Origin IGS: taaaacacaccgaggttgcggtataaaaaagagaagccggaagtttttatcgatatttttcgacgaaaaacttccggcttattattatgctctacatagcgccgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacggcgctatgtagagcataataataagccggaagtttttcgtcgaaaaatatcgataaaaacttccggcttctcttttttataccgcaacctcggtgtgtttta Mask Tandem Repeat Region ================================================ taaaacacaccgaggttgcggtataaaaaagagaagccggaagtttttatcgatatttttcgacgaaaaacttccggcttattattatgctctacatagcgccgtta Find is-nt database================================================ Query_seq: TF1191:TF1192|TF1191:TF1192:possible transcriptional regulator:alpha-amylase:->->:1274040..1274146 107 taaaacacaccgaggttgcggtataaaaaagagaagccggaagtttttatcgatatttttcgacgaaaaacttccggcttattattatgctctacatagcgccgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1191:TF1192|TF1191:TF1192:possible transcriptional regulator:alpha-amylase:->->:1274040..1274146 107 taaaacacaccgaggttgcggtataaaaaagagaagccggaagtttttatcgatatttttcgacgaaaaacttccggcttattattatgctctacatagcgccgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1191:TF1192|TF1191:TF1192:possible transcriptional regulator:alpha-amylase:->->:1274040..1274146 107 taaaacacaccgaggttgcggtataaaaaagagaagccggaagtttttatcgatatttttcgacgaaaaacttccggcttattattatgctctacatagcgccgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaacacaccgaggttgcggtataaaaaagagaagccggaagtttttatcgatatttttcgacgaaaaacttccggcttattattatgctctacatagcgccgtta Predict ORF larger than 30AA ================================================ taaaacacaccgaggttgcggtataaaaaagagaagccggaagtttttatcgatatttttcgacgaaaaacttccggcttattattatgctctacatagcgccgtta 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================================================ taaaacacaccgaggttgcggtataaaaaagagaagccggaagtttttatcgatatttttcgacgaaaaacttccggcttattattatgctctacatagcgccgtta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.9 Tail_Score: -5.24129 Start: 31 End: 83 Full_Region: tatgtagagcataat aataagccggaagtttttcgtcga aaaata tcgataaaaacttccggcttctc ttttttataccgcaa ..............................aataagccggaagtttttcgtcgaaaaatatcgataaaaacttccggcttctc........................ TransTerm Strand: - Conf: 100 HP_score: -13.5 Tail_Score: -4.25873 Start: 33 End: 81 Full_Region: tgtagagcataataa taagccggaagtttttcgtcga aaaata tcgataaaaacttccggcttc tcttttttataccgc ................................taagccggaagtttttcgtcgaaaaatatcgataaaaacttccggcttc.......................... TransTerm Strand: - Conf: 100 HP_score: -15.2 Tail_Score: -4.23386 Start: 36 End: 78 Full_Region: agagcataataataa gccggaagtttttcgtcga aaaata tcgataaaaacttccggc ttctcttttttatac ...................................gccggaagtttttcgtcgaaaaatatcgataaaaacttccggc............................. Find igs database================================================ Query_seq: TF1191:TF1192|TF1191:TF1192:possible transcriptional regulator:alpha-amylase:->->:1274040..1274146 107 taaaacacaccgaggttgcggtataaaaaagagaagccggaagtttttatcgatatttttcgacgaaaaacttccggcttattattatgctctacatagcgccgtta Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: tfor_TF1191_TF1192|possible transcriptional regulator:alpha-amylase|POSITIVE:POSITIVE|[1274040, 1274146]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 taaaacacaccgaggttgcggtataaaaaagagaagccggaagtttttatcgatatttttcgacgaaaaacttccggcttattattatgctctacatagcgccgtta taaaacacaccgaggttgcggtataaaaaagagaagccggaagtttttatcgatatttttcgacgaaaaacttccggcttattattatgctctacatagcgccgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACACACCGAGGUUGCGGUAUAAAAAAGAGAAGCCGGAAGUUUUUAUCGAUAUUUUUCGACGAAAAACUUCCGGCUUAUUAUUAUGCUCUACAUAGCGCCGUUA .............(((.(((((((((.((....(((((((((((((((.((((......))))..))))))))))))))).)).))))))).......))))).... (-34.51) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGGCGCUAUGUAGAGCAUAAUAAUAAGCCGGAAGUUUUUCGUCGAAAAAUAUCGAUAAAAACUUCCGGCUUCUCUUUUUUAUACCGCAACCUCGGUGUGUUUUA .......(((......)))........(((((((((((((((.(((((......))))))))))))))))))))........(((((((......)))))))..... (-36.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 60 13 104 52 tfor:TF1019|5end_N-acetylmuramoyl-L-alanine_amidase_1075367..1075597_POSITIVE 303 77 36 84 44 tfor:TF1474|5end_6-phosphogluconolactonase_1567342..1567572_POSITIVE 302 43 9 77 33 tfor:TF1916|5end_conserved_hypothetical_protein;_possible_ATPase_2068530..2068760_POSITIVE 296 77 33 103 52 tfor:TF1450|5end_periplasmic_serine_protease_1534102..1534332_POSITIVE 291 79 35 231 188 tfor:TF0027|5end_conserved_hypothetical_protein_22866..23096_POSITIVE 287 79 35 169 130 tfor:TF1887|5end_hypothetical_protein_2040301..2040531_POSITIVE 283 80 35 178 135 tfor:TF3118|5end_conserved_hypothetical_protein_3352373..3352603_POSITIVE 277 77 37 180 140 tfor:TF3093|5end_30S_ribosomal_protein_S2_3325244..3325474_POSITIVE 277 100 51 94 30 tfor:TF2881|5end_conserved_hypothetical_protein_3071581..3071811_POSITIVE 277 55 19 159 132 tfor:TF0780|5end_alpha-L-arabinofuranosidase,_precursor_A_831944..832174_POSITIVE 277 44 5 146 105 tfor:TF0505|5end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_530223..530453_POSITIVE 271 100 56 198 152 tfor:TF0828|5end_hypothetical_protein_887090..887320_POSITIVE 270 42 2 127 82 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 270 42 2 87 42 tfor:TF1917|5end_hypothetical_protein_2069997..2070227_POSITIVE 266 78 33 227 188 tfor:TF0990|5end_hypothetical_protein_1045395..1045625_POSITIVE 266 78 36 76 42 tfor:TF0236|5end_multidrug_resistance_protein_261779..262009_POSITIVE 265 52 11 162 111 tfor:TF1332|5end_cytochrome_c-type_synthesis_protein_(cytochrome_c_biogenesis_protein);_ABC_transporter,_permease_1410957..1411187_POSITIVE 263 53 19 69 37 tfor:TF2085|5end_D-alanyl-D-alanine_carboxypeptidase_2252043..2252273_POSITIVE 261 78 33 159 108 tfor:TF2352|5end_phosphotransacetylase_2516688..2516918_POSITIVE 261 77 36 56 11 tfor:TF1931|5end_ATPase/GTPase_2078123..2078353_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 484 80 34 57 11 tfor:TF1191|3end_possible_transcriptional_regulator_1273979..1274129_POSITIVE 287 79 35 129 90 tfor:TF1886|3end_auxin-regulated_protein_2040341..2040491_POSITIVE 283 80 35 138 95 tfor:TF3116|3end_conserved_hypothetical_protein_3352413..3352563_POSITIVE 278 52 11 67 30 tfor:TF1608|3end_sulfate_transporter_1728463..1728613_POSITIVE 277 44 5 146 105 tfor:TF0504|3end_Fe-S_oxidoreductase,_family_2_530303..530453_POSITIVE 275 100 56 63 9 tfor:TF2880|3end_phenylalanyl-tRNA_synthetase,_beta_subunit_3071630..3071780_POSITIVE 272 47 8 119 76 tfor:TF2013|3end_polysaccharide_deacetylase_2169341..2169491_POSITIVE 270 42 2 115 70 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 266 78 36 66 32 tfor:TF0235|3end_hypothetical_protein_261849..261999_POSITIVE 265 52 11 59 8 tfor:TF1331|3end_outer_membrane_protein_1410934..1411084_POSITIVE 261 77 36 56 11 tfor:TF1930|3end_two-component_response_regulator_2078203..2078353_POSITIVE 257 48 10 77 41 tfor:TF0861|3end_HAD-superfamily_hydrolase,_subfamily_IA,_variant_1_family_protein_914122..914272_POSITIVE 256 79 35 69 26 tfor:TF1437|3end_hypothetical_protein_1522361..1522511_POSITIVE 255 42 3 53 14 tfor:TF2164|3end_hypothetical_protein_2341708..2341858_POSITIVE 255 42 3 53 14 tfor:TF0368|3end_hypothetical_protein_385834..385984_POSITIVE 253 76 33 122 73 tfor:TF1445|3end_RNA_polymerase_sigma_factor_1530718..1530868_POSITIVE 251 99 63 142 102 tfor:TF1591|3end_surface_antigen_BspA_1708266..1708416_POSITIVE 249 46 3 79 35 tfor:TF0525|3end_conserved_hypothetical_protein_549584..549734_POSITIVE 247 42 7 30 3 tfor:TF2525|3end_conserved_hypothetical_protein_2705612..2705762_POSITIVE 243 41 5 75 27 tfor:TF3086|3end_conserved_hypothetical_protein_3319949..3320099_POSITIVE