Origin IGS: atcttatctgtttatgaaaacccgtgcaaaattacccacctataaaacagataaataaccctactattcacacctatacccctattgagtcattctgctttcaatatgtcgttttcgggcagta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tactgcccgaaaacgacatattgaaagcagaatgactcaataggggtataggtgtgaatagtagggttatttatctgttttataggtgggtaattttgcacgggttttcataaacagataagat Mask Tandem Repeat Region ================================================ atcttatctgtttatgaaaacccgtgcaaaattacccacctataaaacagataaataaccctactattcacacctatacccctattgagtcattctgctttcaatatgtcgttttcgggcagta Find is-nt database================================================ Query_seq: TF1142:TF1143|TF1142:TF1143:outer membrane cobalamin receptor protein:ABC transporter, ATP-binding/permease component:->->:1221720..1221843 124 atcttatctgtttatgaaaacccgtgcaaaattacccacctataaaacagataaataaccctactattcacacctatacccctattgagtcattctgctttcaatatgtcgttttcgggcagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1142:TF1143|TF1142:TF1143:outer membrane cobalamin receptor protein:ABC transporter, ATP-binding/permease component:->->:1221720..1221843 124 atcttatctgtttatgaaaacccgtgcaaaattacccacctataaaacagataaataaccctactattcacacctatacccctattgagtcattctgctttcaatatgtcgttttcgggcagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1142:TF1143|TF1142:TF1143:outer membrane cobalamin receptor protein:ABC transporter, ATP-binding/permease component:->->:1221720..1221843 124 atcttatctgtttatgaaaacccgtgcaaaattacccacctataaaacagataaataaccctactattcacacctatacccctattgagtcattctgctttcaatatgtcgttttcgggcagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcttatctgtttatgaaaacccgtgcaaaattacccacctataaaacagataaataaccctactattcacacctatacccctattgagtcattctgctttcaatatgtcgttttcgggcagta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 24 End: 122 ....................... M Q N Y P P I K Q I N N P T I H T Y T P I E S F C F Q Y V V F G Q .. atcttatctgtttatgaaaacccgtgcaaaattacccacctataaaacagataaataaccctactattcacacctatacccctattgagtcattctgctttcaatatgtcgttttcgggcagta 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================================================ atcttatctgtttatgaaaacccgtgcaaaattacccacctataaaacagataaataaccctactattcacacctatacccctattgagtcattctgctttcaatatgtcgttttcgggcagta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1142:TF1143|TF1142:TF1143:outer membrane cobalamin receptor protein:ABC transporter, ATP-binding/permease component:->->:1221720..1221843 124 atcttatctgtttatgaaaacccgtgcaaaattacccacctataaaacagataaataaccctactattcacacctatacccctattgagtcattctgctttcaatatgtcgttttcgggcagta Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: tfor_TF1142_TF1143|outer membrane cobalamin receptor protein:ABC transporter, ATP-binding/permease component|POSITIVE:POSITIVE|[1221720,1221843]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 atcttatctgtttatgaaaacccgtgcaaaattacccacctataaaacagataaataaccctactattcacacctatacccctattgagtcattctgctttcaatatgtcgttttcgggcagta atcttatctgtttatgaaaacccgtgcaaaattacccacctataaaacagataaataaccctactattcacacctatacccctattgagtcattctgctttcaatatgtcgttttcgggcagta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUAUCUGUUUAUGAAAACCCGUGCAAAAUUACCCACCUAUAAAACAGAUAAAUAACCCUACUAUUCACACCUAUACCCCUAUUGAGUCAUUCUGCUUUCAAUAUGUCGUUUUCGGGCAGUA ...((((((((((..........(((......))).........))))))))))..................(((..((..((((((((..........))))))).)..))....)))..... (-13.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUGCCCGAAAACGACAUAUUGAAAGCAGAAUGACUCAAUAGGGGUAUAGGUGUGAAUAGUAGGGUUAUUUAUCUGUUUUAUAGGUGGGUAAUUUUGCACGGGUUUUCAUAAACAGAUAAGAU ....(((((.......((((((............((((.....))))...))))))....((((((((((((((((((...)))))))))))))))))).)))))................... (-27.46) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 50 8 189 148 tfor:TF2291|5end_outer_membrane_protein_2446098..2446328_POSITIVE 271 120 79 206 162 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 269 120 71 69 26 tfor:TF1068|5end_conserved_hypothetical_protein;_possible_N-acetylglucosamine_kinase_1138036..1138266_POSITIVE 260 120 72 186 142 tfor:TF0127|5end_conserved_hypothetical_protein_138026..138256_POSITIVE 259 102 61 47 1 tfor:TF0424|5end_outer_membrane_receptor,_TonB-linked_440028..440258_POSITIVE 253 108 69 58 14 tfor:TF0440|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_2_463655..463885_POSITIVE 251 117 71 213 166 tfor:TF2402|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2574582..2574812_POSITIVE 248 120 75 196 146 tfor:TF2036|5end_possible_pyruvate_formate-lyase_activating_enzyme_2196302..2196532_POSITIVE 248 119 82 42 9 tfor:TF0243|5end_conserved_hypothetical_protein_273728..273958_POSITIVE 246 41 1 140 93 tfor:TF2448|5end_conserved_hypothetical_protein_2624962..2625192_POSITIVE 246 120 73 170 116 tfor:TF2305|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2461348..2461578_POSITIVE 246 120 83 116 81 tfor:TF1047|5end_tRNA_pseudouridylate_synthetase_A_(pseudouridylate_synthase_I)_1108483..1108713_POSITIVE 245 97 54 218 159 tfor:TF2605|5end_outer_membrane_protein,_TonB_dependent_receptor_2779855..2780085_POSITIVE 240 120 73 61 1 tfor:TF2260|5end_transfer_region-related_protein,_TraL_2430207..2430437_POSITIVE 240 117 71 131 80 tfor:TF2043|5end_fructokinase_2202267..2202497_POSITIVE 239 120 78 70 15 tfor:TF2495|5end_succinate-semialdehyde_dehydrogenase_(NADP+)_2669456..2669686_POSITIVE 238 120 73 210 166 tfor:TF2253|5end_conjugative_transposon_protein,_TraG_2424950..2425180_POSITIVE 236 118 77 36 8 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 236 111 71 132 85 tfor:TF0475|5end_possible_transcriptional_regulator,_AraC_family_493729..493959_POSITIVE 235 93 65 107 81 tfor:TF2279|5end_hypothetical_protein_2438895..2439125_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 118 73 146 97 tfor:TF2607|3end_conserved_hypothetical_protein_2784645..2784795_POSITIVE 269 120 73 73 24 tfor:TF2659|3end_conserved_hypothetical_protein_2833055..2833205_POSITIVE 269 120 71 69 26 tfor:TF1067|3end_conserved_hypothetical_protein_1138116..1138266_POSITIVE 251 117 73 146 102 tfor:TF0196|3end_conserved_hypothetical_protein_221037..221187_POSITIVE 246 41 1 88 41 tfor:TF2447|3end_lipoprotein_2624990..2625140_POSITIVE 246 119 77 148 109 tfor:TF2173|3end_hypothetical_protein_2346063..2346213_POSITIVE 246 119 77 148 109 tfor:TF0346|3end_hypothetical_protein_367316..367466_POSITIVE 245 97 54 115 56 tfor:TF2604|3end_possible_membrane_transport_protein_2779832..2779982_POSITIVE 243 120 78 145 100 tfor:TF1761|3end_hypothetical_protein_1899579..1899729_POSITIVE 243 120 79 151 118 tfor:TF0886|3end_conjugative_transposon_protein_fragment_938152..938302_POSITIVE 243 120 79 54 21 tfor:TF0885|3end_conjugative_transposon_protein_fragment_938055..938205_POSITIVE 242 118 71 116 51 tfor:TF0673|3end_conserved_hypothetical_protein_717355..717505_POSITIVE 240 117 71 140 89 tfor:TF2042|3end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2202356..2202506_POSITIVE 235 93 65 122 96 tfor:TF2278|3end_conserved_hypothetical_protein_2438990..2439140_POSITIVE 235 120 74 103 51 tfor:TF0260|3end_conserved_hypothetical_protein_291594..291744_POSITIVE 233 118 89 77 48 tfor:TF0862|3end_conserved_hypothetical_protein_fragment_914459..914609_POSITIVE 233 118 74 136 88 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 228 120 73 109 61 tfor:TF0355|3end_transposase_element_373487..373637_POSITIVE 227 120 80 55 6 tfor:TF3133|3end_conserved_hypothetical_protein_3369913..3370063_POSITIVE 225 120 79 143 108 tfor:TF3037|3end_galactokinase_3264266..3264416_POSITIVE