Origin IGS: cgcagttacattataaaaacatgaatactattacaaatatcgcatttttttcagtgattcaaacgacatgaatatgatttaatattatttatgaattaccgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacggtaattcataaataatattaaatcatattcatgtcgtttgaatcactgaaaaaaatgcgatatttgtaatagtattcatgtttttataatgtaactgcg Mask Tandem Repeat Region ================================================ cgcagttacattataaaaacatgaatactattacaaatatcgcatttttttcagtgattcaaacgacatgaatatgatttaatattatttatgaattaccgtta Find is-nt database================================================ Query_seq: TF1288:TF1289|TF1288:TF1289:hypothetical protein:ribosomal protein L11 methyltransferase:->->:1370338..1370441 104 cgcagttacattataaaaacatgaatactattacaaatatcgcatttttttcagtgattcaaacgacatgaatatgatttaatattatttatgaattaccgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1288:TF1289|TF1288:TF1289:hypothetical protein:ribosomal protein L11 methyltransferase:->->:1370338..1370441 104 cgcagttacattataaaaacatgaatactattacaaatatcgcatttttttcagtgattcaaacgacatgaatatgatttaatattatttatgaattaccgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1288:TF1289|TF1288:TF1289:hypothetical protein:ribosomal protein L11 methyltransferase:->->:1370338..1370441 104 cgcagttacattataaaaacatgaatactattacaaatatcgcatttttttcagtgattcaaacgacatgaatatgatttaatattatttatgaattaccgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgcagttacattataaaaacatgaatactattacaaatatcgcatttttttcagtgattcaaacgacatgaatatgatttaatattatttatgaattaccgtta Predict ORF larger than 30AA ================================================ cgcagttacattataaaaacatgaatactattacaaatatcgcatttttttcagtgattcaaacgacatgaatatgatttaatattatttatgaattaccgtta 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================================================ cgcagttacattataaaaacatgaatactattacaaatatcgcatttttttcagtgattcaaacgacatgaatatgatttaatattatttatgaattaccgtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1288:TF1289|TF1288:TF1289:hypothetical protein:ribosomal protein L11 methyltransferase:->->:1370338..1370441 104 cgcagttacattataaaaacatgaatactattacaaatatcgcatttttttcagtgattcaaacgacatgaatatgatttaatattatttatgaattaccgtta Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: tfor_TF1288_TF1289|hypothetical protein:ribosomal protein L11 methyltransferase|POSITIVE:POSITIVE|[1370338, 1370441]|104 HSP 1 e-value: 3.0E-40 bit: 165.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 cgcagttacattataaaaacatgaatactattacaaatatcgcannnnnnncagtgattcaaacgacatgaatatgatttaatattatttatgaattaccgtta cgcagttacattataaaaacatgaatactattacaaatatcgcatttttttcagtgattcaaacgacatgaatatgatttaatattatttatgaattaccgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCAGUUACAUUAUAAAAACAUGAAUACUAUUACAAAUAUCGCAUUUUUUUCAGUGAUUCAAACGACAUGAAUAUGAUUUAAUAUUAUUUAUGAAUUACCGUUA ...................((((((((.(((((.....((((.((((...((.((.......))))...)))).)))).))))).))))))))........... (-11.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGGUAAUUCAUAAAUAAUAUUAAAUCAUAUUCAUGUCGUUUGAAUCACUGAAAAAAAUGCGAUAUUUGUAAUAGUAUUCAUGUUUUUAUAAUGUAACUGCG ...((((.(((((..((..((((.((......)).))))..))))))).))))..((((((..((((((......)))).))..)))))).............. (-10.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 202 60 20 86 44 tfor:TF1758|5end_conserved_hypothetical_protein_1894769..1894999_POSITIVE 197 77 38 208 161 tfor:TF2646|5end_conserved_hypothetical_protein_2814998..2815228_POSITIVE 186 58 20 140 102 tfor:TF0024|5end_conserved_hypothetical_protein;_possible_ATPase_20191..20421_POSITIVE 183 76 32 183 141 tfor:TF1768|5end_conserved_hypothetical_protein;_possible_transposase_1906526..1906756_POSITIVE 183 77 35 131 93 tfor:TF1429|5end_S-adenosyl-methyltransferase_1513927..1514157_POSITIVE 182 70 40 177 142 tfor:TF3079|5end_ribonucleoside-diphosphate_reductase_1,_beta_subunit_3309184..3309414_POSITIVE 182 73 35 214 173 tfor:TF0432|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_452531..452761_POSITIVE 176 80 41 57 12 tfor:TF1325|5end_L-fucose_isomerase_1404000..1404230_POSITIVE 175 68 39 193 166 tfor:TF1500|5end_conserved_hypothetical_protein_1599693..1599923_POSITIVE 174 70 30 209 171 tfor:TF0302|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_328641..328871_POSITIVE 173 77 33 77 30 tfor:TF0437|5end_conserved_hypothetical_protein_460923..461153_POSITIVE 173 71 33 143 96 tfor:TF0014|5end_beta-glucosidase_(beta-D-glucoside_glucohydrolase),_periplasmic_7233..7463_POSITIVE 169 74 39 127 85 tfor:TF2776|5end_hypothetical_protein_2961470..2961700_POSITIVE 169 75 40 164 123 tfor:TF1985|5end_surface_antigen_BspA_2135659..2135889_POSITIVE 169 87 46 170 136 tfor:TF1695|5end_excisionase_1816522..1816752_POSITIVE 168 67 29 211 175 tfor:TF2684|5end_conserved_hypothetical_protein;_possible_CvpA_family_protein_2860692..2860922_POSITIVE 168 72 33 216 178 tfor:TF1800|5end_conserved_hypothetical_protein_1941214..1941444_POSITIVE 168 80 33 191 140 tfor:TF1384|5end_hypothetical_protein_1458010..1458240_POSITIVE 167 59 17 121 65 tfor:TF1321|5end_conserved_hypothetical_protein_1401565..1401795_POSITIVE 167 56 13 175 134 tfor:TF0093|5end_outer_membrane_protein,_TonB_dependent_receptor_100497..100727_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 47 1 85 32 tfor:TF3079|3end_ribonucleoside-diphosphate_reductase_1,_beta_subunit_3310313..3310463_POSITIVE 202 60 20 62 20 tfor:TF1757|3end_chromosome_partitioning_protein_1894825..1894975_POSITIVE 197 77 38 136 89 tfor:TF2645|3end_conserved_hypothetical_protein_2815006..2815156_POSITIVE 186 58 20 102 64 tfor:TF0023|3end_possible_response_element_in_two_component_regulation_20233..20383_POSITIVE 183 77 35 120 82 tfor:TF1428|3end_conserved_hypothetical_protein_1513996..1514146_POSITIVE 182 70 40 139 104 tfor:TF3078|3end_ribonucleoside_diphosphate_reductase,_alpha_subunit_3309226..3309376_POSITIVE 182 73 35 73 32 tfor:TF0431|3end_hypothetical_protein_452470..452620_POSITIVE 182 73 35 106 65 tfor:TF0430|3end_hypothetical_protein_452503..452653_POSITIVE 181 78 41 146 112 tfor:TF0381|3end_cell_cycle_protein_403028..403178_POSITIVE 176 80 41 77 32 tfor:TF1326|3end_hypothetical_protein_1404100..1404250_POSITIVE 173 71 33 115 68 tfor:TF0013|3end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_7285..7435_POSITIVE 167 59 17 101 45 tfor:TF1320|3end_beta-galactosidase_1401625..1401775_POSITIVE 167 56 13 147 106 tfor:TF0092|3end_outer_membrane_protein_100549..100699_POSITIVE 166 77 40 100 63 tfor:TF0602|3end_aminotripeptidase;_peptidase_T_633472..633622_POSITIVE 165 90 42 93 41 tfor:TF2860|3end_hypothetical_protein_3051680..3051830_POSITIVE 164 59 37 107 79 tfor:TF2430|3end_hypothetical_protein_2613204..2613354_POSITIVE 164 77 41 135 102 tfor:TF1983|3end_conserved_hypothetical_protein_2135000..2135150_POSITIVE 162 77 39 124 82 tfor:TF2007|3end_uracil_phosphoribosyltransferase_2159327..2159477_POSITIVE 162 78 32 104 51 tfor:TF0525|3end_conserved_hypothetical_protein_549584..549734_POSITIVE 161 72 40 86 54 tfor:TF2523|3end_NAD(P)H-flavin_oxidoreductase_2702916..2703066_POSITIVE