcacaaaaatagaaaattcaggttggtatattaaagttttgccgttaaataatactaatcacacaacgggctgtcacgctctaatttgtttatttttaaaaagatta Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: tfor_TF0559_TF0560|methanol dehydrogenase regulator, MoxR-like; magnesium chelatase, subunit I:DNA-binding protein|POSITIVE:POSITIVE|[592148,592303]|156 HSP 1 e-value: 1.0E-83 bit: 309.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 agattaaatatattatataattctgatctctgtatgttcatttttgaacgcacaaaaatagaaaattcaggttggtatattaaagttttgccgttaaataatactaatcacacaacgggctgtcacgctctaatttgtttatttttaaaaagatta agattaaatatattatataattctgatctctgtatgttcatttttgaacgcacaaaaatagaaaattcaggttggtatattaaagttttgccgttaaataatactaatcacacaacgggctgtcacgctctaatttgtttatttttaaaaagatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUAAAUAUAUUAUAUAAUUCUGAUCUCUGUAUGUUCAUUUUUGAACGCACAAAAAUAGAAAAUUCAGGUUGGUAUAUUAAAGUUUUGCCGUUAAAUAAUACUAAUCACACAACGGGCUGUCACGCUCUAAUUUGUUUAUUUUUAAAAAGAUUA .......................((((((.(((.((((((....)))))).))).(((((((.......(((((((((.((((.(......).))))...))))))))).......((((......))))...)))))))..........)))))) (-23.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCUUUUUAAAAAUAAACAAAUUAGAGCGUGACAGCCCGUUGUGUGAUUAGUAUUAUUUAACGGCAAAACUUUAAUAUACCAACCUGAAUUUUCUAUUUUUGUGCGUUCAAAAAUGAACAUACAGAGAUCAGAAUUAUAUAAUAUAUUUAAUCU ........(((((.(((.....(((((((..((.....((((((.(((((....))))).))))))))...)))))))...............(((((((((((((.(((((....))))).))))))))).))))........))).)))))... (-27.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 139 114 228 206 tfor:TF2010|5end_hypothetical_protein_2163246..2163476_POSITIVE 261 54 12 216 169 tfor:TF3034|5end_conserved_hypothetical_protein_3259113..3259343_POSITIVE 261 129 87 146 102 tfor:TF3024|5end_periplasmic_protease_3247204..3247434_POSITIVE 245 148 116 107 69 tfor:TF2596|5end_conserved_hypothetical_protein;_possible_lipoprotein_2766667..2766897_POSITIVE 239 128 84 89 42 tfor:TF2986|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_3201818..3202048_POSITIVE 236 141 116 217 186 tfor:TF0087|5end_ABC_transporter,_permease_component_93185..93415_POSITIVE 235 129 109 30 6 tfor:TF0708|5end_possible_alkaline_phosphatase_752173..752403_POSITIVE 233 129 84 183 143 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 232 130 88 49 3 tfor:TF3079|5end_ribonucleoside-diphosphate_reductase_1,_beta_subunit_3309184..3309414_POSITIVE 232 130 85 157 101 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 232 141 108 89 52 tfor:TF2879|5end_tRNA_(guanine-N-1)-methyltransferase_3068254..3068484_POSITIVE 232 94 52 161 122 tfor:TF1812|5end_tryptophan_synthase,_beta_chain_1952696..1952926_POSITIVE 230 129 88 192 139 tfor:TF0248|5end_hypothetical_protein_278249..278479_POSITIVE 226 139 110 113 76 tfor:TF1716|5end_hypothetical_protein_1837442..1837672_POSITIVE 226 131 115 171 151 tfor:TF1523|5end_hypothetical_protein_1630273..1630503_POSITIVE 224 138 110 167 141 tfor:TF3002|5end_helicase-related_protein_3217756..3217986_POSITIVE 224 138 110 112 86 tfor:TF2111|5end_RNA_polymerase_sigma-54_factor_2280506..2280736_POSITIVE 224 93 51 156 119 tfor:TF1721|5end_2,3-bisphosphoglycerate-independent_phosphoglycerate_mutase_1844374..1844604_POSITIVE 224 130 87 87 48 tfor:TF0919|5end_conserved_hypothetical_protein_957541..957771_POSITIVE 224 138 110 181 155 tfor:TF0717|5end_signal_recognition_particle_767654..767884_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 139 114 147 125 tfor:TF2009|3end_octaprenyl-diphosphate_synthase_ispB_2163245..2163395_POSITIVE 275 137 113 106 81 tfor:TF0008|3end_hypothetical_protein_4336..4486_POSITIVE 265 150 114 113 79 tfor:TF0308|3end_hypothetical_protein_334082..334232_POSITIVE 245 148 116 77 39 tfor:TF2595|3end_conserved_hypothetical_protein_2766717..2766867_POSITIVE 235 129 109 30 6 tfor:TF0707|3end_conserved_hypothetical_protein_752253..752403_POSITIVE 232 130 85 135 79 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 232 141 108 38 1 tfor:TF2878|3end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3068283..3068433_POSITIVE 226 131 115 136 116 tfor:TF1522|3end_hypothetical_protein_1630318..1630468_POSITIVE 224 138 110 52 26 tfor:TF2110|3end_transposase_2280526..2280676_POSITIVE 224 93 51 78 41 tfor:TF1720|3end_conserved_hypothetical_protein_1844376..1844526_POSITIVE 224 120 74 71 22 tfor:TF0177|3end_hypothetical_protein_187154..187304_POSITIVE 220 138 115 38 14 tfor:TF2344|3end_ATP/GTP_binding_protein_2508434..2508584_POSITIVE 218 125 87 50 6 tfor:TF2449|3end_undecaprenyl_diphosphate_synthase_2626541..2626691_POSITIVE 218 128 112 57 37 tfor:TF2160|3end_magnesium_chelatase,_subunit_I_2337049..2337199_POSITIVE 218 140 95 138 85 tfor:TF0456|3end_conserved_hypothetical_protein_474172..474322_POSITIVE 217 78 33 140 94 tfor:TF2601|3end_conserved_hypothetical_protein_2775139..2775289_POSITIVE 214 120 87 145 103 tfor:TF0595|3end_hypothetical_protein_628073..628223_POSITIVE 212 96 67 133 105 tfor:TF1417|3end_conserved_hypothetical_protein_1500070..1500220_POSITIVE 212 140 92 101 51 tfor:TF0505|3end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_531103..531253_POSITIVE 211 78 41 36 1 tfor:TF2054|3end_UDP-N-acetylglucosamine_2-epimerase_2219535..2219685_POSITIVE