Origin IGS: agatttcgattgtcgtgcaaaagtaaatactttattgccgacgtacaatttttttttcggattattcagccggattttcggcgggacatcattggtcgcggggcttttcggcttctttcgtatggggcgtgtgccggttctcctgtaaaaaaggcctttacgccggtcctcatcgttggaaaccggtgcaaaggccttggagtataagtgtggataagattggctgttttccgtcctcttgttta .........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 taaacaagaggacggaaaacagccaatcttatccacacttatactccaaggcctttgcaccggtttccaacgatgaggaccggcgtaaaggccttttttacaggagaaccggcacacgccccatacgaaagaagccgaaaagccccgcgaccaatgatgtcccgccgaaaatccggctgaataatccgaaaaaaaaattgtacgtcggcaataaagtatttacttttgcacgacaatcgaaatct Mask Tandem Repeat Region ================================================ agatttcgattgtcgtgcaaaagtaaatactttattgccgacgtacaatttttttttcggattattcagccggattttcggcgggacatcattggtcgcggggcttttcggcttctttcgtatggggcgtgtgccggttctcctgtaaaaaaggcctttacgccggtcctcatcgttggaaaccggtgcaaaggccttggagtataagtgtggataagattggctgttttccgtcctcttgttta Find is-nt database================================================ Query_seq: TF2759:TF2760|TF2759:TF2760:xylose repressor, ROK family:MarR family transcriptional regulator:->->:2944914..2945158 245 agatttcgattgtcgtgcaaaagtaaatactttattgccgacgtacaatttttttttcggattattcagccggattttcggcgggacatcattggtcgcggggcttttcggcttctttcgtatggggcgtgtgccggttctcctgtaaaaaaggcctttacgccggtcctcatcgttggaaaccggtgcaaaggccttggagtataagtgtggataagattggctgttttccgtcctcttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2759:TF2760|TF2759:TF2760:xylose repressor, ROK family:MarR family transcriptional regulator:->->:2944914..2945158 245 agatttcgattgtcgtgcaaaagtaaatactttattgccgacgtacaatttttttttcggattattcagccggattttcggcgggacatcattggtcgcggggcttttcggcttctttcgtatggggcgtgtgccggttctcctgtaaaaaaggcctttacgccggtcctcatcgttggaaaccggtgcaaaggccttggagtataagtgtggataagattggctgttttccgtcctcttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2759:TF2760|TF2759:TF2760:xylose repressor, ROK family:MarR family transcriptional regulator:->->:2944914..2945158 245 agatttcgattgtcgtgcaaaagtaaatactttattgccgacgtacaatttttttttcggattattcagccggattttcggcgggacatcattggtcgcggggcttttcggcttctttcgtatggggcgtgtgccggttctcctgtaaaaaaggcctttacgccggtcctcatcgttggaaaccggtgcaaaggccttggagtataagtgtggataagattggctgttttccgtcctcttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agatttcgattgtcgtgcaaaagtaaatactttattgccgacgtacaatttttttttcggattattcagccggattttcggcgggacatcattggtcgcggggcttttcggcttctttcgtatggggcgtgtgccggttctcctgtaaaaaaggcctttacgccggtcctcatcgttggaaaccggtgcaaaggccttggagtataagtgtggataagattggctgttttccgtcctcttgttta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 35 End: 145 .................................. M P T Y N F F F G L F S R I F G G T S L V A G L F G F F R M G R V P V L L .................................................................................................... Protein_Len: 60 Strand: + Start: 10 End: 204 ......... M S C K S K Y F I A D V Q F F F R I I Q P D F R R D I I G R G A F R L L S Y G A C A G S P V K K A F T P V L I V G N R C ......................................... Protein_Len: 60 Strand: + Start: 27 End: 245 .......................... M L Y C R R T I F F S D Y S A G F S A G H H W S R G F S A S F V W G V C R F S C K K G L Y A G P H R W K P V Q R P W S I Protein_Len: 49 Strand: - Start: 69 End: 215 .................................................................... G S K R R S M M P R P A K R S R E Y P A H A P E G T F F A K V G T R M T P F R H L P R P T Y T H M .............................. Protein_Len: 41 Strand: - Start: 1 End: 123 S K S Q R A F T F V K N G V Y L K K K P N N L R I K P P V D N T A P S K P K K R M .......................................................................................................................... agatttcgattgtcgtgcaaaagtaaatactttattgccgacgtacaatttttttttcggattattcagccggattttcggcgggacatcattggtcgcggggcttttcggcttctttcgtatggggcgtgtgccggttctcctgtaaaaaaggcctttacgccggtcctcatcgttggaaaccggtgcaaaggccttggagtataagtgtggataagattggctgttttccgtcctcttgttta 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================================================ agatttcgattgtcgtgcaaaagtaaatactttattgccgacgtacaatttttttttcggattattcagccggattttcggcgggacatcattggtcgcggggcttttcggcttctttcgtatggggcgtgtgccggttctcctgtaaaaaaggcctttacgccggtcctcatcgttggaaaccggtgcaaaggccttggagtataagtgtggataagattggctgttttccgtcctcttgttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -14.6 Tail_Score: -5.00616 Start: 153 End: 196 Full_Region: acacttatactccaa ggcctttgcaccggtttcca acga tgaggaccggcgtaaaggcc ttttttacaggagaa ........................................................................................................................................................ggcctttgcaccggtttccaacgatgaggaccggcgtaaaggcc................................................. Find igs database================================================ Query_seq: TF2759:TF2760|TF2759:TF2760:xylose repressor, ROK family:MarR family transcriptional regulator:->->:2944914..2945158 245 agatttcgattgtcgtgcaaaagtaaatactttattgccgacgtacaatttttttttcggattattcagccggattttcggcgggacatcattggtcgcggggcttttcggcttctttcgtatggggcgtgtgccggttctcctgtaaaaaaggcctttacgccggtcctcatcgttggaaaccggtgcaaaggccttggagtataagtgtggataagattggctgttttccgtcctcttgttta Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: tfor_TF2759_TF2760|xylose repressor, ROK family:MarR family transcriptional regulator|POSITIVE:POSITIVE|[2944914,2945158]|245 HSP 1 e-value: 1.0E-120 bit: 432.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 agatttcgattgtcgtgcaaaagtaaatactttattgccgacgtacaannnnnnnnncggattattcagccggattttcggcgggacatcattggtcgcggggcttttcggcttctttcgtatggggcgtgtgccggttctcctgtaaaaaaggcctttacgccggtcctcatcgttggaaaccggtgcaaaggccttggagtataagtgtggataagattggctgttttccgtcctcttgttta agatttcgattgtcgtgcaaaagtaaatactttattgccgacgtacaatttttttttcggattattcagccggattttcggcgggacatcattggtcgcggggcttttcggcttctttcgtatggggcgtgtgccggttctcctgtaaaaaaggcctttacgccggtcctcatcgttggaaaccggtgcaaaggccttggagtataagtgtggataagattggctgttttccgtcctcttgttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUUCGAUUGUCGUGCAAAAGUAAAUACUUUAUUGCCGACGUACAAUUUUUUUUUCGGAUUAUUCAGCCGGAUUUUCGGCGGGACAUCAUUGGUCGCGGGGCUUUUCGGCUUCUUUCGUAUGGGGCGUGUGCCGGUUCUCCUGUAAAAAAGGCCUUUACGCCGGUCCUCAUCGUUGGAAACCGGUGCAAAGGCCUUGGAGUAUAAGUGUGGAUAAGAUUGGCUGUUUUCCGUCCUCUUGUUUA ...........((((.((((((((....))))..))))))))...............((((.....((((((.(((((..((((((....(((((.((((.(.(((..(((......)))...))).).)))))))))..))))))....(((((((((.(((((((..(((....)))..))))))).))))))))).................)))))))))))...))))............ (-76.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAAGAGGACGGAAAACAGCCAAUCUUAUCCACACUUAUACUCCAAGGCCUUUGCACCGGUUUCCAACGAUGAGGACCGGCGUAAAGGCCUUUUUUACAGGAGAACCGGCACACGCCCCAUACGAAAGAAGCCGAAAAGCCCCGCGACCAAUGAUGUCCCGCCGAAAAUCCGGCUGAAUAAUCCGAAAAAAAAAUUGUACGUCGGCAAUAAAGUAUUUACUUUUGCACGACAAUCGAAAUCU .......((...((((...(((((...................(((((((((((((((.((((((..((....))..)))))).))))))))))).......))))...((((...(((......(....)..((......))...)))..((....))....)))).......))))).....))))...............((((((((..((((....)))))))).))))..))....... (-71.61) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 487 120 71 55 7 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 486 110 68 54 18 tfor:TF0431|5end_hypothetical_protein_452178..452408_POSITIVE 486 110 68 39 3 tfor:TF0430|5end_hypothetical_protein_452163..452393_POSITIVE 462 130 81 212 156 tfor:TF2159|5end_conserved_hypothetical_protein_2334446..2334676_POSITIVE 455 144 101 220 172 tfor:TF1801|5end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_1944213..1944443_POSITIVE 444 127 83 57 11 tfor:TF1559|5end_glycosyltransferase_1665879..1666109_POSITIVE 441 147 101 214 170 tfor:TF1812|5end_tryptophan_synthase,_beta_chain_1952696..1952926_POSITIVE 441 127 81 79 31 tfor:TF0888|5end_transfer_region-related_protein,_TraN_938392..938622_POSITIVE 425 120 72 184 132 tfor:TF2023|5end_possible_Fe-S_oxidoreductase_2180631..2180861_POSITIVE 425 130 81 74 16 tfor:TF0374|5end_glycerophosphoryl_diester_phosphodiesterase_392527..392757_POSITIVE 422 136 92 207 157 tfor:TF1070|5end_hydrolase_1139704..1139934_POSITIVE 417 140 93 75 23 tfor:TF2208|5end_conserved_hypothetical_protein_2382349..2382579_POSITIVE 416 142 102 158 117 tfor:TF2788|5end_hypothetical_protein_2972201..2972431_POSITIVE 416 147 108 41 9 tfor:TF1811|5end_hypothetical_protein_1952523..1952753_POSITIVE 413 100 58 154 113 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 413 100 58 114 73 tfor:TF1917|5end_hypothetical_protein_2069997..2070227_POSITIVE 413 130 82 212 147 tfor:TF1492|5end_ribonuclease_H-related_protein_1592017..1592247_POSITIVE 412 137 93 226 180 tfor:TF2248|5end_transfer_region-related_protein,_TraB_2422551..2422781_POSITIVE 412 137 94 52 5 tfor:TF1897|5end_conserved_hypothetical_protein;_possible_aminopeptidase_2049259..2049489_POSITIVE 410 134 96 166 126 tfor:TF0775|5end_ABC_transporter,_permease_component_823664..823894_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 444 127 83 57 11 tfor:TF1558|3end_possible_heme_biosynthesis_protein_1665959..1666109_POSITIVE 430 195 152 144 93 tfor:TF0271|3end_oxidase/dehydrogenase_298530..298680_POSITIVE 425 120 72 143 91 tfor:TF2022|3end_conserved_hypothetical_protein_2180670..2180820_POSITIVE 425 130 81 63 5 tfor:TF0373|3end_conserved_hypothetical_protein,_yngK-related_392596..392746_POSITIVE 420 120 71 139 83 tfor:TF2738|3end_30S_ribosomal_protein_S16_2920084..2920234_POSITIVE 420 199 152 56 2 tfor:TF0705|3end_hypothetical_protein_750789..750939_POSITIVE 416 142 102 135 94 tfor:TF2787|3end_30S_ribosomal_protein_S1_2972258..2972408_POSITIVE 413 100 58 142 101 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 401 130 82 143 97 tfor:TF1612|3end_conserved_hypothetical_protein_1729866..1730016_POSITIVE 395 197 151 103 54 tfor:TF2012|3end_conserved_hypothetical_protein_2168720..2168870_POSITIVE 395 209 161 68 6 tfor:TF1298|3end_possible_membrane_protein_1381197..1381347_POSITIVE 395 131 96 149 112 tfor:TF0774|3end_membrane-fusion_protein;_36_kDa_antigen_823730..823880_POSITIVE 395 110 62 134 88 tfor:TF0708|3end_possible_alkaline_phosphatase_753836..753986_POSITIVE 391 109 68 149 105 tfor:TF1923|3end_conserved_hypothetical_protein;_possible_phosphoserine_phosphatase_2072929..2073079_POSITIVE 391 139 91 69 20 tfor:TF0300|3end_hypothetical_protein_325541..325691_POSITIVE 389 180 136 148 93 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 387 120 72 136 81 tfor:TF2468|3end_hypothetical_protein_2646582..2646732_POSITIVE 387 139 92 67 5 tfor:TF1002|3end_replicative_DNA_helicase_1058232..1058382_POSITIVE 386 137 91 147 82 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 385 146 103 40 1 tfor:TF2263|3end_transfer_region-related_protein,_TraN_2432964..2433114_POSITIVE